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PDF file - 53K, Recurrence free survival and miR187 expression in cohort 2

Figure S1. Characterization of MM134, SUM44, CAMA-1 and OCUB-M ILC cell lines.

PDF file - 73K, Association of clinicopathological characteristics of tumours with miR-187 expression in Cohort 1 (n=117) using Pearson's chi-squared test

PDF file - 757K, Ectopic expression of miR187 in SBKR3 cells, phenotypic effects

supplementary data figure legends updated to include wnt11 knockdown data in FigS3 (untracked)

PDF file - 56K

PDF file - 85K, qRT-PCR, standard in vitro functional assays and Western blotting description

PDF file - 414K, miR187 ectopic expression in MCF7, effects on growth, quantification of invasion

PDF file - 73K, Association of clinicopathological characteristics of tumours with miR-187 expression in Cohort 2 (n=470) using Pearson's chi-squared test

PDF file - 68K, Clinicopathological charactistics of tumours in Cohorts 1 and 2

PDF file - 65K, miRNAs associated with poor outcome in breast cancer patient cohorts

Table S3: Cox regression analysis on RATHER RNA-seq data

PDF file - 47K, miR187 expression and patient outcome stratified according to ER status

Background: Anti-HER2 therapies such as trastuzumab used for the treatment of patients with HER2+ metastatic breast cancer (MBC) have led to significant improvements to disease progression. We previously identified cases from the “Thousand Patient HER2 database” project at Saint Vincent’s University Hospital (SVUH) Dublin, of HER2+ MBC long-term durable complete responders to trastuzumab, and reported that Copy Number Aberration (CNA) burden may represent a novel prognostic predictor to trastuzumab response from the exome analysis of in HER2+ MBC “exceptional responders’’ (ExRs). However, whole-genome sequencing (WGS) allows a better understanding of how CNA affects the MBC genome and to-date, the complete genome of this “exceptional” cohort has never been described. Methods: We performed WGS analysis to characterise the CNA profiles of 9 ExRs from our HER2+ MBC cohort treated with trastuzumab. Samples were obtained from patients who never progressed/relapsed for more than 5 years (OS > 60 months). DNA was sequenced from tumours (primary or metastases) and matching control (blood or normal tissue) at a mean depth of 60X and 30X, respectively (18 samples). Somatic single nucleotide variants (SNV) were detected using GATK4 Mutect2 and CNA were identified using Control-FREEC. Results: Eighty-five HER2+ MBC were identified with OS > 60 months, of which 28 were ExRs with bone, lung, liver and lymph metastasis who responded exceptionally to trastuzumab, with a mean OS of 108 months (range 61-236 months). This cohort includes patients who were diagnosed between 31 and 80 years old (median=51). WGS analysis revealed CNA in chr6p21 with amplification of CCND3 and in chr17q12 with amplification of RAD51D. SNV were identified in genes involved in the DNA damage repair (DDR) pathway such as ATM, BRCA2, RAD50 and FANCA. On-going analysis will allow the CNA profiles of all ExRs to be presented and their CNA burden calculated in order to investigate the relationship between whole genome CNA burden and HER2+ MBC patient survival. Conclusion: To our knowledge, this is the first study to sequence the whole genome of HER2+ MBC, never relapse exceptional responders. The identification of the genomic aberrations of these metastatic patients increases our understanding of the mechanisms involved in MBC progression. CNA burden may represent a novel prognostic predictor to trastuzumab response and new outcomes for patients, particularly as MBC is generally termed incurable. Citation Format: Charlotte Andrieu, Laura P. Ivers, Jose Javier Berenguer Pina, Darko Skrobo, Jo Ballot, Alex J. Eustace, Cecily Quinn, Giuseppe Gullo, Naomi Walsh, John P. Crown. Whole genome sequencing of long-term, never relapse exceptional responders HER2+ advanced metastatic breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-24.

Background: In the SUMMIT trial, original cohorts of patients with HR+, HER2-negative (locally assessed), HER2-mutant MBC received N alone or N+F, with promising clinical response rates but abbreviated duration. Clinical progression coincided with emergence of additional HER2 mutations and/or amplification of the mutant allele [Smyth et al. Cancer Discov 2020;10:198–213]. Addition of T to the combination was postulated to prolong response; the combination of N+F+T in heavily pretreated patients with HR+, HER2-mutant MBC who had received CDK4/6 inhibitors (n=51) yielded a confirmed overall response rate (ORR) of 35.3%, median duration of response (DOR) of 14.3 months, clinical benefit rate (CBR) of 47.1%, and median progression-free survival (PFS) of 8.2 months [Jhaveri et al. J Clin Oncol 2022;40:1028]. Seven of these 51 patients were part of a randomized (1:1:1) cohort who received N+F+T, F+T, or F alone. Patients randomized to F+T or F could crossover to N+F+T upon progression. No patients responded to F or F+T; however, one of four patients who crossed over to N+F+T upon progression on F+T responded to the triplet, as did two of six who crossed over upon progression on F. We undertook ctDNA sequencing in patients who responded to N+F+T upfront and after crossover. Methods: Patients with HR+, HER2-negative MBC with activating HER2 mutation(s) and prior CDK4/6i received N+F+T (oral N 240 mg/d with loperamide prophylaxis, im F 500 mg d1, d15, and d29 of cycle 1 then q4w, iv T 8 mg/kg initially then 6 mg/kg q3w) or F+T or F alone. Efficacy endpoints included investigator-assessed ORR and CBR (RECIST v1.1), DOR, and best overall response. ctDNA was collected at baseline, every third cycle during treatment, and at the end of treatment and analyzed by next-generation sequencing. Samples were analyzed using the TEMPUS xF assay. Results: Sequencing results from ctDNA analysis are pending at the time of this abstract submission. Baseline HER2 mutations and co-alterations will be reported and compared with those found in tissue samples. Genomic spectrum and variant allele frequencies in samples taken at baseline, on treatment, and at the end of treatment from patients who experienced complete or partial response to N+F+T and then progressed (n=25) will be sequenced and mechanisms of acquired resistance will be posited. ctDNA genomic profiles of serial time points from patients randomized to F or F+T before and after crossover to N+F+T (n=10) will also be evaluated. Conclusions: Similarities and differences between the mechanisms of acquired resistance to N+F+T, and those previously reported to be associated with progression on N or N+F, will be discussed. Citation Format: Cynthia Ma, James Waisman, Adam M. Brufsky, Eddy S. Yang, Hans Wildiers, John P. Crown, Sarina A. Piha-Paul, Jennifer M. Suga, José Ángel García-Sáenz, Valentina Gambardella, Angel Guerrero, Salomon Stemmer, Ron Bose, Tonya Novara-Demgen, Daniel DiPrimeo, Lisa D. Eli, Komal Jhaveri. Genomic analysis of circulating tumor DNA (ctDNA) from patients with HR+, HER2-mutant metastatic breast cancer (MBC) enrolled in SUMMIT: mechanisms of acquired resistance to neratinib + fulvestrant + trastuzumab (N+F+T) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD17-01.