Genomic Profiling of Metastatic Castration-Resistant Prostate Cancer Samples Resistant to Androgen Receptor Pathway Inhibitors

PURPOSE

The androgen receptor axis inhibitors (ARPI; e.g., enzalutamide, abiraterone acetate) are administered in daily practice for men with metastatic castration-resistant prostate cancer (mCRPC). However, not all patients respond, and mechanisms of both primary and acquired resistance remain largely unknown.

EXPERIMENTAL DESIGN

In the prospective trial MATCH-R (NCT02517892), 59 patients with mCRPC underwent whole-exome sequencing (WES) and/or RNA sequencing (RNA-seq) of samples collected before starting ARPI. Also, 18 patients with mCRPC underwent biopsy at time of resistance. The objectives were to identify genomic alterations associated with resistance to ARPIs as well as to describe clonal evolution. Associations of genomic and transcriptomic alterations with primary resistance were determined using Wilcoxon and Fisher exact tests.

RESULTS

WES analysis indicated that no single-gene genomic alterations were strongly associated with primary resistance. RNA-seq analysis showed that androgen receptor (AR) gene alterations and expression levels were similar between responders and nonresponders. RNA-based pathway analysis found that patients with primary resistance had a higher Hedgehog pathway score, a lower AR pathway score and a lower NOTCH pathway score than patients with a response. Subclonal evolution and acquisition of new alterations in AR-related genes or neuroendocrine differentiation are associated with acquired resistance. ARPIs do not induce significant changes in the tumor transcriptome of most patients; however, programs associated with cell proliferation are enriched in resistant samples.

CONCLUSIONS

Low AR activity, activation of stemness programs, and Hedgehog pathway were associated with primary ARPIs' resistance, whereas most acquired resistance was associated with subclonal evolution, AR-related events, and neuroendocrine differentiation. See related commentary by Slovin, p. 4323.

Abstract P2-08-18: Evaluation of the activity of key actionable oncogenic driving pathways in triple negative breast cancer using OncoSignal™; a novel molecular assay based on transcriptional profile analysis

Introduction: Triple negative breast cancer (TNBC), defined by the absence of expression of estrogen receptor (ER), progesterone receptor, and HER2, is a heterogenous subgroup of breast cancer which currently accounts for a significant proportion of the mortality from the disease. Consequently, there is an urgent need to identify more effective therapy for women with this type of breast cancer. We have recently developed a novel assay, OncoSignal™ which is capable of precisely measuring the activity of seven key signaling pathways through utilizing measurements of mRNA. The assay quantitatively determines the specific activity of ER, androgen receptor, PI3K, MAPK, HedgeHog, Notch, and TGFβ signal pathways via measurement and analysis of mRNA expression from transcriptional targets of these pathways. This approach overcomes some of the limitations of NGS and other methods which analyze only partial components of a complex signaling pathway, producing significant risk of false positive and negative results, and resulting in potentially inaccurate diagnosis and treatment selection. In this study we evaluated oncogenic pathway activation in 88 cases of TNBC using the OncoSignal™ assay. Materials and methods: Samples and pathway scores for TNBC tumors were calculated using a publicly available Affymetrix dataset GSE76275. This study included 88 cases of TNBC obtained at Baylor College of Medicine. OncoSignal™ pathway activity scores (PAS) were calculated from the transcriptional profile for each case. In addition, 10 samples of benign breast tissue were available for analysis of PAS and used as controls for this evaluation. The mean pathway activity scores and ranges were calculated from the benign tissues. The PAS results for each of the 7 oncogenic pathways from the TNBC cases were compared with PAS results from benign tissues. Results: The OncoSignal™ PAS were significantly higher in TNBC compared to benign tissues for MAPK, PI3K, and HH pathways. The PAS of ER and TGFβ pathways were significantly lower in TNBC compared to the benign tissue. MAPK, AR, ER, PI3K, and HH were elevated in 86%, 17%, 8%, 95%, and 94% of TNBC cases respectively. TGFβ pathway, for which oncogenic versus tumor suppressive functionality is contextually determined, showed reduced PAS in 85% of TNBC cases compared to benign tissue controls. Conclusion: OncoSignal™ analysis identifies enhanced targetable oncogenic pathway activity in a majority of TNBC breast cancers. Of interest, 7 of 88 cases (8%) classified as TNBC using IHC methods showed evidence of estrogen receptor signal pathway activation, and 15 (17%) showed elevated AR PAS. PI3K and MAPK had high PAS in over 85% of TNBC cases. Results suggest loss of tumor suppressive function of the TGFβ pathway. We conclude that OncoSignal™ analysis may help identify TNBC tumors with targetable signal transformation pathways.

Citation Format: Genevra Magliocco, Eveline den Biezen, Diederick Keizer, Martijn Akse, Martijn van Zelst, Dianne van Strijp, Saskia Vermeer, Anja van de Stolpe, Anthony Magliocco. Evaluation of the activity of key actionable oncogenic driving pathways in triple negative breast cancer using OncoSignal™; a novel molecular assay based on transcriptional profile analysis [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-08-18.

Abstract 740: A robust rapid mRNA based test to profile simultaneously ER, AR, PI3K and MAPK functional signaling pathway activity for precision oncology

Introduction: OncoSignal test was developed to determine and quantify functional signal transduction pathway activity levels of 4 key oncogenic signaling pathways (ER, AR, PI3K and MAPK), based on the quantitative measurement of mRNA expression levels of the direct target genes. Here we present data of a 4 pathway qPCR test, that can be used in external labs and is able to measure simultaneously the 4 pathway activities in tumor tissue samples possibly providing important information for optimal therapy selection for treatment of breast cancer.

Materials and methods: OncoSignal 4 pathway test was compared between 2 reference laboratories; the Philips service lab in The Netherlands and at Protean BioDiagnostics, a US CAP-certified CLIA service lab. mRNA was isolated from unstained FFPE tissue sections of well characterized breast tissues obtained from 65 patients (retrospective). Annotated areas with at least 50% tumor cells were used (total volume about 0.25mm3). The OncoSignal test was used to measure the signal transduction pathway activity of AR, ER, PI3K and MAPK pathways. IHC staining for ER, PR, Ki67 and HER2 was also available for all samples enabling tumor categorization into conventional breast cancer subtypes.

Results: Excellent inter-lab concordance was found with correlation coefficients of 0.99, 0.99, 0.98 and 0.99 for ER, AR, PI3K and MAPK, respectively. Average absolute difference between pathway activities was 3.6 activity points on a 0-100 activity score scale. All 32 cases passed the criteria set for reproducibility. Of the 65 tested breast cancer samples, 58 could be subtyped based on IHC. Five of the 58 samples failed QC. Of interest, ER IHC positive luminal A (41%) and B (28%) breast cancer showed high variation in ER pathway activity between cases, suggesting that the ER signaling pathway is not the tumor driving pathway in a significant subset of IHC ER positive tumors. As expected the Her2-enriched (17%) and TNBC (17%) sub-groups predominantly had a very low ER pathway activity score. AR pathway activity was most prominent in the HER2 enriched tumor groups, while in TNBC the MAPK pathway was most active.

Conclusion: The OncoSignal 4 pathway test is robust and can be implemented in external (local) labs as shown by the excellent correlation results. The results of the signal pathway activity analysis correlate well with breast subtype classification, however, the assay has the potential to uncover specific pathway activation independent of subtype which may have significant value for precision oncology and targeted therapy selection. The test has potential for wide utilization as it can be performed on conventional FFPE prepared breast specimens, and may be complementary to conventional mutational and IHC analysis for classifying breast cancer and selecting appropriate therapy.

Citation Format: Eveline den Biezen, Saskia Vermeer, Diederick Keizer, Martijn Akse, Martijn van Zelst, Dianne van Strijp, Hannah Park, Anthony Magliocco. A robust rapid mRNA based test to profile simultaneously ER, AR, PI3K and MAPK functional signaling pathway activity for precision oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 740.

Abstract 533: Breast cancer IHC subtypes display heterogenous and independent targetable signaling pathway activity profiles

Background: Primary breast cancer is routinely subtyped using immunohistochemistry (IHC) staining and treatment choice is guided by the subtype. Targeted treatment requires the targeted signaling pathway to be active and tumor driving. IHC staining does not provide reliable information on active signaling pathways, and we reported before that clinical response of ER positive breast cancer patients to neoadjuvant aromatase inhibitor therapy appears to be more closely related to ER pathway activity rather than ER/PR IHC staining. To better understand the role of tumor driving signaling pathways within breast cancer subtypes and potentially improve precision medicine we evaluated signaling pathway activity profiles per IHC subtype, using novel assays to quantitatively measure activity of multiple main tumor driving signal transduction pathways, within tissue samples.

Methods: mRNA-based estrogen (ER) and androgen (AR) receptor, MAPK, PI3K, Hedgehog (HH), TGFβ, Notch, Wnt signal transduction pathway assays have been previously described. Pathway activity scores (PAS) were measured on primary untreated breast cancer samples, and compared to normal breast epithelium, using Affymetrix expression dataset GSE65194 (Institut Marie Curie), excluding the duplicate measures, containing 29 Luminal A, 30 Luminal B, 30 HER2, 41 triple negative (TN) breast cancer and 6 normal breast tissue sample data. Pathway activity scores exceeding the 95th percentile of normal were considered highly active.

Results: PAS thresholds for defining highly active pathway activity were for MAPK 23, AR 29, ER 34, PI3K 42, HH 34, Notch 65, TGFβ 48, Wnt 29. Luminal A was characterized by high ER pathway activity (n=25, 86%, mean PAS 45, SD 10); luminal B by high ER (n=10, 33%; mean PAS 32, SD 11) increased PI3K pathway activity (n=27, 90%; mean PAS 53, SD 10) and increased HH pathway activity (n=23, 77% mean PAS 29, SD 7); HER2 by high AR (n=18, 60%; mean PAS 30, SD 6) increased PI3K pathway activity (n=19, 63%; mean PAS 48, SD8) and increased HH pathway activity (n=27, 90% mean PAS 30 SD 7) ; TNBC by high PI3K (n=37, 90%; mean PAS 53, SD 7) plus high developmental pathway activity (Notch, n=6, 15%; mean PAS 53, SD 12; Wnt, n=28, 68%; mean PAS 31, SD 6). All subtypes had elevated MAPK pathway activity.

Discussion: Each breast cancer subtype based on IHC, had in the overall population a typical pathway activity profile. However within each IHC subtype, a substantial range of pathway activities between patients is observed, suggesting that within same IHC subtypes, clear differences in signal pathway activation can be measured that may provide a novel approach to more effectively select patients for specific precision oncology targeted therapy treatments.

Citation Format: Anthony M. Magliocco, Anja van de Stolpe, Martijn Akse, Eveline den Biezen, Laurent Holtzer. Breast cancer IHC subtypes display heterogenous and independent targetable signaling pathway activity profiles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 533.

Heterogeneity in Signaling Pathway Activity within Primary and between Primary and Metastatic Breast Cancer

Targeted therapy aims to block tumor-driving signaling pathways and is generally based on analysis of one primary tumor (PT) biopsy. Tumor heterogeneity within PT and between PT and metastatic breast lesions may, however, impact the effect of a chosen therapy. Whereas studies are available that investigate genetic heterogeneity, we present results on phenotypic heterogeneity by analyzing the variation in the functional activity of signal transduction pathways, using an earlier developed platform to measure such activity from mRNA measurements of pathways' direct target genes. Statistical analysis comparing macro-scale variation in pathway activity on up to five spatially distributed PT tissue blocks (n = 35), to micro-scale variation in activity on four adjacent samples of a single PT tissue block (n = 17), showed that macro-scale variation was not larger than micro-scale variation, except possibly for the PI3K pathway. Simulations using a "checkerboard clone-size" model showed that multiple small clones could explain the higher micro-scale variation in activity found for the TGFβ and Hedgehog pathways, and that intermediate/large clones could explain the possibly higher macro-scale variation of the PI3K pathway. While within PT, pathway activities presented a highly positive correlation, correlations weakened between PT and lymph node metastases (n = 9), becoming even worse for PT and distant metastases (n = 9), including a negative correlation for the ER pathway. While analysis of multiple sub-samples of a single biopsy may be sufficient to predict PT response to targeted therapies, metastatic breast cancer treatment prediction requires analysis of metastatic biopsies. Our findings on phenotypic intra-tumor heterogeneity are compatible with emerging ideas on a Big Bang type of cancer evolution in which macro-scale heterogeneity appears not dominant.

Abstract 3690: Measuring functional signal transduction pathway activity on breast cancer tissue samples to determine intra-tumor heterogeneity and heterogeneity between primary and metastatic tumors

Background

Treatment with targeted drugs is increasingly used in breast cancer aiming to block the tumor driving pathway(s). Drug choice is often based on a single primary tumor biopsy. It is important to ascertain that biopsied tumor material is representative for the tumor or metastases to treat with respect to tumor driving signaling pathway. Little is known about pathway heterogeneity within primary breast cancer, and between primary and metastatic tumors. A novel analysis method was developed to identify and quantify activity of signal transduction pathways in cancer tissue, based on Bayesian models which infer a pathway activity score from transcription factor target gene mRNA levels (Cancer Res 2014 Jun 1;74(11):2936-45).

Methods

Originally for AffymetrixU133Plus2.0, the pathway analysis was adapted for RT-qPCR enabling use on FFPE tissue. Calibration was performed using tissue samples with known pathway activity. Functional pathway activity of ER, AR, PI3K-FOXO, Hedgehog (HH), TGFbeta, and Wnt pathways was analyzed to assess (1) intra-tumor heterogeneity: 2-5 FFPE blocks of 17 primary breast cancers (9 luminal A, 4 luminal B, 1 HER2, 3 triple negative (TN), as defined by surrogate immunohistochemistry); (2) heterogeneity between primary and associated metastases: 9 patients with FFPE blocks from primary and 12 metastases.

Results

Intra-tumor heterogeneity: In 11 out of 13 Luminal A- and B-like tumors the ER pathway was active in all samples, 1 showed ER pathway heterogeneity; 11 had an active TGFbeta pathway, heterogeneic in 3; in one ER inactive tumor one (out of 5) samples was AR active. In 2 TN tumors TGFbeta and PI3K pathways were combined active, in one TN tumor heterogeneic TGFbeta activity was observed. PI3K pathway activity increased with malignancy grade and showed most intra-tumor variation. Overall, pathway heterogeneity was detected in over one third of tumors, least in Luminal A-like (2/9) compared to Luminal B-like (3/4) and triple negative (1/3) tumors.

Extensive heterogeneity was found between primary breast cancer and metastases, and between metastatic locations of the same patient. ER pathway activity decreased in 5/9 patients and increased in 4/9 patients in one or more metastatic tumors; PI3K became active in metastasis of 2 patients and inactive in 1; the Wnt pathway became active in 3 patients in bone and ileum metastases; TGFbeta was lost in 5 patients, and became active in 1 bone metastasis; HH became active in 1 ovarian and AR in 1 bone metastasis.

Conclusion

Intra-tumor heterogeneity was lower in ER active compared to TN breast cancer, suggesting a need for multiple biopsies to adequately characterize TN for neoadjuvant therapy. Between primary tumor and metastases, heterogeneity was extensive indicating the need for pathway analysis on metastatic tumors prior to targeted treatment.

Citation Format: Anja Van De Stolpe, Anne van Brussel, Cathy Moelans, Marcia A. Inda, Wim Verhaegh, Eveline den Biezen, Paul van Diest. Measuring functional signal transduction pathway activity on breast cancer tissue samples to determine intra-tumor heterogeneity and heterogeneity between primary and metastatic tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3690.