Cis-regulatory elements (CREs) in spinal solitary fibrous tumours (SFT)

Abstract

Spinal Solitary Fibrous Tumour is a rare soft tissue neoplasm. Although a lot of genes are involved in Spinal Solitary Fibrous Tumour progression, survival and metastasis, NGFI-A binding protein 2 (NAB2) - signal transducer and activator of transcription 6 (STAT6) gene fusion is one of the most commonly occurring genetic abnormalities in all types of Solitary Fibrous Tumours (SFT). The interaction of STAT6 (Early Growth Response (EGR) transcriptional activator) and NAB2 (EGR transcriptional repressor) activates the conversion of the transcription repressor to the transcriptional activator and promotes EGR-induced promoter activity. EGR has shown to plays a role in the regulation of cell survival, proliferation and cell death. Cis-regulatory elements (CREs) are genomic sequences in non-coding regions of the genomic DNA which binds with the transcription factors, and they play an essential role in precise control of gene expression. CREs composed of enhancers, suppressors and insulators play pivotal roles in gene expression throughout life and development. They have important role in maintaining the normal homeostasis, preventing organogenesis, tumourigenesis and teratoma formation. In this study, we investigate the non-coding regions in the human genome to detect enhancers and suppressors present in different tissue samples of Spinal SFT using Encyclopedia of DNA Elements (ENCODE). The study of these enhancers and suppressors may be used to develop newer diagnostic and treatment strategies. A total of 75 genes and immunohistochemistry (IHC) markers expressed in Spinal SFT were obtained from PubMed and Google Scholar. CREs were identified using the ENCODE consortium. Protein interaction network was obtained using String v11.0 using the proteins corresponding to these 75 genes. Results obtained from ENCODE were enumerated and web-hosted for public access to design a treatment strategy. This may enable the wet lab scientist design CREs specific for Spinal SFT using the in silico results obtained.