Characterization of Epigenetic and Transcriptional Landscape in Infantile Hemangiomas with ATAC-Seq and RNA-Seq

Abstract

Aim: This study was conducted to reveal epigenetic landscape in infantile hemangiomas (IHs) and identify transcription factors (TFs) and their downstream genes active in IHs. Materials & methods: We performed Assay for Transposase Accessible Chromatin (ATAC-seq)with RNA-seq in three pairs of IHs and their adjacent normal tissues. Functions of candidate TFs were investigated in human umbilical vein endothelial cells (HUVECs). Results: Chromatin of IH tissues is less compact. Some candidate genes and TFs were identified. In HUVECs, SPDEF inhibited cell viability and tube formation, and promoted apoptosis; SOX4 exerted the opposite effect. SPDEF may act through EPHA5, ZBTB46 and SASH1; SOX4 may act through MMP12 and HIVEP3. Conclusion: Epigenetics plays a role in IHs. SPDEF and SOX4 may act in IHs.

Keywords::

• ATAC-seq
• infantile hemangioma
• open chromatin
• RNA-seq
• SOX4
• SPDEF

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2020-0060

Acknowledgments

The authors would like to thank S Liu, X_biol (Jinan, China), for his technical assistance and contribution to the data processing.

Financial & competing interest disclosure

This work was supported by the National Natural Science Foundation of China (grant number 81671927). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

This study was approved by the Institutional Ethics Review Board of Shandong Provincial Hospital Affiliated to Shandong University (No. 2017-051). Written informed consents were signed by the guardians of the children.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China (grant number 81671927). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript