Genomic characterization of thymic epithelial tumors in a real-world dataset

BACKGROUND

Thymic epithelial tumors (TETs) are rare neoplasms arising in the mediastinum, including thymic carcinomas and thymomas. Due to their rarity, little is known about the genomic profiles of TETs. Herein, we investigated the genomic characteristics of TETs evaluated in a large comprehensive genomic profiling database in a real-world setting.

METHODS

We included data from two different cohorts: Foundation Medicine Inc. (FMI) in the United States and the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) in Japan. Samples profiled were examined for all classes of alterations in 253 genes targeted across all assays. Tumor mutational burden (TMB) and microsatellite instability (MSI) were also evaluated.

RESULTS

A total of 794 patients were collected in our study, including 722 cases from FMI and 72 cases from C-CAT. In the FMI data, CDKN2A (39.9%), TP53 (30.2%) and CDKN2B (24.6%) were frequently altered in thymic carcinoma, versus TP53 (7.8%), DNMT3A (6.8%), and CDKN2A (5.8%) in thymoma. TMB-high (≥10 mutations/Mb) and MSI were present in 7.0% and 2.3% of thymic carcinomas, and 1.6% and 0.3% of thymomas, respectively. Within C-CAT data, CDKN2A (38.5%), TP53 (36.5%) and CDKN2B (30.8%) were also frequently altered in thymic carcinoma, while alterations of TSC1, SETD2 and LTK (20.0% each) were found in thymoma.

CONCLUSIONS

To the best of our knowledge, this is the largest cohort in which genomic alterations, TMB and MSI status of TETs were investigated. Potential targets for treatment previously unbeknownst in TETs are identified in this study, entailing newfound opportunities to advance therapeutic development.

The surface and internal features of pubic hair: A comparative study with those of scalp hair

Although pubic hair has been a subject of public interest, little is known about its structure or characteristics beyond its curly and coarse appearance. In this study, we investigated the surface and internal features of pubic hair from Korean males and compared them to those of scalp hair from the same donors. Our findings indicate that the cuticle layer of pubic hair has a greater number of scales than that of scalp hair, resulting in a thicker cuticle layer overall. Fourier-transform infrared (FT-IR) spectroscopy analysis showed that the protein in the cortex layer of pubic hair was less affected by exposure to urine or ammonia than the protein in the cortex layer of scalp hair. This suggests that the cuticle layer of pubic hair, which is thicker and composed of more scales, acts as a physical barrier that protects the hair's internal structure. Furthermore, we observed that the secondary and tertiary structures of keratin in the pubic hair cuticle layer are essentially different from those in scalp hair. Based on these findings, we hypothesize that the thickened cuticle layer in pubic hair may have evolved as a defence mechanism against chemical damage from urine, urea and ammonia.

First Evidence of Axial Shape Asymmetry and Configuration Coexistence in ^{74}Zn: Suggestion for a Northern Extension of the N=40 Island of Inversion

The excited states of N=44 ^{74}Zn were investigated via γ-ray spectroscopy following ^{74}Cu β decay. By exploiting γ-γ angular correlation analysis, the 2_{2}^{+}, 3_{1}^{+}, 0_{2}^{+}, and 2_{3}^{+} states in ^{74}Zn were firmly established. The γ-ray branching and E2/M1 mixing ratios for transitions deexciting the 2_{2}^{+}, 3_{1}^{+}, and 2_{3}^{+} states were measured, allowing for the extraction of relative B(E2) values. In particular, the 2_{3}^{+}→0_{2}^{+} and 2_{3}^{+}→4_{1}^{+} transitions were observed for the first time. The results show excellent agreement with new microscopic large-scale shell-model calculations, and are discussed in terms of underlying shapes, as well as the role of neutron excitations across the N=40 gap. Enhanced axial shape asymmetry (triaxiality) is suggested to characterize ^{74}Zn in its ground state. Furthermore, an excited K=0 band with a significantly larger softness in its shape is identified. A shore of the N=40 "island of inversion" appears to manifest above Z=26, previously thought as its northern limit in the chart of the nuclides.

Heart failure with improved ejection fraction (HFimpEF) in patients treated with sacubitril/valsartan (SV)

Introduction

Several studies demonstrated that patients with improvement of left ventricular ejection fraction (LVEF) and symptoms had good prognosis in heart failure with reduced ejection fraction (HFrEF). Based on these results, new classification of HF according to LVEF was currently proposed. Sacubitril/valsartan (SV) is recommended as one of the first-line therapy of HFrEF patients. SV reduced hospitalization for HF and cardiovascular mortality compared to enalapril in PARADIGM-HF trial. However, it is unclear that patients with improvement of LVEF also have better prognosis compared to patients without LVEF improvement among patients treated with SV.

Purpose

We aimed to evaluate the clinical characteristics and outcomes of heart failure with improved ejection fraction (HFimpEF) in heart failure with reduced ejection fraction (HFrEF) patients treated with SV.

Methods

We analyzed 230 patients with HFrEF taking SV in a multicenter retrospective cohort (RECORD-SV registry) from 2017 to 2019. Enrolled 230 patients were performed baseline and 1-year follow-up echocardiography. Based on 2 echocardiographic results, we defined “HFimpEF” as HF with a baseline LVEF ≤40%, ≥10% increase from baseline LVEF and a follow-up measurement of LVEF >40%. Others were defined as “Persistent HFrEF”. We analyzed and compared clinical characteristics and outcomes between two groups. Primary endpoint was a composite outcome of all-cause death and hospitalization for HF (HHF).

Results

From 230 patients, 65 patients with HFimpEF and 165 patients with Persistent HFrEF were analyzed. The median follow-up duration was 557 days (interquartile range 364 to 727 days). Patients with HFimpEF had a higher prevalence of female gender (50.8% vs. 30.3%) and de novo HF (44.6% vs. 21.2%). There were no significant differences for age, etiology (ischemic vs. non-ischemic), diabetes, atrial fibrillation, hypertension, and HF medications including SV dose between two groups. Patients with HFimpEF showed lower rate of all-cause death or HHF as a primary endpoint compared to patients with persistent HFrEF (6.2% vs. 22.4%; IPTW adjusted HR 0.24; 95% CI 0.13–0.46; p<0.001) (Table 1). It was also shown that HFimpEF patients had a reduced risk of primary endpoint in the Kaplan-Meier curves compared with persistent HFrEF (Log-rank p=0.045) (Figure 1). We demonstrated that Non-prior MI (adjusted OR 7.29; 95% CI 1.50–35.36; p=0.014) and de novo HF (adjusted OR 4.33; 95% CI 1.70–11.04; p=0.002) were independent prognostic factors of HFimpEF in HFrEF patients treated with SV.

Conclusions

HFimpEF patients had better clinical outcomes compared to those with persistent HFrEF in HFrEF patients treated with SV. Non-prior MI and de novo HF were independent predictors of HFimpEF in patients treated with SV.

Funding Acknowledgement

Type of funding sources: None.

AB0339 EFFICACY, PHARMACOKINETICS AND SAFETY BETWEEN CT-P13 AND CHINA-APPROVED INFLIXIMAB: 54 WEEK RESULT FROM A PHASE III RANDOMIZED CONTROLLED TRIAL IN CHINESE PATIENTS WITH ACTIVE RHEUMATOID ARTHRITIS

Background

CT-P13 is an approved biosimilar to EU-approved and US-licensed Infliximab (INX) for the indications of rheumatoid arthritis (RA), adult and paediatric Crohn’s disease, adult and paediatric ulcerative colitis, ankylosing spondylitis, psoriatic arthritis and psoriasis.

Objectives

The purpose of this study was to demonstrate equivalence of efficacy and compare PK and safety profiles of CT-P13 and China-approved INX.

Methods

In this randomized, double blinded, multicenter, parallel-group, phase III study, patients with active RA who had been responding inadequately to methotrexate for at least 3 months, were randomized to receive either CT-P13 or China-approved INX. Patients were treated with doses of 3 mg/kg at Weeks 0, 2, 6, then every 8 weeks up to Week 54. Prior to dosing at Week 30, patients randomized to China-approved INX underwent a second randomization either to continue China-approved INX or to switch to CT-P13 at Week 30. Results of patients who underwent transition to CT-P13 were included in the China-approved INX group. The primary efficacy endpoint was change in DAS28 (CRP) from baseline to Week 14, which was analyzed using an analysis of covariance. Equivalence was determined if the 90% CI for the estimate of treatment difference was entirely contained within the predefined equivalence margin of -0.6 to 0.6.

Results

270 patients were randomly assigned to 2 treatment groups in a 1:1 ratio (136 and 134 patients in the CT-P13 and China-approved INX groups, respectively) and 184 patients completed the study. The least square mean change (standard error) of DAS28 (CRP) from baseline to Week 14, -1.566 [0.1419] and -1.547 [0.1491], was similar between the CT-P13 and China-approved INX groups, respectively. The 90% CI for the estimate of treatment difference (-0.29, 0.25) was contained within the predefined equivalence margin, which demonstrated therapeutic equivalence between the groups. The mean actual values for DAS28 (CRP) decreased from baseline to Week 54 and were similar between the groups (Figure 1). Additional efficacy endpoints, including ACR responses (ACR20 at Week 14; 60.6%, 54.8% and at Week 54; 65.1%, 60.6% in the CT-P13 and China-approved INX groups, respectively), EULAR responses, CDAI, and SDAI, were similar between the groups, even after switching at Week 30. During the study, mean serum INX concentrations were similar between the groups. Between Weeks 14 and 22, mean (percent coefficient of variation) AUCτ were 11156333.615 (44.796) ng·h/mL and 11462884.280 (51.057) ng·h/mL, and Cmax,ss were 66577.2 (31.4) ng/mL and 66356.1 (21.0) ng/mL in the CT-P13 and China-approved INX groups, respectively, which were similar between the groups. Most treatment-emergent AEs were grade 1 or 2 in intensity. One malignancy was reported in the CT-P13 group and no deaths were reported. The proportions of patients with anti-drug antibodies were similar between the groups, even after switching at Week 30. The overall safety profile of CT-P13 was comparable to that of China-approved INX and no new safety issues were observed (Table 1).

Table 1.

Summary of Safety Results

Number of patients (%)CT-P13 (N=136)China-approved Infliximab (N=133)Treatment-emergent AEsTotal115 (84.6%)107 (80.5%)Related97 (71.3%)86 (64.7%)Treatment-emergent serious AEsTotal17 (12.5%)12 (9.0%)Related10 (7.4%)6 (4.5%)Infusion related reaction/ hypersensitivity/anaphylactic reactionsTotal(=Related)20 (14.7%)19 (14.3%)InfectionsTotal45 (33.1%)43 (32.3%)Related36 (26.5%)40 (30.1%)

Note: Summary is presented for the safety population who received at least 1 dose (full or partial) of study drug.

Conclusion

The study demonstrated that efficacy of CT-P13 is equivalent to that of China-approved INX. Also, the PK and safety profiles of CT-P13 were comparable to those of China-approved INX. No loss of efficacy or difference in safety or immunogenicity was observed after switching from China-approved INX to CT-P13 at Week 30.

Disclosure of Interests

Jonathan Kay Consultant of: Boehringer Ingelheim GmbH; Pfizer Inc.; Samsung Bioepis; Sandoz Inc., Grant/research support from: Pfizer Inc. (paid to UMass Chan Medical School), Xiaofeng Zeng Grant/research support from: Celltrion, Inc, Lin Chen Grant/research support from: Celltrion, Inc, Kaijiang Tang Grant/research support from: Celltrion, Inc, guixiu shi Grant/research support from: Celltrion, Inc, Lin Liu Grant/research support from: Celltrion, Inc, Lijun Wu Grant/research support from: Celltrion, Inc, Yi Liu Grant/research support from: Celltrion, Inc, Jiankang Hu Grant/research support from: Celltrion, Inc, Shengyun Liu Grant/research support from: Celltrion, Inc, Zheng Yi Grant/research support from: Celltrion, Inc, Sung Hyun Kim Employee of: Celltrion, Inc, YunJu Bae Employee of: Celltrion, Inc, JeeHye Suh Employee of: Celltrion, Inc, Seungjin Rhee Employee of: Celltrion, Inc, SeulGi Lee Employee of: Celltrion, Inc, Chankyoung Hwang Employee of: Celltrion, Inc

THU0186 CLINICAL EVALUATION OF THE IMMUNOGENICITY TO CT-P13 FOR SUBCUTANEOUS USE IN PATIENTS WITH ACTIVE RHEUMATOID ARTHRITIS: 1-YEAR CLINICAL RESULTS FROM A MULTICENTER, RANDOMIZED CONTROLLED PIVOTAL TRIAL

Background:

Novel subcutaneous infliximab (CT-P13 SC) was developed to augment the flexibility in therapeutic use of infliximab and noninferiority (NI) of CT-P13 SC versus CT-P13 intravenous (IV) was demonstrated for efficacy in patients with rheumatoid arthritis (RA) [1]. CT-P13 SC 120mg biweekly showed consistent higher therapeutic trough levels during the treatment period, which helps in maintaining efficacy over time. Since immunogenicity has clinical importance in patients using anti-TNF alpha agents and there is a general presumption that SC route is more immunogenic than IV route, this needs careful assessment.

Objectives:

Immunogenicity assessment of CT-P13 SC with further impact analysis has been performed on the pivotal data set [1] to determine whether there was any correlation between the magnitude of anti-drug antibody (ADA) positivity and clinical outcomes in RA patients.

Methods:

The immune response against CT-P13 in human serum was detected using an electrochemiluminescence (ECL) platform with an Affinity Capture Elution (ACE) step. An ADA ECL ACE assay showed ability to detect ADA at low levels in all samples regardless of residual drug in serum (25 ng/mL ADA in the presence of 80 μg/mL of CT-P13 in RA serum). To investigate the impact of ADA titer on PK, efficacy and safety, key clinical parameters were assessed by visit based ADA titer quartile. All patients who had ‘Positive’ ADA status result at each visit were included in the analysis and categorized into 4 groups using the 25th, 50th, 75th percentiles of ADA titer result, respectively.

Results:

The four subgroups categorized by quartiles at each visit from week 22 to week 54 were: 1st (ADA titer ≤ 3), 2nd (3 < ADA titer ≤ 9), 3rd (9 < ADA titer ≤ 27) and 4th (27 < ADA titer). There was a trend for pre-dose concentration to decrease as ADA titer increases for both CT-P13 SC and CT-P13 IV arms as expected (Figure 1). Patients in the 1st and 2nd subgroup maintained the sufficient therapeutic drug concentration level. Figure 2 shows the correlation between ADA titer and efficacy outcomes where the change from baseline of DAS28 (CRP) and the proportion of patients achieving ACR20 were lower in the 3rd and 4th subgroups. The ADA impact was especially apparent in the 4th subgroup where the mean pre-dose concentration of the patients was below the therapeutic drug concentration level (1 μg/mL), which led to worse efficacy outcomes in both arms, IV as well as SC. Nevertheless, no impact of ADA on safety profile in both arms was observed. A neutralizing antibody (NAb) method with enhanced drug tolerance but limited performance was also developed and clinical consequences of NAb titer in terms of PK, efficacy and safety were not different from the results with ADA.

Conclusion:

The analysis of both ADA positivity and titer is clinically meaningful in the prediction of PK profile and clinical response. CT-P13 SC administration did not result in a greater incidence of ADA compared to the CT-P13 IV and there were no clinical differences depending on the formulation.

References:

[1]Westhovens R, et al. Annals of the Rheumatic Diseases 2019;78:1158-1159.

Disclosure of Interests:

Rene Westhovens Grant/research support from: Celltrion Inc, Galapagos, Gilead, Consultant of: Celltrion Inc, Galapagos, Gilead, Speakers bureau: Celltrion Inc, Galapagos, Gilead, DaeHyun Yoo Grant/research support from: Celltrion, Inc, Consultant of: Celltrion, Inc, Speakers bureau: Celltrion Healthcare, Inc, Piotr Wiland Grant/research support from: Celltrion, Inc, Speakers bureau: Novartis, Pfizer, Abbvie, Gedeon-Richter, Lilly, Roche, Sandoz, Marek Zawadzki Grant/research support from: Celltrion, Inc, Delina Ivanova Grant/research support from: Celltrion, Inc, Alfredo Berrocal Grant/research support from: Celltrion, Inc, Speakers bureau: Pfizer, Elias Chalouhi Grant/research support from: Celltrion, Inc, Éva Balázs Grant/research support from: Celltrion, Inc, Consultant of: Amgen, Sergii Shevchuk Grant/research support from: Celltrion, Inc, Sang Joon Lee Shareholder of: Celltrion, Inc, Employee of: Celltrion, Inc, Sung Hyun Kim Shareholder of: Celltrion, Inc, Employee of: Celltrion, Inc, JeeHye Suh Employee of: Celltrion, Inc, Chankyoung Hwang Employee of: Celltrion, Inc, Dae Seok Choi Shareholder of: Celltrion, Inc, Employee of: Celltrion, Inc

Recurrent hyperactive ESR1 fusion proteins in endocrine therapy-resistant breast cancer

Background

Estrogen receptor-positive (ER-positive) metastatic breast cancer is often intractable due to endocrine therapy resistance. Although ESR1 promoter switching events have been associated with endocrine-therapy resistance, recurrent ESR1 fusion proteins have yet to be identified in advanced breast cancer.

Patients and methods

To identify genomic structural rearrangements (REs) including gene fusions in acquired resistance, we undertook a multimodal sequencing effort in three breast cancer patient cohorts: (i) mate-pair and/or RNAseq in 6 patient-matched primary-metastatic tumors and 51 metastases, (ii) high coverage (>500×) comprehensive genomic profiling of 287-395 cancer-related genes across 9542 solid tumors (5216 from metastatic disease), and (iii) ultra-high coverage (>5000×) genomic profiling of 62 cancer-related genes in 254 ctDNA samples. In addition to traditional gene fusion detection methods (i.e. discordant reads, split reads), ESR1 REs were detected from targeted sequencing data by applying a novel algorithm (copyshift) that identifies major copy number shifts at rearrangement hotspots.

Results

We identify 88 ESR1 REs across 83 unique patients with direct confirmation of 9 ESR1 fusion proteins (including 2 via immunoblot). ESR1 REs are highly enriched in ER-positive, metastatic disease and co-occur with known ESR1 missense alterations, suggestive of polyclonal resistance. Importantly, all fusions result from a breakpoint in or near ESR1 intron 6 and therefore lack an intact ligand binding domain (LBD). In vitro characterization of three fusions reveals ligand-independence and hyperactivity dependent upon the 3' partner gene. Our lower-bound estimate of ESR1 fusions is at least 1% of metastatic solid breast cancers, the prevalence in ctDNA is at least 10× enriched. We postulate this enrichment may represent secondary resistance to more aggressive endocrine therapies applied to patients with ESR1 LBD missense alterations.

Conclusions

Collectively, these data indicate that N-terminal ESR1 fusions involving exons 6-7 are a recurrent driver of endocrine therapy resistance and are impervious to ER-targeted therapies.

P6445Stress hyperglycemia and in-hospital mortality in patients with ST-segment elevation myocardial infarction

Introduction

Stress hyperglycemia is common in acute ill patients and associated with poor clinical outcomes. Some studies demonstrated the association of stress hyperglycemia and poor outcomes in acute MI. However, current results for the impact of stress hyperglycemia on mortality in acute MI who underwent PCI are insufficient.

Purpose

We aimed to evaluate the impact of stress hyperglycemia on clinical outcomes of patients with STEMI underwent primary PCI in large scale multi-center registry.

Methods

From 2007 to 2014, in 1,538 patients of the INTERSTELLAR (Incheon-Bucheon Cohort of Patients Undergoing Primary PCI for Acute ST-Elevation Myocardial Infarction) cohort, 997 patients without diabetes who underwent primary PCI for STEMI were retrospectively analyzed. We defined random glucose more than 200mg/dl at admission without diabetic history or results of HbA1C more than 6.5% as stress hyperglycemia. The primary endpoint was in-hospital all-cause death and the secondary endpoint was all-cause death within 1 year after index PCI.

Results

From 997 nondiabetic cohort population, 117 patients with stress hyperglycemia and 880 patients without stress hyperglycemia were enrolled. Baseline characteristics including age, sex, hypertension, hyperlipidemia, atrial fibrillation, left main disease, and multivessel disease were not significantly different between two groups. However, systolic blood pressure was lower (111.2±39.2 vs. 125.5±28.1, p<0.001) and hypoxic liver injury was frequent (31.0% vs. 20.1%, p=0.007) in stress hyperglycemia. In-hospital and 1-year all-cause mortality were higher in stress hyperglycemia (13.7% vs. 2.7%, p<0.001; 15.4% vs. 3.8%, p<0.001, respectively). However, there is no significant difference in post-discharge mortality rate. Stress hyperglycemia was a significant independent predictor of in-hospital death (adjusted OR: 5.67, 95% CI: 2.40–13.39; p<0.001). Hypotension (defined less than 90mmHg) and left ventricular dysfunction (defined less than 40% of LVEF on echocardiography) were significantly associated with stress hyperglycemia (adjusted OR: 5.72, 95% CI: 3.33–9.82; p<0.001; adjusted OR: 2.38, 95% CI: 1.49–3.82; p<0.001, respectively).

Landmark analysis of all-cause death

Conclusions

In nondiabetic patients who underwent primary PCI for STEMI, stress hyperglycemia is significantly associated with an increased in-hospital all-cause mortality but did not increase post-discharge mortality within 1 year.

Reducing off target viral delivery in ovarian cancer gene therapy using a protease-activated AAV2 vector platform

Gene therapy is a promising strategy for treating metastatic epithelial ovarian cancer (EOC). However, efficient vector targeting to tumors is difficult and off-target effects can be severely detrimental. Most vector targeting approaches rely on surface receptors overexpressed on some subpopulation of cancer cells. Unfortunately, there is no universally expressed cell surface biomarker for tumor cells. As an alternative, we developed an adeno-associated virus (AAV) based "Provector" whose cellular transduction can be activated by extracellular proteases, such as matrix metalloproteinases (MMP) that are overexpressed in the tumor microenvironments of the most aggressive forms of EOC. In a non-tumor bearing mouse model, the Provector demonstrates efficient de-targeting of healthy tissues, especially the liver, where viral delivery is <1% of AAV2. In an orthotopic HeyA8 tumor model of EOC, the Provector maintains decreased off-target delivery in the liver and other tissues but with no loss in tumor delivery. Notably, approximately 10% of the injected Provector is still detected in the blood at 24 h while >99% of injected AAV2 has been cleared from the blood by 1 h. Furthermore, mouse serum raised against the Provector is 16-fold less able to neutralize Provector transduction compared to AAV2 serum neutralizing AAV2 transduction (1:200 vs 1:3200 serum dilution, respectively). Thus, the Provector appears to generate less neutralizing antibodies than AAV2. Importantly, serum against AAV2 does not neutralize the Provector as well as AAV2, suggesting that pre-existing antibodies against AAV2 would not negate the clinical application of Provectors. Taken together, we present an EOC gene delivery vector platform based on AAV with decreased off-target delivery without loss of on-target specificity, and greater immunological stealth over the traditional AAV2 gene delivery vector.

Comprehensive genomic profiles of metastatic and relapsed salivary gland carcinomas are associated with tumor type and reveal new routes to targeted therapies

Background

Relapsed/metastatic salivary gland carcinomas (SGCs) have a wide diversity of histologic subtypes associated with variable clinical aggressiveness and response to local and systemic therapies. We queried whether comprehensive genomic profiling could define the tumor subtypes and uncover clinically relevant genomic alterations, revealing new routes to targeted therapies for patients with relapsed and metastatic disease.

Patients and methods

From a series of 85 686 clinical cases, DNA was extracted from 40 µm of formalin-fixed paraffin embedded (FFPE) sections for 623 consecutive SGC. CGP was carried out on hybridization-captured, adaptor ligation-based libraries (mean coverage depth, >500×) for up to 315 cancer-related genes. Tumor mutational burden was determined on 1.1 Mb of sequenced DNA. All classes of alterations, base substitutions, short insertions/deletions, copy number changes, and rearrangements/fusions were determined simultaneously.

Results

The clinically more indolent SGC including adenoid cystic carcinoma, acinic cell carcinoma, polymorphous low-grade adenocarcinoma, mammary analog secretory carcinoma, and epithelial-myoepithelial carcinomas have significantly fewer genomic alterations, TP53 mutations, and lower tumor mutational burden than the typically more aggressive SGCs including mucoepidermoid carcinoma, salivary duct carcinoma, adenocarcinoma, not otherwise specified, carcinoma NOS, and carcinoma ex pleomorphic adenoma. The more aggressive SGCs are commonly driven by ERBB2 PI3K pathway genomic alterations. Additional targetable GAs are frequently seen.

Conclusions

Genomic profiling of SGCs demonstrates important differences between traditionally indolent and aggressive cancers. These differences may provide therapeutic options in the future.

Abstract P3-05-03: Metaplastic breast cancers: Genomic profile, mutational burden and TILs

Background: Metaplastic breast cancers (MPBC) are rare, typically triple negative aggressive tumors composed of both, adenocarcinoma and metaplastic elements. Recent evidence that TNBC and MPBC can respond vigorously to immune checkpoint inhibitor therapy (Adams et al, ASCO 2017 and npj Breast Cancer 2017) has prompted the following comprehensive genomic profiling (CGP) and histopathologic assessment of tumor infiltrating lymphocytes (TIL) designed to uncover potential biomarkers of immunotherapy response for MPBC, including mutational burden, Microsatellite Instability (MSI) status and gene amplification of 9p21.4 (or CD274, which includes the PD-L1 locus).

Methods: 12,214 locally aggressive, relapsed and metastatic breast malignancies (mBM) were subjected to CGP using DNA extracted from 40 µm of FFPE sections and adaptor ligation-based libraries to a mean coverage depth &gt;650X for up to 315 cancer-related genes. The results were analyzed for all classes of genomic alterations (GA) including base substitutions, insertions and deletions, select rearrangements, and copy number changes. Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA. MSI status was determined by an algorithm based on the sequencing results. TIL were assessed on archived H&E tumor sections and enumerated per guidelines established by the TIL Working Group (Salgado, Ann Oncol 2015) in a subset of MPBC with the highest TMB and compared with low TMBC cases.

Results: 165 of mBM cases were MPBC (1.4%) and are included in this study. All patients were female with a median age of 60 (range 24-86). 165 of the MPBC cases (100%) harbored a wide variety of GA involving more than 100 individual genes. The most common GA were identified in TP53 (65%), followed by PIK3CA (37%). No cases of MSI hi status (0/103) and only one case with amplification of 9p21.4 (1/165, 0.6%) were observed. Most MPBC had a low mutational burden, with a median TMB of 2.7 mutations/Mb (range 0-39.6). Only 11/165 tumors (6.7%) were found to have a TMB over 10 mutations/Mb, including 3 cases (1.8%) with TMB &gt;20. Tumor sections were available for TIL review from 9/11 cases with highest TMB, as well as 11 control cases with lowest TMB. TIL were more frequently observed in high versus low TMB MPBC, with median TIL percentage of 40 and 20 (range 10-80 and range 10-60), respectively, although this difference was not statistically significant (Wilcoxon rank-sum test, p=0.15).

Conclusions: Genomic profiling in the largest cohort of MPBC reported to date confirms that MPBC is enriched for TP53 and PIK3CA mutations and many tumors harbor targetable GA. The frequently observed tumoral PD-L1 expression in MPBC is not based on gene amplification as amplification of 9p21.4 is rare. Most tumors had a low mutation burden, and no significant association of TIL with TMB was observed, suggesting additional processes underlying MPBC immunogenicity.

Citation Format: Taff J, Suh J, Singh B, Denkert C, Troxel AB, Ross JS, Adams S. Metaplastic breast cancers: Genomic profile, mutational burden and TILs [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 P3-05-03.

Abstract P5-21-20: Integrating comprehensive genomic profiling with treatment decisions – Experience gained while treating 139 advanced breast carcinomas

Background: Comprehensive Genomic Profiling (CGP) using next-generation sequencing (NGS) technology can provide insight into potentially clinically relevant genomic alterations (CRGA) within a patient's breast cancer. For example, HER2 amplification status and targetable short variants (SV), acquired ESR1 or BRCA1/2 resistance mutations, and the presence of targetable alterations in the PI3K kinase. We retrospectively reviewed CGP results and subsequent outcomes at one cancer center to illustrate the experience of using molecular subtyping to inform treatment decisions.

Methods: DNA extracted from FFPE tumor tissue or blood samples obtained during routine clinical care for patients (n=139) with predominantly relapsed, refractory or metastatic breast cancer was analyzed by hybrid-capture, NGS for all classes of GA: 1. base substitutions, 2. insertion and deletions, 3. rearrangements, and 4. copy number changes. Treatment decisions based on comprehensive genomic profiles were captured retrospectively. Tumor mutational burden (TMB), scored as mutations (mut)/Mb, was calculated on 0.8-1.2 Mb of sequenced DNA. Alterations affecting the ERBB family included amplification of or oncogenic mutations in ERBB2 (HER2), ERBB3, and EGFR.

Results: From Jan 2013 to May 2017, FFPE tissue samples for 136 patients with advanced breast cancer were analyzed by CGP and 3 additional patients had circulating tumor DNA analyzed for alterations; 11 patients received profiling on multiple biopsies. Tumors analyzed were carcinomas (Ca) NOS (n=84), invasive ductal Ca (n=46), invasive lobular Ca (n=7), a neuroendocrine Ca, and a phyllodes tumor. In total, 118/139 (84.9%) samples harbored CRGA in a targetable pathway: PI3K/MTOR (n=67; 48.2%), CDK cell-cycle (n=40; 28.8%), ERBB family (n=24; 17.3%), FGFR (n=24; 17.3%), ESR1 (n=16; 11.5%), homologous repair (HRD)( n=14; 10.1%), and RAS/RAF/MEK (n=11; 7.9%). Targetable alterations in other cancer-related kinases were found in 10 (7.2%) samples and 10 (7.2%) samples were TMB high (≥20 mut/Mb) or had CD274 (PD-L1) amplification. There were 3 patients (2.1%) with HER2 short variants detected in the absence of ERBB2 amplification; these patients may respond to HER2-targeted therapies but would be HER2-negative by IHC. Many samples had alterations in ≥1 pathway, and overlap is particularly high for the CDK and FGFR pathways (12 samples). Alterations in pathways targeted by MTOR inhibitors, HER2-targeted therapies, or the CDK inhibitors were found in 93/136 (66.9%) tumors. Evaluation of outcomes for these 139 patients is ongoing and will be presented.

Conclusions: Genomic profiling of breast carcinomas, using either tissue or liquid biopsies, provides potentially actionable information to guide treatment decisions. Overall, 84.9% of patient samples harbored oncogenic alterations in a targetable pathway, with two-thirds of tumors having alterations in pathways targeted by therapies with FDA approval for breast cancer and 7.2% of patients having high levels of TMB or amplification of PD-L1, suggesting that checkpoint inhibitors may be relevant options.

Citation Format: Mahtani R, Gay LM, Chung J, Hartmaier R, Sokol E, Elvin JA, Daniel S, Ramkissoon S, Severson E, Suh J, Vergilio J-A, Stephens PJ, Ross JS. Integrating comprehensive genomic profiling with treatment decisions – Experience gained while treating 139 advanced breast carcinomas [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 P5-21-20.

Abstract PD8-01: CDH1 mutated classic and pleomorphic invasive lobular breast carcinomas differ in genomic signatures and opportunities for targeted and immunotherapies

Background: Typically defined by negative IHC staining for E-cadherin, classic (CILC) and pleomorphic (PILC) are often combined as a single breast cancer subtype. We queried whether patients with relapsed metastatic disease, mCILC and mPILC, would harbor contrasting genomic alterations (GA)and that molecular information could further differentiate the 2 tumor types and thereby influence therapy selection.

Methods: DNA was extracted from 40 µm of FFPE sections of 10,784 invasive breast carcinomas. 454 (4%) CDH1 mutated mILC were selected including 428 classic mCILC (94%) and 26 mPLIC (6%) subtypes. Comprehensive genomic profiling (CGP) was performed on hybridization-captured, adaptor ligation-based libraries to a mean coverage depth &gt;600X for up to 315 cancer-related genes. Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA.

Results: mCILC and mPILC patients featured a median age of 63 years (Table). Slide based ER+ status and HER2+ status was significantly different in both groups (P&lt;0.0001). The frequency of base substitutions in ESR1 was significantly higher in mCILC, and this difference was also significantly higher in mCILC metastasis biopsies exposed to hormonal therapy than in pre-treatment primary tumors (P&lt;0.0001). ERBB2 (HER2) GA (amp + non-amp) detected by CGP were higher in mPILC than mCILC in both pre-and post-treatment samples (P&lt;0.0001 for both). The ERBB2 GA frequency was nearly twice as high after hormonal therapy in both mCILC and mPILC. ESR1 and ERBB2 GA were mutually exclusive overall and especially in the mCILC group. PIK3CA GA were the most frequent GA in both mCILC and mPILC. TP53 GA were significantly more frequent in mPILC than mCILC. At 19%, the frequency of TMB &gt; 15 mutations/MB in mPILC was more than twice as frequent than in mCILC (P=0.046). All (100%) of both the CILC and PILC groups were negative for mis-match repair deficiency or MSI high status. mCILC and mPILC patients with post primary therapy associated ESR1 and ERBB2 GA responding to targeted and immunotherapies will be presented.

Contrasting Clinical and Genomic Features of CILC and PILC Classic CILC (428 cases)Pleomorphic PILC (26 cases)Median Age6363*ER+98%74%*HER2 IHC/FISH+12 (3%)6 (22%)ESR1 GA Primary Pre-Rx6%0%ESR1 GA Metastatic Post-Rx17%0%ERBB2 GA Primary Pre-Rx7%18%ERBB2 GA Metastatic Post-Rx12%34%Other Significant GAPIK3CA (55%), CCND1 (21%), TP53 (17%), ARID1A, AKT3, MDM4, PTEN (all 11%)PIK3CA (58%), TP53 (30%), AKT1 22%), FGFR4, CCND1, PTEN (all 17%)TMB median (mut/Mb)2.73.6TMB &gt; 15%8%19%*when clinical status available

Conclusions: CGP of mCILC and mPILC reveals significant differences in the panorama of GA both in pre-treatment primary and metastatic disease lesions especially in therapy-impacting GA in ESR1 and ERBB2. mCILC is more often driven by ESR1 GA and mPILC by ERBB2 GA. Although both mCILC and mPILC feature subsets of tumors with high TMB, this is more frequent for mPILC likely indicating different potentials for immunotherapies to benefit these patients.

Citation Format: Ross JS, Chung J, Elvin JE, Vergilio J-A, Ramkissoon S, Suh J, Severson E, Daniel S, Frampton GM, Fabrizio D, Hartmaier RJ, Albacker LA, Ali SM, Schrock AB, Miller VA, Stephens PJ, Gay LM. CDH1 mutated classic and pleomorphic invasive lobular breast carcinomas differ in genomic signatures and opportunities for targeted and immunotherapies [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 PD8-01.

Abstract P1-05-07: Comprehensive genomic profiling of clinically malignant phyllodes tumors of the breast reveals frequent mutation of NF1 and other genes associated with PI3K and RAS pathway activation

Background: Malignant or metastatic breast phyllodes tumors (MPT) are exceptionally rare, and the underlying genomic drivers are still being elucidated. Recent studies report frequent mutations in the RAS and PI3K pathways but have not commonly reported mutations in NF1. Comprehensive genomic profiling (CGP) can measure mutation load (TMB) and identifies all four classes of oncogenic alterations, including rearrangements and copy number loss that commonly affect tumor suppressors such as NF1, and can direct personalized treatment strategies.

Methods: CGP using hybridization capture of 3,769 exons from up to 315 cancer-related genes and select introns of 28 genes commonly rearranged in cancer was applied to ≥50ng of DNA extracted from 21 consecutive MPT and sequenced to high, uniform median coverage (&gt;400X). TMB was determined as mutations/Mb on 1.1 Mb of sequenced DNA.

Results: The 21 MPT featured a median age of 51 yrs (range 14-70 yrs). CGP was performed on the primary MPT in 15 cases and on metastasis biopsies in 6 cases. TMB for all MPT was low (&lt;10 mut/Mb), and all evaluable tumors (17/21) were microsatellite stable (MSS). The most commonly mutated genes were TP53 (57.1%), TERT (56.3%), NF1 (52.4%), MED12 (38.1%), CDKN2A/B (33.3%), and MLL2 (33.3%). 19/21 (90.5%) MPT harbored clinically relevant genomic alterations (CRGA) associated with therapies available on the market or under investigation in late stage clinical trials. Additional alterations in the PI3K/AKT/MTOR, RAS/RAF/MEK, and FGFR pathways were identified (see table); the PI3K/ATK/MTOR pathway was mutated in 10/21 (47.6%) of samples. Although CDKN2A/B loss was found in 6/11 tumors with NF1 mutation and only 1/10 NF1 wild-type samples, the co-occurrence was not significant (p&lt;0.07). No significant correlation exists between the occurrence of NF1 mutations and mutation of MED12, TERT, the PI3K pathway, or other genes in the RAS/RAF pathway (NRAS, BRAF, EGFR). Targetable KIAA1549-BRAF or FGFR3-TACC3 fusions were identified in 2/21 (9.5%) tumors. Responses to targeted treatments will be presented.

Conclusions: More than 90% of MPT feature CRGA, including alteration of NF1, which was by far the most common targetable GA in this study. 52.4% of MPT had alterations predicted to result in loss of NF1 activity. NF1 mutation does not significantly co-occur with mutations in any other gene or pathway commonly altered in MPT. Other tumors with underlying NF1 mutations have responded to the MEK inhibitor selumetinib, suggesting MEK inhibitors may be relevant for the treatment of MPT. Other targetable alterations, including known gene fusions, are common in MPT. Thus, MPT may benefit from combination targeted therapy, warranting further investigation in the clinical trial setting.

  Total Mutation NumberPathwayTotal Cases (n=21)Short VariantsCopy NumberRearrangementsRAS/RAF/MEK    NF111 (52.4%)722BRAF3 (14.3%)301NRAS2 (9.5%)300PI3K/AKT/MTOR    PIK3CA4 (19%)310PTEN4 (19%)130STK112 (9.5%)110AKT11 (4.8%)100FBXW71 (4.8%)001TSC21 (4.8%)010PIK3R11 (4.8%)100FGFR    FGFR11 (4.8%)100FGFR31 (4.8%)001Other    EGFR2 (9.5%)020BRCA21 (4.8%)100PDGFRA1 (4.8%)010KIT1 (4.8%)010

Citation Format: Gay LM, Elvin JA, Vergilio J-A, Suh J, Ramkissoon S, Ali S, Schrock A, Hirshfield K, Ganesan S, Miller VA, Stephens PJ, Ross JS. Comprehensive genomic profiling of clinically malignant phyllodes tumors of the breast reveals frequent mutation of NF1 and other genes associated with PI3K and RAS pathway activation [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 P1-05-07.

Abstract P1-05-08: Comprehensive genomic profiling of 8,654 breast carcinoma reveals therapeutically targetable molecular subtypes beyond those defined by hormone-receptor expression

Background: Breast carcinomas (BC) are commonly classified into 4 subtypes based on hormone receptor expression: basal, luminal A, luminal B, and HER2 overexpressed. Comprehensive genomic profiling (CGP) reveals targetable genomic alterations (GA) across all four mutation classes, as well measuring tumor mutational burden (TMB), and can redefine BC classification into therapeutically relevant subtypes. Testing with immunohistochemistry or hotspot testing can miss a substantial number of targetable alterations and cannot measure TMB.

Methods: DNA was extracted from 40 µm of FFPE sections for 8654 consecutive BCs. CGP was performed on hybridization-captured, adaptor ligation-based libraries (mean coverage &gt;500X) for up to 315 cancer-related genes and select introns from up to 28 genes frequently rearranged in cancer. Sequences were analyzed for substitutions, small insertions/deletions, copy number changes, and rearrangements. TMB was determined by counting non-driver, non-germline alterations across 1.1 Mbp of sequenced DNA. Clinically relevant GA (CRGA) are GA linked to therapies on the market or under evaluation in clinical trials. Immunotherapy (IO) sensitivity is defined as TMB &gt;20 mut/Mbp or mutation of specific DNA repair pathways.

Results: The table below outlines 7 distinct functional or signal transduction pathways commonly altered in BC. Several are targetable with therapies that are FDA approved for an oncology indication. Mutations can also be found in other targetable kinases such as RET, ROS1, and RAF. 6959 (80.4%) tumors harbor a GA in at least one pathway, and 2697 (31.2%) BC harbor alterations in just one pathway (unique cases). Only 9.8% of BC would be HER2-positive by IHC. Almost 4% (352/8654) of cases harbor rearrangements or gene fusions that may not be detectable with other assays. Mutations in ESR1 characterize an eighth category of tumors with acquired resistance to endocrine therapy; 796/8654 (9%) samples harbor ESR1 alterations.

Conclusions: CGP can identify CRGA and TMB that can stratify tumors by predicted sensitivity to a variety of therapies, including HER2- or mTOR-targeted therapies, immunotherapies, and other kinase inhibitors. 80% of BC harbor targetable GA, and 30% of samples harbor mutations in only one pathway. CGP can provide crucial information for identifying which of several treatment modalities is most appropriate for these 30% of patients. High levels of TMB and most GA would not be identified by IHC or hotspot testing, but can be detected by next-generation sequencing. CGP is a powerful tool for guiding treatment across therapeutically distinct, but targetable, pathways.

 PI3K/AKT/mTOR pathwayFGFR pathwayCDK pathwayERBB pathwayHR deficientIO sensitiveOther kinasesTotal Cases43752650268512941266419424% Total Cases51%31%31%15%15%5%5%Unique Cases14422262312743094858% Unique Cases17%3%3%3%4%1%1%TherapiesEverolimus, TemsirolimusPazopanib, PonatinbPalbociclibTrastuzumab, Pertuzumab, Afatinib, Lapatinib, NeratinibOlaparibPembrolizumab, Nivolumab, Atezolizumab, IpilumumabSorafenib, Regorafenib, Dabrafenib, Vemurafenib, Crizotinib, Cabozantinib, Sunitinib

Citation Format: Ross JS, Gay LM, Elvin JA, Suh J, Vergilio J-A, Ramkissoon S, Schrock A, Ali S, Miller VA, Stephens PJ. Comprehensive genomic profiling of 8,654 breast carcinoma reveals therapeutically targetable molecular subtypes beyond those defined by hormone-receptor expression [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 P1-05-08.

Biocomputing nanoplatforms as therapeutics and diagnostics

Biocomputing nanoplatforms are designed to detect and integrate single or multiple inputs under defined algorithms, such as Boolean logic gates, and generate functionally useful outputs, such as delivery of therapeutics or release of optically detectable signals. Using sensing modules composed of small molecules, polymers, nucleic acids, or proteins/peptides, nanoplatforms have been programmed to detect and process extrinsic stimuli, such as magnetic fields or light, or intrinsic stimuli, such as nucleic acids, enzymes, or pH. Stimulus detection can be transduced by the nanomaterial via three different mechanisms: system assembly, system disassembly, or system transformation. The increasingly sophisticated suite of biocomputing nanoplatforms may be invaluable for a multitude of applications, including medical diagnostics, biomedical imaging, environmental monitoring, and delivery of therapeutics to target cell populations.