In-Depth Analysis Of The Genomic Landscape Of 91 Metastatic Neuroendocrine Tumors Reveals Subtype-Heterogeneity And Potential Therapeutic Targets

Background: Metastatic neuroendocrine tumors (mNET) form a clinically and genetically heterogeneous malignancy, characterized by distinct prognosis based upon primary tumor localization, functionality, grade and proliferation index, and a wide variation in treatment outcome. To get a better insight into this heterogeneity in prognosis and outcome, and also to reveal putative novel treatment targets, we here analyzed the mutational landscape of 91 metastatic mNET biopsies derived from whole-genome sequencing (WGS). Material and Methods: Between May 2016 and July 2018, 91 mNET patients from 14 Dutch hospitals were included in the study protocol (NCT01855477) of the Center for Personalized Cancer Treatment (CPCT). Patients with mNET were categorized by primary location into midgut (N = 44), pancreas (N = 26), lung (N = 5), unknown (N = 12) and other (N = 4). The WGS of matched peripheral blood and tumor tissues was performed on a HiSeq X Ten system to sequencing depths of 38x and 105x, respectively, and subsequently aligned to the human reference genome (GRCh37) and analyzed for somatic mutations, mutational signatures, copy-number alterations and structural variants with the GRIDSS, PURPLE, LINX suite, GISTIC2 and in-house algorithms. Results: The overall mutational landscape of mNET is hallmarked by a relative stable diploid tumor genome and low median tumor mutational burden (TMB) of 1.32 (IQR: 0.91 - 2.1) mutations per genomic Mb. Differences in median TMB relating to primary location were observed; ranging from 1.1 (midgut), 1.49 (pancreas), 2.87 (lung) to 4.18 (unknown); six mNET had high tumor mutational burden (TMB ≥ 10), but without microsatellite-instability signatures. In addition, we observed striking evidence of somatic aberrations due to alkylating agents (sig. 11), combined with the highest cohort-wide TMB (39.6) for a single patient treated with streptozocin prior to biopsy. Three mNETs revealed MUTYH-related alterations (sig. 18) and furthermore, we detected chromothripsis (n = 6) and APOBEC-related regional hypermutation (kataegis; n = 11). Midgut-derived mNET (n = 44) predominantly harbored somatic alterations in CDKN1B (n = 11) and CDKN2A/B (n = 7). Strikingly, no somatic driver mutation was seen in almost half of these midgut-derived mNET (n = 21). Pancreatic mNET (n = 26) predominantly harbored alterations in MEN1 (n = 8), TP53 (n = 8), ATRX (n = 6), CDKN2A/B (n = 6) and DAXX (n = 5). In total, 39 mNET (43%) showed clinically-actionable somatic alterations for current on- and off-label NET therapies. Conclusion: This study comprises the largest WGS repository of mNET to date, and demonstrates the genetic heterogeneity of mNET linked to primary localization. Several potential therapeutic targets were identified which are worthwhile to explore for their clinical value in the treatment of mNET patients. Citation Format: Job van Riet, Harmen J. van de Werken, Edwin Cuppen, Ferry A. L. M. Eskens, Margot E. Tesselaar, Linde M. van Veenendaal, Heinz-Josef Klumpen, Wouter Dercksen, Gerlof D. Valk, Martijn P. J. K. Lolkema, Stefan Sleijfer, Bianca Mostert. In-depth analysis of the genomic landscape of 91 metastatic neuroendocrine tumors reveals subtype-heterogeneity and potential therapeutic targets [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 5673.