Intrinsic Subtypes Research Articles

Abstract PD7-08: Gene Expression Profiling of Breast Cancer Brain Metastasis shows enrichment for non-luminal subtypes with potential prognostic implications

Abstract Background: The incidence of breast cancer (BC) brain metastases (BM) is increasing as a result of both improved diagnostic techniques and longer survival due to better treatment approaches. However, the biological complexity of BCBMs is still poorly understood. We here evaluate the genomic profile of BCBMs and assess its prognostic implications. Methods: Clinical data and BM samples (FFPE) from BC patients undergoing neurosurgery (2003-2019) at three institutions were collected. Hormone receptor (HR) and HER2 status were evaluated on the BCBM. RNA extracted from BM samples was used to measure the expression of 758 BC–related genes and 18 housekeeping genes using the Breast Cancer 360 Panel on an nCounter platform (NanoString Technologies). Intrinsic molecular subtyping was determined using the previously reported PAM50 subtype predictor (Parker et al. JCO 2009). Median overall survival from neurosurgery (OS) was calculated using the Kaplan-Meier method. The correlations between expression of each gene/PAM50 signature, BC subtype and OS were studied using univariate and multivariate Cox-models. Results: Sixty-five BCBM samples were analyzed: 32% (N=21) were HR+/HER2-, 38% (N=25) HER2+ and 29% (N=19) HR-/HER2-. With a median follow-up of 33 months, no clinical variable was significantly associated with OS, despite a trend towards a shorter survival for patients with HR-/HER2- BMs, as compared to patients with HR+/HER2- and HER2+ subtypes (median OS 9.4 versus 22.1 and 20.0 months, respectively, log-rank p=NS). The intrinsic subtype distribution, as assessed by gene-expression profiling, was 37% Basal-like, 46% HER2-enriched (HER2-E), 15% Luminal B and 2% Normal-like. Non-luminal subtypes (basal-like and HER2-E) were extensively represented, both overall and in each BC subtype (52% in HR+/HER2- subgroup, 96% in HER2+ subgroup, see Table). The PAM50 basal-like signature was significantly associated with a worse OS (HR 2.7, 95% CI 1.0-7.2, p=0.045), even after correcting for BC subtype (HR 5.2, 95% CI 1.1-23.4, p=0.032). In fact, even within the subgroup of HR+/HER2- BCBMs, the PAM50 basal-like signature was strongly associated with a worse OS (HR 92.6, 95% CI 5.0-1860.1, p=0.003) and patients with basal-like HR+/HER2- BCBMs presented a median OS similar to patients with HR-/HER2- BCBMs (mOS 9.0 vs 9.4 months). We identified 36 genes whose high expression was significantly associated with a worse OS (p< 0.05) and one gene (LINC02381) whose high expression was significantly associated with better OS (p< 0.05); for 33 of these genes (BCL11A, BMP2, BNIP3, CAV1, CDH3, CDK6, CKB, CRYAB, CXCL12, EGFR, EYA4, FOXC1, FZD8, FZD9, GABRP, GAS1, GDF5, GPC4, IL6, KRT17, KRT5, KRT6B, KRT7, LAMB3, LINC02381, MYC, NOTCH1, PRKX, PSAT1, RUNX3, SNAI1, SPRY2, TTYH1), the association was confirmed even after correcting for BC subtype (p< 0.05). Conclusions: Non-luminal intrinsic subtypes are extensively represented in resected BCBMs, even if clinically classified as HR+/HER2-. Our data suggest that basal-like genomic features might be enriched in BCBMs and might be associated with worse survival. Distribution of PAM50 intrisic subtyping on the 65 brain metastases evaluated according to hormone receptor (HR) and HER2 status Citation Format: Gaia Griguolo, Maria Vittoria Dieci, Susan Fineberg, claudia Pinato, Michele Bottosso, Luc Bauchet, Federica Miglietta, Jack Jacob, Giovanni Zarrilli, Valérie Rigau, Maria Cristina Guarascio, Francesca Zanconato, Francesca Schiavi, Matteo Fassan, William Jacot, Stefano Piccolo, Amelie Darlix, Valentina Guarneri. Gene Expression Profiling of Breast Cancer Brain Metastasis shows enrichment for non-luminal subtypes with potential prognostic implications [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD7-08.

Abstract P2-11-05: Effects of Intrinsic Subtypes and 21-gene Assay on the Early and Late Recurrence Risks in Patients with Early Stage HER2+ Breast Cancer: An Analysis of the North Central Cancer Treatment Group (NCCTG) N9831 (Alliance) Trial

Abstract Background: We previously demonstrated that intrinsic subtypes were associated with prognosis for early recurrence risk in patients (pts) with early-stage HER2-positive (HER2+) BC treated with trastuzumab (H) in the N9831 trial. Here, we evaluated the prognostic value of Intrinsic subtypes and 21-gene assay and the risk of early and late recurrence in the N9831 trial. Methods: NanoString custom code set, which included PAM50 and housekeeping genes, was used to quantify mRNA and generated intrinsic subtypes and risk of recurrence (ROR) score from the N9831 trial in Arms A and C: Arm A chemotherapy alone and arm C concurrent H. Quantitative RT-PCR of 21 genes, calculation of the axis, including estrogen axis (ER, PGR, BCL2, SCUBE2), HER2 axis (GRB7, HER2), proliferation axis (Ki67, STK15, Survivin, CCNB1, MYBL2), invasion axis (MMP11, CTSL2), and recurrence score (RS) risk group assignment (RS group 1 and 2: RS < 31 and RS group 3: RS ≥ 31) were performed using Oncotype DX assay. Cox regression models for RFS were used for analysis. Early recurrence was defined as a recurrence that occurred at ≤ 5 years, and late recurrence was defined as recurrence at > 5 years. Results: A total of 783 patients (Arm A 409 and Arm C 374) were included in this analysis. Using multivariate Cox regression analysis to evaluate the risk of early recurrence in patients who received chemotherapy alone in arm A, both invasion genes (MMP11 HR 1.23, 95%CI 1.05-1.44, p 0.01 and CTSL2 HR 1.36, 95%CI 1.1-1.69, p 0.005) and invasion axis (HR 1.64, 95%CI 1.26-2.13, p < 0.001) were associated with a higher rate of early recurrence. CD68 was associated with improved outcomes (HR 0.56, 95%CI 0.38-0.83, p 0.004). For the risk of early recurrence in patients treated with trastuzumab in arm C, ER (HR 0.85, 95%CI 0.74-0.97, p 0.02), PR (HR 0.78, 95%CI 0.64-0.94, p 0.008), and estrogen axis (HR 0.7, 95%CI 0.57-0.87, p 0.001) were associated with improved outcomes. Invasion axis (HR 1.61, 95%CI 1.08-2.41, p 0.02), Oncotype Dx risk group (3 vs. 1 and 2, HR 8.89, 95%CI 1.27-1124, p 0.02), and basal subtype (HR 2.77, 95%CI 1.1-5.95, p 0.03) were also significantly associated with worse outcomes. For risk of late recurrence, in arm A, ER (HR 1.22, 95%CI 1.04-1.44, p 0.02), PR (1.26, 95%CI 1.05-1.5, p 0.01), and estrogen axis (1.39, 95%CI 1.09-1.77, p 0.008) were associated with worse outcomes. Oncotype Dx risk group (3 vs. 1 and 2, HR 0.4, 95%CI 0.16-0.98, p 0.05) was associated with improved outcomes. However, neither individual gene, axis, nor intrinsic subtypes were associated with the risk of late recurrence in patients treated with trastuzumab. Conclusions: For risks of early recurrence, the invasion genes/axis were associated with increased risks of recurrence in patients with early-stage HER2+ BC regardless of trastuzumab treatment. Among patients treated with trastuzumab, ER genes/axis, Oncotype Dx risk group, and intrinsic subtype were prognostic for risks of recurrence in the first five years. For risks of late recurrence, ER genes/axis and Oncotype Dx risk group were prognostic but only in patients treated with chemotherapy alone. The ER genes/axis were associated with less recurrence in the first five years but worse after five years, reflecting a higher risk of late recurrence in ER/PR+ HER2+ BC patients treated with chemotherapy alone. However, none of the individual gene, axis, or intrinsic subtypes were associated with the risk of late recurrence in patients treated with trastuzumab. Therefore, future studies are needed to identify biomarkers for the risk of late recurrence in HER2+ BC patients treated with adjuvant trastuzumab. Support: BCRF-19-161; U10CA180821, U10CA180882, Genentech. https://acknowledgments.alliancefound.org; Clinicaltrials.gov Identifier: NCT00005970 Citation Format: Saranya Chumsri, Zhuo Li, Nadine Norton, Alvaro Moreno-Aspitia, Gerardo Colon-Otero, Keith L. Knutson, Antonio C. Wolff, Edith A. Perez, E. A. Thompson. Effects of Intrinsic Subtypes and 21-gene Assay on the Early and Late Recurrence Risks in Patients with Early Stage HER2+ Breast Cancer: An Analysis of the North Central Cancer Treatment Group (NCCTG) N9831 (Alliance) Trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-11-05.

Abstract P4-02-13: Homologous recombination deficiency, RB-loss gene signatures, intrinsic subtype and response to neoadjuvant treatment in HR+/HER2- early breast cancer: a correlative analysis of two phase II trials

Abstract Background: Hormone-receptor (HR)+/HER2- breast cancer (BC) is a biologically heterogeneous disease. Homologous recombination deficiency (HRD) and BRCA mutations have been previously reported to be associated with worse outcomes in HR+/HER2- metastatic BC patients receiving CDK4/6 inhibitors and endocrine therapy. Here, we assess the relation between HRD and RB-loss signatures, intrinsic subtyping, the PAM50-based chemo-endocrine score, and response to chemotherapy-based therapy and endocrine treatment in HR+/HER2- early BC. Methods: GIADA is a multicentric neoadjuvant phase II trial that treated premenopausal patients with Luminal B (LumB)-like BC (HR-positive, HER2-negative, with Ki67>20% and/or histologic Grade 3) with a combination of chemotherapy, immunotherapy and endocrine treatment. Expression of 758 genes on baseline tumor samples from all 43 patients was quantified by nCounter platform. The LETLOB phase II trial randomized postmenopausal women with clinical stage II-IIIA HR+/HER2- BC to neoadjuvant letrozole + lapatinib or letrozole + placebo for 6 months (Guarneri, JCO 2014). Gene-expression data (Affymetrix platform) from pre-treatment frozen core-biopsies was available from 66 out of 92 pts enrolled. Intrinsic subtype was assigned using a research-based PAM50 subtype predictor. A published HRD signature (Peng, Nat Commun 2014) and a signature of RB loss (RBsig), previously reported to potentially predict resistance to CDK4/6 inhibitors in HR+/HER2- BC (Malorni, Oncotarget 2016) were computed. The PAM50 based chemo-endocrine score (CES) was calculated using published definition (Prat, CCR 2017). Higher values of CES indicate increased endocrine sensitivity, while lower values indicate chemosensitivity. Association between genomic signatures was assessed through Pearson’s correlation coefficient. Association of genomic signatures with pCR was assessed through logistic regression and association with PEPI scores was assessed through Kruskal-Wallis test. Results: HRD signature levels were significantly higher in non-luminal (Basal-like and HER2-enriched) tumors as compared to Luminal (A or B) tumors (p>0.001 in the GIADA trial, p=0.021 in the LETLOB trial). Moreover, higher levels of HRD signature were associated with higher levels of RB-loss signature (Pearson correlation 0.355, p=0.020 in the GIADA trial; Pearson correlation 0.942, p< 0.001 in the LETLOB trial), higher levels of Basal-like signature (Pearson correlation 0.502, p< 0.001 in the GIADA trial; Pearson correlation 0.373, p=0.002 in the LETLOB trial) and lower levels of CES (Pearson correlation -0.422, p=0.005 in the GIADA trial; Pearson correlation -0.763, p< 0.001 in the LETLOB trial), indicative of higher chemosensitivity. In the GIADA trial, higher levels of HRD signature (p=0.018) and RBloss signature (p=0.073) and lower levels of CES (p=0.007) were associated with higher pCR rates after chemo, endocrine and immunotherapy. In the LETLOB trial, lower levels of HRD signature (p=0.068) and RBloss signature (p=0.042) and higher levels of CES (p=0.050) were associated with higher sensitivity to endocrine treatment (lower PEPI scores, 0 vs 1-3 vs 4 or more, after neoadjuvant letrozole). Conclusions: In HR+/HER2- early BC, HRD gene signatures, RB-loss gene signatures and non-luminal (especially Basal-like) intrinsic subtyping are associated with each other and associated with higher sensitivity to chemotherapy-based therapy and lower sensitivity to endocrine treatment. These observations might help correctly tailor systemic therapy, including biologic agents, in patients with HR+/HER2- early and advanced BC. Citation Format: Gaia Griguolo, Federica Miglietta, Laia Paré, Daniele G. Generali, Antonio Frassoldati, Antonino Musolino, Simon Spazzapan, Grazia Vernaci, Tommaso Giarratano, Marcello Lo Mele, Giancarlo Bisagni, Federico Piacentini, Enrico Tagliafico, Katia Cagossi, Francesca Schiavi, Claudia Pinato, Aleix Prat, Valentina Guarneri, Maria Vittoria Dieci. Homologous recombination deficiency, RB-loss gene signatures, intrinsic subtype and response to neoadjuvant treatment in HR+/HER2- early breast cancer: a correlative analysis of two phase II trials [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-02-13.

Abstract PD18-04: Prognostic implications of PIK3CA mutation by hormone receptor status and intrinsic subtype in early stage HER2-positive breast cancer: a correlative analysis from CALGB 40601

Abstract Background PIK3CA mutations have been described in 20-25% of early-stage HER2-positive breast tumors [1], and are associated with reduced pathologic complete response (pCR) rate after chemotherapy and anti-HER2 agents [2]. However, the independence of this finding and association with long-term outcomes within HER2+ patients is still largely unknown. Here, we studied the prognostic implications of PIK3CA mutations by hormone receptor (HR) status and intrinsic subtype in patients with early stage HER2+ breast cancer enrolled in CALGB 40601. Method In CALGB 40601, gene expression profiling by RNA sequencing (RNAseq) with PAM50-determined intrinsic subtype and PIK3CA mutations from whole exome sequencing (WES) were obtained from 184/305 (60%) pretreatment core biopsies. We examined the association of PIK3CA mutations with pCR and event free survival (EFS) by HR status and intrinsic subtype using logistic and Cox regression analyses. Results PIK3CA mutations were found in 32 patients (32/184, 17%). The most frequent mutation was H1047R (12/32,38%), followed by E545K (7/32,22%) and E542K (5/32,16%). PIK3CA mutations were present in 20% and 15% of HR-positive and HR-negative BC subpopulations, respectively. Within Luminal-B, Luminal-A and HER2-Enriched breast tumors, PIK3CA mutations occurred in 36%, 10% and 19% respectively. In the overall population there was lower rate of pCR in mutated-PIK3CA patients than wild-type (34% vs 49%). Using only the subset of patients treated with neoadjuvant trastuzumab-based therapy as standard of care (excluding the lapatinib plus paclitaxel arm), we found a statistically significant lower pCR rate among PIK3CA-mutated tumors using logistic regression model (30% vs 54%, OR=0.30, p=0.045). At a median follow-up of 9.1 years, the presence of PIK3CA mutation was significantly associated with worse EFS in the overall study population (HR 2.58, 95% CI 1.24- 5.35, p=0.011). In a multivariable model including pCR status, HR status and intrinsic subtype (HER2-E vs. not), PIK3CA mutation was independently and significantly associated with worse EFS (HR 2.18, 95% CI 1.04- 4.56, p=0.039). The negative impact of PIK3CA mutation on EFS was statistically significant only in patients with HR-positive (HR 3.6, 95% CI 1.45-8.96, p=0.06) and luminal breast tumors (HR 4.84, 95% CI 1.08-21.7, p=0.039), but not in HR-negative and non-luminal subtypes. Conclusion In our study, the presence of PIK3CA mutation was significantly associated with lower pCR rates in patients treated with chemotherapy plus trastuzumab. Moreover, in uni- and multivariable Cox models, PIK3CA mutations were associated with worse long-term survival, which appeared to be driven by HR-positive and luminal HER2-positive breast tumors.

Abstract P2-11-12: Pattern of distant relapse according to intrinsic molecular subtype in patients with HER2-positive breast cancer: a combined analysis of ShortHER, CherLOB, and two institutional cohorts

Abstract Background: All intrinsic molecular subtypes are represented among HER2-positive breast cancer, with implications on clinical outcome and treatment sensitivity. The impact of molecular subtypes on the pattern and site of relapse is largely unexplored. Methods: 677 patients with HER2-positive early breast cancer from the Shorther trial (n=437), the CherLOB trial (n=84) and two Institutional cohorts (Istituto Oncologico Veneto IRCCS Padova n=39 and Hospital Clinic Barcelona n=117) were included. Only patients with available PAM50 intrinsic molecular subtyping were considered. We analyzed the incidence of distant relapse (at any site and at specific sites) as the first event. Cumulative incidence was estimated according to competing risk analysis (Fine and Gray’s method). Competing risk regression was used to calculate the subdistribution Hazard Ratios (subHR) and their 95% Confidence Interval (CI). Results: The distribution of molecular subtypes was: 130 LumA (19%), 75 LumB (11%), 347 HER2-e (51%), 46 Basal (7%), 79 Normal (12%). Median follow up was 8.4 years (95%CI 8.2-8.6). The 10-yr cumulative incidence rates of distant relapse as first event were: LumA 7.9%, LumB 14.8%, HER2-e 14.7%, Basal 15.5%, Normal 10.4% (HER2-e vs LumA: SubHR 2.21, 95%CI 1.05-4.64, p=0.037). Table 1 shows the 5-yr and 10-yr cumulative incidence rates of distant metastases at specific sites (as first event) according to intrinsic subtype. HER2-e enriched and Basal tumors were more prone as compared to other subtypes to develop brain and lung metastasis as first event, respectively. Isolated brain metastases without extracranial disease occurred only in patients with HER2-e tumors. All brain metastases as first event occurred within 5 years from diagnosis. Bone-only disease as first event was less frequent in HER2-e and Basal subtype (subHR HER2-e vs LumA: 0.32, 95%CI 0.10-10.4. p=0.058). Next, we analyzed the frequency of site-specific first metastasis among patients who experienced a distant metastasis as first event (n=77). Lung metastases were more frequent in Basal tumors (LumA 25.0%, LumB 20.0%, HER2-e 24.4%, Basal 71.4%, Normal 0.0%, p=0.037) and bone metastases were more frequent in Luminal tumors (LumA 100.0%, LumB 60.0%, HER2-e 31.1%, Basal 42.9%, Normal 57.1%, p=0.006). Among 45 HER2-e patients with a first distant relapse, 25.6% were diagnosed with a brain metastasis and 15.6% had brain-only disease. Conclusions: Molecular subtypes influence the metastatic behaviour of clinically HER2-positive breast cancer. These results, if further validated, may have implication in planning personalized monitoring strategies. Table 1. 5-yr and 10-yr cumulative incidence rates of distant metastasis at specific sites (as first event) according to intrinsic subtype. Citation Format: Maria Vittoria Dieci, Giancarlo Bisagni, Stefania Bartolini, Antonio Frassoldati, Daniele Giulio Generali, Federico Piacentini, Gaia Griguolo, Enrico Tagliafico, Fara Brasó-Maristany, Nuria Chic, Francesca Porra, Roberto Vicini, Roberto D’Amico, Sara Balduzzi, Aleix Prat, PierFranco Conte, Valentina Guarneri. Pattern of distant relapse according to intrinsic molecular subtype in patients with HER2-positive breast cancer: a combined analysis of ShortHER, CherLOB, and two institutional cohorts. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-11-12.

Abstract P6-01-46: Independent validation of the HER2DX genomic test in HER2-positive breast cancer treated with neoadjuvant docetaxel, carboplatin, trastuzumab +/- pertuzumab (TCH/TCHP): a correlative analysis from a multicenter academic study

Abstract Background: HER2DX (Prat et al. EBiomedicine 2022) is a 27-gene prognostic (risk-score) and predictive (pathological complete response [pCR]-score) assay in early-stage HER2+ breast cancer based on clinical data and the expression of 4 gene signatures (immune, proliferation, luminal differentiation and HER2 amplicon). Here, we aim to evaluate, for the first time, the ability of HER2DX to predict pCR following neoadjuvant TCH or TCHP in HER2+ disease. Methods: Standardized HER2DX was performed in a central lab on baseline pre-treatment FFPE tumor biopsies from the GOM-HGUGM-2018-05 study in Spain, a consecutive retrospective series of patients (pts) with newly diagnosed stage I-III HER2+ breast cancer eligible for neoadjuvant therapy. Pts received standard 6 cycles of docetaxel, carboplatin and trastuzumab (TCH) or TCH with pertuzumab (TCHP) regimens. Primary aim was to test the ability of HER2DX pCR score to predict pCR (ypT0/is ypN0). Secondary objectives were to test the ability of HER2DX pCR score to predict pCR independently of clinical-pathological variables and the PAM50 subtype (HER2-enriched versus not), and to evaluate the association of HER2DX pCR score with the HER2DX risk-score. Logistic regression and receiver-operator curve (ROC) analysis were assessed. Statistical analyses were performed in R code 4.0.5. Results: HER2DX was evaluated in 155 pts (97%) enrolled in the study with available RNA (as of June 2022). Mean age of pts was 50 (range 22-74) and 55.2% of pts (n=85) were pre-menopausal. Clinical T2-4 disease represented 77.4% of cases (n=120), clinical node-positive disease (cN1-3) represented 63.9% of cases (n=99), and 68.0% of tumors (n=105) were hormone receptor-positive. The overall pCR rate was 57.4% (95% confidence interval [CI] 50-65): 52.2% (95% CI 40-64) with TCH (n=67) and 61.4% (95% CI 50-72) with TCHP (n=88). The proportion of HER2DX low-, medium- and high-pCR groups was 34.2%, 34.8% and 31.0%, respectively. HER2DX pCR score (as a continuous variable from 0 to 100) was significantly associated with pCR (odd ratio [OR]=1.03, p=5.91e-07). The pCR rates in HER2DX pCR-high and pCR-low groups were 75.0% and 28.0% (OR=7.6, 95% CI 3.2-19.1, p=7.14e-06), respectively. In pts treated with TCHP, the pCR rates in HER2DX pCR-high and pCR-low groups were 85.7% and 27.3% (OR=16.0, 95% CI 4.3-59.01, p=3.2e-05), respectively. The AUC ROC of HER2DX pCR score (as a continuous variable) and pCR status was 0.746 (in all pts) and 0.812 (in pts treated with TCHP). HER2DX pCR score was significantly associated with pCR independently of hormone receptor status, Ki67, age, menopausal status, pertuzumab use, clinical stage and PAM50 HER2-enriched subtype. The proportion of HER2DX low- and high-risk of relapse disease was 32.0% and 68.0%, respectively. The correlation of HER2DX pCR score and HER2DX risk-score was weak (coefficient=-0.17), as previously described. Proportion of cases according to both HER2DX scores and absolute difference of pCR rates between TCHP and TCH in each combined group is shown in Table. Conclusion: The HER2DX genomic test predicts pCR following neoadjuvant TCH or TCHP regimens independently of clinical-pathological variables and intrinsic subtype. The combination of both HER2DX scores might help better tailor systemic therapy in patients with newly diagnosed stage I-III HER2+ breast cancer. Citation Format: Coralia Bueno-Muiño, Isabel Echavarria, Sara López-Tarruella, Roche-Molina Marta, María del Monte-Millán, Tatiana Massarrah, Yolanda Jerez Gilarranz, Blanca Herrero, Salvador Gámez, Iván Márquez-Rodas, María Cebollero-Presmanes, Nevado Santos Manuel, Pilar de la Morena Barrio, Francisco Ayala de la Peña, José Ángel García-Sáenz, Fernando Moreno Antón, Álvaro Rodríguez Lescure, Teresa Quintanar, Diego Malón-Giménez, Laura Rodriguez-Lajusticia, Ana Isabel Ballesteros García, Dulce Bañón Torres, Lucía Villarejo, Nerea Lobato, Ainhoa Arias, Inmaculada Ocaña, Enrique Álvarez, Laia Paré, Mercedes Marín-Aguilera, Patricia Galván, Fara Brasó-Maristany, Ana Vivancos, Patricia Villagrasa, Joel S Parker, Charles M. Perou, Aleix Prat, Miguel Martín. Independent validation of the HER2DX genomic test in HER2-positive breast cancer treated with neoadjuvant docetaxel, carboplatin, trastuzumab +/- pertuzumab (TCH/TCHP): a correlative analysis from a multicenter academic study [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-01-46.

Abstract PD11-04: PD11-04 Primary results of SOLTI-1503 PROMETEO phase 2 trial of Combination of Talimogene Laherparepvec (T-VEC) with Atezolizumab in patients with residual breast cancer after standard neoadjuvant multi-agent chemotherapy

Abstract Background: Residual disease (RD) following neoadjuvant chemotherapy (NAC) in early HER2-negative breast cancer (BC) remains an unmet medical need. However, no therapies to date have tested their activity directly in chemo-resistant RD. Here, we hypothesized that combining an oncolytic virus such as T-VEC with atezolizumab may offer clinical benefit in patients (pts) with RD after standard NAC. To our knowledge, PROMETEO is the first trial that examines the activity of immunotherapy in pts with RD prior to surgery. Methods: PROMETEO (NCT03802604) is a single-arm, open-label, multicenter phase II trial. Women with triple-negative BC (TNBC) or hormone receptor-positive/HER2-negative (HR+/HER2-) BC with baseline (i.e., before NAC) ki67 ≥ 20% were eligible. RD was confirmed with a magnetic resonance imaging (MRI) showing a tumor diameter ≥ 10 mm and a core-biopsy detecting the presence of invasive cells. Before surgery, T-VEC was administered intratumorally on week 1 (106 pfu/mL), then in week 4 and every 2 weeks thereafter (108 pfu/mL) for 4 injections. Atezolizumab (840 mg) was administered intravenously every 2 weeks for 4 infusions, starting at week 4. Surgery was performed in < 3 weeks after completing the treatment. The primary objective was to evaluate the efficacy of the combination, measured by the rate of residual cancer burden (RCB) class 0/1 at surgery. Tumor samples collected at 5 timepoints (before NAC, during screening period, after first dose of T-VEC, after first dose of T-VEC and atezolizumab and at surgery) were mandatory to assess gene expression, tumor-infiltrating lymphocytes (TILs), immune cells PD-L1 IHC (SP142), tumor mutational burden (TMB) by FoundationOne and other translational endpoints. Results: Between Dec 2018 to Feb 2022, 28 pts were enrolled: 20 pts with HR+/HER2- disease and 8 pts with TNBC. Median age was 47 (range 31-71) and 71% of pts were premenopausal. At diagnosis before NAC, clinical stage II disease represented 60.7%, cN+ 60.7%, median Ki-67 was 37.5% (range 20%-95%), high TILs (≥10%) 37%, median TMB was 3 (0-19) and only 1 of 27 pts (3.7%) had a PD-L1-positive tumor. After NAC, mean tumor size by MRI was 28.3 mm (10-93). Two pts discontinued from the trial (1 withdrawal of consent and 1 COVID infection). The completion of 5 cycles of treatment was achieved by 73% of pts. The overall RCB-0/1 rate was 25% (7 of 28, 95% IC 10.7 – 44.9%), all with RCB 0 (pathologic complete response [pCR]). The pCR rate was 30% in HR+/HER2- disease and 12.5 % in TNBC. Radiological response by MRI was achieved by 3 of 28 pts (10.7%). Interestingly, none of the 7 pts with a pCR had radiological response (stable disease n=5, progressive disease [PD] n=2). Six pts (21.4%) had radiological PD and had RCB 2/3. Overall, 27 (96%) patients had at least one treatment-emergent adverse event (TEAE) of any grade. Most common grade 1 or 2 AEs were fever (11 pts, 39.3%), ALT increased (9 pts, 32.1%), AST increased (8 pts, 28.6%), arthralgia (6 pts, 21.4%) and anemia (6 pts, 21.4%). Grade 3 reversible neutropenia occurred in 1 patient. Across all pts, significant increases (p< 0.001) in TILs, immune genes and immune PDL1+ cells were observed after 1 dose of TVEC, 1 dose of the combination and at surgery. Intrinsic subtype changes at surgery occurred in 73.1% of cases, mostly (46.1%) Luminal A/B converting to Normal-like. At surgery, 19 of 26 (73.1%) of tumors were PDL1+. Conclusions: Two months of T-VEC in combination with atezolizumab induced a pCR in a subgroup of pts with chemoresistant HER2- breast cancer. This effect is probably related to the immune activation provoked by the combined treatment. Interestingly, a high discrepancy was observed between the pre-surgical radiological imaging and the actual surgical pathological report. Pre-operative window-of-opportunity trials in this context might provide important clues regarding the activity of novel treatment strategies. Citation Format: Tomás Pascual, Maria Vidal, Juan Miguel Cejalvo, Estela Vega, Esther Sanfeliu, Sergi Ganau, Ana Julve, Esther Zamora, Ignacio Miranda, Ana Delgado, Begoña Bermejo, Luis de la Cruz-Merino, Manel Juan, Patricia Galván, Xavier Gonzalez-Farré, Juan Manuel Ferrero-Cafiero, Patricia Villagrasa, Mafalda Oliveira, Aleix Prat. PD11-04 Primary results of SOLTI-1503 PROMETEO phase 2 trial of Combination of Talimogene Laherparepvec (T-VEC) with Atezolizumab in patients with residual breast cancer after standard neoadjuvant multi-agent chemotherapy [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD11-04.

Abstract PD10-07: PD10-07 Low plasma estradiol, low expression of estrogen responsive genes and TP53 mutations are associated with poor anti-proliferative response to aromatase inhibitors

Abstract Background: Aromatase inhibitors (AIs) are highly effective at reducing recurrences and mortality in postmenopausal patients with estrogen receptor positive breast cancer (ER+ BC). Poor anti-proliferative (Ki67) response or ER+ BCs to AIs after 2 weeks is associated with worse long-term outcomes. Factors that relate to the degree of the response may identify markers and/or mechansims of resistance. Methods: The PeriOperative Endocrine Therapy for Individualizing Care (POETIC) trial randomized 4,480 with ER+ BC to 2 weeks’ AI before surgery or no presurgical treatment. All patients within the bottom 15% of Ki67 responders to AI (poor responders [PRs]; n=177 with RNA extracted) were selected from and matched to good responders (GRs) within the 50% showing the best response (n=190). Matching was based on baseline Ki67 levels as measured by immunohistochemistry (IHC). Response to AI was measured by the percentage change in Ki67 after 2 weeks’ treatment. PRs were further divided into groups expressing high ESR1 (PRs ESR1HIGH; n=119) and low ESR1 (PRs ESR1LOW; n=58) levels since there were very few GRs with low ESR1. RNAseq, targeted exome DNA sequencing of 87 BC/resistance related genes and measurement of plasma estradiol levels by mass spectrometry were performed to understand mechanisms of de novo resistance. Intrinsic subtypes were estimated from RNAseq data. Results: More than 90% of PRs ESR1LOW were non-luminal subtypes with low expression of estrogen-responsive genes. In contrast, 11% of PRs ESR1HIGH were non-luminal compared to 4% of GRs but only HER2-enriched subtypes were significantly higher in PR ESR1HIGH (p=0.05, Fisher exact). While AI treatment had limited impact on Ki67 IHC values in PRs ESR1HIGH, PGR expression was more than 2-fold lower after 2 weeks of AI. Gene-set enrichment analysis showed significantly lower expression of estrogen-response genes in PRs ESR1HIGH compared to GRs (FDR< 10-9) at baseline despite similar percentage of Luminal subtypes in PRs ESR1HIGH and GRs. Plasma estradiol levels were correlated with expression of estrogen-response genes (FDR=0.01) and levels were significantly lower in PRs ESR1HIGH compared to GRs (p=0.003, Mann Whitney). PRs ESR1HIGH had significantly more mutations in RB1, TP53, ARID1B and DNAH11 genes (p< 0.05, Fisher exact). TP53 mutations were significantly enriched in Luminal-A PRs ESR1HIGH compared to GRs (22% and 3% respectively; p=0.003, Fisher exact), but not in Luminal-B tumors (23% and 15% mutated respectively). Discussion and conclusions: In approximately 33% of PRs, de novo AI resistance was associated with and most likely due to low expression of ER/ESR1 and estrogen-responsive genes in non-luminal tumors. In the remaining tumors, AI treatment still impacted some estrogen responsive genes but had limited downstream impact on suppressing proliferation. This might be due to mutations including in TP53 that limit suppression of proliferation downstream of estrogen signaling. The proportion of Luminal tumors in GRs and PRs ESR1HIGH was similar, suggesting better outcome of Luminal-A tumors on AI is likely due to their better intrinsic prognosis rather than better response to endocrine therapy. Citation Format: Eugene F. Schuster, Elena López-Knowles, Anastasia Alataki, Lila Zabaglo, Elizabeth Folkerd, David Evans, Kally Sidhu, Holly Tovey, Perry Maxwell, Nicholas Turner, Stephen Johnston, Manuel Salto-Tellez, Maggie Chon U Cheang, John Robertson, Ian Smith, Judith Bliss, Mitch Dowsett. PD10-07 Low plasma estradiol, low expression of estrogen responsive genes and TP53 mutations are associated with poor anti-proliferative response to aromatase inhibitors [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD10-07.

Abstract P2-23-13: Highly proliferative estrogen receptor-positive breast cancer is associated with better response to neoadjuvant chemotherapy but worse clinical outcome

Abstract Introduction: Highly proliferative cancers are known to respond better to neoadjuvant chemotherapy (NAC), and pathological complete response (pCR) is a surrogate for survival benefit in breast cancer. Ki67 is the most commonly used cell proliferation marker; however, conventional immunostaining is subjected to variability by the assessor and the institution including the antibody used. To this end, we used the Ki67 gene expression to identify highly proliferative breast cancer and investigated whether it is associated with better response to NAC and survival by intrinsic subtype. Materials and Methods: Total of 6623 breast cancer patients from 11 independent cohorts with full transcriptome and clinical data were analyzed. The top 20% of Ki67 gene expression in each cohort were defined as highly proliferative group based on previous studies using immuno-staining. Results: Highly proliferative breast cancer was associated with high proliferation score, and all five cell proliferation-related gene sets in the Hallmark collection; E2F Targets, G2M Checkpoint, Mitotic Spindle, and Myc Targets v1 and v2 were enriched by gene set enrichment analysis in multiple cohorts regardless of subtype. MKI67 gene expression increased with higher grade in both ER-positive breast cancer and TNBC in multiple cohorts, but no clear association with staging was observed. Highly proliferative ER-positive breast cancer was significantly associated with worse disease-free, disease-specific, and overall survival consistently in METABRIC and GSE96058 cohorts, and showed a trend toward worse overall survival in TCGA; however, this was not the case in TNBC. Further, we found that highly proliferative tumor was significantly associated with better pathologic complete response (pCR) rate in six of the eight neoadjuvant chemotherapy cohorts of ER-positive breast cancer, but only two for TNBC. We also found that highly proliferative ER-positive breast cancer was associated with abundant silent and non-silent mutations, increased intra-tumoral heterogeneity, and homologous recombination defect scores when compared to lower proliferation groups, and this was not seen in TNBC in TCGA cohort. Although DNA repair gene set was enriched in the highly proliferative ER-positive breast cancer, it was also associated with higher neoantigen activity, higher infiltration of tumor infiltrating lymphocytes including Th1 cells, Th2 cells, regulatory T cells, and M1 macrophages, as well as with enrichment of Interferon-gamma response gene set consistently in 3 large cohorts. In contrast, several stromal cell fractions were decreased in this group. Conclusions: Highly proliferative ER-positive breast cancer is significantly associated with pCR after NAC with increased tumor infiltrating lymphocytes, but is not a surrogate for survival, which are not the case in TNBC. Citation Format: Rongrong Wu, Yoshihisa Tokumaru, Mariko Asaoka, Masanori Oshi, Li yan, Takashi Ishikawa, Kazuaki Takabe. Highly proliferative estrogen receptor-positive breast cancer is associated with better response to neoadjuvant chemotherapy but worse clinical outcome [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-23-13.

Abstract OT1-07-01: Omission of SLNB in triple-negative and HER2-positive breast cancer patients with radiologic and pathologic complete response in the breast after NAST: a single-arm, prospective surgical trial (EUBREAST-01 trial, GBG 104)

Abstract Background: Currently, axillary surgery for breast cancer is considered a staging procedure that does not seem to influence breast cancer mortality since the risk of developing metastasis depends mainly on the biological behavior of the primary (seed-and-soil model). Based on this, postsurgical therapy should be considered based on biological tumor characteristics. Retrospective data of cancer registry trials showed a strong correlation between breast pathologic complete response (pCR) and nodal pCR depending on intrinsic subtypes. Improvements in systemic treatments for breast cancer have increased the rates of pCR in patients receiving neoadjuvant systemic therapy (NAST), offering the opportunity to decrease, and perhaps eliminate, surgery in patients who have a pCR. Trial design: The EUBREAST network designed a clinical trial (NCT04101851) in which only patients with the highest likelihood of having a pCR after NAST (triple-negative or HER2-positive breast cancer) will be included, and type of surgery will be defined according to the response to NAST rather than on the classical T and N status at presentation. In the ongoing trial, axillary surgery will be eliminated (no axillary sentinel lymph node biopsy [SLNB]) for initially clinical node-negative (cN0) patients with radiologic complete remission (rCR) and a breast pCR (ypT0/ypTis) as determined in the lumpectomy specimen. The trial design is a multicenter single-arm study with a limited number of patients (N=440 as the screening population with an expected 80% pCR-rate) which might give practice-changing results in a short period, sparing the time and the costs of a randomized comparison. Patients will be recruited in European countries (Austria, Germany, Italy, and Spain) over 36 months. Inclusion criteria: -Written informed consent -Histologically confirmed unilateral primary invasive carcinoma of the breast (core biopsy). Multifocal or multicentric tumors are allowed if breast-conserving surgery (BCS) is planned. -Age at diagnosis at least 18 years -imaging techniques with estimated tumor stage between cT1-T3 before NAST -triple-negative (TNBC) or HER2-positive invasive breast cancer -TNBC is defined by: ER-negative (< 10% positive cells in IHC) and PgR-negative (< 10% positive cells in IHC), HER2-negative -clinically and sonographically tumor-free axilla before core biopsy (cN0/iN0) -in cases with cN0 and iN+, a negative core biopsy or fine-needle aspiration biopsy of the sonographically suspected lymph node is required -no evidence for distant metastasis (M0) -standard NAST with rCR -planned BCS with postoperative external whole-breast irradiation (conventional fractionation or hypofractionation) Primary objective: 3-year rate of axillary recurrence-free survival (ARFS) after BCS Statistics: The calculated total case number for per-protocol analysis is N=350, and the expected total number of screened patients is N=440. The assumption for acceptable 3-year ARFS ≥98.5% in the experimental arm is based on previous study findings. Timelines: -First patient in: January 2021 -Last patient in: December 2023 -Primary outcome analysis: Q1/2027 Current accrual: In June 2022, 150 patients were recruited in Germany and Italy. Contact: Prof. Dr. Toralf Reimer (eubreast-01@kliniksued-rostock.de), study chair Dr. Oreste D. Gentilini (gentilini.oreste@hsr.it), study co-chair Funding by Else Kroener-Fresenius Foundation, German Society of Senology, University of Rostock (Germany), and San Raffaele Hospital (Milan, Italy) Citation Format: Toralf Reimer, Thorsten Kuehn, Angrit Stachs, Anke Kleine-Tebbe, Nikola Bangemann, Andrea Stefek, Carolin Hammerle, Jörg Heil, Antje Nixdorf, Gabriele Bonatz, Agnieszka Nolte, Isabel T. Rubio, Florentia Peintinger, Keyur Mehta, Sibylle Loibl, Edoardo Botteri, Oreste Davide Gentilini. Omission of SLNB in triple-negative and HER2-positive breast cancer patients with radiologic and pathologic complete response in the breast after NAST: a single-arm, prospective surgical trial (EUBREAST-01 trial, GBG 104) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT1-07-01.

Abstract P1-04-10: Association of stromal tumor infiltrating lymphocytes (sTILs) in pretreatment biopsies in different molecular subtypes of HER2+/ER+ breast cancer: Assessment of NRG Oncology/NSABP B-52

Abstract Background: The primary aim of the NRG Oncology/NSABP B-52 clinical trial was to test if estrogen deprivation (ED) administered concomitantly with neoadjuvant docetaxel, carboplatin, trastuzumab, and pertuzumab (TCHP), would improve the pCR rate in patients with HER2+/ER+ early breast cancer. A numerical increase in the pCR rate was observed with ED (46.1% v 40.9%), but the difference was not statistically significant. The purposes of this study were to assess the association of sTILs in pretreatment biopsies with pCR in the total population and within the molecular subtypes of breast cancer and to assess changes in sTILs between pre- and on-treatment biopsies. The secondary endpoints of recurrence-free interval (RFI) and overall survival (OS) are currently being analyzed and will be presented along with association of these endpoints with sTILs in pretreatment biopsies in the total cohort and within molecular subtypes. Methods: Scoring of sTILs on routine H&E slides from pre-treatment biopsies with sufficient tumor from 249 of the 315 patients (79%) entered in B-52 were performed by one of two pathologists (SKM, RSM). Both pathologists scored sTILs on a subset of 64 patients to document concordance. Wilcoxon two-sided test, box and whisker plots, and forest plots were used to assess associations with pCR. Molecular subtypes were determined utilizing RNA-seq data and AIMS subtyping method. On-treatment biopsies were available in 46 patients and were scored and compared to paired baseline samples. Results: Good concordance between pathologists was established with an inter-pathologist difference of ˂20% difference between scores in 92% of cases. sTILs in pre-treatment samples were associated with pCR across both arms of the trial (p=0.0074) and in the TCHP+ED arm (p=0.033), but not in the TCHP arm (p=0.093). The distribution of intrinsic subtypes was 34% luminal B, 29% luminal A, 28% HER2E, 5.8% normal, and 2.7% basal, with no significant differences between the arms. Presence of sTILs showed a trend for association with pCR in HER2E pre-treatment samples (p=0.054) but not in non-HER2E (p=0.75). Similarly, sTILs were associated with pCR in non-luminal tumors (p=0.055) but not in luminal tumors (p=0.44). Stratification by treatment arm and menopausal status suggested sTILs are associated with pCR in premenopausal women treated with TCHP (OR: 1.04, 95% CI=1.00-1.09). Interestingly, decreases in the sTIL scores with treatment were associated with pCR in the TCHP+ED arm (p=0.01) but not in the TCHP arm. Analysis of RFI and OS on B-52 is ongoing and will be presented along with associations of sTILs with intrinsic subtypes for RFI and OS. Conclusions: Although a positive correlation between sTILs and pCR was observed, the clinical utility appears limited because of the extensive overlap in the TIL scores between pCR and non-pCR tumors. Significance for a positive association of sTILs with pCR was detected in HER2E but not in luminal tumors. This may be due to the molecular differences of the subtypes, or the make-up of the TILs, or both. The association of a decrease in sTILs with TCHP+ED treatment needs further investigation. The small number of samples is a limitation of the study; however, the B-52 protocol specified that the collection of the B-52 samples was for the purpose of exploratory analysis. Our results highlight the molecular heterogeneity of the HER+/ER+ patient population and suggests that different treatment strategies may be required in future treatment regimens for this patient population. Support: NSABP Foundation; BCRF; 3U10CA180868-03S2, -180822; UG1CA189867; Genentech. Citation Format: Katherine L. Pogue-Geile, Sai K. Maley, Rim S. Kim, Ying Wang, Roberto Salgado, Corey Lipchik, Huichen Feng, Reena S. Cecchini, Samuel A. Jacobs, Ashok Srinivasan, Eleftherios (Terry) Mamounas, Charles E. Geyer Jr, Priya Rastogi, C. Kent Osborne, Soonmyung Paik, Norman Wolmark, Peter C. Lucas, Mothaffar Rimawi. Association of stromal tumor infiltrating lymphocytes (sTILs) in pretreatment biopsies in different molecular subtypes of HER2+/ER+ breast cancer: Assessment of NRG Oncology/NSABP B-52 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-04-10.

Abstract P4-09-05: Characterization and validation of biologically-driven HER2-positive breast cancer subgroups in the ALTTO and NeoALTTO clinical trials

Abstract Background: Tumor and microenvironment features, including luminal phenotype as well as metabolic, immune and stroma activation, impact prognosis and treatment response in HER2-positive breast cancer. Here, we aimed to identify subgroups depicting biological processes associated with prognosis in patients receiving adjuvant trastuzumab in the phase III ALTTO trial, and to validate their biological and prognostic characteristics in the phase III neoadjuvant NeoALTTO trial. Methods: By applying a case-control approach (1:2), we selected from the ALTTO trastuzumab arm 134 and 268 patients with and without a distant relapse respectively, matched for clinicopathological characteristics. In ALTTO, RNA was obtained from FFPE tumor cores from surgical samples. RNA sequencing (RNAseq) data available from 254 frozen pre-treatment samples were used for validation in patients receiving trastuzumab and/or lapatinib in NeoALTTO. The Absolute Intrinsic Molecular Subtyping (AIMS) was used to compute PAM50 subtypes. Prognostic genes were identified using a multivariable Cox proportional hazard model (controlling for clinicopathological characteristics and PAM50 HER2-enriched [HER2-E] vs others) for distant relapse-free survival (DRFS). Clusters were identified using non-negative matrix factorization (NMF) and k-means clustering, and characterized with gene expression profiling and Gene Set Variation Analysis (GSVA, hallmark gene sets from MSigDB). Aiming at identifying the subgroups in external cohorts, we identified relevant genes to develop group-specific signatures with LASSO regression, and used the derived scores to build a multinomial classifier. Results: The case-control cohort includes a high-risk population, with higher proportions of >2cm, node positive and G3 tumors compared to the whole ALTTO trastuzumab arm. RNAseq data were generated for 386/402 patients. NMF and k-means clustering performed on genes associated with DRFS (false discovery rate < 0.05) identified 4 groups with distinct biological characteristics and prognosis: immune-enriched (IM, N = 69), proliferative/metabolic (P/M, N = 87, characterized by glycolysis, cholesterol homeostasis and proliferation pathways), mesenchymal/stroma-enriched (M/S, N = 76, characterized by epithelial-mesenchymal transition, angiogenesis and TGF-beta signaling), and hormone receptor positive-enriched (N = 154), further divided into PAM50 HER2-E (N = 91) and non-HER2-E (N = 63, LUM, mainly luminal A/B tumors). The IM and LUM groups presented better DRFS (91% and 87% 5-year DRFS, respectively) compared to the others (5-year DRFS of 72%, 58% and 51% for HER2-E, M/S and P/M, respectively). The gene expression-based classifier identified the same 5 groups in NeoALTTO. GSVA analysis and comparisons among the 5 groups showed similar results in the two studies. Of interest, we observed significant differences in event-free survival in NeoALTTO (P = 0.035 and P = 0.041 in the whole population and in the subgroup with residual disease, respectively), with IM and LUM presenting better outcomes compared to the other groups. Sensitivity to neoadjuvant treatment as described by pathological complete response (pCR, ypT0/is ypN0) differed across the groups, with LUM presenting lower pCR rates (8%) compared to HER2-E (40%), IM (35%), P/M (32%), and M/S (32%). Conclusions: Five biologically-driven HER2-positive breast cancer subgroups were identified in ALTTO, highlighting the heterogeneity of this disease. Of note, their biological features and clinical behavior were validated in the NeoALTTO population, suggesting the robustness of our findings. IM and LUM tumors could be considered for treatment de-escalation approaches. Additional validation in cohorts receiving standard (neo)adjuvant therapies is warranted. Citation Format: Mattia Rediti, David Venet, Andrea Joaquin Garcia, Dominique Agbor-Tarh, Marion Maetens, Delphine Vincent, Samira Majjaj, Sarra El-Abed, Takayuki Ueno, Serena Di Cosimo, Martine Piccart, Lajos Pusztai, Sherene Loi, Roberto Salgado, Giuseppe Viale, Françoise Rothé, Christos Sotiriou. Characterization and validation of biologically-driven HER2-positive breast cancer subgroups in the ALTTO and NeoALTTO clinical trials [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-09-05.

Abstract P3-09-01: Characterization of residual disease after neoadjuvant selective estrogen receptor degrader (SERD) therapy using tumor organoids in the I-SPY Endocrine Optimization Protocol (EOP)

Abstract Background: Treatment of estrogen receptor (ER)-positive breast cancer with selective estrogen receptor degraders (SERDs) frequently results in the loss or reduction of ER expression. Whether these changes are due to on-target effects of SERDs degrading ER or arise as a mechanism of tumor resistance with associated changes in cellular phenotypes remains unknown. It is critical to distinguish between these possibilities to accurately assess treatment response and determine the most appropriate subsequent therapy. To this end, we created and conducted molecular analyses on patient-derived organoid cultures from post-treatment tissue in patients receiving neoadjuvant SERD therapy for early-stage ER+ breast cancer in the I-SPY2 Endocrine Optimization Protocol (EOP). Methods: The I-SPY2 EOP study is a prospective, randomized substudy within the I-SPY TRIAL testing the oral SERD amcenestrant alone or in combination with letrozole or abemaciclib in stage 2/3 ER+ Her2-negative breast cancer. Enrollment is ongoing, with patients receiving amcenestrant neoadjuvantly for 6 months until the day before surgery. Tumor tissue is collected at baseline, 3 weeks, and at surgery. Organoids were generated from post-treatment surgical samples. Organoid cultures were optimized based on established methods (Dekkers et al., Nature Protocols, 2021) to assess ER levels and activity. Pre- and post-treatment tissue samples were also assessed for ER, PR, Ki67, and GATA3, a luminal marker and transcription factor that is functionally linked with ER, via immunohistochemistry. Results: In 7 patients with both pre- and post-treatment tissue samples including fresh surgical samples for organoid generation, the ER in baseline tumor tissue was >=90% in all patients, PR ranged from 40-90%, and Ki67 ranged from 5-30%. In post-treatment surgical tissue from these cases, ER ranged from 0-30%, PR from 0-50%, Ki67 from < 1%-10%, and GATA3 was positive in 5 of 5 cases tested to-date. The creation of organoids from residual disease at surgery was attempted for these 7 patients, with organoids successfully propagated in 5 cases thus far. 3 of 5 organoid cultures were ready for analysis and in all cases strong ER and PR expression in organoids was observed after culture for > 1 month in the absence of amcenestrant. Detailed gene expression profiling (including Mammaprint/Blueprint) and gene set enrichment analyses (GSEA) to assess for intrinsic breast cancer subtype and ER activity in each sample and corresponding organoid culture are in progress and will be reported with the full dataset. Conclusion: Patient-derived organoid culturing of residual disease after neoadjuvant endocrine therapy is feasible. Neoadjuvant treatment with a SERD can render ER and PR low or absent at the time of surgical resection, which does not necessarily imply the presence of endocrine therapy resistant disease. The use of organoids and additional IHC markers (GATA3) demonstrate that receptor negativity may be an indicator of the drug hitting its target, suggesting ER signaling is still intact. In general, patient-derived tumor organoid cultures modeling residual disease states can be a useful adjunct to existing methods used to monitor the effects of neoadjuvant endocrine therapy and is being explored in the I-SPY EOP trial. Citation Format: Jennifer Rosenbluth, Christopher J. Schwartz, Tam Binh Bui, Shruti Warhadpande, Pravin Phadatare, Sigal Eini, Michael Bruck, Julissa Molina-Vega, Kami Pullakhandam, Nicole Schindler, Lamorna A. Brown Swigart, Christina Yau, Gillian Hirst, Rita Mukhtar, Karthik V. Giridhar, Olufunmilayo I. Olopade, Kevin Kalinsky, Cheryl A. Ewing, Jasmine M. Wong, Michael D. Alvarado, Laura Van’t Veer, Laura J. Esserman, Jo Chien. Characterization of residual disease after neoadjuvant selective estrogen receptor degrader (SERD) therapy using tumor organoids in the I-SPY Endocrine Optimization Protocol (EOP) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-09-01.

Abstract PD17-05: Development and Validation of a Composite Biomarker Predictive of Palbociclib + Endocrine Treatment Benefit in Early Breast Cancer: PENELOPE-B and PALLAS Trials

Abstract Background: The PENELOPE-B (NCT01864746) and PALLAS (NCT02513394) trials are large prospective, randomized, phase III trials that evaluated adjuvant palbociclib (PAL) + endocrine treatment (ET) vs ET in patients with hormone receptor–positive/human epidermal growth factor receptor 2–negative (HER2–) early breast cancer (EBC). Both studies did not meet the primary endpoint of improving invasive disease-free survival (iDFS). We conducted biomarker analyses to identify patients who might benefit from PAL + ET in EBC. Methods: Resected tumor tissue was collected from consenting patients. Gene expression analyses were conducted using the HTG EdgeSeq Oncology Biomarker Panel including 2549 genes. Based on 91 genes from the HTG panel, the intrinsic molecular subtypes were calculated using Absolute Intrinsic Molecular Subtyping (AIMS). Potential predictive treatment biomarkers were established in PENELOPE-B (n=906 with resected tissue) as the development set using an outcome-oriented approach based on iDFS with a selection procedure that maximized the log-rank statistic to estimate a standard Z score–based optimal cutoff. Independent validation was conducted on PALLAS (n=2085; PENELOPE-B-like with resected tissue and HTG data). Hazard ratios and corresponding 95% CIs were calculated using the Cox proportional hazards model, and iDFS distributions between treatment arms were compared using the log-rank test. Interaction between treatment and biomarker status was assessed. Results: Patient baseline characteristics were well balanced, with no differences in iDFS between the intent-to-treat set and the biomarker set for both trials. Approximately 73% of patients (PENELOPE-B [n=663] and PALLAS [n=1516]) had luminal A subtypes whereas only 7.1 % (PENELOPE-B [n=64]) and 8.3 % (PALLAS [n=172]) had a luminal B subtype. AIMS subtypes showed overall similar prognostic patterns for iDFS between PENELOPE-B and PALLAS. The biomarker-defined subgroup found in PENELOPE-B with optimal cutoff demonstrated a preferential benefit from PAL + ET (n=364 [96 events]; hazard ratio [95% CI], 0.63 [0.42, 0.95]; P=0.025). Independent validation of the PALLAS subgroup using the pre-defined optimal cutoff confirmed a significant benefit from PAL + ET (n=916 [70 events]; 0.55 [0.34–0.90]; P=0.015) while not in the rest of the patients (interaction p=0.0025). Significant treatment effects remained (0.55 [0.34–0.89]; P=0.015) after adjusting for the randomization stratification factors of PALLAS. Conclusions: The composite predictive biomarker defined from PENELOPE-B was independently validated in a prospectively defined retrospective analysis of a subset of patients selected from PALLAS. The composite biomarker identified a subset of EBC patients deriving benefit from the addition of PAL to ET. This patient stratification approach can potentially be applied to future adjuvant clinical trials for treatment of hormone receptor–positive/HER2– EBC. Citation Format: Sibylle Loibl, Carsten Denkert, Yuan Liu, Erik S. Knudsen, Angela DeMichele, Zhe Zhang, Julia Teply-Szymanski, Martin Filipits, Peter A. Fasching, Michael Gnant, Shibing Deng, Marija Balic, Federico Rojo, Mark Watson, Chetan Deshpande, Nicholas Turner, Otto Metzger, Kathy Puyana Theall, Agnieszka Witkiewicz, Olga Valota, W. Fraser Symmans, Erica L. Mayer. Development and Validation of a Composite Biomarker Predictive of Palbociclib + Endocrine Treatment Benefit in Early Breast Cancer: PENELOPE-B and PALLAS Trials [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD17-05.

Abstract P3-06-02: TATEN TRIAL (SOLTI-1716) Targeting non-Luminal disease by PAM50 with pembrolizumab + paclitaxel in Hormone Receptor-positive/HER2-negative (HR+/HER2-) metastatic breast cancer (MBC): interim analysis

Abstract Background Within HR+/HER2- disease, patients with non-luminal subtypes of breast cancer (HER2-enriched [HER2-E] and Basal-like) have poorer prognosis than those with luminal subtypes, may be more sensitive to chemotherapy, and have higher expression of immune-related genes and tumor infiltrating lymphocytes (TILs). Here, we report the interim efficacy and safety data of the TATEN trial (NCT04251169), the first study designed to evaluate pembrolizumab and paclitaxel in HR+/HER2-negative, PAM50 non-luminal, metastatic breast cancer (MBC). Methods TATEN is a single-arm, multicenter phase II study evaluating pembrolizumab in combination with paclitaxel in patients with HR+/HER2-, PAM50 non-luminal, MBC. Key inclusion criteria include progression to prior CDK4/6 inhibitors, presence of measurable disease by RECIST V1.1, no prior chemotherapy for MBC, and ECOG 0-1. Patients receive pembrolizumab at 200 mg every 3 weeks (on D1 of each 21-day cycle, beginning at cycle 1) in combination with weekly paclitaxel at 80 mg/m2, beginning at cycle 2. The primary endpoint is to evaluate overall response rate (ORR), defined as the rate of complete (CR) and partial response (PR) according to RECIST V1.1. Secondary endpoints include clinical benefit rate (CBR; CR + PR + stable disease >24 weeks), progression free survival, overall survival, safety, and predictive biomarkers. Tumor samples collected during advanced/metastatic disease are mandatory to assess PAM50 and other translational endpoints. This study had a planned interim analysis after 15 patients were evaluable for ORR based on a Simon’s two stage design with 80% power and a type I error rate of 0.05. Stage I of the trial would be considered successful if at least 6 patients achieved a PR and/or CR. In that case, the trial would recruit up to 46 evaluable patients for a target ORR ≥ 41. Here we report results from the patients who received at least one dose of combination treatment and had a first, post-baseline, tumor assessment according to RECIST v1.1 (evaluable population). Results From July 2020 to December 2021, 119 patients were screened, and 25 PAM50 non-luminal tumors were identified (21%). From these, 17 (68%) patients were recruited, and 15 were evaluable for primary endpoint. Two patients discontinued the trial before the first dose of pembrolizumab and paclitaxel, because of clinical progressive disease (PD). Baseline patient characteristics were as follows: median age 53 years (range: 40-77), ECOG 0 52.9%, de novo MBC at diagnosis 29.4%, and visceral disease 64.7% (including 53.3% with liver metastasis). Ten patients had received paclitaxel treatment in the adjuvant setting. Regarding PAM50 intrinsic subtype, two patients had basal-like and 13 HER2-E tumors. At the time of data cut-off (May 17,2022), 8 patients (53.3%) had stopped their treatment because of PD and 2 (13.3%) due to toxicity. Five patients (33.3%) were still on treatment. The ORR was 53.3 % (8 of 15, 95% CI 26.6-78.7), meeting the pre-specified ORR for the first stage of the trial. The CBR was 86.6% (13 of 15, 95%CI 59.5-98.34), and median PFS was 7.5 months (95% CI: 5.6 – 10.2). Overall, all patients experienced treatment-related adverse events (TRAEs) of any grade, while 53.3% of patients experienced grade 3 TRAEs. No grade 4 or 5 TRAEs were reported in the evaluable population. Correlative analysis including gene expression analysis and centralized TILs scoring and PD-L1 IHC will be presented. Conclusions The first stage of TATEN combining pembrolizumab with paclitaxel after progression to CDK4/6 inhibitors in patients with HR+/HER2-negative, PAM50 non-luminal MBC met its pre-specified endpoint. Completion of the stage II part of the trial with the inclusion of up to 46 patients is warranted to assess the activity of this combination in this group of patients. Correlative studies to find predictive biomarkers of response to this regimen are ongoing and will be presented at the meeting. This study was funded by MSD. Citation Format: Aleix Prat, Tomás Pascual, Montserrat Muñoz, Cristina Hernando, Silvia Vazquez, Salvador Blanch, Manuel Alva, Mafalda Oliveira, Esther Sanfeliu, Lorea Villanueva, Fara Brasó-Maristany, Nuria Chic, Eva Ciruelos. TATEN TRIAL (SOLTI-1716) Targeting non-Luminal disease by PAM50 with pembrolizumab + paclitaxel in Hormone Receptor-positive/HER2-negative (HR+/HER2-) metastatic breast cancer (MBC): interim analysis [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-06-02.

Abstract P6-14-09: Non-canonical Wnt/Ror2 signaling regulates tumor cell invasion and dissemination in breast cancer through cell-matrix crosstalk

Abstract BACKGROUND: Metastasis is the main cause of mortality for breast cancer patients. The early steps of cancer metastasis require that tumor cells actively invade and disseminate from the primary tumor to distant organs. Cell-extracellular matrix (ECM) interactions represent fundamental interactions during tumor invasion and metastasis, yet how particular signal-transduction factors prompt the conversion of tumor cells into migratory populations capable of systemic dissemination remains elusive. OBJECTIVES: Wnt signaling is a known regulator of cell fate, migration, and polarity during various key biological processes. We previously discovered an inverse correlation between the canonical Wnt signature and a non-canonical Wnt receptor, Ror2, across breast cancers in TCGA. The objective of this study is to investigate how canonical and non-canonical Wnt signaling orchestrate tumor cell behavior during cancer invasion and metastasis. METHODS: We used clinically relevant syngeneic TP53-null Genetically Engineered Mouse Model (GEMM) tumors that molecularly reflect the different breast cancer intrinsic subtypes. In vivo transplantation of GEMM models and in vitro 3D tumor organoids were employed to elucidate the molecular mechanism underlying the migration, invasion, and metastasis of tumor cells upon genetic perturbation of Wnt/Ror2 signaling. RESULTS/DISCUSSION: From 3-dimensional (3D) tumor organoid models, we identified novel transcriptional alterations encompassing cell-cell adhesion, cytoskeletal remodeling, and ECM organization upon Ror2 loss. At protein levels, we discovered a significant increase in collagen fibril organization and integrin-α5 and integrin-β3 expression following Ror2 depletion. In addition, the matrisomal protein fibronectin (FN) was concomitantly upregulated and assembled in Ror2-deficient tumor cells at sites of invasion. Consequently, we observed FAK activation and actin cytoskeleton alterations in Ror2-deficient tumor cells, leading to a promigratory tumor cell behavior. The altered cytoskeleton and cell-ECM interaction enhanced the rigidity of the Ror2-depleted cells. Furthermore, Inhibition of either integrin or FAK activation abrogated the increased invasion driven by Ror2-loss. Unexpectedly, these changes were distinct from processes regulated by Wnt/ß-catenin activation. From both spontaneous metastasis and experimental metastasis models, we discovered a shift from canonical to non-canonical Wnt signaling throughout the progression of lung metastasis, indicating that the balance of Wnt signaling may serve as a switch to dictate cell functions at different stages of metastatic development. Consistently, we found enhanced initial colonization in the lungs when Ror2 is depleted in these breast cancer cells. Together, these studies provide new insight into how canonical and alternative Wnt pathways coordinate cell-cell and cell-ECM exchanges during breast cancer progression and metastasis. Supported by grant NIH-CA016303 Citation Format: Hongjiang Si, Na Zhao, Andrea Pedroza, Chad Creighton, Jeffrey Rosen, Kevin Roarty. Non-canonical Wnt/Ror2 signaling regulates tumor cell invasion and dissemination in breast cancer through cell-matrix crosstalk [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-14-09.

Abstract P5-14-04: Genomic characterization of hormone receptor-positive advanced breast cancer with high tumor mutational burden: fresh-frozen tissue genomic analysis from MUTATION-1 study (KCSG BR17-04)

Abstract Background The hormone receptor (HR)-positive metastatic breast cancer (MBC) patients show a diverse range of tumor mutational burden (TMB), but its biological and clinical implication has been largely unrevealed. Here we report genomic landscape of 117 HR+ MBC patients who were included in the pre-screening tissue genomic analysis of MUTATION-1 study (SABCS 2021; Abs P1-19-03) according to TMB of tumors. Patients and method The MUTATION-1 study (NCT03608865) enrolled HR-positive MBC patients who received prior ≥ 1 line of systemic therapy, and performed prescreening with whole exome sequencing (WES) and RNA-seq of fresh-frozen tissue of metastatic or recurred tumors. Patients who met upper 30% of TMB were eligible for treatment phase and received durvalumab plus tremelimumab. This study analyzed 117 prescreening tissues of MUTATION-1 study patients for mutation and transcriptomic landscape analysis. (WES, n=117; RNA-seq, n=107) Results The 117 patients showed diverse TMB (range 0~21.7 mut/Mb, median 2.0 mut/Mb) and genomic alterations. The most frequently mutated gene included PIK3CA (29.1%), TP53 (27.4%), ESR1 (23.9%), GATA3 (19.7%), and MAP3K1 (12.0%). There was no association between patient survival and TMB. We estimated single base substitution (SBS) mutational signature of patients with SigMA algorithm. The patients were classified according to their dominant mutational signatures: APOBEC (25.6%), HRD (41.0%), clockwise (28.2%), SBS8, and SBS17. The APOBEC patients showed higher TMB (median 3.47 mut/Mb) and higher mutation prevalence in PIK3CA (63.3% vs. 29.1%), ARID1A (16.7% vs. 6.0%), and NF1 (16.7% vs. 6.8%) compared with other patients. The high TMB positively correlated with time from MBC diagnosis to biopsy. Tumors with TMB ≥ 5 mut/Mb were exclusively found in patients diagnosed as MBC ≥ 36 months before the timing of biopsy. In the matched RNA-seq analysis, TMB was higher in luminal B and HER2-enriched intrinsic subtype patients than basal or luminal A subtype. The high TMB (≥ 3.16 mut/Mb, cutoff used for treatment phase patient selection) patients showed upregulation of G2/M checkpoint, MYC, E2F1, and MTORC1 signature compared to low TMB patients. In the tumor microenvironment analysis by CIBESORT, PIK3CA mutant patients showed lower score of cytotoxic T cell than others. Conclusions The high TMB in HR+ breast cancer was associated with longer time duration from MBC diagnosis to biopsy, high APOBEC signature, and cell cycle/MYC signature gene upregulation. Further therapeutic targeting of high TMB patients is warranted based on their genomic and immunologic characteristics. Citation Format: Min Hwan Kim, Yohan Yang, Eunyoung Kim, Yong Wha Moon, Gun Min Kim, Seul-Gi Kim, Yee Soo Chae, Jieun Lee, Jae Ho Jeong, Kyung-Hun Lee, Han Jo Kim, Joo Young Jung, Su-Jin Koh, Kyoung Eun Lee, Hee-Jun Kim, Kyong Hwa Park, Seungtaek Lim, Yeon Hee Park, Sangwoo Kim, Joo Hyuk Sohn. Genomic characterization of hormone receptor-positive advanced breast cancer with high tumor mutational burden: fresh-frozen tissue genomic analysis from MUTATION-1 study (KCSG BR17-04) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-14-04.

Abstract P5-03-02: Adiposity and immune-related gene expression in the breast tumor microenvironment

Abstract Background: Extreme adiposity has been associated with tumor progression and increased mortality after a breast cancer diagnosis, but the underlying mechanisms remain unclear. Pre-clinical and in vitro analyses suggest that higher levels of adiposity impair anti-tumor immunity, but studies in human breast cancer patients are lacking. Previously, we found that higher levels of subcutaneous adiposity had stronger associations with breast cancer outcomes than did higher levels of visceral adiposity or overall obesity measured by BMI, underscoring the importance of measuring adipose tissue distribution as well as overall body size to understand the adiposity-cancer link. Methods: We identified women with a first-primary, stage 2 or 3 invasive breast cancer diagnosed and treated at Kaiser Permanente Northern California between 2005 and 2015. Using diagnostic computed tomography scans collected as part of routine clinical care, we measured subcutaneous (SAT) and visceral adipose tissue (VAT) areas in cm2 at the third lumbar vertebra. We calculated body mass index (BMI) from clinically-collected height and weight. We isolated RNA from 251 FFPE breast tumors collected at biopsy or excision; these were a preliminary, random sample within each immunohistochemical subtype groups from an ongoing study that will analyze 1400 breast tumors. We verified RNA quality prior to performing NanoString BC 360™ assays to calculate the PAM50 molecular intrinsic subtype and measure the expression levels of genes related to immune cell abundance and anti-tumor immune activity. Using linear regression models, we examined the mean change in log2 gene expression (dependent variables) associated with each adiposity exposure (BMI, SAT and VAT as independent variables). Results: Mean (SD) age at diagnosis was 56 (13); a majority of women were either overweight (BMI 25- < 30-kg/m2: 30%) or obese (BMI>30-kg/m2: 35%), and most were diagnosed with stage 2 (61%) vs. stage 3 (39%) breast cancer with representation from each PAM50 subtype: n (%) Luminal A, 46 (18%) Luminal B, 56 (22%), HER2-overexpressing 26 (27%), and 82 (33%) basal-like. In unadjusted analyses, expression of genes related to macrophages, PD-1 and TIGIT increased with increasing subcutaneous adiposity, whereas expression of genes related to mast cells decreased (see Table 1). We found a similar (though non-significant) pattern for BMI. Associations with increasing visceral adiposity were closer to the null. After adjusting for PAM50 subtype, age and stage at diagnosis, only the association of increasing subcutaneous adiposity with increasing PD-1 expression remained statistically significant. Conclusion: Excess subcutaneous adiposity was associated with increased PD-1 expression, whereas excess visceral adiposity or obesity defined by BMI were not. These results from the first 251 samples of an ongoing study of 1400 tumors provide evidence from human breast cancer patients to demonstrate the importance of measuring body composition to assess adipose tissue distribution and support the hypothesis that excess adiposity impairs anti-tumor immunity. Association of Adiposity Measures with Immune-Related Gene Expression in the Breast Tumor Microenvironment (n=251 patients with stage 2-3 breast cancer at Kaiser Permanente Northern California) 195% Confidence Interval 2A 1-unit increase represents a doubling in the log expression level of the genes in the signature Citation Format: Deborah A. Dillon, Elizabeth M. Cespedes Feliciano, Alexa Zimbalist, En Cheng, Bette J. Caan, Wendy Y. Chen, Elizabeth A. Mittendorf, Roberto Bonfim Pimenta Peixoto, Tabata Alves Domingos, Krishan Taneja, Ashka Patel. Adiposity and immune-related gene expression in the breast tumor microenvironment [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-03-02.

Abstract PD13-02: PD13-02 Exploratory gene expression analysis of coopERA Breast Cancer (BC): a study evaluating neoadjuvant giredestrant versus anastrozole alone and in combination with palbociclib in ER-positive, HER2-negative untreated early BC

Abstract Background: Endocrine therapy remains the mainstay treatment for ER+ BC. CDK4/6 inhibitors induce cell cycle arrest and decrease tumor cell proliferation, as measured by the biomarker Ki67, when used in combination with aromatase inhibitors (AI) such as anastrozole (A). Giredestrant is an oral, well-tolerated, and highly potent selective ER degrader (SERD) that achieves robust ER suppression and has demonstrated antitumor activity in the metastatic setting either as monotherapy or in combination with the CDK4/6 inhibitor palbociclib. The randomized, phase 2 coopERA Breast Cancer study (NCT04436744) evaluated giredestrant in postmenopausal women with untreated ER+/HER2- early BC and met its primary endpoint, demonstrating superior Ki67 suppression with giredestrant vs A after two weeks of single agent treatment. This suppression was maintained at surgery where giredestrant vs A was evaluated in combination with palbociclib. Here, we present gene expression analysis and associations with Ki67 response. Methods: 221 eligible patients with measurable ER+/HER2– untreated early BC and baseline Ki67 ≥ 5% were randomized 1:1 to receive 30 mg oral daily (PO QD) giredestrant or 1 mg PO QD A on Days 1–14 of a neoadjuvant window-of-opportunity phase, followed by four 28-day cycles of PO QD giredestrant or A with 125 mg PO QD palbociclib on Days 1–21 before surgery. FFPE specimens were collected at baseline, week 2 and surgery; and RNA-sequencing (seq) was performed. Gene expression analysis included ER pathway activity, PAM50 intrinsic subtypes, and other pathway analyses, assessed by Ki67 response. Results: 112 and 92 patients had paired tumor samples at baseline/week 2 and baseline/surgery, respectively, that were evaluable for RNA-seq and Ki67. The trend for greater Ki67 protein suppression by giredestrant vs A from baseline to week 2 was maintained in the RNA-seq evaluable subset. Interestingly, the same subset revealed similar suppression of both proliferation gene signatures and ER pathway activity between A and giredestrant. PAM50 subtyping showed that 69% of tumors were luminal (Lum) A and 29% were LumB at baseline. Less than 1% were classified as basal or HER2. Interestingly, giredestrant (G) showed greater suppression of both Ki67 and ER pathway activity vs A in LumB tumors (Ki67: -82% [G] vs -62% [A]; ER activity: -0.83 [G] vs -0.66 [A]) compared to LumA at week 2 (Ki67: -74% [G] vs -71% [A]; ER activity: -0.60 [G] vs -0.70 [A]). Moreover, at week 2, 83% (13/18) of LumB tumors at baseline transitioned into a LumA subtype after giredestrant treatment compared to 46% (5/11) of A-treated tumors. Giredestrant-treated tumors also achieved lower mean ER pathway activity compared to those treated with A at surgery (p=0.023). Gene set enrichment analysis showed downregulation of cell-cycle and ER-related pathways at week 2 and surgery in both treatment arms. A subset of cytokine signaling and immune response pathways were increased at week 2 compared to baseline after treatment with A but not with giredestrant. These pathways were also associated with Ki67 resistance (Ki67 ≥ 7.4%) in A-treated tumors. This was consistent with differential expression analysis of samples collected at week 2, in which cytokine signaling pathways were enriched in A compared to giredestrant. Notably, IL12 signaling was enriched in tumors resistant to A but not giredestrant. Conclusions: Giredestrant has a greater effect on Ki67 protein suppression in ER+/HER2- early BC compared to A, which is more pronounced in LumB tumors. This benefit may involve differential regulation of cytokine and immune responses. These exploratory findings reveal novel mechanisms that may differentiate the activity of SERDs vs AIs, which warrant further validation. Citation Format: Alejandro M. Chibly, Tharu M. Fernando, Ciara Metcalfe, Marc Hafner, Gilbert Owusu-Manu, Sara Hurvitz, Aditya Bardia, Peter A. Fasching, Yeon H. Park, Vanesa Quiroga, Jutta Steinseifer, Pablo Perez-Moreno, Heather M. Moore. PD13-02 Exploratory gene expression analysis of coopERA Breast Cancer (BC): a study evaluating neoadjuvant giredestrant versus anastrozole alone and in combination with palbociclib in ER-positive, HER2-negative untreated early BC [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD13-02.

Abstract HER2-06: HER2-06 Outcome analysis of HER2-zero or HER2-low hormone receptor-positive (HR+) breast cancer patients - characterization of the molecular phenotype in combination with molecular subtyping

Abstract Background: Breast cancer with low HER2 expression (HER2-low) is of high clinical relevance because of new therapeutic options with antibody-drug conjugates. We have recently shown in a large cohort from neoadjuvant clinical trials that HER2-low breast cancer has different molecular characteristics as well as different clinical outcomes compared to HER2-zero. Considering the positive correlation between HER2-low expression and hormone receptor positivity observed consistently in many investigations, we have extended our analysis to HR+ tumors from the post-neoadjuvant PenelopeB trial. In PenelopeB, patients with HR+ breast cancer and residual disease after neoadjuvant chemotherapy (NACT) were randomized to post-neoadjuvant palbociclib versus placebo in addition to endocrine therapy. We evaluated the molecular phenotype and clinical outcomes of HER2-low compared to HER2-zero patients. Methods: A total of 1250 patients were randomized, HER2 status was available for 1151 tumors from pretherapeutic core biopsy, determined mainly by local pathology, and from 1213 tumors from the post-NACT sample, determined as part of central pathology. For 1119 patients a paired HER2-status was both available. HER2-zero was defined as IHC0 and HER2-low-positive was defined as IHC1+ or IHC2+/ISH-. Gene expression analysis of 2549 genes using the HTG oncology biomarker panel was performed in 620 pretherapeutic biopsies and 780 post-NACT residual tumor samples, with 539 paired gene expression samples. Breast cancer subtypes were determined using the AIMS approach. Results: In pretherapeutic biopsies, 695 tumors (60%) were HER2-low and 457 (40%) were HER2-zero. A HER2-low status in the biopsy was significantly linked to improved iDFS (HR 0.76 (0.60-0.96; p=0.02). In residual tumors, 632 tumors (60%) were HER2-low and 581 (40%) were HER2-zero, without any prognostic impact of HER2 low status. In addition, a shift of HER2-low-status comparing core biopsy and residual tumor was observed in 415 (37%) of 1119 tumors. 161 (14%) had a shift from HER2-zero to HER2-low and 254 (23%) shifted from HER2-low to HER2-zero. A shift from HER2-zero to HER2-low in the post-NACT samples was significantly linked to reduced iDFS (HR 1.43 [95%CI 1.01-2.01]), p=0.04), compared to HER2-low group, while a shift from HER2-low to HER2-zero was associated with better iDFS compared to HER2-zero group, although not statistically significant (p=0.17). We did not observe a significant correlation of HER2-low status and AIMS molecular subtypes. In particular, the HER2-enriched (HER2E) subtype was assigned to only 4.3% of HER2-zero and 3.1% of HER2-low tumors. Significant iDFS differences were observed for HER2-low-status in combination with AIMS subtypes (lumB/basal/HER2E vs. lumA/normL; overall p-value < 0.0001) for both pretherapeutic biopsies and residual tumor. Patients with post-NACT HER2-low tumors had an improved survival in the subgroups of aggressive AIMS subtypes (lumB/basal/HER2E), but not in the less aggressive AIMs subtypes (lumA/normL), with a positive test for interaction (p=0.02). For the pre-NACT samples a similar, but non-significant trend was observed. We evaluated a total of 620 core biopsies for differences in gene expression comparing HER2-low and HER2-zero tumors. A total of 417 genes were statistically significantly different, but in a hierarchical clustering there was no clear separation of HER2-low and HER2-zero tumors. Conclusions: In the PenelopeB cohort of HR+ tumors, a HER2-low status in pretherapeutic core biopsies is related to improved disease-free survival, especially for those tumors that have a more aggressive intrinsic subtype. A shift of HER2-low status was observed before and after chemotherapy, indicating an adaptation of the pathway activity to therapy-induced stress, which might become relevant for future diagnostic and therapeutic approaches. Citation Format: Carsten Denkert, Miguel Martín, Michael Untch, Hervé R. Bonnefoi, Erik S. Knudsen, Seock-Ah Im, Angela DeMichele, Agnieszka Witkiewicz, Laura Van ’t Veer, Sung-Bae Kim, Harry D. Bear, Nicole McCarthy, Karen Gelmon, Frederik Marmé, José Ángel García-Sáenz, Nicholas Turner, Federico Rojo, Martin Filipits, Lesley-Ann Martin, Peter A. Fasching, Christian Schem, Catherine M. Kelly, Toralf Reimer, Masakazu Toi, Hope Rugo, Michael Gnant, Andreas Makris, Yuan Liu, Karsten Weber, Sivaramakrishna Rachakonda, Sibylle Loibl. HER2-06 Outcome analysis of HER2-zero or HER2-low hormone receptor-positive (HR+) breast cancer patients - characterization of the molecular phenotype in combination with molecular subtyping [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr HER2-06.