Profiling of transcriptional and epigenetic changes during directed endothelial differentiation of human embryonic stem cells identifies FOXA2 as a marker of early mesoderm commitment
- Lynsey Howard†1,
- Ruth M Mackenzie†1,
- Nikolay A Pchelintsev2,
- Tony McBryan2,
- John D McClure1,
- Martin W McBride1,
- Nicole M Kane1,
- Peter D Adams2,
- Graeme Milligan3 and
- Andrew H Baker1Email author
© Howard et al.; licensee BioMed Central Ltd. 2013
Received: 8 February 2013
Accepted: 21 March 2013
Published: 24 April 2013
Differentiation of vascular endothelial cells (ECs) in clinically relevant numbers for injection into ischaemic areas could offer therapeutic potential in the treatment of cardiovascular conditions, including myocardial infarction, peripheral vascular disease and stroke. While we and others have demonstrated successful generation of functional endothelial-like cells from human embryonic stem cells (hESCs), little is understood regarding the complex transcriptional and epigenetic changes that occur during differentiation, in particular during early commitment to a mesodermal lineage.
We performed the first gene expression microarray study of hESCs undergoing directed differentiation to ECs using a monolayer-based, feeder-free and serum-free protocol. Microarray results were confirmed by quantitative RT-PCR and immunocytochemistry, and chromatin immunoprecipitation (ChIP)-PCR analysis was utilised to determine the bivalent status of differentially expressed genes.
We identified 22 transcription factors specific to early mesoderm commitment. Among these factors, FOXA2 was observed to be the most significantly differentially expressed at the hESC–EC day 2 timepoint. ChIP-PCR analysis revealed that the FOXA2 transcription start site is bivalently marked with histone modifications for both gene activation (H3K4me3) and repression (H3K27me3) in hESCs, suggesting the transcription factor may be a key regulator of hESC differentiation.
This enhanced knowledge of the lineage commitment process will help improve the design of directed differentiation protocols, increasing the yield of endothelial-like cells for regenerative medicine therapies in cardiovascular disease.
KeywordsGene expression Epigenetics Endothelial differentiation Embryonic stem cells Transcription factors
The directed differentiation of human embryonic stem cells (hESCs) towards endothelial cell (EC) lineages offers therapeutic potential in the treatment of myocardial infarction, peripheral vascular disease and stroke . While successful derivation of endothelial-like cells from hESCs has been demonstrated [2–5], relatively little is understood regarding early commitment to mesoderm and subsequent specification .
To commit to a specified lineage, pluripotent cells must undergo radical transcriptional change , partly regulated by miRNAs [2, 3]. Recent studies suggest epigenetic influences also play a significant role in the determination of cell fate . Indeed, the poised transcriptional state classically associated with pluripotent hESCs is maintained via effects at the chromatin level with gene expression determined by post-translational modification of histones . While some histone marks, such as trimethylation of lysine 4 of histone H3 (H3K4me3), are associated with gene activation, others, such as trimethylation of lysine 27 of histone H3 (H3K27me3), are associated with repression. However, around 3,000 developmental regulatory genes in embryonic stem cells are labelled with both H3K4me3 and H3K27me3 , allowing the genes to be rapidly activated upon differentiation or to remain silenced during commitment to lineages not requiring their expression. Unsurprisingly, these bivalently marked genes are proposed to be master regulators of the differentiation process, although their role in endothelial differentiation has not been extensively investigated to date.
The study described herein was designed to profile transcriptional and epigenetic changes during early hESC commitment to a mesodermal and endothelial-like fate with a view to improving understanding of this process and to optimise the generation of ECs for regenerative medicine purposes.
hESC lines SA461 (Cellartis, Dundee, UK), H1 and H9 (WiCell Research Institute, Madison, WI, USA) and RC10 (Roslin Cells Ltd, Edinburgh, UK) were cultured in a monolayer-based, serum-free and feeder-free system. Pluripotency was maintained and endothelial differentiation induced as previously described . Primary human saphenous vein endothelial cells (HSVECs) were isolated on the day of surgery by standard collagenase digestion based on a modified version of the protocol described by Jaffe and colleagues . HSVECs were then cultured as previously described . All participants gave written informed consent. The study was approved by the West of Scotland Ethics Committee (06/S0703/110) and complies with the principles of the Declaration of Helsinki.
Data were quantile normalised and background subtracted in Genome Studio (Illumina®) and were then exported to Partek® Genomics Suite™ (Partek® Inc., St. Louis, MO, USA) and visualised using principle component analysis . An error-weighted analysis of variance with a false discovery rate multiple testing adjustment threshold of 0.05 was used to identify differentially expressed probe sets , which were then uploaded to Ingenuity Pathway Analysis software (2009; Ingenuity® Systems, Redwood City, CA, USA) and analysed to identify dynamic gene expression.
In silico prediction of bivalency
H3K27me3 and H3K4me3 data from the H9 chromatin immunoprecipitation (ChIP)-sequencing dataset of Ku and colleagues  were mined and integrated with microarray data to give an in silico prediction of the bivalent status of genes.
SICER software (http://home.gwu.edu/~wpeng/Software.htm) was used to determine enriched domains for each histone modification using a stringent E value of 0.1, a window size of 200 and gap sizes of 200, 400, 600, 800 and 1,000 base pairs . For each gene within the Ensembl gene set (NCBI36.1), the transcription start site (TSS) was determined and an interval spanning ±2 kb around the TSS was defined.
For a specific gap size, if the TSS contained enriched domains for both H3K27me3 and H3K4me3 marks, then this gene was classified as bivalent. The bivalency score was defined as the count of gap sizes where a gene was considered bivalent. A score of 0 would thus indicate that the gene was never classified as bivalent, while a score of 5 indicated that the gene was found to be bivalent regardless of the gap size chosen.
TaqMan® quantitative RT-PCR
First-strand cDNA was synthesised from 1 μg DNase-treated total RNA using TaqMan Reverse Transcription Reagents (Applied Biosystems, Life Technologies Ltd., Paisley, UK). TaqMan® Gene Expression Assays for CXXC1 (Hs00969406_g1), EHMT2 (Hs00938384_g1), FOXA2 (Hs00232764_m1), L3MBTL2 (Hs01002038_g1), MLL3 (Hs01005539_m1), RBM14 (Hs01056358_m1), TAF6L (Hs01008038_m1), TFAP4 (Hs01558245_m1), TSC22D3 (Hs00608272_m1), UBTF (Hs00610733_g1), USF2 (Hs01100995_g1) and ZNF35 (Hs01071488_m1) were used with TaqMan® Endogenous Controls, 18S (Hs99999901_s1) or UBC (Hs00824723_m1) (Applied Biosystems, Life Technologies). Relative quantitation of gene expression was calculated using the comparative (ΔΔCt) method .
Immunocytofluorescence experiments were carried out as previously described . Primary antibodies utilised were mouse anti-OCT4 primary antibody (SC5279, 1:200; Santa Cruz Biotechnology Inc., Dallas, TX, USA) and goat anti-FOXA2 primary antibody (AF2400, 1:50; R&D Systems Europe Ltd., Abingdon, UK). Secondary antibodies were Alexafluor-488 donkey anti-goat (A11055; Invitrogen, Life Technologies Ltd., Paisley, UK) and Alexafluor-555 goat anti-mouse (A21424; Invitrogen). ProLong Gold with 4′,6-diamidino-2-phenylindole (Invitrogen) was used for nuclear counterstaining.
Chromatin immunoprecipitation and PCR identification
ChIP assays were performed based on a modified version of the method of Rai and colleagues . Chromatin was prepared from pluripotent H9s and SA461s, and H3K4me3 and H3K27me3 were immunoprecipitated using Dynabeads® M-280 sheep anti-rabbit IgG (Invitrogen) and H3K4me3 (AB8580; Abcam, Cambridge, UK) and H3K27me3 (C36B11; Cell Signaling Technology, Beverly, MA, USA) specific antibodies. Immunoprecipitations with total H3 (AB1791; Abcam) and control IgG (M7023; Sigma-Aldrich Company Ltd., Dorset, UK) were included as positive and negative controls, respectively.
Using the University of California Santa Cruz Genome Browser, primer pairs were designed to span the FOXA2 TSS (Additional files 1, 2 and 3) and DyNAmo™ SYBR® Green quantitative PCR (Thermo Fisher Scientific UK Ltd., Loughborough, UK) was performed on immunoprecipitation eluates, in addition to 2% chromatin input not subjected to immunoprecipitation. Quantitative PCR data were normalised to IgG negative control and displayed as fold enrichment.
Values are presented as mean ± standard error of the mean. Data from multiple groups were analysed using repeated-measures analysis of variance. Significant differences were determined by Tukey post-hoc testing and P <0.05 (two-tailed) was considered significant.
Gene expression analysis of endothelial differentiation
Principle component analysis of global transcription data, designed to detect early transcriptional changes during directed differentiation (Figure 1A), revealed sufficient separation of cell groups. As expected, HSVECs were clearly distinct from all hESC-derived cells, and hESC–EC on day 4 and day 10 were divergent compared with day 0 and day 2 timepoints (Figure 1B).
A large number of significantly differentially expressed probe sets was observed at each of the three differentiation timepoints, as compared with day 0 (Figure 1C). Comparison of samples from day 10 hESC–EC with HSVEC samples revealed differential expression of 6,133 different probe-sets, defining markedly different cells (Figure 1C).
Differentially expressed human embryonic stem cell–endothelial cell day 2 transcription factor-encoding genes
Entrez gene name
Ankyrin repeat, family A (RFXANK-like), 2
Achaete-scute complex homolog 2 (Drosophila)
CXXC finger protein 1
DNA (cytosine-5)-methyltransferase 3-like
Euchromatic histone-lysine N-methyltransferase 2
Forkhead box A2
GA binding protein transcription factor, beta subunit 1
Histone deacetylase 5
l(3)mbt-like 2 (Drosophila)
Myeloid/lymphoid or mixed-lineage leukemia 3
MAX binding protein
Retina and anterior neural fold homeobox 2
RNA binding motif protein 14
RFX1 (includes EG:100038773)
Regulatory factor X, 1 (influences HLA class II expression)
Small nuclear RNA activating complex, polypeptide 4, 190 kDa
Steroid receptor RNA activator 1
TAF6-like RNA polymerase II, p300/CBP-associated factor-associated factor, 65 kDa
Transcription factor AP-4 (activating enhancer binding protein 4)
TSC22 domain family, member 3
Upstream binding transcription factor, RNA polymerase I
Upstream transcription factor 2, c-fos interacting
Zinc finger protein 35
To confirm day 2 differential expression of FOXA2 at the protein level, SA461s, H1s and RC10s were stained using anti-FOXA2 antibodies. Expression of the pluripotency marker OCT4 was observed in day 0 pluripotent cells but diminished by hESC–EC day 2 (Figure 2C). FOXA2, although present in a subset of pluripotent cells, was abundantly expressed at day 2. Interestingly, FOXA2 did not co-localise with OCT4 (Figure 2C).
Epigenetic analysis of FOXA2
On aligning in silico data with differentially expressed genes identified via microarray analysis, a large proportion (2,684/3,883) achieved a bivalency score of 5 and was therefore predicted to be bivalently marked.
To the best of our knowledge, this study describes the first global gene expression profiling of hESCs at intermediate timepoints during their directed differentiation to an endothelial-like lineage using a monolayer-based, feeder-free and serum-free protocol. The study is also the first to identify transcription factors potentially specific to early mesoderm commitment, including FOXA2 which we show to be bivalently marked at the TSS. In addition, we report that cells at day 10 of the differentiation process remain genetically distinct from mature endothelial cells, supporting our previous findings that this timepoint yields progenitor-type cells, capable of further differentiation in vivo.
Rapid and transient FOXA2 mRNA upregulation was identified and confirmed at the protein level, suggesting the hepatocyte nuclear factor may represent a marker of early mesoderm lineage commitment. A member of the forkhead class of DNA binding proteins, FOXA2 has been shown to bind and open compacted chromatin at histones H3 and H4  and is one of the first transcription factors to bind target genes on differentiation . Traditionally endoderm associated, FOXA2 has not, as far as we are aware, previously been linked to hESC–EC differentiation. However, with cells used for microarray analyses likely to represent a somewhat heterogeneous population containing precursors for both endoderm and mesoderm germ layers [18, 19], further investigation utilising purified cell populations will be required to confirm the importance of FOXA2 in early EC commitment.
Epigenetic control of transcription is now known to play a major role in cell fate determination and, as stated, we have identified the FOXA2 TSS as being bivalently marked in pluripotent hESCs, displaying histone modifications associated with both gene activation and repression. Conceivably, FOXA2 may therefore be a marker of early mesoderm lineage commitment and a potential regulator of hESC-EC commitment. Such enhanced knowledge of the complex commitment process is likely to prove important for optimising the design and development of directed endothelial differentiation protocols.
This study is the first to generate global gene expression profiles for hESCs undergoing directed differentiation to ECs using a monolayer-based, serum-free and feeder-free system, and is the first to identify transcription factors, including FOXA2, likely to be specific for early mesoderm lineage commitment.
Histone H3 trimethylated on lysine 27
Histone H3 trimethylated on lysine 4
Human embryonic stem cell
Primary human saphenous vein endothelial cell
Polymerase chain reaction
Transcription start site.
The authors acknowledge Dr Peter Burton, Miss Wendy Crawford and Dr Wai Kwong Lee for technical assistance. This work was supported by the Medical Research Council (G0800122-1/1) and the British Heart Foundation (SP/10/005/28298). AHB is supported by the British Heart Foundation Chair of Translational Cardiovascular Sciences (CH/11/2/28733).
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