Abstract GS2-03: Highly recurrent transcriptional remodeling events in advanced endocrine resistant ER-positive breast cancers

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 < 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.

Epigenetic silencing of tumor suppressor candidate 3 confers adverse prognosis in early colorectal cancer

Colorectal cancer (CRC) is a biologically and clinically heterogeneous disease. Even though many recurrent genomic alterations have been identified that may characterize distinct subgroups, their biological impact and clinical significance as prognostic indicators remain to be defined. The tumor suppressor candidate-3 (TUSC3/N33) locates to a genomic region frequently deleted or silenced in cancers. TUSC3 is a subunit of the oligosaccharyltransferase (OST) complex at the endoplasmic reticulum (ER) which catalyzes bulk N-glycosylation of membrane and secretory proteins. However, the consequences of TUSC3 loss are largely unknown. Thus, the aim of the study was to characterize the functional and clinical relevance of TUSC3 expression in CRC patients' tissues (n=306 cases) and cell lines. TUSC3 mRNA expression was silenced by promoter methylation in 85 % of benign adenomas (n=46 cases) and 35 % of CRCs (n =74 cases). Epidermal growth factor receptor (EGFR) was selected as one exemplary ER-derived target protein of TUSC3-mediated posttranslational modification. We found that TUSC3 inhibited EGFR-signaling and promoted apoptosis in human CRC cells, whereas TUSC3 siRNA knock-down increased EGFR-signaling. Accordingly, in stage I/II node negative CRC patients (n=156 cases) loss of TUSC3 protein expression was associated with poor overall survival. In sum, our data suggested that epigenetic silencing of TUSC3 may be useful as a molecular marker for progression of early CRC.

A randomised phase III trial comparing two dose-dense, dose-intensified approaches (EPC and PM(Cb)) for neoadjuvant treatment of patients with high-risk early breast cancer (GeparOcto)

518

Background: The sequential use of intense does-dense (idd) epirubicin, paclitaxel, cyclophosphamide (EPC) and weekly paclitaxel/liposomal doxorubicin (+/- carboplatin (Cb) in triple negative breast cancer (TNBC) (PM(Cb)) are considered highly efficient regimens for high-risk early stage breast cancer (BC). Methods: GeparOcto (NCT02125344) patients (pts) received 18 weeks (wks) either EPC (3x E 150mg/m² q2w followed by 3x P225 mg/m² q2w followed by 3x C 2000mg/m² q2) or PM(Cb) (12x P 80mg/m² plus M 20 mg/m² q1w, plus Cb AUC 1.5 q1w in TNBC). For HER2+ BC trastuzumab 6 (8) mg/kg q3w and pertuzumab 420 (840) mg q3w cycles were given concomitantly with P and C. Pts with histologically confirmed, cT1c - cT4a-d BC and central receptor assessment were included. Pts with HER2+ or TNBC were eligible irrespective of nodal status, luminal B-like tumours only if pN+. Primary objective compared pathologic complete response (pCR) rates (ypT0/is ypN0). Sample size calculations assumed a pCR rate of 50% for EPC and 60% for PM(Cb), requiring 950 pts to show superiority of PM(Cb). Secondary objectives compared pCR rates within the stratified subgroups (BC subtype, HER2+ vs HER2- HR+ vs HER2- HR-), amongst others. Results: 961 pts were recruited between 12/2014 and 05/2016, 945 started treatment. Median age was 48 years, 4% T3, 2% T4d, 46% N+, 82% ductal invasive, 66% G3 tumors; 40% were HER2+, 43% TNBC. 347 pts reported SAEs (176 EPC/171 PM(Cb)) and 2 pts died. 35 pneumonias (2 EPC vs 33 PM(Cb)) and 18 pneumonitis (3 EPC vs 15 PM(Cb)) were reported. 16.4% pts with EPC and 33.8% with PM(Cb) discontinued treatment (p<0.001), mainly due to AEs (47 EPC vs 113 PM(Cb)). Mean treatment duration was 17 wks with EPC and 16 wks with PM(Cb). pCR rate was 48.3% with EPC and 47.6% with PM(Cb)(OR 0.97 (95%CI 0.75-1.25), p=0.876). pCR rate in TNBC was 48.5% with EPC and 51.7% with PM(Cb); in HER2+ 62.0% vs 57.4% and in Luminal B 14.1% vs 14.6%. Conclusions: In high-risk early stage breast cancer pts pCR rates of idd EPC compared to weekly PM(Cb) were not significantly different. PM(Cb) appeared to be less feasible. Clinical trial information: NCT02125344.

Tumor-Infiltrating Lymphocytes: A Promising Biomarker in Breast Cancer

There is clear evidence that the immune system plays an essential role in tumor defense. By determining tumor-infiltrating lymphocytes (TILs), the individual immunological response becomes more apparent and measurable. In breast cancer, high levels of TILs are associated with a more favorable clinical course. In this review, we describe how TILs are determined with emphasis on daily routine diagnostics. We further discuss their impact as a prognostic and predictive biomarker in the neoadjuvant and adjuvant therapy setting as well as in residual disease. We also discuss their potential future implications on further stratifying prognostic subgroups of breast cancer, thereby possibly influencing future therapy considerations.

[Molecular pathology for breast cancer: Importance of the gene expression profile]

Gene expression arrays are currently used to guide therapy decisions in breast cancer. The indications for gene expression tests are especially important in the group of hormone receptor negative, HER2 positive tumors to decide whether endocrine therapy alone is sufficient or additional chemotherapy is necessary. In this group of luminal tumors conventional clinicopathological parameters are often not suitable to select patients who would benefit from an endocrine therapy alone. Gene expression tests can provide additional information and, therefore, support decision-making and avoid unnecessary chemotherapy. There are a variety of test systems available which poses the questions of which tests should be selected for which patients and how the test results should be evaluated in a direct comparison. This report provides information about three currently available gene expression tests (i.e. OncotypeDx®, Endopredict® and PAM50/Prosigna®), comments on similarities and differences and discusses the impact on therapy decisions. The focus of this article is on a discussion of clinical studies that have compared the different molecular tests in the same clinical study cohort. These investigations allow a first comparative evaluation of the various assays for breast cancer.