Genomic heterogeneity of ALK fusion breakpoints in non-small-cell lung cancer.

Abstract

In lung adenocarcinoma, canonical EML4-ALK inversion results in a fusion protein with a constitutively active ALK kinase domain. Evidence of ALK rearrangement occurs in a minority (2-7%) of lung adenocarcinoma, and only ~60% of these patients will respond to targeted ALK inhibition by drugs such as crizotinib and ceritinib. Clinically, targeted anti-ALK therapy is often initiated based on evidence of an ALK genomic rearrangement detected by fluorescence in situ hybridization (FISH) of interphase cells in formalin-fixed, paraffin-embedded tissue sections. At the genomic level, however, ALK rearrangements are heterogeneous, with multiple potential breakpoints in EML4, and alternate fusion partners. Using next-generation sequencing of DNA and RNA together with ALK immunohistochemistry, we comprehensively characterized genomic breakpoints in 33 FISH-positive lung adenocarcinomas. Of these 33 cases, 29 (88%) had detectable DNA level ALK rearrangements involving EML4, KIF5B, or non-canonical partners including ASXL2, ATP6V1B1, PRKAR1A, and SPDYA. A subset of 12 cases had material available for RNA-Seq. Of these, eight of eight (100%) cases with DNA rearrangements showed ALK fusion transcripts from RNA-Seq; three of four cases (75%) without detectable DNA rearrangements were similarly negative by RNA-Seq, and one case was positive by RNA-Seq but negative by DNA next-generation sequencing. By immunohistochemistry, 17 of 19 (89%) tested cases were clearly positive for ALK protein expression; the remaining cases had no detectable DNA level rearrangement or had a non-canonical rearrangement not predicted to form a fusion protein. Survival analysis of patients treated with targeted ALK inhibitors demonstrates a significant difference in mean survival between patients with next-generation sequencing confirmed EML4-ALK rearrangements, and those without (20.6 months vs 5.4 months, P<0.01). Together, these data demonstrate abundant genomic heterogeneity among ALK-rearranged lung adenocarcinoma, which may account for differences in treatment response with targeted ALK inhibitors.

• Authors: Jason N Rosenbaum, Ryan Bloom, Jason T Forys, Jeff Hiken, Jon R Armstrong, Julie Branson, Samantha McNulty, Priya D Velu, Kymberlie Pepin, Haley Abel, Catherine E Cottrell, John D Pfeifer, Shashikant Kulkarni, Ramaswamy Govindan, Eric Q Konnick, Christina M Lockwood, Eric J Duncavage
• Journal: Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc (Mod Pathol) Vol. 31 Issue 5 Pg. 791-808 (05 2018) ISSN: 1530-0285 [Electronic] United States
• PMID: 29327716 (Publication Type: Journal Article)

Chemical References

• EML4-ALK fusion protein, human
• Oncogene Proteins, Fusion
• Protein Kinase Inhibitors
• Pyrimidines
• Sulfones
• Crizotinib
• ALK protein, human
• Anaplastic Lymphoma Kinase
• ceritinib

Topics

• Adult
• Aged
• Aged, 80 and over
• Anaplastic Lymphoma Kinase (antagonists & inhibitors, biosynthesis, genetics)
• Carcinoma, Non-Small-Cell Lung (enzymology, genetics, pathology)
• Chromosome Breakpoints
• Crizotinib (therapeutic use)
• Female
• Gene Rearrangement
• High-Throughput Nucleotide Sequencing
• Humans
• In Situ Hybridization, Fluorescence
• Lung Neoplasms (enzymology, genetics, pathology)
• Male
• Middle Aged
• Molecular Targeted Therapy
• Oncogene Proteins, Fusion (genetics)
• Protein Kinase Inhibitors (therapeutic use)
• Pyrimidines (therapeutic use)
• Sulfones (therapeutic use)
• Survival Analysis