Discovery and Characterization of Recurrent, Targetable ALK Fusions in Leiomyosarcoma

Abstract

Soft tissue sarcomas such as leiomyosarcoma (LMS) pose a clinical challenge because systemic treatment options show only modest therapeutic benefit. Discovery and validation of targetable vulnerabilities is essential. To discover putative kinase fusions, we analyzed existing transcriptomic data from LMS clinical samples. Potentially oncogenic ALK rearrangements were confirmed by application of multiple RNA-sequencing fusion detection algorithms and fluorescence in situ hybridization (FISH). We functionally validated the oncogenic potential and targetability of discovered kinase fusions through biochemical, cell-based (Ba/F3, NIH3T3 and murine smooth muscle cell) and in vivo tumor modelling approaches. We identified ALK rearrangements in 9 of 377 (2.4%) LMS patients, including a novel KANK2-ALK fusion and a recurrent ACTG2-ALK fusion. Functional characterization of the novel ALK fusion, KANK2-ALK, demonstrates it is a dominant oncogene in Ba/F3 or NIH3T3 model systems, and has tumorigenic potential when introduced into smooth muscle cells. Oral monotherapy with targeted ALK kinase inhibitor lorlatinib significantly inhibits tumor growth and prolongs survival in a murine model of KANK2-ALK leiomyosarcoma. These results provide the first functional validation of a targetable oncogenic kinase fusion as a driver in a subset of leiomyosarcomas.Overall, these findings suggest that some soft tissue sarcomas may harbor previously unknown kinase gene translocations, and their discovery may propel new therapeutic strategies in this treatment-refractory cancer. IMPLICATIONA subset of leiomyosarcomas harbor previously unrecognized oncogenic ALK fusions that are highly responsive to ALK inhibitors and thus these data emphasize the importance of detailed genomic investigations of leiomyosarcoma tumors.

CDKN2C-Null Leiomyosarcoma: A Novel, Genomically Distinct Class of TP53/RB1–Wild-Type Tumor With Frequent CIC Genomic Alterations and 1p/19q-Codeletion

“…A minor subset of CDKN2C -null and/or 1p/19q-codeleted LMS harbored activating fusions in ALK , BRAF , FGFR1 , and NTRK1 , for which targeted inhibitors may be of utility. 9 …”

CDKN2Chomozygous loss identifies a distinct subtype ofTP53/RB1-wildtype leiomyosarcoma with frequentCICgenomic alterations and 1p/19q-codeletion

“…A subset of CDKN2C-null and/or 1p/19q codeleted LMS also harbored activating fusions in ALK, for which ALK inhibitors may be of utility. 9 Other rare targetable activating fusions were present within the CDKN2C-null cohort, including in BRAF, FGFR1, and NTRK1.…”

“…7 LMS has demonstrated occasional potentially targetable genomic alterations (GAs), but novel targeted therapeutic agents have not been widely used. 8,9,10 Herein, we describe a novel recurrent genomic signature of CDKN2C homozygous loss in leiomyosarcoma primarily from the uterus, with significantly low frequency of TP53 and RB1 genomic alterations.…”

Spindle cell neoplasm with EML4‐ALK gene fusion presenting as an intraosseous vertebral mass

“…Fusions involving the ALK (anaplastic lymphoma kinase) gene have been described in a wide spectrum of neoplasms. Not only are they present in a subset of anaplastic large cell lymphoma, but they can also be detected in approximately 50% of IMT, 14 5% to 6% of lung adenocarcinomas 15 and 2.4% of leiomyosarcomas, 13 as well as other neoplasms 16 . In addition, targetable activating point mutations in ALK have been described in a subset of neuroblastoma and anaplastic thyroid carcinoma 16 …”

“…These findings have also been crucial to the identification of potential therapeutic targets. For example, ALK inhibitors, which are routinely used in the treatment of ALK fusion‐positive nonsmall cell lung carcinoma, 4 also represent a potential tool to treat mesenchymal neoplasms harboring ALK fusions such as inflammatory myofibroblastic tumor (IMT), 5‐10 epithelioid inflammatory myofibroblastic sarcoma, 9,11,12 and leiomyosarcoma 13 …”