Abstract GS2-03: Highly recurrent transcriptional remodeling events in advanced endocrine resistant ER-positive breast cancers
Authors: Priedigkeit N , Vareslija D , Basudan A , Watters RJ , Lucas PC , Davidson NE , Blohmer J-U , Denkert C , Machleidt A , Heppner BI , Brufsky AM , Oesterreich S , Young L , Lee AV 
Published: February 2018

Abstract
BACKGROUND: Although individual cancers are driven by heterogeneous processes, cancer mortality has a near universal cause—therapy resistance, recurrence and metastasis to vital organs. Characterizing more advanced tumors has borne valuable insight into cancer progression, yet studies of longitudinally collected breast cancer specimens are scarce given lengthy periods of cancer dormancy. In this study, we aimed to create the most comprehensive characterization of gene expression alterations to date between patient-matched pairs of primary and advanced ER-positive breast cancers.
MATERIALS/METHODS: Hybrid-capture RNA-sequencing was performed on 50 patient-matched pairs of primary and advanced ER-positive tumors from various recurrence sites (9 brain, 11 bone, 3 GI, 10 ovary, 17 local). Time to recurrence was up to 14.1 years with a median of 3.4 years. A shared variant analysis confirmed all paired samples were patient-matched. 1,380 cancer-related genes were analyzed for outlier expression fold-changes in matched recurrences versus primary tumors. Pair-specific, outlier fold-change thresholds were defined as Q1/Q3 +/- [1.5 X IQR]; using each pairs' fold-change values across all genes as the distribution. These discrete, longitudinal transcriptional remodeling events (LTREs) were assessed for recurrence across all sites and analyzed for enrichments within specific cohorts (Fisher's exact tests), such as locoregional vs. distant recurrences. To determine if LTREs represent acquired vulnerabilities, ex vivo and in vivo experiments targeting a recurrent, druggable LTRE gain of RET was performed.
RESULTS: The majority of advanced cancers were transcriptionally similar to patient-matched primaries with 23 of 33 distant metastases retaining PAM50 assignments of the matched primary—shifts to HER2 (n=4, 12%) or Luminal B (n=5, 15%) subtypes accounted for most metastatic discordances. Despite this intrinsic conservation, remarkably recurrent gene-level LTRE gains and losses were observed in advanced disease. Recurrent LTRE gains included NCAM1 [42%], FGFR4 [40%], IBSP [36%], ROBO2 [36%] and SPP1 [30%]. Notable LTRE losses included RELN [42%] and ESR1 [26%]. NCAM1 LTREs showed the most significant enrichments (p &lt; 0.001) in distant disease (20 of 33, 61%) versus locoregional disease (1 of 17, 6%). A prominent LTRE enriched in brain metastasis (BrM) was RET (p-value = 0.003), expression of which showed outlier gains in 56% of ER-positive BrM. Marked anti-tumor activity was demonstrated with the RET inhibitor cabozantinib in ex vivo explant cultures of patient resected BrMs (n=3) and a BrM patient-derived xenograft.
CONCLUSIONS: Taken together, these results demonstrate profound, recurrent and metastatic site-specific LTREs in advanced breast cancers, which may be essential to our understanding of endocrine-therapy resistance and metastasis. Although current emphasis for longitudinal clinical profiling of tumors is on DNA-level alterations, these results suggest LTREs as a compelling, shared mechanism of cancer progression. Given remarkably high recurrence rates of specific LTREs across multiple cohorts, further preclinical and clinical investigations of LTREs are demanded, especially considering some (i.e. FGFR4 and RET) are readily druggable.
Citation Format: Priedigkeit N, Vareslija D, Basudan A, Watters RJ, Lucas PC, Davidson NE, Blohmer J-U, Denkert C, Machleidt A, Heppner BI, Brufsky AM, Oesterreich S, Young L, Lee AV. Highly recurrent transcriptional remodeling events in advanced endocrine resistant ER-positive breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS2-03.