Abstract P3-08-04: Transient state change, but not permanent subtype change, after HER2-targeted therapy for HER2-positive breast cancer

Background: In CALGB 40601 (Alliance, NCT00770809), a neoadjuvant phase III trial of paclitaxel and trastuzumab with or without lapatinib for 12 weeks for patients with HER2-positive breast cancer, 33% of pretreatment tumors were Luminal A subtype, however, 69% of post-treatment samples with residual disease were Luminal A subtype. In addition, 71% of Luminal B (12/17) and 67% of HER2-Enriched (6/9) tumors changed into Luminal A, while 80% of Luminal A (20/24) remained Luminal A (Carey et al. J Clin Oncol. 2016). It is not known whether this shift to Luminal A was transient or permanent.

Methods: We selected matched pairs of pre- and post-treatment 40601 samples with tumor purity >10% based upon DNA analyses to ensure all samples contained tumor. PAM50 intrinsic subtyping was applied to the 40601 samples gene expression data using a two-step normalization process based on The Genome Cancer Atlas, and PAM50 training set. In addition, a HER2-enriched expression subtype patient-derived xenograft (PDX) tumor called WHIM35, was studied and was either untreated (n=10), or treated with lapatinib at 220 mg/kg for 1 week (wk) (n=5), for 2 wks (n=8), or for 3 wks (n=4). We also treated WHIM35 tumors with lapatinib for 2 wks (on) and then removed laptinib for 1 wk (off) (n=6), or for 2 wks on and 2-4 wk off (n=6), and finally for 3 wks on, and 1 wk off (n=3). PAM50 intrinsic subtyping was applied to the PDX gene expression data and subtype assessed as well as a genomic-based proliferation score. ANOVA p-values were calculated by comparing median values across all gene signature or correlation scores.

Results: We found 10 pairs of 40601 samples that kept their tumor purity values, however, their subtype changed to Luminal A after treatment (i.e., in the residual disease), and in these cases no minor tumor subclone became a dominant clone in the post treatment sample. Pretreatment subtypes were 6 Luminal B, 3 Luminal A, and 1 HER2-enriched. The tumor purity values did not change after the treatments, but correlation to Luminal A was significantly higher (p=0.01), while correlation to HER2-enriched (p=0.004) and proliferation signature scores (p=0.003) were significantly lower in the post-treatment samples. Among the WHIM35 PDX tumors, one sample changed its subtype from HER2-enriched to Luminal A after the lapatinib treatment and the rest remained HER2-enriched, suggesting environmental differences between patient samples and the PDX model. However, correlation to Luminal A was significantly higher in all lapatinib treated WHIM35 samples (p=8.3e-12), and notably went back to the initial low levels just one week after removing lapatinib. Likewise, correlation to HER2-enriched (p=1.2e-10) and proliferation signature scores (p=6.2e-12) also got lower while treated with lapatinib, but went back to the initial levels after cessation of treatment.

Conclusions: Our findings suggest that the apparent subtype change during HER2-targeting therapy is not permanent, but is more likely a transient state change from a HER2-enriched subtype into a more Luminal A-like state. When we plan additional treatment strategies using residual disease phenotypes, it may not be clear what is the true subtype of the sample due to this inherent plasticity.

Citation Format: Tanioka M, Parker JS, Henry LN, Tolaney S, Dang C, Krop IE, Harris L, Polley M, Berry DA, Winer EP, Carey LA, Perou CM. Transient state change, but not permanent subtype change, after HER2-targeted therapy for HER2-positive breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-08-04.

Abstract P5-04-27: Investigating the incidence of ESR1 gene amplification in breast cancers resistant to multiple endocrine agents

Background: Around 70% of all breast cancers (BCs) are estrogen receptor positive (ER+), but some do not respond to endocrine therapy (ET) and many eventually develop resistance. ESR amplification (ESRA) linked to an increase in ESR1 gene expression is known to occur in some cancers that are endocrine resistant. However, the incidence of ESRA has been the object of debate and its clinical significance remains unclear. This study aimed to investigate the incidence of ESRA in BCs resistant to multiple sequential ETs and optimise a fluorescence in-situ hybridisation (FISH) methodology to robustly detect ESRA.

Methods: Two unique cohorts have been studied:

(A) 20 post-menopausal women with ER+ BC with acquired resistance to letrozole, subsequently treated with up to 4 different lines of ET. Serial RNA and DNA from 3-5 cancer samples per patient (58 samples from 20 patients) were analysed by Ribo0-RNAseq and DNA exome sequencing;

(B) 18 post-menopausal women who developed ER+ BC recurrences on 1st line adjuvant letrozole, then on 2nd line tamoxifen and subsequently on 3rd line exemestane. Tissues were collected at the time of each surgery.

We have optimised a FISH method to assess ESRA in these tissues.

Results: In cohort A, 6/20 patients developed ESR1 gene amplification (ESRA) at some point during treatment. In 5 of these cases, ESRA was only found while on 2nd or 3rd line exemestane but was not present on acquired resistance to previous letrozole or tamoxifen. 1 patient had ESRA at the time of first recurrence on letrozole.

The FISH method showed concordance with the genomic analysis. This suggests that ESRA may be associated with BCs that are treated with and then become resistant to exemestane.

ESRA is also evident in samples from Cohort B, which includes 18 exemestane resistant cases. The complete analysis is ongoing.

Conclusions:

· ESRA can be seen in ER+ recurrent BCs.

· ESRA may be associated with BCs treated with 2nd or 3rd line exemestane.

· The frequency of ESRA in endocrine and exemestane resistance can now be ascertained using an optimised FISH-based method, which is more cost-effective than alternative genomic and biochemical methods.

Citation Format: Turnbull AK, Martinez-Perez C, Mok S, Tanioka M, Fernando A, Renshaw L, Keys J, Wheless A, Garrett A, Parker J, He X, Sims AH, Carey LA, Perou CM, Dixon JM. Investigating the incidence of ESR1 gene amplification in breast cancers resistant to multiple endocrine agents [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-27.

Abstract P5-04-14: Tracking ESR1 mutation clonal evolution in breast cancer using in situ mutation detection

Background: Approximately 70% of breast cancers (BCs) are estrogen receptor positive (ER+). Not all ER+ cancers respond to endocrine therapy (ET) and many eventually develop acquired resistance. Next-generation sequencing (NGS) has shown ESR1 mutations (ESRMs) are present in 10-50% of recurrent/metastatic cancers treated with aromatase inhibitors (AIs). Many of these mutations are located in the ligand-binding domain of ER, so they can lead to constitutive activation. This suggests ESRMs are a major mechanism of acquired resistance to endocrine therapy (ET) and numerous studies have shown a link between ESRMs and reduced sensitivity to 2nd line ET. The aim of this project was to investigate the incidence and clonal evolution of common ESRMs in BCs resistant to multiple sequential ETs using NGS, as well as novel PCR and in situ mutation detection methods.

Methods: We have optimised an allele-specific real-time PCR (rtPCR) assay and an in situ mutation detection method (ER-ISMD) for the assessment of ESRMs. Both have been designed to identify a missense gain-of-function D538G mutation with a single nucleotide-resolution in formalin-fixed paraffin-embedded (FFPE) BC tissues.

Two unique cohorts have been studied:

(A) 20 post-menopausal women (PMW) with ER+ BC who acquired resistance to letrozole and were treated with up to 4 subsequent lines of ET. Serial RNA and DNA from 3-5 cancer samples per patient (58 samples from 20 patients) were analysed by Ribo0-RNAseq, DNA exome sequencing, rtPCR and ER-ISMD.

(B) 150 PMW with ER+ BC who developed local (n=79), lymph node (n=59) or distant (n=12) recurrences on 1st line adjuvant letrozole, anastrozole or tamoxifen. Of these, 48 patients developed subsequent recurrences on 2nd line ET. Tissue samples from each recurrence and matched primary BC were collected.

Results: In cohort A, 5/20 patients (20%) had expansion of a D538G ESR1 mutation clone at time of resistance 1st line ET (3:letrozole, 1:anastrozole, 1:tamoxifen). The mutant allele frequency (MAF) increased further in the 4 BCs treated with 2nd line ET (2:tamoxifen, 2:exemestane) and further still in the 1 BC who received 3rd line exemestane. 0/6 patients with ESRM responded to subsequent ET. Allele-specific rtPCR and ER-ISMD have been used to validate these findings and also identified low frequency ESRM clones in the sequential samples prior to the development of clinical resistance, that were not reported by NGS. Both methods have also been applied to screen tissues from patients in cohort B, where ESRMs have also been identified in recurrent samples. Complete analysis is currently ongoing.

Conclusions:

· ESRMs develop and expand in some BCs as a mechanism for acquired resistance to ET and are associated with a lack of response to subsequent standard ETs.

· Allele-specific rtPCR can detect ESRMs and is more cost-effective and easier to use than NGS for ER mutation analysis.

· Some ESRMs predate clinical resistance.

· ER-ISMD is a novel approach that allows for identification and visualisation of the distribution of mutant clones in morphologically intact FFPE tissue.

· ER-ISMD has the potential to become a clinically useful tool to help direct the use of 2nd line ET in routine care.

Citation Format: Martinez-Perez C, Turnbull AK, Tanioka M, Fernando A, Renshaw L, Keys J, Wheless A, Garrett A, Parker J, He X, Sims AH, Carey LA, Perou CM, Dixon JM. Tracking ESR1 mutation clonal evolution in breast cancer using in situ mutation detection [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-14.

Abstract P3-06-17: Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis

Background: Transcriptomic analyses of clinical samples can help improve our understanding of disease aetiology, drug effectiveness, assign molecular subtypes and derive prognostic signatures for clinical decision-making. The success of early microarray studies relied heavily on sample quality and predominantly fresh frozen (FF) tissues to generate reliably robust data. The emergence of next-generation microarray and sequencing-based technologies from formalin-fixed paraffin-embedded (FFPE) tissues provides an opportunity to study archival clinical tissues with long-term follow-up. Here we assess 9 technologies, which vary in resolution, cost and RNA requirements, with matched FF and FFPE tissues from the same patient.

Methods: Sequential tumour biopsies were taken pre-treatment and on-treatment (at 14-days and 3-months) from 11 postmenopausal patients with oestrogen receptor positive breast cancer treated with 3 months of neoadjuvant letrozole. Half of each sample was snap frozen in liquid nitrogen and half was FFPE, RNA was extracted from both. Transcriptomic analyses were performed using 9 technologies: Illumina Beadarray, Affymetrix U133A, Affymetrix Clariom S, NanoString nCounter, AmpliSeq Transcriptome, Lexogen QuantSeq and IonXpress RNAseq, Tempo-Seq BioSpyder and Qiagen UPX3'.

Results: Success rates for generating robust expression profiles from FFPE tissues were 100% all except the Illumina BeadChip (22%) and AmpliSeq Transcriptome (83%) , which varied by the age of tissue. With the total number and position of probes/primers/counts varying widely between approaches, in total 7305 genes were represented across all of the whole-genome technologies tested.

Clear batch effects were evident when comparing data from FF and FFPE tissues and when comparing between different technologies. Standard batch correction approaches such as XPN and ComBat minimised technical bias effect and increased the correlations between matched samples (FF and FFPE) to R>0.9, irrespective of the technology used.

When analysed by multi-dimensional scaling following batch correction, samples clustered by treatment time-point. When ranked by expression of 60 proliferation genes, reported by us to change with letrozole treatment, samples ordered again by time-point, consistent with our previous findings, and paired samples clustered together.

Conclusions:

· Robust gene expression profiles can be reliably generated from FFPE tissues and are comparable to those derived from FF tissue using established transcriptomic approaches.

· A range of new technologies are available for the study of FFPE tissues; these vary in cost, resolution and RNA requirements to fit the user's needs.

· Gene expression data from biologically similar studies, generated using different technologies, can be reliably integrated for robust meta-analysis, subject to appropriate batch correction analysis.

Citation Format: Turnbull AK, Selli C, Martinez-Perez C, Fernando A, Renshaw L, Keys J, Figueroa JD, He X, Tanioka M, Munro A, Murphy L, Fawkes A, Clark R, Coutts A, Perou CM, Carey LA, Dixon JM, Sims AH. Unlocking the transcriptomic potential of formalin-fixed paraffin embedded breast cancer tissues for high-throughput genomic analysis [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-17.

Abstract GS3-02: Invasive disease-free survival and gene expression signatures in CALGB (Alliance) 40601, a randomized phase III neoadjuvant trial of dual HER2-targeting with lapatinib added to chemotherapy plus trastuzumab

Purpose

Dual HER2 targeting increases pathologic complete response (pCR) rate to neoadjuvant therapy and improves outcomes in both early and metastatic HER2-positive disease. CALGB 40601 is a randomized phase III trial examining the impact of dual HER2 blockade consisting of trastuzumab (H) and lapatinib (L) added to paclitaxel (T) on pCR, considering tumor and microenvironment molecular features. We previously found that pCR was numerically but not significantly increased with dual therapy, and that tumor molecular subtype and evidence of immune activation significantly and independently affected pCR (Carey et al, JCO 2016). In this secondary analysis, we sought to evaluate the effects of treatment arm and gene expression-defined subgroups on invasive disease free survival (IDFS).

Patients and Methods

Patients (Pts) with stage II to III HER2-positive breast cancer underwent tumor biopsy followed by random assignment with equal probabilityto paclitaxel plus trastuzumab alone (TH) or with the addition of lapatinib (THL) for 16 weeks before surgery. A paclitaxel plus lapatinib (TL) arm was closed early based on reports of futility from other trials. A secondary endpoint was IDFS, defined as the time from surgery until local or distant recurrence, new primary, or death from any cause, whichever was first. Gene expression signatures were identified by RNA sequencing.

Results

Between 12/2008 and 2/2012, 305 pts were enrolled. 261 pts had IDFS and gene expression information available (THL, n = 103; TH, n =101; TL, n = 57); there were no significant differences in clinical characteristics between this subset and the entire population. The median IDFS follow-up was 4.6 years with 40 IDFS events having occurred (THL, n=7; TH, n=19; TL, n=14). IDFS was significantly longer in the THL arm compared to standard TH (HR=0.34; 95% CI: 0.14-0.82; p=0.02). IDFS was also significantly longer among pCR than non-pCR pts (HR=0.40; 95% CI: 0.19-0.81; p=0.01), and did not differ by hormone receptor (HR) status, clinical stage, tumor size, race, menopausal status or age. Among gene expression signatures, only immune activation measured by an IgG signature was associated with longer IDFS (HR=0.71; 95% CI: 0.51-0.98; p=0.04); this signature was previously also associated with pCR. Multivariate analysis showed dual therapy (HR=0.35; p=0.02), pCR (HR=0.36; p=0.01), IgG (HR=0.69; p=0.05), and molecular subtype (LumA vs HER2E, HR=0.24, p=0.005) were associated with longer IDFS. A subgroup analysis by hormone receptor status revealed that among pts with HR+ disease, pts with luminal A experienced longer IDFS (HR=0.23; p=0.02) compared to those with luminal B or HER2-enriched molecular subtypes.

Conclusion

Dual HER2-targeting with lapatinib added to 16 weeks of TH produced significantly longer IDFS than TH alone, despite modest effects on pCR. Similar to pts with HER2-negative disease, pts with luminal A had better IDFS than those with other molecular subtypes. Immune activation as measured by RNA-based signature independently predicted both pCR and IDFS.

Support: U10CA180882, U10CA180821, U24CA196171, P50-CA58823, Susan G Komen, BCRF

Citation Format: Krop IE, Hillman D, Polley M-Y, Tanioka M, Parker J, Huebner L, Henry NL, Tolaney SM, Dang C, Harris L, Berry DA, Perou CM, Partridge A, Winer EP, Carey LA. Invasive disease-free survival and gene expression signatures in CALGB (Alliance) 40601, a randomized phase III neoadjuvant trial of dual HER2-targeting with lapatinib added to chemotherapy plus trastuzumab [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 GS3-02.

Abstract P2-09-05: Independent validation of the PAM50-based chemo-endocrine score (CES) in hormonal receptor positive (HR+)/HER2+ breast cancer (BC) treated with neoadjuvant (NA) anti-HER2-based therapy

Background. HER2+/HR+ BC is heterogeneous and subgroups with different treatment sensitivities need to be identified. We previously reported a PAM50-based CES in HR+/HER2-negative BC (Prat et al. CCR 2016). Here, we evaluated the association of CES with pathologic complete response (pCR) following anti-HER2-based therapy in HR+/HER2+ BC across 6 NA studies.

Methods. Intrinsic subtype and clinico-pathological data were obtained from 6 NA clinical studies (CHERLOB, OptiHERHEART[OHH], PAMELA, LPT109096, ICO and CALGB 40601 [CALGB is part of the Alliance for Clinical Trials in Oncology]). All patients (pts) received chemotherapy (CT) and trastuzumab, except for pts in the PAMELA study who did not receive CT. A second anti-HER2 agent (lapatinib or pertuzumab) was included in the NA of all pts in OHH and PAMELA and in one of the treatment arms in CHERLOB, LPT and C40601. CES was evaluated as a continuous variable, and categorically (CES-E[endocrine-sensitive], CES-U[uncertain] and CES-C[chemo-sensitive]) using the previously reported cut-offs. In all studies, except CHERLOB and C40601, ERBB2 mRNA levels were measured using the nCounter platform. pCR in the breast was the endpoint. We first performed statistical analyses in each dataset individually, and then in a dataset with combined patient-level data. Univariate and multivariable logistic regressions analyses were used.

Results. A total of 345 pts were included in the analysis. In the combined cohort, CES-E, CES-U and CES-C were identified in 27.5%, 23.7% and 48.6% of the pts, respectively. Table 1 summarizes the distribution and pCR rates by CES groups. In the combined cohort, CES-C was associated with higher pCR rates compared to CES-U and CES-E independent of tumor size, nodal status, anti-HER2 treatment (single vs. dual HER2 blockade), intrinsic subtype (HER2-enriched [HER2E] versus not) and study (Table 2). In the PAMELA trial (no CT), CES-C was also found associated with higher pCR rates compared to CES-E (31.6% vs. 0%). Concordant with this finding, CES-C tumors showed higher ERBB2 mRNA levels than non-CES-C (P<0.01).

Conclusion. CES shows clinical validity for predicting CT/HER2-targeting sensitivity in HER2+/HR+ BC beyond intrinsic subtype and clinicopathologic characteristics. HER2+/HR+/CES-E tumors, which represent ˜20% of all HER2+ tumors, show low sensitivity to anti-HER2 regimens (with and without CT); other treatment strategies might be needed for this group.

Support: U10CA180882;U10CA180821;U24CA196171;P50-CA58823;BCRF;Komen.

Table 1. Distribution and pCR rates of CES-E, CES-U and CES-C groups across studies.n(%pCR)LPTCHERLOBOHHICOPAMELAC40601TOTALCES-E00/9(0)1/5(20)0/7(0)0/14(0)16/60(27)17/95 (18)CES-U0/1(0)4/15(27)5/7(71)4/13(30)2/25(8)10/21(47)25/82 (30)CES-C20/29(69)12/32(37)22/28(78)15/29(52)12/38(32)3/6(50)84/162(52)P0.330.080.040.03<0.01<0.01<0.01

Table 2. Association of CES, intrinsic subtype, clinicopathologic variables and study with pCR in a multivariable model (including type of study). OR95% CIPCES   CES-E1  CES-U2.91.2-7.0<0.01CES-C6.22.3-16.4<0.01T3-4 vs T1-20.40.2-0.90.02N+ vs N00.90.4-1.70.68HER2E vs not2.21.1-4.30.02AntiHER2: 2vs12.90.7-3.20.20

Citation Format: Pascual T, Tanioka M, Dieci MV, Pernas S, Gavila J, Guarnieri V, Cortes J, Llombart A, Conte P, Oliveira M, Paré L, Galván P, Perou CM, Prat A, Carey L. Independent validation of the PAM50-based chemo-endocrine score (CES) in hormonal receptor positive (HR+)/HER2+ breast cancer (BC) treated with neoadjuvant (NA) anti-HER2-based therapy [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 P2-09-05.

Abstract P4-04-02: Characterising the effects of neoadjuvant endocrine therapy on primary cancers and nodal metastasis

Background: Approximately 40% of ER+ breast cancer present with nodal metastasis. To date, there has been no comparison of the molecular response of primary cancers and metastases to ET. Recent evidence suggests that nodal metastases have different clones and subclones compared to the primary tumour. The aim of this study is to characterise the molecular response of primaries and nodal metastases to ET.

Methods: A unique set of 7 post-menopausal women with ER-positive breast cancer had biopsies taken from the primary tumour and a positive lymph node at diagnosis and at surgery following 3-12 months of neoadjuvant letrozole. 14-day and 3-6 month on-treatment biopsies from the primary tumour and involved nodes were also taken from the same patients, giving a total of 75 samples. Lymph node FFPE blocks were stained for cytokeratin and macro-dissected to enrich for tumour tissue. RNA and DNA were extracted and Ribo0-RNAseq, DNA exome sequencing and somatic mutation detection using UNCeqR performed. Whole-transcriptome AmpliSeq targeted-sequencing has been analysed for 4 patients.

Results: Multi-dimensional scaling and hierarchical clustering analysis based on all transcripts and the 500 most variably expressed genes revealed that primaries and nodal metastases are strongly associated at diagnosis but some nodes diverge during ET treatment. Analysis of estrogen-responsive proliferation-associated genes (n=60) in nodal metastasis revealed a reduction in expression of the majority of genes with ET. However, the expression levels of some remained high in the on-treatment node samples in all 4 patients analysed compared with the matched primary tumour on treatment. In particular, expression of genes involved in DNA replication and regulation of cell cycle including MCM6 and RRM2 (DNA replication), ASPM and CEP55 (mitosis) and CDKN3 (regulation of cell cycle) persisted at high levels in nodal metastases, but reduced in the primary cancers. Similarly, primary tumours had increased levels of ECM remodeling genes (n=60) as treatment continued, while levels in the nodal metastasis were heterogeneous on-treatment. Full genome sequencing results will be available by December 2017.

Discussion

· This is the first study to investigate genomic and transcriptomic changes with ET in both primary cancers and nodal metastases.

· On-treatment changes in nodal disease are heterogeneous between patients and within the same patient.

· Nodal metastases do respond to ET with reduced levels of proliferation-associated genes.

· Some proliferation-associated genes appear to maintain higher expression in nodal disease.

· Patterns of gene expression observed in some nodal metastases are consistent with profiles previously described by us for ET resistance and recurrent disease.

· Nodal metastases may accumulate mutations during treatment with ET and on-going analysis will clarify this.

Citation Format: Dixon JM, Turnbull AK, Tanioka M, Parker J, He X, Fernando A, Renshaw L, Keys J, Thomas JS, Sims AH, Carey LA, Perou CM. Characterising the effects of neoadjuvant endocrine therapy on primary cancers and nodal metastasis [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 P4-04-02.

Abstract P4-03-01: Causes of endocrine therapy resistance: An in-depth genomic analysis of resistant multidrug ER+ breast cancers

Background: 70% of all breast cancers (BCs) are ER+. Not all ER+ cancers respond to endocrine therapy (ET) and many eventually develop resistance. The aim was to perform in-depth genomic analysis of both primary resistant BCs, that do not respond to ET, and cancers which progress (>40% increase in size) after an initial response as they acquire resistance (AQR) to ET.

Methods: A unique series of 48 post-menopausal women with ER+ BC received neoadjuvant ET using letrozole (L) or anastrozole (A) (mean treatment duration 17 months, range 3-67). 13/48 received up to 4 lines of ET.

12/48 responded to A or L, 16/48 had primary resistance and 20/48 had AQR.

Of 20 with AQR, 13 had 2nd line ET with A or tamoxifen (T). 6 had 3rd line ET with exemestane (E) and 1 had 4th line megestrol acetate (MA). Serial RNA & DNA from 3-5 cancer samples/patient (226 samples) had Ribo0-RNAseq, DNA exome sequencing and somatic mutation detection using UNCeqR. We have data so far on 29 patients: 5 responders, 4 with primary resistance and 20 AQR, the full cohort will be complete shortly.

Results:

ESR1 Mutations (ESRM): 1/5 responders had an ESRM (E380Q) at diagnosis. This clone disappeared with response to L. 5/20 patients with AQR (25%) had clonal expansion of an ESRM during 1st line ET (L:4, A:1). 4 had a chr6:152419926[lowbar]A:G (D538G) ESRM and 1 had a novel ESRM. Of the 5 with ESRM acquired during 1st line ET, the mutant allele fraction (MAF) increased further in the 4 who had 2nd ET (3:T, 1:E) and increased further for the 2 who had 3rd line E.

ESR1 Amplification (ESRA):

5 patients developed ESRA. 3/5 developed ESRA on 2nd or 3rd line E that was not present on AQR to 1st line L or A and 2nd line T. The other 2 developed ESRA on L. 2/5 with ESRA had concomitant CYP19A1 amplification. One patient with ESRA that developed on 3rd line E subsequently responded to MA. No patients with primary resistance to 1st line ET had an ESRM or ESRA.

PIK3CA mutations (PIK3M): 5/20 with AQR had PIK3M (25%). 3/7 had PIK3M at diagnosis and in 3 MAF increased between 1st and 2nd line ET. 2/7 developed PIK3M when resistant to 2nd line ET, 1 of the 2 had ESRA. 2 patients responsive to L had PIK3M at diagnosis and MAF decreased with therapy.

Other Mutations: Unique mutations with limited commonality developed and new clones expanded in the remaining cancers during primary and acquired resistance. Clonality analysis of AQR samples to different ETs showed proliferation of specific clones, characterised by novel sets of mutations, which typically became the dominant clone at the time of resistance to a particular agent.

Summary: 13/20 with acquired resistance had ESRM, ESRA, or PIK3M in resistant tumours: 1 had all 3, 2 ERSM + ESRA, 1 ERSA + PIK3CA, 4 ESRM only, 2 ESRA only and 3 had PIK3M only.

Conclusions:

• Endocrine resistance is complex

• ESRM or ESRA is uncommon at diagnosis and does not explain primary ET resistance

• ESRM (in particular the D538G mutation) occurs in one-third of patients with acquired resistance. 2nd line ET results in clonal selection and expansion of ESRM cells. Assessing recurrences for ESRM by in situ detection has clinical utility

• ESRA is only seen in heavily ET-pre-treated tumours, with its significance being unknown.

Citation Format: Dixon JM, Turnbull AK, Tanioka M, Wheless A, Garrett A, Martinez-Perez C, Parker J, He X, Sims AH, Thomas JS, Carey LA, Perou CM. Causes of endocrine therapy resistance: An in-depth genomic analysis of resistant multidrug ER+ 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 P4-03-01.

Abstract S3-05: Integrated analysis of multidimensional genomic data on CALGB 40601 (Alliance), a randomized neoadjuvant phase III trial of weekly paclitaxel (T) and trastuzumab (H) with or without lapatinib (L) for HER2-positive breast cancer

Background: RNA profiling and mutational analyses in CALGB 40601 (NCT00770809) found significant impact on pathologic complete response (pCR) rates from tumor (intrinsic subtype, p53 mutation) and microenvironmental (immune cell) features. Integrated analysis across platforms is needed to better understand the roles of these different factors with respect to response to HER2-targeted therapies.

Methods: We performed a comprehensive genomic analyses on pCR, defined as no invasive tumor in the breast, by integrating clinicopathological information with somatic mutation status, 422 segment-level DNA Copy Number Alterations (CNAs), and 510 gene expression signatures using mRNAseq and DNA exome sequencing from 213 pre-treatment tumors. Excluding 48 samples in the TL arm that was closed early due to futility, and 4 Normal-like tumors, the dataset consisted of 161 patients from TH and THL arms including 47 HER2-enriched (HER2E), 8 Basal-like, 54 Luminal A, and 52 Luminal B, all of whom received H. The main analysis was performed using the Elastic Net on multivariate logistic regression models for predicting pCR. The samples were divided into a training and a test set, then models were built to predict pCR by 10-fold cross-validation in the training set, then applying the best model onto the test set to construct ROC curves and evaluate prediction accuracy by calculating area under ROC (AUC). We also used the DawnRank, a network-based bioinformatics tool that integrates DNA and RNA data to identify driver genes, to find predictors of resistance to H-containing therapies.

Results: Among clinicopathological factors, clinical estrogen/progesterone receptor (ER/PgR) status and intrinsic subtype by PAM50 were statistically associated with pCR, but treatment arm (TH vs THL) and stage were not. In the Elastic Net analysis, the models incorporating either gene signatures (AUC: 0.724) or CNAs (AUC: 0.777) were more predictive of response than mutation status model (AUC: 0.635). Gene signatures and CNAs were further combined with either mutation status (AUC: 0.773), clinical ER/PgR status (AUC: 0.787) or ER/PgR status plus intrinsic subtype (AUC: 0.784). The combination with the highest AUC comprised gene signatures, CNAs, and ER/PgR status, and demonstrated that CNAs at Chromosome (Chr.) 6p, 10q22, or 11q23, the signature of Correlation to HER2E, and a T-cell signature, positively predicted pCR and that Luminal and PgR gene signatures were negative predictors. The CN gain of Chr.6p, which contains the HLA genes, predicted for pCR and was associated with higher expression of HLA genes and B cell / IgG signatures. The CN loss of Chr.11q23 including CD3D, CD3E, and CD3G was also identified by DawnRank as a region associated with resistance.

Conclusions: Tumor genetics (CNAs), tumor RNA subtype (HER2E, Luminal), and the microenvironment (immune cells) were independently predictive of response to H-containing therapies and biologically and clinically important for HER2-positive breast cancer, supporting integrated RNA- and DNA-based tumor assessments to clarify response to HER2-targeting.

Support: U10CA031946/033601/180821/180882/180888.

Citation Format: Tanioka M, Fan C, Carey LA, Hyslop T, Pitcher BN, Parker JA, Hoadley KA, Henry NL, Tolaney S, Dang C, Krop IE, Harris L, Berry DA, Mardis E, Perou CM, Winer EP, Hudis CA. Integrated analysis of multidimensional genomic data on CALGB 40601 (Alliance), a randomized neoadjuvant phase III trial of weekly paclitaxel (T) and trastuzumab (H) with or without lapatinib (L) for HER2-positive breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S3-05.

Abstract P5-03-05: Genomic analysis and efficacy of entinostat in basal-like and HER2-overexpressing models

Background. The histone deacetylase inhibitor Entinostat has been under development for patients with metastatic estrogen receptor-positive breast cancer, and its use in Basal-like and HER2-overexpressing breast cancer has been limited. Here we provide results of a study using cell-lines and genetically engineered mouse (GEM) models of breast cancer to examine the effects of Entinostat and combination therapies on multiple in vitro and in vivo models.

Methods. Breast cancer cell lines SKBR3, BT474 and MCF-7 were treated with or without Entinostat at their IC50 doses and their gene expression profiles determined. Two breast cancer GEM models (MMTV-neu and C3-Tag) were used to test the efficacy of Entinostat alone, or in combination with cyclophosphamide, or a murine version of an anti-mouse PD1 immune checkpoint inhibitor.

Results: Entinostat was an effective in vitro drug with IC50 ranging from 700 to 1500 nM. Supervised analysis of gene expression data coming from treated cell lines showed induction of multiple major histocompatibility complex (MHC) class I/II genes on 6p21. In addition, several MHC genes were also upregulated in C3-Tag treated by Entinostat; because of these findings, the GEM models are currently being treated with the combination of Entinostat and the anti-mouse PD-1 inhibitor. In vivo, GEM tumors treated only with Entinostat were observed to have high objective response rates of 88% and 33% in MMTV-Neu and C3-Tag, respectively. The combination with cyclophosphamide provided significant improvements in the C3-Tag mice over either agent alone, with 11 of 17 mice achieving a CR or PR, and an extension of overall survival (98 days vs 33 days); Entinostat (42d, p=0.002) and Cytoxan (47d, p=0.001).

Conclusions. Entinostat showed anti-tumor activity in vitro and in vivo, and was synergistic with cyclophosphamide in the Basal-like C3-Tag mouse model. The upregulation of MHC genes induced by Entinostat at RNA level suggested the interaction with immune response, which is currently under study and will be presented.

Citation Format: Tanioka M, Usary J, Darr DB, Harrell CJ, Perou CM. Genomic analysis and efficacy of entinostat in basal-like and HER2-overexpressing models. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-03-05.

Increased halogenated tyrosine levels are useful markers of human skin ageing, reflecting proteins denatured by past skin inflammation

BACKGROUND

Photoageing of skin is thought to be caused by protein denaturation, which can be induced by ultraviolet radiation. Previous studies have also reported that inflammation is related to protein denaturation; however, the influence of inflammation on skin ageing has not been explored in detail.

AIM

To investigate the possible connection between inflammation and protein denaturation, which might lead to skin ageing, we focused on halogenated tyrosine as a denatured substance produced during the inflammation process.

METHODS

We measured halogenated tyrosine in aged human skin. Inflammatory cells and halogenated tyrosine were detected by immunohistochemistry using antibodies to mast-cell tryptase, neutrophilic myeloperoxidase and halogenated tyrosine. Finally, using elastic van Gieson (EVG) staining, we investigated whether the sites of halogenated tyrosine coincided with the sites at which proteins were denatured.

RESULTS

Immunohistochemical analysis indicated that both inflammatory cells and halogenated tyrosines increased with ageing in both photoexposed and photoprotected skin. EVG staining confirmed that the localization of halogenated tyrosine was close to the sites at which protein was denatured.

CONCLUSIONS

Our investigations indicate a possible connection between skin ageing and inflammation, suggesting that halogenated tyrosine could be a useful marker of ageing skin.

Prognostic factors in cutaneous squamous cell carcinoma: is patient delay in hospital visit a predictor of survival?

The patient's delay in the visit to a hospital seems to play an important role in prognosis in invasive cutaneous squamous cell carcinoma (SCC). This report explored prognostic factors of cutaneous SCC focusing on patient delay in hospital visit. Data of 117 Japanese patients who were treated for invasive cutaneous SCC in our facility between 2000 and 2010 were used for analysis. A multivariate Cox proportional-hazard modelling revealed that a pair of TNM stage (hazard ratio, 5.0; 95% CI, 1.8 to 13.9) and poorer histological differentiation (hazard ratio, 3.2; 95% CI, 0.93 to 10.3), and a pair of tumour size (hazard ratio, 1.02; 95% CI, 1.004 to 1.04) and rapid growth (hazard ratio, 8.25; 95% CI, 1.29 to 52.7) were a prognostic factor whereas patient delay in hospital visit was not. However, patient delay in hospital visit was correlated with larger tumour size.

Perturbations of both nonregulatory and regulatory FOXP3+ T cells in patients with malignant melanoma

BACKGROUND

'FOXP3+ regulatory T cells' (Tregs) are reported to be increased in tumour-bearing hosts including patients with melanoma, leading to tumour immune suppression. However, this idea is challenged by recent evidence that the 'FOXP3+ Treg' fraction in fact contains activated 'nonregulatory' T cells. Also, FOXP3+ T cells are reported to have functionally and kinetically distinct subsets.

OBJECTIVES

To investigate whether either or both of regulatory and 'nonregulatory' FOXP3+ T cells are perturbed in patients with melanoma.

METHODS

FOXP3+ T cells were classified into three subsets, namely CD45RO+FOXP3(low) nonregulatory T cells, CD45RO+FOXP3(high) effector Tregs, and CD45RO-FOXP3(low) naïve Tregs, according to their expression levels of FOXP3 and CD45RO. The percentage and cytokine production of these FOXP3+ T-cell subsets were assessed by flow cytometry.

RESULTS

Both regulatory and nonregulatory T cells were increased in patients with melanoma. Moreover, we found three unexpected perturbations in FOXP3+ T-cell subsets: (i) patients with melanoma showed higher frequencies of FOXP3(low) nonregulatory T cells, which decreased and normalized after tumour removal; (ii) FOXP3(low) naïve Tregs containing higher frequencies of interferon-γ+ cells increased with tumour progression; and (iii) CD45RO+FOXP3(high) effector Tregs were pronouncedly infiltrated around tumour tissues.

CONCLUSIONS

These findings demonstrate that patients with melanoma have distinct and differential perturbation of both regulatory and nonregulatory FOXP3+ T cells. The degree of perturbation is associated with tumour burden and progression, suggesting that the perturbation reflects fundamental pathophysiological processes in patients with melanoma. The presented analysis provides a practical approach to investigate the immunological environment of cancer patients.

Phase I study of LY2181308, an antisense oligonucleotide against survivin, in patients with advanced solid tumors

PURPOSE

LY2181308 is an antisense oligonucleotide that complementarily binds to survivin mRNA and inhibits its expression in tumor tissue. This phase I dose escalation study evaluated the tolerability, pharmacokinetics, and anticancer activity of LY2181308 in Japanese.

METHODS

Patients with solid tumors refractory to standard therapy received LY2181308 (400, 600, or 750 mg) as a 3-h intravenous infusion for 3 consecutive days and thereafter once a week.

RESULTS

LY2181308 was administered to 14 patients, aged 44-73 (median 60) years. Flu-like syndrome, prolonged prothrombin time-international normalized ratio (PT-INR), thrombocytopenia, and fatigue were common reversible grade 1/2 toxicities. The dose-limiting toxicity was reversible grade 3 elevation of ALT/AST/γ-GTP in 1 patient treated at the 750-mg dose. Pharmacokinetic analysis showed a long terminal half-life of 21 days and an extensive tissue distribution of LY2181308. In 12 evaluable patients, one patient had stable disease, while the remaining 11 patients had progressive disease.

CONCLUSIONS

LY2181308 monotherapy is well tolerated up to 750 mg with a manageable toxicity, the pharmacokinetic profile warrants further evaluation of LY2181308 in combination with cytotoxic agents or radiotherapy.

Predictors of recurrence in breast cancer patients with a pathologic complete response after neoadjuvant chemotherapy

Background:

Although a pathologic complete response (pCR) after neoadjuvant chemotherapy is associated with favourable outcomes, a small proportion of patients with pCR have recurrence. This study was designed to identify factors predictive of recurrence in patients with pCR.

Methods:

A total of 449 breast cancer patients received neoadjuvant chemotherapy, and 88 evaluable patients had a pCR, defined as no evidence of invasive carcinoma in the breast at surgery. The clinical stage was II in 61 patients (69%), III in 27 (31%). All patients received taxanes and 92% received anthracyclines. Among 43 patients with HER2-positive tumours, 27 received trastuzumab. Cox regression analyses were performed to identify predictors of recurrence.

Results:

Median follow-up was 46.0 months. There were 12 recurrences, including 8 distant metastases. The rate of locoregional recurrence was 10.4% after breast-conserving surgery, as compared with 2.5% after mastectomy. Multivariate analysis revealed that axillary metastases (hazard ratio (HR), 13.6; P<0.0001) and HER2-positive disease (HR, 5.0; P<0.019) were significant predictors of recurrence. Five of six patients with both factors had recurrence. Inclusion of trastuzumab was not an independent predictor among patients with HER2-positive breast cancer.

Conclusion:

Our study results suggest that HER2 status and axillary metastases are independent predictors of recurrence in patients with pCR.

Prospective Study of Ice Gel Pack as Less Expensive Alternative for Prevention of Skin and Nail Toxicity in Patients with Breast Cancer Receiving Docetaxel

Background: Docetaxel (DTX)-induced nail and skin toxicity can be prevented by frozen glove. We investigate whether we can use cooling gel pad (CGP), which is available less than 10 dollars in Japan, as less expensive alternative.Method: Patients (pts) with breast cancer receiving DTX as preoperative or post operative chemotherapy were eligible for this study. Two CGPs, which were refrigerated for eight hours beforehand, were used to cover patient's hand from 15 minutes before to 15minutes after DTX administration. To reduce discomfort from icing, pts were wearing cotton glove during CGP usage. If pts felt CGP as too cold during the cooling process, they were allowed to remove CGP tentatively until they felt comfort. Another hand was not covered as the control. Nail and skin toxicity were assessed at each cycle by CTCAEver.3.0 and documented by photography. Fisher's exact probability test was used. Satisfaction and discomfort of CGP covering was assessed by pts using two item questionnaires. All patients gave written informed consent. The protocol was approved by institutional review board.Result: From October 2006 to September 2008, 50 pts were enrolled to this study. All the patients were female, and received DTX 75mg/m2 in every three weeks schedule for four cycles. Most of patients received DTX after anthracycline-containing regimen. Both nail (10% v 66%, p&lt;0.0001) and skin (0% v 34%, p&lt;0.0001) toxicity was reduced in CGP covered hands. Nail toxicity was grade (G) 0 in 90% v 34%, G1 in 10% v 42%, G2 in 0% v 22%, and G3 in 0% v 2%, for CGP covered and the control hand, respectively. Skin toxicity was G0 in 100% v 66%, G1 in 0% v 4%, G2 in 0% v 30% in CGP covered hand and the control hand, respectively. About the timing of toxicity occurrence, “after the first cycle” was most common, 13 pts (39%) in nail change and 7 pts (41%) in skin toxicity. In the questionnaires, 94% were satisfied with CGP covering.Discussion: The iced CGP cover method reduced the incidence and severity of nail and skin toxicity associated with DTX, even if patients wear cotton glove and remove CGP for a while, in case of excess coldness. This method has no adverse effect, and patients were satisfied with the effect. The iced CGP may be considered as a new, effective and less expensive method for prevention of nail and skin toxicity caused by DTX.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1114.

Malignant melanoma derived from cerebriform intradermal naevus

We report a case of malignant melanoma (MM) derived from cerebriform intradermal naevus (CIN) in a 66-year-old Japanese man. The patient had cutis verticis gyrata (CVG) on the posterior area of the scalp at birth. He noticed a dome-shaped nodule at the centre of the CVG at 66 years of age. Histopathological examination found a nodule of MM arising within an extensive area of intradermal naevus. There was no metastasis to lymph nodes or other organs. To our knowledge, only two cases of CIN in which MM had later developed have been reported. We estimated that the incidence of melanoma from CIN including our case is 4.5% (3 of 67 reported cases), which seems to be comparable to the frequency of malignant alteration of giant pigmented naevi. This suggests that pathological examination is recommended for CVG, and once pathological diagnosis of CIN is confirmed, long clinical follow-ups are necessary for detecting development of MM.

Plasma biomarkers predictive for disease control duration in the phase I study of E7080, a multitarget kinase inhibitor

e14524

Background: E7080 is an oral multi-targeted kinase inhibitor of VEGFRs, PDGFRs, FGFRs and c-kit. In the phase I study for advanced solid tumors, E7080 was repeated every 3 weeks (twice daily by 2 wks-on/ 1 wk-off). The toxicities were manageable and the preliminary antitumor activity including one partial response was observed at doses up to MTD [ASCO 2008; abstract 3527]. This study was conducted to evaluate whether the change of plasma biomarkers in the E7080 phase I study could predict the antitumor activity or the disease control duration. Methods: The treatment duration was determined as a period from the first dosing to treatment failure. Plasma angiogenic proteins and circulating endothelial cells (CEC)/ progenitor cells (CEP) were measured in blood samples collected on Days 1 (pre-dose), 8 and 15 of Cycles 1 and 2. CEC and CEP population with (+) or (-) c-kit expression were analyzed by FACS. Correlation was determined by Spearman's rank correlation coefficient (r) and test for non-correlation (p). Results: 19 (76%) out of 25 evaluable patients had PR/SD including 6 (24%) patients with the treatment duration of ≥180 days. VEGF increase and sVEGFR1 and -R2 decreases in plasma were seen with the increased dose of E7080. But these changes had no correlations with disease control. E7080 decreased c-kit(+) CEC and CEP, but not c-kit(-) population. Importantly, patients showing the decrease of c-kit(+) CEC in Cycle 1 had received E7080 treatment for significantly longer duration (r=-0.468, p=0.018). The decrease of c- kit(+) CEC diminished during treatment-off for final 7 days in Cycle 1 and repeatedly decreased in Cycle 2 treatment. The decrease of c- kit(+) ratio in CEP correlated with the increase of plasma SCF (r=-0.457, p=0.021) and SDF1 (r=-0.466, p=0.018), but not with VEGF or thrombopoietin. Conclusions: The change of c-kit(+) CEC correlated with the disease control duration in the phase I study of E7080. SCF and SDF1 may play a role in c-kit(+) CEP accumulation. C-kit(+)-selective changes of CEC could be a candidate biomarker to predict the disease control duration in anti-angiogenic therapy of E7080.

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Secondary platinum therapy in patients with uterine cervical cancer previously treated with platinum chemotherapy

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Background: Second-line chemotherapy after the front-line platinum based regimens including concurrent chemoradiation (CCRT) has not been established for patients with advanced or recurrent cervical cancer. Platinum based regimens are often selected, but the predictive and prognostic factors of secondary platinum therapy are unclear. We therefore evaluated the relative influence of platinum free interval ( PFI ) between the completion of front-line regimen and the institution of second-line regimen. Methods: This retrospective review was undertaken of 65 patients who received ≥ 2 platinum-based regimens and were assessable for secondary response in National Cancer Center Hospital between 1996 and 2008. We analyzed independent predictive factors associated with secondary response by logistic regression model and prognostic factors associated with subsequent survival by Cox regression model. Results: The median age was 54 years old (range, 28 to 73). The median follow-up of subsequent survival was 11.0 months (1.1 to 66.6). The median PFI was 11.1 months (0.7 to 77.6). Overall secondary response rate was 40%, while response rate for 36 patients after CCRT was 36%. The response increases in frequency with longer PFI ( Table ). Univariate and multivariate analyses using logistic regression model showed PFI for ≥ 9 months (odds ratio [OR] = 0.28; P =.04), PS 0 (OR = 0.19; P =.006) and maximum tumor diameter ≥ 30 mm (OR = 0.23; P =.02) were independent predictive factors of secondary response. Univariate and multivariate analyses using Cox regression model revealed PFI for ≥ 9 months (hazard ratio [HR] = 0.44; P =.005), PS 0 (HR = 0.30; P =.000) and histology of squamous cell carcinoma (HR = 2.20; P =.02) were independent prognostic factors of subsequent survival. Conclusions: Our exploratory study demonstrates that platinum free interval has both predictive and prognostic value for secondary platinum-based treatment for patients with advanced or recurrent cervical cancer.

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Extensive skin necrosis of the arm in a patient with complex regional pain syndrome

We report a 36-year-old woman with complex regional pain syndrome (CRPS) type 1 presenting with extensive skin necrosis of the left arm. The patient cooled her arm with ice packs to ease severe pain due to CRPS, in spite of repeated cautions against frostbite injury. The regions of skin necrosis corresponded with the sites where she had applied ice packs. We considered that the severe skin necrosis in our case was due to a self-induced frostbite injury.