Image: A positive test with the Break Apart fluorescence in situ hybridization (FISH) Probe kit for anaplastic lymphoma kinase gene (ALK) (Photo courtesy of Abbott Molecular).
Activation of tyrosine kinase proto-oncogenes, through gene fusions, has been found in lung adenocarcinomas and they are highly sensitive to selective kinase inhibitors.
A fluorescence in situ hybridization (FISH) assay was used to simultaneously determine the genomic status of anaplastic lymphoma kinase (ALK) and v-ros avian UR2 sarcoma virus oncogene homolog (ROS1) and to identify the presence of genetic rearrangements in human colorectal adenocarcinoma (CRC) specimens.
Scientists at the University of Colorado School of Medicine (Aurora, CO, USA) used a FISH assay to test for the oncogenic gene rearrangements in 236 tumor samples of colorectal cancer collected from patients enrolled in a large, Australian clinical trial. The tissue microarrays (TMA) were prepared using formalin fixed paraffin embedded (FFPE) CRC tissue specimens from 268 patients.
The TMA slides were subjected to a FISH assay using a novel 4-color, 4-target ALK/ROS1 Break Apart probe (Abbott Molecular; Des Plaines, IL, USA) developed to determine genomic status of ALK and ROS1 in the same cells. The FISH assays were performed using the Zymed Spot-Light Tissue Pretreatment kit (Invitrogen; Carlsbad, CA, USA) in the TMAs. To identify the fusion partner for ALK and ROS1, reverse transcriptase polymerase chain reaction (RT-PCR) was carried out using the Invitrogen SuperScript III First-Strand Synthesis System with previously published ALK and ROS1 primers.
The scientists found one patient carrying the ALK rearrangement, confirming previous findings, and demonstrated the first finding of ROS1 as an oncogenic driver of colorectal cancer; in this case, they found it in 2 of the 236 tumor samples. Surprisingly, these gene alterations tended to coexist in colorectal tumors along with other molecular alterations. Tumors that were positive for ALK rearrangements were also positive for another well-defined molecular alternation known as Kirsten ras oncogene homolog (KRAS). ROS1 mutations occurred in one specimen along with the known, oncogenic mutation, v-raf murine sarcoma viral oncogene homolog B (BRAF).
Dara Aisner, MD, PhD, a molecular pathologist, and lead author said, “This is a case in which we have all the background science as we know that when ALK and ROS1 improperly fuse with other genes, the result can be oncogenic. We have drugs that target these oncogenes and we even have tests to determine who has the gene rearrangements and so should benefit from these drugs. The important piece missing was finding these oncogenes in other cancers, and now we've filled in that piece in colorectal cancer.” The study was published on December 2, 2013, in the journal Molecular Cancer Research.
University of Colorado School of Medicine