<p>Patients with NSCLCs Harboring Internal Inversions or Deletion Rearrangements of the <em>ALK</em> Gene Have Durable Responses to ALK Kinase Inhibitors</p>

Abstract

Background: ALK fusions are targetable drivers in non-small-cell lung cancer (NSCLC). However, patients with NSCLC harboring ALK rearrangements without a fusion partner identified in DNA have also been shown to respond to ALK inhibitors. We aimed to characterize complex ALK variants that may predict sensitivity to multiple approved ALK inhibitors. Methods: Comprehensive genomic profiling (CGP) of DNA isolated from formalin-fixed paraffin-embedded (FFPE) tumor tissue or blood-based circulating tumor DNA was performed for 39,159 NSCLC patients during routine clinical care. For a subset of cases, RNA sequencing was performed, and prior ALK test results and clinical treatment information were collected from treating physicians. Results: We queried the Foundation Medicine NSCLC database and identified ALK internal inversions, as well as internal deletions, as the sole ALK rearrangements in 6 (0.02%) and 3 (0.01%) of cases, respectively. In cases with ALK internal inversions, RNA testing identified an EML4-ALK fusion in 2/2 cases evaluated, and 3/3 patients treated with ALK inhibitors had durable responses. A single patient with an ALK internal deletion and clinical data available responded to multiple ALK inhibitors. RNA data available for a subset of non-NSCLC cases suggest that ALK internal deletions removing a portion of the N-terminus are drivers themselves and do not result in ALK fusions. Fluorescence in situ hybridization (FISH) results were inconsistent for both classes of DNA events. Conclusion: Rare internal inversions of ALK appear to be indicative of ALK fusions, which can be detected in RNA, and response to ALK inhibitors in patients with NSCLC. In contrast, ALK internal deletions are not associated with ALK fusions in RNA but likely represent targetable drivers themselves. These data suggest that CGP of DNA should be supplemented with immunohistochemistry or RNA-based testing to further resolve these events and match patients to effective therapies.

ALK Deletion Exons 2 to 19: Case Report of a Rare ALK Inhibitor–Responsive Lung Cancer Driver Oncogene

“…These variants account for 0.01% of cases with ALK activation in large cohorts of ALK genomic aberrations. 1 We report a lung adenocarcinoma with a previously undescribed somatic ALK deletion of exons 2 to 19 ( Fig. 1 A – E ).…”

“…The previous case in literature of an ALK deletion–positive metastatic lung adenocarcinoma also disclosed prolonged responses to ALK inhibitors—sequential crizotinib and alectinib. 1 Of note, both cases with ALK nonkinase domain deletions (between introns and exons 1 to 19) and also changes involving ALK intragenic internal inversions (usually between introns 8 to 19) disclosed diagnostic tests with ALK IHC plus ALK fluorescence in situ hybridization (FISH) positivity in patterns similar to more common ALK -rearranged lung cancers, albeit some cases did not have typical positivity using A LK FISH. 1 All clinical studies that led to the regulatory approval of crizotinib, 2 alectinib, 3 brigatinib, 4 and lorlatinib 5 enrolled cases in which the tumor was diagnosed using nonsequencing-based ALK detection methods (IHC or FISH) and is plausible to speculate that a few tumors with ALK deletions or interval inversions were included.…”

“… 1 Of note, both cases with ALK nonkinase domain deletions (between introns and exons 1 to 19) and also changes involving ALK intragenic internal inversions (usually between introns 8 to 19) disclosed diagnostic tests with ALK IHC plus ALK fluorescence in situ hybridization (FISH) positivity in patterns similar to more common ALK -rearranged lung cancers, albeit some cases did not have typical positivity using A LK FISH. 1 All clinical studies that led to the regulatory approval of crizotinib, 2 alectinib, 3 brigatinib, 4 and lorlatinib 5 enrolled cases in which the tumor was diagnosed using nonsequencing-based ALK detection methods (IHC or FISH) and is plausible to speculate that a few tumors with ALK deletions or interval inversions were included. ALK internal inversions may be indicative of more extensive ALK rearrangements when orthogonal testing is used whereas A LK internal deletions are true driver events with ALK signaling activation in preclinical models of similar changes.…”

“…ALK internal inversions may be indicative of more extensive ALK rearrangements when orthogonal testing is used whereas A LK internal deletions are true driver events with ALK signaling activation in preclinical models of similar changes. 1 …”

“…The ALK intragenic rearrangement change with loss of intron 1 to intron 19 and resulting in deletion of exons 2 to 19 is illustrated. In addition, some of the other reported ALK deletions in lung cancer 1 —involving deletions of intron 1 to 18, intron 3 to 19, and intron 12 to 19—are also represented. ( B , C ) Resected left lung invasive nonmucinous adenocarcinoma ( B ) exhibiting strong and diffuse ALK staining ( C ) by means of D5F3 immunohistochemistry (×400 original magnification).…”