Next-generation transcriptomic analysis in cancer vascular research
Posted: 3 September 2015 |
Over the past decade significant advances have been made in the fields of genomic and transcriptomic profiling, inspired by the advent of next-generation sequencing (NGS). Yet despite the considerable promise of these new technologies, uptake has been slow. The focus of this review is the use of next-generation transcriptomic analysis in the field of cancer endothelial biology, highlighting its advantages and a few of the disadvantages compared with current-generation technologies.
NGS is an emerging technology for genomic, epigenomic and transcriptomic profiling, which can be performed more rapidly than traditional Sanger sequencing and in far greater depth than microarray technologies. NGS technologies have been used in a wide variety of fields from sequencing of bacterial and viral genomes, searching for patient-specific genetic variations and profiling of DNA-binding proteins by ChIP-Seq, to characterising the transcriptomes of cells, tissues and organisms by RNA-Seq. NGS covers a wide variety of technologies but primarily operates by sequencing DNA or RNA samples in a massively multiplexed manner, generating images, from which short sequence reads can be determined, aligned to a reference genome and converted to genomic data.
Tumours are highly dependant on their vasculature to support their growth, being unable to expand beyond 2mm in size or metastasise in the absence of vessels to supply nutrients, remove waste products and propagate tumour cells around the body. Considerable effort has been expended to investigate the mechanisms by which tumour vasculature develops, as well as examining its distinctiveness from the vessels of healthy tissues, with the aim of depriving the tumour of its blood supply. The vast majority of transcriptomic analysis involved in this work has been performed using microarray technologies, though SAGE and cDNA library analysis have also been used (reviewed in). The advent of highthroughput next-generation analysis offers the opportunity for new discoveries to be made in this field, discoveries which are not possible with older technologies, and this will contribute to refinement and improvement of vessel-targeted anti-cancer therapies…