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Purpose:Young age at breast cancer diagnosis correlates with unfavorable clinicopathologic features and worse outcomes compared with older women. Understanding biological differences between breast tumors in young versus older women may lead to better therapeutic approaches for younger patients.Experimental Design:We identified 100 patients ≤35 years old at nonmetastatic breast cancer diagnosis who participated in the prospective Young Women's Breast Cancer Study cohort. Tumors were assigned a surrogate intrinsic subtype based on receptor status and grade. Whole-exome sequencing of tumor and germline samples was performed. Genomic alterations were compared with older women (≥45 years old) in The Cancer Genome Atlas, according to intrinsic subtype.Results:Ninety-three tumors from 92 patients were successfully sequenced. Median age was 32.5 years; 52.7% of tumors were hormone receptor-positive/HER2-negative, 28.0% HER2-positive, and 16.1% triple-negative. Comparison of young to older women (median age 61 years) with luminal A tumors (N = 28 young women) revealed three significant differences: PIK3CA alterations were more common in older patients, whereas GATA3 and ARID1A alterations were more common in young patients. No significant genomic differences were found comparing age groups in other intrinsic subtypes. Twenty-two patients (23.9%) in the Young Women's Study cohort carried a pathogenic germline variant, most commonly (13 patients, 14.1%) in BRCA1/2.Conclusions:Somatic alterations in three genes (PIK3CA, GATA3, and ARID1A) occur at different frequencies in young versus older women with luminal A breast cancer. Additional investigation of these genes and associated pathways could delineate biological susceptibilities and improve treatment options for young patients with breast cancer.See related commentary by Yehia and Eng, p. 2209

ImportanceBiomarkers to guide the use of pertuzumab in the treatment of early-stage ERBB2 (formerly HER2)-positive breast cancer beyond simple ERBB2 status are needed.ObjectiveTo determine if use of the HER2DX genomic assay (Reveal Genomics) in pretreatment baseline tissue samples of patients with ERBB2-positive breast cancer is associated with response to neoadjuvant trastuzumab-based chemotherapy with or without pertuzumab.Design, Setting, and ParticipantsThis is a retrospective diagnostic/prognostic analysis of a multicenter academic observational study in Spain performed during 2018 to 2022 (GOM-HGUGM-2018-05). In addition, a combined analysis with 2 previously reported trials of neoadjuvant cohorts with results from the assay (DAPHNe and I-SPY2) was performed. All patients had stage I to III ERBB2-positive breast cancer, signed informed consent, and had available formalin-fixed paraffin-embedded tumor specimens obtained prior to starting therapy.ExposuresPatients received intravenous trastuzumab, 8 mg/kg, loading dose, followed by 6 mg/kg every 3 weeks in combination with intravenous docetaxel, 75 mg/m2, every 3 weeks and intravenous carboplatin area under the curve of 6 every 3 weeks for 6 cycles, or this regimen plus intravenous pertuzumab, 840 mg, loading dose, followed by an intravenous 420-mg dose every 3 weeks for 6 cycles.Main Outcome and MeasuresAssociation of baseline assay-reported pathologic complete response (pCR) score with pCR in the breast and axilla, as well as association of baseline assay-reported pCR score with response to pertuzumab.ResultsThe assay was evaluated in 155 patients with ERBB2-positive breast cancer (mean [range] age, 50.3 [26-78] years). Clinical T1 to T2 and node-positive disease was present in 113 (72.9%) and 99 (63.9%) patients, respectively, and 105 (67.7%) tumors were hormone receptor positive. The overall pCR rate was 57.4% (95% CI, 49.2%-65.2%). The proportion of patients in the assay-reported pCR-low, pCR-medium, and pCR-high groups was 53 (34.2%), 54 (34.8%), and 48 (31.0%), respectively. In the multivariable analysis, the assay-reported pCR score (as a continuous variable from 0-100) showed a statistically significant association with pCR (odds ratio [OR] per 10-unit increase, 1.43; 95% CI, 1.22-1.70; P P P P = .77). A statistically significant interaction between the assay-reported pCR score and the effect of pertuzumab in pCR was observed.Conclusions and RelevanceThis diagnostic/prognostic study demonstrated that the genomic assay predicted pCR following neoadjuvant trastuzumab-based chemotherapy with or without pertuzumab. This assay could guide therapeutic decisions regarding the use of neoadjuvant pertuzumab.

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Pattern of HER2 amplification in the subset of HER2 heterogeneous tumors. Heatmap generated using data from central pathology evaluation of HER2 heterogeneity. The graphic includes patients classified as HER2 heterogeneous depicted in each row. The color code to the right of the heatmap refers to the percentage of HER2 amplified cells per core biopsy tumor area. Core biopsy tumor areas, A, B and C were obtained from core biopsy site 1 and D, E and F from core biopsy site 2.

Mechanisms driving resistance to cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) in hormone receptor–positive (HR+) breast cancer have not been clearly defined. Whole-exome sequencing of 59 tumors with CDK4/6i exposure revealed multiple candidate resistance mechanisms including RB1 loss, activating alterations in AKT1, RAS, AURKA, CCNE2, ERBB2, and FGFR2, and loss of estrogen receptor expression. In vitro experiments confirmed that these alterations conferred CDK4/6i resistance. Cancer cells cultured to resistance with CDK4/6i also acquired RB1, KRAS, AURKA, or CCNE2 alterations, which conferred sensitivity to AURKA, ERK, or CHEK1 inhibition. Three of these activating alterations—in AKT1, RAS, and AURKA—have not, to our knowledge, been previously demonstrated as mechanisms of resistance to CDK4/6i in breast cancer preclinically or in patient samples. Together, these eight mechanisms were present in 66% of resistant tumors profiled and may define therapeutic opportunities in patients.Significance:We identified eight distinct mechanisms of resistance to CDK4/6i present in 66% of resistant tumors profiled. Most of these have a therapeutic strategy to overcome or prevent resistance in these tumors. Taken together, these findings have critical implications related to the potential utility of precision-based approaches to overcome resistance in many patients with HR+ metastatic breast cancer.This article is highlighted in the In This Issue feature, p. 1079

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Intratumor heterogeneity is postulated to cause therapeutic resistance. To prospectively assess the impact of HER2 (ERBB2) heterogeneity on response to HER2-targeted therapy, we treated 164 patients with centrally confirmed HER2-positive early-stage breast cancer with neoadjuvant trastuzumab emtansine plus pertuzumab. HER2 heterogeneity was assessed on pretreatment biopsies from two locations of each tumor. HER2 heterogeneity, defined as an area with ERBB2 amplification in >5% but P < 0.0001, adjusted for hormone receptor status). Single-cell ERBB2 FISH analysis of cellular heterogeneity identified the fraction of ERBB2 nonamplified cells as a driver of therapeutic resistance. These data suggest HER2 heterogeneity is associated with resistance to HER2-targeted therapy and should be considered in efforts to optimize treatment strategies.Significance:HER2-targeted therapies improve cure rates in HER2-positive breast cancer, suggesting chemotherapy can be avoided in a subset of patients. We show that HER2 heterogeneity, particularly the fraction of ERBB2 nonamplified cancer cells, is a strong predictor of resistance to HER2 therapies and could potentially be used to optimize treatment selection.See related commentary by Okines and Turner, p. 2369.This article is highlighted in the In This Issue feature, p. 2355

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Supplementary Table from Somatic and Germline Genomic Alterations in Very Young Women with Breast Cancer

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Purpose:Young age at breast cancer diagnosis correlates with unfavorable clinicopathologic features and worse outcomes compared with older women. Understanding biological differences between breast tumors in young versus older women may lead to better therapeutic approaches for younger patients.Experimental Design:We identified 100 patients ≤35 years old at nonmetastatic breast cancer diagnosis who participated in the prospective Young Women's Breast Cancer Study cohort. Tumors were assigned a surrogate intrinsic subtype based on receptor status and grade. Whole-exome sequencing of tumor and germline samples was performed. Genomic alterations were compared with older women (≥45 years old) in The Cancer Genome Atlas, according to intrinsic subtype.Results:Ninety-three tumors from 92 patients were successfully sequenced. Median age was 32.5 years; 52.7% of tumors were hormone receptor-positive/HER2-negative, 28.0% HER2-positive, and 16.1% triple-negative. Comparison of young to older women (median age 61 years) with luminal A tumors (N = 28 young women) revealed three significant differences: PIK3CA alterations were more common in older patients, whereas GATA3 and ARID1A alterations were more common in young patients. No significant genomic differences were found comparing age groups in other intrinsic subtypes. Twenty-two patients (23.9%) in the Young Women's Study cohort carried a pathogenic germline variant, most commonly (13 patients, 14.1%) in BRCA1/2.Conclusions:Somatic alterations in three genes (PIK3CA, GATA3, and ARID1A) occur at different frequencies in young versus older women with luminal A breast cancer. Additional investigation of these genes and associated pathways could delineate biological susceptibilities and improve treatment options for young patients with breast cancer.See related commentary by Yehia and Eng, p. 2209

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Supplementary Figure from Somatic and Germline Genomic Alterations in Very Young Women with Breast Cancer

FGFR alterations in different cohorts

Supplementary Data from Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER+ Metastatic Breast Cancer

Figure S1. REMARK diagram Figure S2. NanoString Tumor Inflammation Signature by breast cancer intrinsic subtype Figure S3. NanoString individual gene expression changes by cohort Table S1. Pre-treatment immune microenvironment and response to preoperative therapy Table S2. Tissue-based immune biomarkers in patients with pathologic complete response Table S3. References for classification of genes as M1-like or M2-like

Purpose:Hormone receptor–positive/HER2-negative (HR+/HER2−) breast cancer is associated with low levels of stromal tumor-infiltrating lymphocytes (sTIL) and PD-L1, and demonstrates poor responses to checkpoint inhibitor therapy. Evaluating the effect of standard chemotherapy on the immune microenvironment may suggest new opportunities for immunotherapy-based approaches to treating HR+/HER2− breast tumors.Experimental Design:HR+/HER2− breast tumors were analyzed before and after neoadjuvant chemotherapy. sTIL were assessed histologically; CD8+ cells, CD68+ cells, and PD-L1 staining were assessed immunohistochemically; whole transcriptome sequencing and panel RNA expression analysis (NanoString) were performed.Results:Ninety-six patients were analyzed from two cohorts (n = 55, Dana-Farber cohort; n = 41, MD Anderson cohort). sTIL, CD8, and PD-L1 on tumor cells were higher in tumors with basal PAM50 intrinsic subtype. Higher levels of tissue-based lymphocyte (sTIL, CD8, PD-L1) and macrophage (CD68) markers, as well as gene expression markers of lymphocyte or macrophage phenotypes (NanoString or CIBERSORT), correlated with favorable response to neoadjuvant chemotherapy, but not with improved distant metastasis-free survival in these cohorts or a large gene expression dataset (N = 302). In paired pre-/postchemotherapy samples, sTIL and CD8+ cells were significantly decreased after treatment, whereas expression analyses (NanoString) demonstrated significant increase of multiple myeloid signatures. Single gene expression implicated increased expression of immunosuppressive (M2-like) macrophage-specific genes after chemotherapy.Conclusions:The immune microenvironment of HR+/HER2− tumors differs according to tumor biology. This cohort of paired pre-/postchemotherapy samples suggests a critical role for immunosuppressive macrophage expansion in residual disease. The role of macrophages in chemoresistance should be explored, and further evaluation of macrophage-targeting therapy is warranted.

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Background: Although immune checkpoint inhibitors (ICI) are most widely used in PD-L1 positive, metastatic triple-negative breast cancer (TNBC), the clinical utility of ICI in other tumor subtypes and patient populations is not well defined. In this study, we measured infiltration of multiple immune cell populations in primary and metastatic HR+ tumors to infer potential benefit from ICI. We investigated how risk stratifying features such as pathologic grade and Oncotype Dx scores affect immune cell infiltration across subtypes. Lastly, we compared immune cell infiltration in breast tumors from younger versus older women, as our pre-clinical studies demonstrated differential enrichment of immune response pathways by age and association with improved response to ICI. Methods: ImmunoProfile, a multiplexed immunofluorescence (IF) assay, was performed on FFPE tissue from 167 archived breast cancer tumors from the Dana-Farber Cancer Institute (HR+/HER2- n=124, HER2+ n=21, TNBC n=22). Unmatched samples were obtained from either primary breast (HR+/HER2- n=104, HER2+ n=13, TNBC n=15) or metastatic core biopsies. IF staining signal was measured for T cell markers CD8 and co-localized CD8/PD-1, T regulatory cell marker FOXP3, PD-L1 and PD1 expression on tumor cells as well as PD-L1 expression on inflammatory cells. Inflammatory, tumoral (TPS) and combined inflammatory and tumor (CPS) pathologic PD-L1 scores were calculated. PD-L1 staining was also assessed by IHC (E1L3N) staining and compared to multiplexed IF stains. IF staining signal (Vectra analyzed, log2+1 transformed) was analyzed against clinical and pathologic variables, including tumor subtype, primary versus metastatic status, pathologic grade, and Oncotype Dx score, using non-parametric statistical comparisons. Given the decline in adaptive immunity that occurs with normal physiological aging and our own group’s previous reports, we also explored whether immune cell staining signal associated with age. Results: TPS, CPS, and inflammatory PD-L1 scores strongly correlated between IHC and IF staining methods (Spearman r = 0.660, 0.683, 0.638 respectively, p < 2.2e-16). When HR+/HER2- (n=124), HER2+ (n=21) and TNBC (n=22) cases were analyzed separately, there was no statistical difference between unmatched primary and metastatic cases in any of the analyzed immune cell population stains for any subtype. When all primary cases were analyzed, TNBC showed higher CD8, CD8/PD1, PD1 (all p < 0.05), and FOXP3 staining as well as IF CPS, TPS and inflammatory PD-L1 scores (all p < 0.005) than HR+ cases. HR+/HER2- cases from women < age 65 (n=56) showed higher intra-tumoral CD8 (p=0.039), PD1 (p=0.043), and CD8/PD1 (p=0.022) than cases from women > age 65 (n=38). There was a statistically significant step-wise increase in IF staining of all immune cell populations with increasing pathologic grade (I, II, III) as well as Oncotype Dx scores (< 11, 11-25, >25) among primary HR+/HER2- cases (n=74). Conclusions: Strong correlations between PD-L1 scores based on IF and IHC methods suggest clinical utility for multiplexed IF immune cell staining in therapeutic planning. ImmunoProfile demonstrated the previously known pattern that primary TNBC contains higher immune cell infiltration than HR+ or HER2+ tumors. Women < age 65 with HR+ cancer showed higher levels of CD8 and PD1 stained populations, suggesting there may be greater utility of ICI in younger patients. Lastly, the association of higher pathologic grade and Oncotype Dx score with increasing immune cell infiltration supports exploration of ICI in biologically unfavorable primary HR+ cancers. Citation Format: Tess A. O'Meara, Tanya E. Keenan, Adrienne G. Waks, Kristen D. Felt, Bijaya Sharma, Scott Rodig, Melissa Hughes, Nancy U. Lin, Judith Agudo, Jennifer L. Guerriero, Sandra S. McAllister, Elizabeth Mittendorf, Sara Tolaney. Multiplexed immunofluorescence staining of intra-tumoral immune cell populations and associations with immunohistochemical, clinical, and pathologic variables in breast cancer [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 P1-04-05.

Background: Immunological differences between HER2+ breast tumors that are HR+ versus HR- have not been widely explored. DAPHNe was a single-arm prospective clinical trial enrolling patients with clinical anatomic stage II-III HER2+ breast cancer to neoadjuvant treatment with THP. Here, we examine differential expression of immune-related proteins between HR+/HER2+ and HR-/HER2+ tumors in pre-treatment biopsies from trial participants, and analyze correlates of pathologic response to THP, overall and by HR status. Methods: A baseline research biopsy was required in all participants prior to initiation of neoadjuvant therapy. All patients received 12 weeks of neoadjuvant THP; 5 patients also received neoadjuvant AC given incomplete clinical response to THP, and are excluded from residual cancer burden (RCB) analyses. The trial primary endpoint, feasibility of de-escalation to antibody doublet therapy only (HP) following pCR, was previously reported. Protein expression profiling of baseline research biopsies was performed on the NanoString GeoMx® platform using a 58-protein immune cell profiling panel. Regions of interest (ROI; up to 12 per slide) were identified by a pathologist based on tumor cell, immune cell, and/or T cell presence, and all ROI were segmented into tumor vs stroma. Protein data quality controls were normalized by isotypes. Linear mixed effect models were used for differential expression comparisons; p-values were estimated using Satterthwaite’s method. Results: 97 pre-treatment breast tumor specimens were analyzed: 64 patients had HR+ tumors, 32 HR-, 1 unknown; 67 patients had favorable (RCB 0/1) response to preop therapy, 30 patients had unfavorable response (RCB 2/3). Multiple significant differences were observed between protein expression in HR+ versus HR- tumors (Table 1). Multiple immune cell types, as well as checkpoint proteins PD-L1 and IDO1, were higher in HR- patients, whereas checkpoint proteins B7-H3 and TIM3 were higher in HR+ patients. In the overall population, higher HER2 and PD-L1 expression were significant predictors of favorable RCB response, while higher ER alpha and Bcl-2 expression were significant predictors of unfavorable RCB response (Table 2). Conclusions: As anticipated, the strength of HER2 expression and ER expression were the most significant predictors of favorable and unfavorable RCB response to neoadjuvant THP, respectively. This highly multiplexed protein expression analysis demonstrated significant differences between the immune microenvironment of HR+ and HR- HER2+ breast tumors, implying that distinct immunological targets should be explored in the treatment of HER2+ breast cancer according to HR status. Table 1.Differences between HR+/HER2+ and HR-/HER2+ patientsStroma compartmentTumor compartmentHigher in HR+ER alpha* (fold-change 2.25)ER alpha* (8.94)Fibronectin (1.68)Bcl-2* (1.98)B7-H3 (1.44)Fibronectin* (1.90)PR (1.69)TIM-3 (1.37)Higher in HR-CD27* (fold-change 1.36)IDO1 (1.50)IDO1 (1.77)S100B (1.44)CD45 (1.45)MART1 (1.33)CD3 (1.35)CD20 (1.34)STING (1.33)CD4 (1.30)ICOS (1.30)CD45RO (1.28)CD40 (1.28)CD127 (1.27)VISTA (1.25)PD-L1 (1.24)4-1BB (1.21)*FDR p-value < 0.05 (otherwise, p-value < 0.05). Table 2: Predictors of RCB response Overall populationHigher in RCB 0/1HER2* (fold-change 3.75)PD-L1 (1.25)Higher in RCB 2/3ER alpha* (2.44)Bcl-2 (1.46)HR+/HER2+ patientsStroma compartmentTumor compartmentHigher in RCB 0/1HER2* (fold-change 4.28)HER2* (4.21)CTLA4 (1.64)Higher in RCB 2/3Bcl-2* (2.18)*FDR p-value < 0.05 (otherwise, p-value < 0.05).HR-/HER2+ patients are not shown in Table 2 as only 2 HR- patients had unfavorable RCB response. Citation Format: Adrienne G. Waks, Ying Huang, Tyler Hether, Esther R Ogayo, Sapana Kadel, Jillian Alberti, Sara M Tolaney, Ian E Krop, Prajan Divakar, Otto Metzger, Madison L O'Donnell, Sarah Church, Eric P Winer, Jennifer L. Guerriero, Elizabeth A Mittendorf. Correlation of immune-related protein expression with hormone receptor (HR) status and pathologic response to neoadjuvant paclitaxel/trastuzumab/pertuzumab (THP) among patients with early-stage HER2+ breast cancer [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 P2-07-03.

Background: The optimal systemic therapy strategy, neoadjuvant vs adjuvant therapy, for patients with small clinically node negative HER2+ breast cancers is uncertain. The goal of this study was to evaluate the incidence of pathologic nodal disease in cT1-2 N0 HER2+ patients, treated with upfront surgery or neoadjuvant chemotherapy (NAC), to better define selection criteria for initial treatment approach. Methods: Our prospectively maintained database was queried for cT1-2 N0 HER2+ breast cancer patients diagnosed 2/12/2015 - 10/13/2020 (after publication of the Adjuvant Paclitaxel and Trastuzumab trial). Patients without axillary surgery were excluded (n =23). HER2 positivity was defined per ASCO/CAP guidelines. Pre-NAC and/or pre-operative axillary ultrasound was not routinely performed. Patient characteristics and rates of pN+ disease were compared by treatment strategy using Chi square and Wilcoxon rank-sum tests. Nodes with isolated tumor cells were considered negative (pN0) in the upfront surgery setting but positive (pN+) after NAC. Logistic regression determined factors associated with pN+ disease. Results: A total of 579 eligible patients were identified; 368 (63.6%) were treated with upfront surgery and 211 (36.4%) with NAC. Upfront surgery patients were older (median 55 years [range 23-88] vs 49 [24-79], p Table 1.Pathologic nodal stage among upfront surgery and NAC patientsUpfront Surgery (N=368)pN+pN0P valuecT category< 0.001T1mi (N=48)6 (10.4%)42 (89.6%)T1a (N=26)3 (11.5%)23 (88.5%)T1b (N=87)7 (8.0%)80 (92.0%)T1c (N=154)38 (24.7%)116 (75.3%)T2 (N=53)19 (35.8%)34 (64.2%)NAC (N=211)ypN+ypN0P valuecT category0.719T1b (N=7)1 (14.3%)6 (85.7%)T1c (N=30)5 (16.7%)25 (83.3%)T2 (N=174)20 (11.5%)154 (88.5%) Citation Format: Anna Weiss, Adrienne G. Waks, Alison Laws, Sara M. Tolaney, Eric P. Winer, Elizabeth A. Mittendorf, Ann H. Partridge, Tari A. King. Pathologic nodal staging and systemic therapy among patients with cT1-2N0 HER2+ breast cancer: A prospective single institution cohort 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 P2-13-02.