Gene Expression Detection Assay for Cancer Clinical Use

Narrandes, Shavira; Xu, Wayne

It is generally accepted that driver gene mutations initialize cancer development. Protooncogenes, such as Ras, are transcribed into products such as receptors, growth factors, transcription factors, and signaling enzymes for cellular proliferation. 1 Gain-of-function mutations in proto-oncogenes, resulting in dominant oncogenes that differ from their proto-oncogenes or are over-expressed, occur by point mutations, localized reduplication, or chromosomal translocation. An oncogene therefore disrupts a cell's normal activity and can lead to uncontrolled cell division, and ultimately cancerous cells. Genes for the inhibition of cell growth are termed tumor-suppressor genes and include APC and TP53; the loss or under-expression of these genes also results in an uncontrolled cell division. 1, 2 Therefore, by analyzing gene expression levels and the biological pathways associated with the genes involved in a cancer, one can study the difference between normal cell and cancerous cell pathways to determine the genetic origin of the faulty pathway, thereby identifying potential targets for treating cancer. The potential subtypes of that cancer can be identified through class discovery, the identification of novel cancer subtypes, and class prediction, the assignment of tumor samples to pre-defined classes in order to aid in predicting the outcome. 3 Gene expression analysis also allows for biomarker and gene signature discovery. The use of gene expression profiling and development of gene biomarkers/ signatures for cancer allows for the diagnosis, progression and aggressiveness analyses, prognosis, prediction of therapeutic treatment, and/or Ivyspring International Publisher identification of patients who would benefit from therapeutic treatment to better understand the disease and its biology. 4 Various assay technologies have been developed for gene expression analysis (Fig 1) . For example, qRT-PCR amplifies a gene of interest and uses fluorescent probes or dyes to depict the gene expression; NanoString nCounter uses probe pairs to anneal to a region of RNA and detect genes; DNA microarrays allow cDNA targets to hybridize to probes on a solid slide and can use fluorescence to detect genes; Illumina MiSeq RNA-Seq bridge amplifies nucleic acid samples to create clusters, which are then interpreted by the MiSeq system; and lastly, tissue microarrays (TMAs) study circular punches from tissue sample blocks with labelled probes or antibodies to determine the gene expression. Each of these assays has been used in diagnosis, prognosis, and treatment prediction for a variety of cancers. Some assays have been commercialized for clinical cancer use. For example, Afirma® is a microarray test for thyroid cancer diagnosis and the Oncotype DX qRT-PCR test is for guiding breast cancer treatment. Many assays are under investigation in clinical trials or studies.