Abstract 2730: Early development of ALK clinical genetic biomarkers for cancer
Authors: Freeman Angela B. , Horn Candice , Thomas James E. , Landschulz Katherine 
Published: February 2011

Abstract
Anaplastic lymphoma kinase (ALK, Chr 2) is an orphan transmembrane receptor tyrosine kinase that is activated in non-small cell lung cancer (NSCLC), neuroblastoma, and anaplastic large cell lymphomas (ALCL). Genetic activation of ALK can occur as a result of gene amplification, kinase-domain point mutations, or by fusion of the kinase domain to structural genes such as echinoderm microtubule associated protein-like 4 (EML4). Ultimately this leads to further activation of downstream effector proteins-including STAT3, AKT or ERK-enhanced cell proliferation, and disease.
A study of 602 cancer cell lines found that neuroblastoma, NSCLC and ALCL cells harboring ALK translocations and amplifications were particularly responsive to treatment with ALK inhibitor therapy (McDermott et al, 2008). Recently, somatic and germline missense mutations were also identified in the ALK kinase domain and linked to 8.4% of hereditary and spontaneous pediatric neuroblastomas (Mosse et al., 2008). The ALK mutations were found to cause an increase in ALK expression that when knocked down resulted in an inhibition of cancer cell growth (Mosse et al., 2008). These results suggest that ALK point mutations have similar functional consequences in neuroblastoma as ALK structural variations and could therefore confer cancer cell sensitivity to ALK inhibitor therapy.
Although few studies have investigated this to date, the ALK point mutations may result in similar functional consequences for other cancer cell types. If so, the ALK mutations may be ideal genetic biomarkers to identify patients who would be clinically responsive to ALK inhibitor therapy. Therefore, we sought to better understand a subset of these ALK somatic mutations, their frequency in other cancer types, and potential as clinical biomarkers for cancer drug response.
We designed and developed custom allelic discrimination assays to genotype three ALK activating mutations; M1166R, F1174L and R1275Q in DNA extracted from 23 cancer cell lines and 47 tumor samples. Although no neuroblastoma samples were included, these 70 samples represented a dozen different cancer types and tissues, including prostate, breast, ovary, lung, liver and pancreas. We also generated synthetic oligonucleotide allele controls to establish the necessary heterozygous and homozygous genotype clusters for automated genotype calling.
Our data showed that the ALK mutations were monomorphic wildtype in all 70 cancer samples tested. These results suggest that the 12.4% frequency of the ALK mutations observed in neuroblastoma may be very specific and play a particular role in that disease. More studies are required to elucidate if these ALK mutations may provide tools for additional cancer patient stratification, including predicted disease progression and response beyond the previously identified ALK translocations and amplifications.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2730.