ALK Fusions

Anaplastic lymphoma kinase (ALK) is a member of the insulin receptor subfamily of tyrosine kinase receptors; it was first identified in 1994 in the setting of anaplastic large-cell lymphoma (ALCL) as a fusion protein arising from a translocation between the nucleophosmin (NPM) and ALK genes.1,2,3 In its normal (i.e., non-rearranged) state, the ALK protein is expressed in neuronal cells, and it is believed to function in the development of the nervous system, although its exact ligand and role in development remain largely unknown.1,4 The activation of ALK is linked to several intracellular signaling pathways, including the mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and the JAK-STAT signaling pathway.1 Gene fusions involving ALK are being increasingly recognized in various cancers, and the resulting fusion proteins share common features, including the break points within the ALK gene, which invariably retain the tyrosine kinase domain, and an N-terminal fusion partner that results in the oligomerization and constitutive activation of the kinase. 1,4

EML4-ALK Fusion

In 2007, another fusion gene between ALK and the echinoderm microtubule-associated protein like 4 gene (EML4) was identified in lung cancers5; the resultant protein was found to function as a bona fide transforming oncogene when expressed in Mouse 3T3 cells, causing them to form foci and subcutaneous tumors in immunocompromised mice. Moreover, the EML4-ALK oncogene was detected in 5 individuals (6.7%) in a sampling of 75 non-small cell lung cancer (NSCLC) patients, and these patients were found to differ from those patients having the epidermal growth factor receptor (EGFR) mutation.5

In 2007, Rikova and colleagues also identified ALK as one of the most commonly activated receptor tyrosine kinases in a comprehensive, large-scale analysis of 41 NSCLC cell lines and 150 NSCLC tumors using phosphoproteomics methodology. N-terminal fusions of ALK to EML4 and another gene, TRK-fused gene (TFG), were identified in this study.6 Since then, other ALK gene fusions with TFG, KIF5B, and KLC1 have been identified in NSCLC, but EML4-ALK appears to be the most common, with more than 20 different variants of the fusion identified. Importantly, all fusions retain the ALK tyrosine kinase domain and therefore the relevant signaling activity of the receptor.1

Like other kinase fusions in cancer, replacement of the 5′ end with other gene sequences, such as EML4 and TFG, allows dimerization or oligomerization of the intracellular kinase domain to occur independent of ligand binding. This results in constitutive kinase activity, hyperactivation of the associated intracellular signaling pathways, and ultimately uncontrolled proliferation and/or survival.1,6 Gene sequence encoding the ALK kinase domain is necessary for its transforming potential since “kinase-dead” mutants of the EML4-ALK fusion are unable to transform Mouse 3T3 cells.5,6 Similarly, inhibition of ALK kinase activity with small molecule inhibitors leads to arrested cell growth and apoptosis, validating its potential as a therapeutic target for lung and other cancers.1

ALK Fusions in Lung Cancer

There is evidence to suggest a distinct set of clinical characteristics for NSCLC patients whose tumors harbor ALK fusions. NSCLC patients with ALK rearrangements have been noted generally to be younger than the average age of patients with lung cancer and to have a light (10 or fewer pack-years) or no smoking history; histologically, these patients also tend to have adenocarcinoma, and signet-ring cells have been commonly observed.7

In a study of 103 Chinese NSCLC patients, ALK rearrangements were detected in a total of 12 patients (11.6%), and all of these rearrangements were found to be variants of the previously described EML4-ALK rearrangement.3 Notably, this study also found patients with the EML4-ALK rearrangement to be predominantly of the adenocarcinoma subtype (10 of 12 patients). In addition, as compared with non-ALK rearrangement patients, those with ALK rearrangements had significantly fewer pack years of smoking history (5.0 vs. 18.5; P<0.01) and were significantly younger (53 years vs. 61 years; P=0.03); however, we did not observe sufficient evidence for improved survival in the patients with ALK rearrangements (P=0.15).3

ALK Fusions in Melanoma and Thyroid Cancers

Although most widely studied in the setting of lymphoma and NSCLC to date, ALK fusions have been noted at a low frequency in other tumor types. A genomic analysis of 140 Spitzoid neoplasms, including 75 Spitz nevi, 32 atypical Spitz tumors, and 33 Spitzoid melanomas, detected ALK rearrangement in a total of 14 patients (10%) across the total sample, with 8, 5, and 1 patients testing positive for rearrangements across the respective subtypes.8 N-terminal fusion partners identified for ALK in this study included the previously described TPM3-ALK and a novel partner, DCTN1. The fusion protein resulting from the DCTN1-ALK rearrangement was further shown to have an increased phosphorylation state relative to the wild-type ALK protein, with increased phosphorylation of downstream signaling molecules, suggesting that like other ALK fusions it, too, is constitutively activated.8 In mouse xenograft models, expression of the fusion protein resulting from the DCTN1-ALK rearrangement was also shown to be oncogenic, causing the development of rapidly growing tumors when injected into immunocompromised mice.8

In a comprehensive assessment of kinase fusions across different cancers, ALK rearrangements were observed in 3 of 498 thyroid cancers (0.6%), 5 of 513 lung adenocarcinomas (1.0%), 1 of 250 bladder urothelial cancers (0.4%), 1 of 91 rectal adenocarcinomas (1.0%), and 1 of 198 kidney papillary cell carcinomas (0.5%).9 Several novel fusion partners for ALK were also identified in this study, including TPM1-ALK (in bladder cancer), SMEK2-ALK (in rectal adenocarcinoma), and GTF2TRD1-ALK (in thyroid cancer), further adding to the range of fusion partners that have been observed across cancer types.9

ALK Fusion Testing

In a guideline statement from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology, the recommendation was made to use the presence of ALK fusions to guide patient selection for therapy with an ALK inhibitor in patients with advanced-stage adenocarcinoma, regardless of sex, race, smoking history, or other clinical risk factors. This guidance further suggests that ALK testing be prioritized over other molecular predictive tests, once EGFR molecular testing has been completed.10 The growing range of ALK fusions that have been identified across different cancer types (Table 1) highlights the importance of ALK as a potential cancer therapy target for the subset of patients having these fusions.

The STARTRK-2 trial is enrolling patients with NTRK, ROS1, and ALK fusions.

More information is available at www.startrktrials.com.

Table 1: Examples of ALK Rearrangements Across Different Cancers.

Frequency is only given if assessed in 2 or more studies (adapted from Shaw 2013).

Cancer Type Fusion Gene Estimated Frequency
NSCLC EML4 – ALK
TFG – ALK
KIF5B* – ALK
KLC1 – ALK
STRN – ALK
3 – 7%
Colorectal Cancer C2orf44 – ALK

EML4 – ALK

< 1%
Breast Cancer EML4 – ALK < 1%
Squamous Cell Esophageal Cancer TPM4 – ALK < 1%
Renal Cell Cancer VCL – ALK
TPM3 – ALK
EML4 – ALK
< 1%
Renal Medullary Cancer VCL – ALK < 1%

ALK, anaplastic lymphoma kinase; C2orf44, chromosome 2 open reading frame 44; EML4, echinoderm microtubule-associated protein-like 4; KIF5B, kinesin family member 5B; KLC1, kinesin light chain 1; STRN, striatin; TFG, TRK-fused gene; TPM, tropomyosin; VCL, vinculin

 

References

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