title: Intact or broken-apart RNA: an alternative concept for ALK fusion screening in non-small cell lung cancer (NSCLC).
abstract: Anaplastic lymphoma kinase (ALK) break-apart fluorescent in situ hybridization (FISH) is currently used in diagnostics for the selection of non-small cell lung cancer (NSCLC) patients to receive crizotinib. We evaluated ALK status in NSCLC with a novel ALK mRNA test based on the break-apart FISH concept, which we called break-apart transcript (BAT) test. ALK5' and ALK3' transcript patterns were established with qPCR for ALK-expressing controls including fusion-negative neuroblastomas, as well as fusion-positive anaplastic large cell lymphomas and NSCLC. The BAT test was evaluated on 271 RNA samples from routinely processed paraffin NSCLC tissues. Test results were compared with ALK FISH (n=121), immunohistochemical (IHC) analysis (n=86), and automated quantitative analysis (AQUA, n=83). On the basis of the nonoverlapping ALK BAT patterns in ALK-expressing controls (P<0.0001), 8/174 adenocarcinomas (4.6%) among 259 informative NSCLC were predicted as fusion positive. Overall concordance for paired method results was high (94.1% to 98.8%) but mainly concerned negative prediction because of the limited availability of positive-matched cases. Tumors with 100% cytoplasmic IHC staining of any intensity (n=3) were positive for AQUA, FISH, and BAT test; tumors with lower IHC positivity and different staining patterns were AQUA-negative. Upon multiple reevaluations, ALK gene status was considered as originally misinterpreted by FISH in 3/121 cases (2.5%). Tumors with >4 ALK gene copies were associated with longer overall survival upon first-line chemotherapy. In conclusion, application of the ALK BAT test on routinely processed NSCLC tissues yields the same fusion partner independent information as ALK break-apart FISH but is more robust and cost-effective. The BAT concept may be considered for the development of further drug-predictive translocation tests.
authors.affiliation: *Department of Pathology †Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research ∥Department of Medical Oncology, "Papageorgiou" Hospital, Aristotle University of Thessaloniki School of Medicine ¶Department of Pathology, "Papageorgiou" Hospital, Thessaloniki §Second Department of Internal Medicine, Division of Oncology, Attikon University Hospital #Department of Pathology, Children's Hospital "Aglaia Kyriakou" ††Second Department of Medical Oncology, Hygeia Hospital, Athens, Greece ‡Department of Pathology, Yale University School of Medicine, New Haven, CT **Department of Pathology, Wayne State University, Detroit, MI.
authors.forename: Vassiliki
authors.initials: V
authors.lastname: Kotoula
authors.forename: Mattheos
authors.initials: M
authors.lastname: Bobos
authors.forename: Maria
authors.initials: M
authors.lastname: Vassilakopoulou
authors.forename: Eleftheria
authors.initials: E
authors.lastname: Tsolaki
authors.forename: Sofia
authors.initials: S
authors.lastname: Chrisafi
authors.forename: Amanda
authors.initials: A
authors.lastname: Psyrri
authors.forename: George
authors.initials: G
authors.lastname: Lazaridis
authors.forename: Kyriaki
authors.initials: K
authors.lastname: Papadopoulou
authors.forename: Ioannis
authors.initials: I
authors.lastname: Efstratiou
authors.forename: Catherine
authors.initials: C
authors.lastname: Michail-Strantzia
authors.forename: Larisa V
authors.initials: LV
authors.lastname: Debelenko
authors.forename: Paris
authors.initials: P
authors.lastname: Kosmidis
authors.forename: George
authors.initials: G
authors.lastname: Fountzilas
mesh_terms: D000368:Aged; D000077548:Anaplastic Lymphoma Kinase; D000970:Antineoplastic Agents / Q000627:therapeutic use; D002289:Carcinoma, Non-Small-Cell Lung / Q000175:diagnosis* / Q000188:drug therapy / Q000401:mortality; D000077547:Crizotinib; D003951:Diagnostic Errors; D005260:Female; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D008175:Lung Neoplasms / Q000175:diagnosis* / Q000188:drug therapy / Q000401:mortality; D008297:Male; D008875:Middle Aged; D009367:Neoplasm Staging; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D011237:Predictive Value of Tests; D011379:Prognosis; D011720:Pyrazoles / Q000627:therapeutic use; D011725:Pyridines / Q000627:therapeutic use; D012333:RNA, Messenger / Q000032:analysis*; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics*; D016019:Survival Analysis; D014178:Translocation, Genetic / Q000235:genetics
chemical_list: D000970:Antineoplastic Agents; D015514:Oncogene Proteins, Fusion; D011720:Pyrazoles; D011725:Pyridines; D012333:RNA, Messenger; D000077547:Crizotinib; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D020794:Receptor Protein-Tyrosine Kinases