KLC1-ALK: A Novel Fusion in Lung Cancer Identified Using a Formalin-Fixed Paraffin-Embedded Tissue Only

Abstract

The promising results of anaplastic lymphoma kinase (ALK) inhibitors have changed the significance of ALK fusions in several types of cancer. These fusions are no longer mere research targets or diagnostic markers, but they are now directly linked to the therapeutic benefit of patients. However, most available tumor tissues in clinical settings are formalin-fixed and paraffin-embedded (FFPE), and this significantly limits detailed genetic studies in many clinical cases. Although recent technical improvements have allowed the analysis of some known mutations in FFPE tissues, identifying unknown fusion genes by using only FFPE tissues remains difficult. We developed a 5′-rapid amplification of cDNA ends-based system optimized for FFPE tissues and evaluated this system on a lung cancer tissue with ALK rearrangement and without the 2 known ALK fusions EML4-ALK and KIF5B-ALK. With this system, we successfully identified a novel ALK fusion, KLC1-ALK. The result was confirmed by reverse transcription-polymerase chain reaction and fluorescence in situ hybridization. Then, we synthesized the putative full-length cDNA of KLC1-ALK and demonstrated the transforming potential of the fusion kinase with assays using mouse 3T3 cells. To the best of our knowledge, KLC1-ALK is the first novel oncogenic fusion identified using only FFPE tissues. This finding will broaden the potential value of archival FFPE tissues and provide further biological and clinical insights into ALK-positive lung cancer.

Testing for ALK rearrangement in lung adenocarcinoma: a multicenter comparison of immunohistochemistry and fluorescent in situ hybridization

“…13,14 Other less common 5 0 fusion partners have been described including kinesin family member 5B (KIF5B), TRKfused gene (TFG) and kinesin light chain 1 (KLC1). 8,15,16 ALK rearrangements have been reported to occur at frequencies that range from 0.4 to 15% in NSCLC, 7,17 although some series include selected patient populations likely to be enriched for ALK rearrangements. Most series, however, report an incidence of around 3-4% in unselected NSCLC populations.…”

Tackling ALK in non-small cell lung cancer: the role of novel inhibitors

“…Variants v1, v2, v3a and v3b of EML4-ALK fusion gene are the most commonly detected, together accounting for more than 90% of variants in some series (20). Although more uncommon, other ALK fusion partners have been identified as TFG (TRK-fused gene), KIF5B, PTPN3 and KLC1 (21)(22)(23). The different EML4 variants and the further partner genes do not seem to significantly impact on biology and sensitivity of ALK-rearranged malignant cells and tumors to specific inhibitors (24-26) although a putative role in conditioning response to treatments has been reported in vitro (27).…”

The Current Landscape of Anaplastic Lymphoma Kinase (ALK) in Non-Small Cell Lung Cancer: Emerging Treatment Paradigms and Future Directions

“…Also Ou et al recently reported that the emergence of ALK -resistant mutations occurred more commonly in patients with variant 3 EML4-ALK rearrangement than in patients with variant 1 tumors [4]. Other rarer ALK fusions occur such as KIF5B-ALK [5], KLC1-ALK [6], and ALK-PTPN3 [7], but they collectively are less frequent than the ALK-EML4 rearrangement [8], and therefore little is known about their clinical significance with respects to different response to ALK TKIs. In general, patients with ALK -rearranged NSCLC tend to be younger, never smokers, and have lung adenocarcinoma, though rarely patients with other lung cancer histologies have also been found to harbor this mutation [9].…”