Abstract 794: Molecular analysis of archival inflammatory myofibroblastic tumor tissue samples from EORTC 90101 “CREATE” and correlation with response to crizotinib
Authors: Lee Che-Jui , Schöffski Patrick , Modave Elodie , Boeckx Bram , Lambrechts Diether , Debiec-Rychter Maria , Sciot Raf , Sufliarsky Jozef , Gelderblom Hans , Blay Jean-Yves , Wozniak Agnieszka 
Published: September 2020

Abstract
About 50% of inflammatory myofibroblastic tumors (IMFTs) harbor rearrangements of anaplastic lymphoma kinase (ALK), the most common driver in this rare tumor. EORTC 90101 “CREATE” is so far the only prospective, disease-specific phase II clinical trial performed in IMFT. It showed high antitumor activity of crizotinib, an ALK/ROS1/MET-inhibitor. This activity was mainly seen in ALK-rearranged IMFT, but the trial results suggested that other molecular events may also contribute to crizotinib sensitivity. Here we present results of an in-depth molecular analysis of archival IMFTs collected from patients within the CREATE trial with the aim to identify other molecular alterations, which could be responsible for response to crizotinib. DNA from archival IMFTs (primary tumor or metastatic lesion) was used for low-coverage whole genome sequencing to identify genomic regions of gains or losses. Whole exome sequencing (WES) was used to assess the mutational landscape, and mutations affecting cancer consensus genes (CCGs) were analyzed in more detail. Correlative and statistical analysis were used to assess the association between molecular findings and clinical outcomes of IMFT patients. In 24 IMFTs analyzed, the recurrent whole-arm copy number losses were: 22q (58% of cases), 16p (33%), 16q (29%), 13q (29%), 19q (29%), 19p (25%), 6p (25%), 6q (21%) and 18q (21%). Loss of chromosome 19 was found to be associated with shorter progression-free survival in patients receiving crizotinib (p = 0.008). Moreover, 2p21 (including EPAS1, SIX2, EML4 from the CCG set) was frequently amplified (54% of cases), while recurrent losses were observed at 22q12.3 (71%, ISX), 7q36.3 (54%, MNX1), 10q26.3 (54%, MGMT, DUX4), 1p36.32 (50%, RPL22, SKI, TNFRSF14, CAMTA1, PRDM16), 8p23.3 (50%, ARHGEF10), 12q24.33 (46%, POLE), and 11q13.4 (33%, CCND1). No significant correlations were found between focal copy number alterations and crizotinib response. A complex genetic rearrangement involving chromosome 2, identified in 2 ALK-rearranged cases, was likely consistent with chromothripsis, a form of genomic instability related to cancer development. WES was performed in 22 cases with an average of 392 alterations per sample. When considering non-synonymous mutations in CCG, a total of 178 mutations were identified, affecting 143 genes with an average of 7 per case. Mutations in 30 CCGs, identified in ≥ 2 cases, were mainly related to DNA damage/repair mechanism, WNT, RB1-TP53, and RTK-RAS-PI3K signaling. In a case with no ALK rearrangement and ALK immunopositivity, a single base substitution in ALK (p.N571K) was identified. In conclusion, we identified multiple molecular alterations in archival IMFTs and provided further insight in the molecular profile of this ultra-rare malignancy, which may potentially lead to the identification of novel therapeutic targets for IMFT patients.
Citation Format: Che-Jui Lee, Patrick Schöffski, Elodie Modave, Bram Boeckx, Diether Lambrechts, Maria Debiec-Rychter, Raf Sciot, Jozef Sufliarsky, Hans Gelderblom, Jean-Yves Blay, Agnieszka Wozniak. Molecular analysis of archival inflammatory myofibroblastic tumor tissue samples from EORTC 90101 “CREATE” and correlation with response to crizotinib [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 794.