Gene Expression Detection Assay for Cancer Clinical Use

Narrandes, Shavira; Xu, Wayne

In one study, FISH was used to assess HER2 transcript distribution in a fresh frozen HER2-positive human breast cancer tissue section and KRAS in wild-type and mutant cells. Padlock probes, oligonucleotides that are circularized following hybridization to a target sequence that is complementary to the probe ends, were designed to detect the cDNA molecules. Rolling circle amplification can then be used to amplify the circularized padlock probes. HER2 expression varied, as expected, and a somatic point mutation was identified in KRAS. 60 23 small molecule inhibitors and antibodies that target MET, a proto-oncogene, and its ligand, hepatocyte growth factor (HGF), have been developed and tested in over 240 clinical trials in 2014. 61 One study analyzed MET expression and activity in a matched set of FFPE vs. fresh frozen tumor samples consisting of 20 cases of gastric cancer using both FISH and IHC. It was found that RNA FISH can be used to confirm findings obtained by IHC and potentially may replace IHC for certain targets if no suitable antibodies are available. RNA FISH is a valid platform for testing predictive biomarkers for patient selection. 62 MicroRNAs (miRNAs) are excellent tumor biomarkers because of their cell-type specificity and abundance. A reliable multicolor miRNA FISH technique was developed that enables miRNA visualization in FFPE tissues. They tested two skin tumors, basal cell carcinoma (BCC) and Merkel cell carcinoma (MCC), to visualize differentially expressed miRNAs in FFPE tumor samples. 63 qRT-PCR analysis and FISH was applied in a study to assess miRNA expression in the HER2-positive breast cancer cells. It was found that miR-489 was expressed at a significantly lower level in tumor tissues compared to the adjacent normal tissues and directly targets HER2. 64 FISH can also be used for LncRNA expression detection in cancer. For example, one study used RNA FISH to investigate the association between LncRNA AK023391 expression and the clinicopathological characteristics and prognosis of gastric cancer patients. 65 A separate study demonstrated two antisense lncRNAs at the 5' (5'aHIF-1α) and 3' (3'aHIF-1α) ends of the human HIF-1α gene in kidney tumor tissues using RNA FISH. 66