BACKGROUND: Neoadjuvant Endocrine Therapy (NET) is seldom used in breast cancer management except in patients with several comorbidities or in elderly patients in which chemotherapy is not an option. Clinical response with NET is not typically achieved until after several months of treatment. In the NET setting, reduction of Ki67 (< 10%) after 2-4 weeks has been used as a predictor of positive response, but studies such as ALTERNATE have questioned this association. It remains uncertain whether a single gene or protein can adequately predict outcomes or inform how NET alters a variety of cancer genes and global tumor biology. This study evaluated the effect of short-term NET on the tumor genomics of patients with early-stage breast cancer (EBC) by comparing whole transcriptome gene expression changes in matched pre- and post-NET tumor samples. METHODS: In this single-institution FLEX substudy performed at Johns Hopkins, patients (n=30) with matched pre- and post-treatment specimens who received at least two weeks of NET between 2019 – 2021 were included. Premenopausal and male patients with breast cancer received Tamoxifen (n=10) and postmenopausal women received either Letrozole (n=10) or Exemestane (n=10). Limma R package was used for quantile normalization and differential gene expression analysis. Significant differentially expressed genes (DEGs) had a false discovery rate of < 0.05 and >2-fold change. Pathway enrichment analysis was performed using Reactome. For patients with available clinical information, changes in immunohistochemistry (IHC) between pre- and post-NET were quantified using absolute values, and the median percent change was reported, with significance assessed using the Wilcoxon test. The observational FLEX trial (NCT03053193) enrolls patients with EBC who have MammaPrint (MP) with or without BluePrint testing and consent to clinically annotated full transcriptome data collection. MammaPrint classifies tumors as having a Low Risk (LR) or High Risk (HR) of distant recurrence. BluePrint is a molecular subtyping assay, and together with MammaPrint, tumors are classified as Luminal A-Type (MP LR), Luminal B-Type (MP HR), HER2-Type, or Basal-Type. RESULTS: Transcriptional profiles between pre- and post-NET samples were distinct with short-term NET inducing 774 DEGs. The majority of significant DEGs (n=748) such as MGAT1, IQGAP3, and PRC1, which are associated with tumor aggressiveness and metastasis, were downregulated in post-NET samples. Upregulated genes in post-NET tumors, such as FOS, JUN, and EGR1, are involved in estrogen signaling and NF-κB pathways and are associated with better outcomes. Among the 30 patients, 7 (6 Luminal B and 1 Basal) remained MP HR and 16 remained MP LR (Luminal A) pre- and post-NET, 1 changed from LR (Luminal A) pre-NET to HR (Luminal B) post-NET, and 6 changed from HR (Luminal B) pre-NET to LR post-NET (Luminal A). The median percent change by IHC in matched pre- and post-NET tissue was 2.5% for estrogen receptor (ER) (range: 0-50%; p=0.750), 22% for progesterone receptor (PR) (range: 0-81%; p=0.097), and 9% for Ki67 (range: 0-43%; p=0.026). CONCLUSIONS: In this study, significant gene expression changes were discovered within a shorter timeframe than when clinical responses are usually observed in the NET setting. This could indicate biological complexity and diverse response pathways, which may be more informative when combined with a single IHC biomarker (ER/PR/Ki67). Results from this study should be confirmed using a larger cohort. Future studies will determine the significance of these DEGs and their impact on outcomes, and will further define gene expression changes by endocrine therapy type (tamoxifen versus aromatase inhibitors). ACKNOWLEDGMENTS: We would like to thank Lynn and Robert Downing for their generous support of our study. Citation Format: Mehran Habibi, Danijela Jelovac, Rima Couzi, Cesar Augusto Santa-Maria, Catherine Klein, Marissa White, Nivali Naik, Jennifer Wei, Yen Huynh, Architha Ellappalayam, Lisa E. Blumencranz, Erin B. Yoder, Patricia Dauer, Bas van der Baan, William Audeh. Impact of neoadjuvant endocrine therapy on tumor transcriptome in patients with early-stage breast cancer from the FLEX 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 P5-09-02.

BACKGROUND: Immune checkpoint inhibitors in combination with chemotherapy have demonstrated an improvement of pathologic complete response (pCR) in patients with HR-HER2- and MammaPrint (MP) High Risk, HR+HER2- tumors in the I-SPY2 TRIAL. However, not all patients benefit from immune checkpoint blockade and these new agents come with additional financial burden and significant long-lasting side effects such as adrenal insufficiency. Thus, it is imperative to better understand who benefits. Response Predictive Subtypes (RPS) were developed in the I-SPY2 TRIAL using pre-treatment expression data from 987 MP High Risk patients; 39% of HR+HER2- tumors and 63% of HR-HER2- tumors were identified as immune sensitive. In I-SPY2.2, RPS tumor classification uses ImPrint, a 53-gene signature that has been independently validated to predict the likelihood of a pCR with PD1-PDL1 immune checkpoint inhibitors with high sensitivity and specificity. Using a real-world dataset of 10,000 patients enrolled in the FLEX trial, we identified immune sensitive (ImPrint+) patients within immunohistochemistry (IHC) subtypes and within MP and BluePrint (BP) subgroups. METHODS: FLEX (NCT03053193) is an ongoing registry trial with 97 sites open in the United States and 2 international sites. Patients enrolled in FLEX have early-stage breast cancer and receive standard of care MP testing with or without BP molecular subtyping and consent to clinically annotated full genome data collection. MP is a 70-gene risk of distant recurrence signature that classifies patients as Low Risk or High Risk. MP High Risk can be further stratified into High 1 and High 2, which have demonstrated differences in chemosensitivity and pCR rates in the I-SPY2 TRIAL (NCT01042379). BP, an 80-gene molecular subtyping signature, categorizes patients’ tumors as Luminal-, HER2- or Basal-Type. RESULTS: Of the 10,021 patients, 9.1% of the FLEX patient population are ImPrint+ and are predicted to have a meaningful pCR rate with immune checkpoint inhibitors. Younger (≤ 50 years) or pre/peri-menopausal patients, patients with larger or node-positive tumors, and patients of Black or Latin race/ethnicity independently had a higher likelihood of having ImPrint+ tumors (Table 1). ImPrint+ tumors were identified in all clinical subtypes by IHC. There is a higher likelihood of ImPrint+ tumors being MP High 2 or BP Basal-Type tumors. Within BP Basal tumors, 74.7% of HR+ and 66.0% of HR- tumors were ImPrint+. CONCLUSIONS: The focus of immune therapy trials has been on patients with HR-HER2-, MP High Risk patients. Indeed, most patients who are predicted to benefit have MP High 2 or BP Basal-Type tumors, including some HR+ patients, which is consistent with I-SPY2 results. Importantly, this large real-world dataset enables the identification of populations who may benefit from immune therapy outside of traditional clinical trial populations and supports the testing of checkpoint inhibitors in the immune-positive subtype. Younger women and patients of Black or Latin race/ethnicity who typically have more aggressive tumors also have higher proportions of ImPrint+ tumors. Thus, it is critical that these populations be included in clinical trials. This first look at immune sensitivity in over 10,000 FLEX patients with ImPrint generates preliminary data and hypotheses that will be explored in future FLEX substudies, including an analysis of lobular cancers and long-term outcomes in ImPrint+ patients across all races and ages. Table 1. Clinical characteristics of ImPrint+ and ImPrint- tumors. Citation Format: Adam M. Brufsky, Midas Kuilman, Rita Mukhtar, Denise M. Wolf, Christina Yau, Joyce O’Shaughnessy, Cathy Graham, Vijayakrishna K. Gadi, Pat Whitworth, Alexander Hindenburg, Ian Grady, Gordon Srkalovic, Kent Hoskins, Ajay Dhakal, Cynthia Ma, Natasha Hunter, Jennifer Crozier, Blanche Mavromatis, Lorenza Mittempergher, Christine Finn, Shraddha Modh, Erin B. Yoder, Patricia Dauer, Andrea Menicucci, Bas van der Baan, William Audeh, Laura J. Esserman. ImPrint immune signature in 10,000 early-stage breast cancer patients from the real-world FLEX database [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 PD9-08.

Background Neoadjuvant chemotherapy (NCT) increases the feasibility of surgical resection by downstaging large primary breast tumors and nodal involvement, which may result in surgical de-escalation and improved outcomes. This subanalysis from the Multi-Institutional Neo-adjuvant Therapy MammaPrint Project I (MINT) trial evaluated the association between MammaPrint and BluePrint with nodal downstaging. Patients and Methods The prospective MINT trial (NCT01501487) enrolled 387 patients between 2011 and 2016 aged ≥ 18 years with invasive breast cancer (T2–T4). This subanalysis includes 146 patients with stage II–III, lymph node positive, who received NCT. MammaPrint stratifies tumors as having a Low Risk or High Risk of distant metastasis. Together with MammaPrint, BluePrint genomically (g) categorizes tumors as gLuminal A, gLuminal B, gHER2, or gBasal. Results Overall, 45.2% ( n = 66/146) of patients had complete nodal downstaging, of whom 60.6% ( n = 40/66) achieved a pathologic complete response. MammaPrint and combined MammaPrint and BluePrint were significantly associated with nodal downstaging ( p = 0.007 and p < 0.001, respectively). A greater proportion of patients with MammaPrint High Risk tumors had nodal downstaging compared with Low Risk ( p = 0.007). When classified with MammaPrint and BluePrint, more patients with gLuminal B, gHER2, and gBasal tumors had nodal downstaging compared with HR+HER2−, gLuminal A tumors ( p = 0.538, p < 0.001, and p = 0.013, respectively). Conclusions Patients with genomically High Risk tumors, defined by MammaPrint with or without BluePrint, respond better to NCT and have a higher likelihood of nodal downstaging compared with patients with gLuminal A tumors. These genomic signatures can be used to select node-positive patients who are more likely to have nodal downstaging and avoid invasive surgical procedures.

Background: As more patients with early-stage breast cancer receive neoadjuvant endocrine therapy (NET), there is a need for reliable biomarkers that can identify patients with HR+ HER2-tumors who are likely to benefit from NET. NBRST (NCT01479101) compared the prognostic value of the 70-gene risk classification and 80-gene molecular subtyping signatures with conventional pathological classification methods in response to neo-adjuvant therapy. We evaluated the association of these signatures with clinical response and 5-year outcome of patients treated with NET. Methods: 1091 patients with early-stage breast cancer scheduled to receive neoadjuvant therapy were prospec-tively enrolled into NBRST, and a sub-analysis of 67 patients treated with NET was performed. Patients received standard of care genomic testing using the 70-gene and 80-gene signatures and were treated with NET, per physician's discretion. The primary endpoint was pathologic partial response (pPR) and secondary endpoints were distant metastasis-free survival (DMFS) and overall survival (OS). Clinical benefit was defined as having a pPR or stable disease (SD) with NET.Results: Overall, 94.4% of patients with genomically (g) Luminal A-Type (50.0% pPR and 44.4% SD) and 95.0% with Luminal B-Type tumors (55.0% pPR and 40.0% SD) exhibited clinical benefit. At 5 years, patients with gLuminal B tumors had significantly worse DMFS (75.6%, 95% CI 50.8-89.1) than patients with gLuminal A (91.1%; 95% CI 74.8-97.1; p = 0.047), with a similar trend for OS, albeit not significant (81.0%, 95% CI 56.9-92.4 and 91.1%, 95% CI 74.8-97.1, respectively; p = 0.13).Conclusions: Genomic assays offer a broader understanding of the underlying tumor biology, which adds preci-sion to pathology as a preoperative risk classifier. Patients with 70-gene signature Low Risk, gLuminal A tumors treated with endocrine therapy alone have excellent 5-year outcomes. Most patients with genomically-defined Luminal A-and B-Type tumors respond well to NET, suggesting these patients may be safely treated with NET, while those with gLuminal B tumors will also require post-operative chemotherapy or CDK4/6 inhibitors to improve long-term outcomes. Overall, these findings demonstrate that genomic classification, defined by the combined 70-and 80-gene signatures, is associated with tumor response and prognostic of long-term outcomes.

Background The Neoadjuvant Breast Symphony Trial (NBRST) demonstrated the 70-gene risk of distant recurrence signature, MammaPrint, and the 80-gene molecular subtyping signature, BluePrint, precisely determined preoperative pathological complete response (pCR) in breast cancer patients. We report 5-year follow-up results in addition to an exploratory analysis by age and menopausal status. Methods The observational, prospective NBRST (NCT01479101) included 954 early-stage breast cancer patients aged 18–90 years who received neoadjuvant chemotherapy and had clinical and genomic data available. Chemosensitivity and 5-year distant metastasis-free survival (DMFS) and overall survival (OS) were assessed. In a post hoc subanalysis, results were stratified by age (≤ 50 vs. > 50 years) and menopausal status in patients with hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2−) tumors. Results MammaPrint and BluePrint further classified 23% of tumors to a different subtype compared with immunohistochemistry, with more precise correspondence to pCR rates. Five-year DMFS and OS were highest in MammaPrint Low Risk, Luminal A-type and HER2-type tumors, and lowest in MammaPrint High Risk, Luminal B-type and Basal-type tumors. There was no significant difference in chemosensitivity between younger and older patients with Low-Risk (2.2% vs. 3.8%; p = 0.64) or High-Risk tumors (14.5% vs. 11.5%; p = 0.42), or within each BluePrint subtype; this was similar when stratifying by menopausal status. The 5-year outcomes were comparable by age or menopausal status for each molecular subtype. Conclusion Intrinsic preoperative chemosensitivity and long-term outcomes were precisely determined by BluePrint and MammaPrint regardless of patient age, supporting the utility of these assays to inform treatment and surgical decisions in early-stage breast cancer.

PURPOSE The prospective Neoadjuvant Breast Registry Symphony Trial compared the 80-gene molecular subtyping signature with clinical assessment by immunohistochemistry and/or fluorescence in situ hybridization in predicting pathologic complete response (pCR) and 5-year outcomes in patients with early-stage breast cancer. METHODS Standard-of-care neoadjuvant chemotherapy combined with trastuzumab or trastuzumab plus pertuzumab was given to patients with human epidermal growth factor receptor 2 (HER2)–positive tumors (n = 295). pCR was the primary end point, with secondary end points of distant metastasis-free survival and overall survival at 5 years. RESULTS Among clinically defined HER2-positive (cHER2) tumors, the 80-gene assay identified 29.5% (87 of 295) as Luminal-Type (cHER2/gLuminal), 14.9% (44 of 295) as Basal-Type (cHER2/gBasal), and 55.6% (164 of 295) as HER2-Type (cHER2/genomically classified as HER2 [gHER2]). Patients with cHER2/gHER2 tumors had a higher pCR rate (61.6%) compared with non-gHER2 tumors (26.7%; P < .001). Dual targeting for cHER2/gHER2 tumors yielded a higher pCR rate (75%) compared with those treated with single HER2-targeted therapy (54%; P = .006). For cHER2/gBasal tumors, the 42.9% pCR rate observed with dual targeting was not different from that with trastuzumab alone (46.4%; P = .830). Among those with cHER2/gBasal tumors, 5-year distant metastasis-free survival (68.6%; 95% CI, 49.1 to 81.9) was significantly worse than in patients with cHER2/gLuminal tumors (88.9%; 95% CI, 78.0 to 94.6) and cHER2/gHER2 tumors (87.4%; 95% CI, 80.2 to 92.2; P = .010), with similar corresponding overall survival differences. CONCLUSION The 80-gene assay identified meaningful genomic diversity in patients with cHER2 disease. Patients with cHER2/gHER2 tumors, who benefitted most from dual HER2-targeted therapy, accounted for approximately half of the cHER2 cohort. Genomically Luminal tumors had low pCR rates but good 5-year outcomes. cHER2/gBasal tumors derived no benefit from dual therapy and had significantly worse 5-year prognosis; these patients merit special consideration in future trials.

PURPOSE The 80-gene molecular subtyping signature (80-GS) reclassifies a proportion of immunohistochemistry (IHC)-defined luminal breast cancers (estrogen receptor–positive [ER+], human epidermal growth factor receptor 2–negative [HER2–]) as Basal-Type. We report the association of 80-GS reclassification with neoadjuvant treatment response and 5-year outcome in patients with breast cancer. METHODS Neoadjuvant Breast Registry Symphony Trial (NBRST; NCT01479101 ) is an observational, prospective study that included 1,069 patients with early-stage breast cancer age 18-90 years who received neoadjuvant therapy. Pathologic complete response (pCR) and 5-year distant metastasis-free survival (DMFS) and overall survival (OS) were assessed in 477 patients with IHC-defined ER+, HER2– tumors and in a reference group of 229 patients with IHC-defined triple-negative breast cancer (TNBC). RESULTS 80-GS reclassified 15% of ER+, HER2– tumors (n = 73) as Basal-Type (ER+/Basal), which had similar pCR compared with TNBC/Basal tumors (34% v 38%; P = .52), and significantly higher pCR than ER+/Luminal A (2%; P < .001) and ER+/Luminal B (6%; P < .001) tumors. The 5-year DMFS (%, [95% CI]) was significantly lower for patients with ER+/Basal tumors (66% [52.6 to 77.3]), compared with those with ER+/Luminal A tumors (92.3% [85.2 to 96.1]) and ER+/Luminal B tumors (73.5% [44.5 to 79.3]). Importantly, patients with ER+/Basal or TNBC/Basal tumors that had a pCR exhibited significantly improved DMFS and OS compared with those with residual disease. By contrast, patients with ER+/Luminal B tumors had comparable 5-year DMFS and OS whether or not they achieved pCR. CONCLUSION Significant differences in chemosensitivity and 5-year outcome suggest patients with ER+/Basal molecular subtype may benefit from neoadjuvant regimens optimized for patients with TNBC/Basal tumors compared with patients with ER+/Luminal subtype. These data highlight the importance of identifying this subset of patients to improve treatment planning and long-term survival.

TPS7088 Background: Genomic expression profiles have enabled the classification of breast cancers into molecular sub-types and provide prognostic information about the metastatic potential of the tumor, both of which have implications for the personalized treatment of breast cancer beyond clinical and pathological features. However, to precisely stratify tumors into actionable subgroups, full genome expression data should be combined with comprehensive clinical information. The FLEX Registry aims to aggregate a large, real-world dataset, which will enable discovery of novel genomic profiles, particularly for patient subsets that are underrepresented in traditional clinical trials and will contribute to improved precision in the management of breast cancer. Methods: The FLEX Registry (NCT03053193) is a multi-center, prospective, observational trial for patients with Stage I, II, and III breast cancer. Patients with stage I-III breast cancer who receive the 70-gene signature risk of recurrence test, with or without the 80-gene signature molecular sub-typing test, on a primary tumor are eligible for enrollment. The primary objective of FLEX is to create a large scale, population-based registry that links complete clinical data with full genome expression data to elucidate new prognostic and/or predictive gene associations in a real-world setting. The FLEX Registry employs a shared study infrastructure to develop and investigate hypotheses for targeted subset analyses and/or clinical trials based on full genome expression data. The adaptable protocol is designed to be amended with the inclusion of targeted sub-studies. Patients enrolled in the initial study are eligible for inclusion in sub-studies for which they meet all eligibility criteria and additional consent is not required. Data will be collected on patients from diagnosis through 10 years of follow-up and any necessary additional clinical data will be collected as specified in the appendix protocols. Target enrollment is a minimum of 10,000 patients; >4,000 patients have enrolled since April 2017 at more than 80 sites, including seven National Cancer Institute-designated comprehensive cancer centers. The FLEX collaborative platform enables participating investigators the opportunity to author their own sub-study protocols, as approved by the FLEX Steering Committee. Fifteen sub-studies have been approved for investigation within the FLEX Registry. Clinical trial information: NCT03053193 .

Abstract Background: The risk of distant recurrence gene signature, MammaPrint (MP), together with the molecular subtyping gene signature, BluePrint (BP), stratifies breast tumors into Luminal A, Luminal B, HER2, and Basal subtypes, independent of immunohistochemistry (IHC) or fluorescent in situ hybridization (FISH) expression. In the Neoadjuvant Breast Registry Symphony Trial (NBRST), MP and BP identified patients likely to respond to neoadjuvant treatment with higher accuracy compared to conventional methods. Here, we report 5-year follow up (FU) data in breast cancer (BC) patients from the NBRST registry with discordant clinical and genomic subtyping.Methods: This prospective study enrolled 1072 early-stage BC patients from 2009-2014 who received MP and BP testing. Patients received neoadjuvant therapy following standard of care and consented to 5 years post-surgery FU. IHC determined hormone receptor (HR) status, including ER and PR, and IHC and/or FISH determined HER2 status. Median FU for distant metastasis free survival (DMFS) and overall survival (OS) was 4.6 and 5 years, respectively. Differences in DMFS and OS was assessed by Kaplan Meier analysis and log-rank test.Results: Overall, BP reclassified 22% of tumors into different molecular subtypes compared to IHC/FISH (Table). BP reclassified 17% of ER+HER2- tumors as BP Basal, with higher pathological complete response (pCR) rates compared to ER+/BP Luminal tumors (36% vs. 4%). ER+/BP Basal patients had similar pCR rates as triple negative BC (TNBC)/BP Basal patients (36% vs. 37%) following neoadjuvant treatment, and pCR correlated with improved survival outcomes. The 5-year DMFS and OS probabilities were lower in ER+/BP Basal patients compared to TNBC/BP Basal patients and were substantially lower compared to ER+/BP Luminal patients (P < 0.001). There were 106 HR-HER2+ patients, of whom BP reclassified 23.6% to Basal and 2.8% as Luminal B; the remaining 73.6% were confirmed HER2 by BP. The 5-year DMFS and OS probabilities were worse in HER2+/BP Basal patients compared to HER2+/BP HER2 patients. Of 142 triple positive (TP, ER+PR+HER2+) patients, BP classified 55% as Luminal, 39% as HER2, and 6% as Basal, with higher pCR rates observed in BP Basal and BP HER2 tumors compared to BP Luminal. The 5-year DMFS and OS probabilities were substantially lower in TP/BP Basal patients compared to TP/BP HER2 and TP/BP Luminal patients (P < 0.05 and P < 0.04). Of clinical HER2+ patients (HR+ or HR-) that received pertuzumab, patients that reclassified as BP Basal had worse OS compared to BP HER2 patients (P < 0.04).Conclusion: ER+HER2- and HER2+ patients that reclassified as BP Basal are more likely to achieve pCR and have improved survival, demonstrating the clinical utility of BP in the neoadjuvant setting. These patients may benefit from optimized chemotherapy used for TNBC, including novel emerging treatments such as PD-1 and PARP1 inhibitors, in addition to HER2-targeted therapy. Furthermore, HER2+ tumors that were confirmed HER2 by BP may have high response rates to regimens containing TDM-1. Lastly, BP identified a subgroup of triple positive BC patients, who reclassified as BP Luminal, that may avoid overtreatment. Overall, molecular subtyping using MP and BP is more accurate in stratifying patients and predicting treatment responses and 5-year disease outcomes than conventional methods and thus, facilitates successful treatment decisions. Clinical subtypeFrequency of BP classificationBluePrint subtypepCR%5-yr DMFS (95% CI)5-yr OS (95% CI)TNBC (n=236)0.42% (1/236)Luminal A100% (1/1)N/AN/A2.54% (6/236)Luminal B16.67% (1/6)N/AN/A1.27% (3/236)HER233.33% (1/3)N/AN/A95.76% (226/236)Basal36.73% (83/226)100% (pCR)100% (pCR)60.5% (50.5-69.1)(non-PCR)64.3%(52.1-71.2) (non-PCR)ER+HER2- (n=520)28.84% (152/520)Luminal A1.97% (3/152)91.1% (84.0-95.2)94.6% (88.3-97.6)52.37% (276/520)Luminal B5.43% (15/276)75.2% (69.0-80.4)84.5% (79.0-88.7)1.33% (7/520)HER214.29% (1/7)N/AN/A17.46% (92/520)Basal35.9%(33/92)84.1% (67.8-92.5) (pCR)86.3% (70.1-94.1) (pCR)54.6% (42.0-65.5) (non-pCR)57% (43.7-68.2) (non-pCR)HR-HER2+ (n=106)2.83% (3/106)Luminal B66.67% (2/3)100%100%73.59% (78/106)HER269% (54/78)82.8% (69.9-90.5)88.6% (76.0-94.8)23.58% (25/106)Basal40% (10/25)79.0% (52.5-91.7)79.0% (52.5-91.7)Triple Positive (n=142)12.68% (18/142)Luminal A22.22% (4/18)88.8% (76.5-94.8)94.5% (83.8-98.2)42.25% (60/142)Luminal B11.67%(7/60)38.73% (55/142)HER244.44% (24/55)87.5% (72.0-94.7)97.9% (83.8-98.2)6.34% (9/142)Basal55.56%(5/9)62.5% (22.9-86.1)70.0% (22.5-91.8)HER2+ (HR+ or HR-)treated with pertuzumab (n=105)28.6%(30/105)Luminal37% (11/30)84.7% (63.8-94.1)92.2%(71.8-98.0)57%(60/105)HER282% (49/60)91.4% (78.3-96.8)92.9%(79.2-97.7)14%(15/105)Basal40% (6/15)66.0%(31.1-86.3)64.0% (29.1-85.1) Citation Format: Pat Whitworth, James Pellicane, Jr, Paul Baron, Peter Beitsch, Laura Lee, Michael Rotkis, Angela Mislowsky, Carrie Dul, Charles Nash, Bichlien Nguyen, Mary Murray, Paul Richards, Mark Gittleman, Stephanie Akbari, Shiyu Wang, Andrea Menicucci, Erin B Yoder, Lisa Blumencranz, William Audeh. Molecular subtyping by BluePrint improves prediction of treatment responses and survival outcomes in patients with discordant clinical and genomic classification [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS4-04.

Abstract Background: Triple negative breast cancers (TNBC) are more aggressive, have a worse prognosis, and few targeted therapies compared to other BC subtypes. TNBC is molecularly heterogeneous, with at least 4 distinct subtypes: basal-like immune-activated (BLIA), basal-like immunosuppressed (BLIS), luminal androgen receptor (LAR), and mesenchymal (MES). The molecular subtyping gene signature, BluePrint (BP), classifies breast tumors into Luminal, HER2, or Basal subtype based on the assessment of downstream signaling pathways and independently of IHC expression. Compared to IHC-defined TNBC, a higher frequency of BLIS or BLIA subtypes and fewer LAR or MES tumors were reported in BP-defined Basal tumors. To advance our understanding of TNBC heterogeneity, we evaluated the relationship between gene expression signatures, TNBC subtype and BluePrint, in IHC-defined TNBC. Methods: The FLEX registry (NCT03053193) is an ongoing, prospective study evaluating primary tumors from stage I-III BC patients who receive the risk of distant recurrence gene signature, MammaPrint (MP), and BP testing and consent to clinically annotated full transcriptome data collection. This analysis includes 204 IHC-defined TNBC patients. TNBC subtypes BLIA, BLIS, LAR, and MES were derived using an adjusted version of the Burstein centroid signature. BP classified patient samples into Luminal, HER2, and Basal subtypes. A proportion of tumors may exhibit a secondary but less pronounced activated pathway or BP subtype. Therefore, each BP subtype was divided into single activated or mixed subtype based on BP indices. Results: Of 204 TNBC tumors, 84% were classified as Basal by BP, most of which were BLIS (65%), followed by BLIA (22%), with a low frequency of MES (8%) and LAR (5%) subtypes (Table). Approximately 14% of TNBCs were reclassified as Luminal by BP, most of which were LAR (76%), whereas 24% were MES. Clustering analysis revealed similar gene expression profiles between Basal-BLIS and Basal-BLIA tumors. Interestingly, the transcriptional profile of Basal-MES and Basal-LAR tumors were similar to Luminal-MES and Luminal-LAR tumors. BP Basal indices distinguished between different TNBC subtypes. The Basal pathway was predominantly activated in 90% of BP Basals (single activated tumors), most of which were either BLIS or BLIA (96%), whereas 10% of BP Basals were mixed subtype and more likely to classify as LAR (53%) or MES (35%). Approximately 25% of the BP Basal gene signature overlapped with the TNBC subtype gene signature. Expression of 18 and 12 genes out of 28 genes that make up the BP basal signature were significantly different in Basal-BLIA/BLIS compared to LAR or MES, respectively (P < 0.05). PRR15 and CAPN13 were significantly differentially expressed between LAR and MES within Basals. Conclusion: BP reclassified a subgroup of TNBC tumors to Luminal, explaining the discrepancy in the distribution of TNBC subtypes between IHC-defined TNBC and BP Basal tumors. Furthermore, BP indices distinguished between single activated and mixed subtypes, which correlated with different TNBC subtypes. These data suggest that molecular classification by BP adds further precision in classifying TNBC patients and sheds new light on the heterogeneity of these tumors. These findings have clinical implications in stratifying patients and identifying successful targeted treatment options. Future studies are warranted to investigate treatment response and prognosis in these molecular subgroups. BasalLuminalHER2TotalBLIA370037BLIS11100111LAR1022335MES147021Total172 (84.3%)29 (14.2%)3 (1.5%)204 (100%) Citation Format: Virginia G. Kaklamani, Cathy Graham, Karen L. Tedesco, Abirami Sivapiragasam, Jennifer A. Crozier, Apurva N. Shah, Yuan Yuan, Josien Haan, Andrea Menicucci, Michelle L. Bolner, Shiyu Wang, Lorenza Mittempergher, Erin Yoder, William Audeh, FLEX Investigators' Group. Using blueprint to elucidate the molecular heterogeneity of triple negative breast cancers [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-05.

Abstract Background: Male breast cancer (MaBC) is rare, comprising <1% of all breast cancers in the United States. The low incidence of MaBC limits the ability to conduct clinical trials specifically for this population. Due to the paucity of research on MaBC, current understanding regarding MaBC biology, pathology, and treatment strategies has been primarily based on evidence extrapolated from research on female breast cancer (FBC) patients. Traditional diagnostic biomarkers such as ER, PR, and HER2, as well as newer multi-gene prognostic signatures, are employed when making treatment decisions for both MaBC and FBC. However, limited empirical data is available to support the use of identical laboratory biomarkers and molecular signatures in both MaBC and FBC. The 70-gene risk of distant recurrence signature, MammaPrint (MP), and the 80-gene molecular subtyping signature, BluePrint (BP), are commonly used to help make treatment decisions for both MaBC and FBC patients. To support the clinical utility of MP and BP in MaBC, this study aims to elucidate whether significant molecular biological differences exist between MaBC and FBC. To address this knowledge gap, we evaluated and compared 1) MP index results within Low Risk (LR) and High Risk (HR) groups, 2) MP and BP gene expression, and 3) differentially expressed genes within the full genome and their associated biological pathways between tumors from MaBC and FBC. Methods: This analysis included a total of 817 breast tumor samples sent to Agendia, Inc. (Irvine, CA) for MP and BP testing. Full-transcriptome microarray data were available for 1) a subset of 400 post-menopausal FBC patients enrolled in the FLEX Registry (NCT03053193) and 2) 80 MaBC pateints, 32 of whom enrolled in the FLEX registry and 48 non-study patients for whom data were limited to metadata and quality metrics routinely captured for diagnostic testing. Data from all patients were de-indentified. Differences in mean MP indices between FBC (N=400) and MaBC (N=417) according to MP Risk classification (LR or HR) were analyzed using a Z-test. Differential gene expression analysis was performed using the R-limma package in which gene expression data were quantile normalized. Pathway analyses were performed using GOseq. Differentially expressed genes (DEGs) were identified between FBC (N=400) and MaBC (N=80) for whom full transcriptome microarray data were available. DEGs were defined as those with a fold change of > 2 and an adjusted P value of < 0.05. Results: All patients in this study had hormone positive, HER2 negative early-stage breast cancer. There was no statistical difference in the average MP index between MaBC and FBC classified as MP LR (P=0.273) or those classified as MP HR (P=0.692). Gene expression comparison revealed 166 DEGs between MaBC (N=80) and FBC (N=400), 99 DEGs between MP HR MaBC (N=42) and MP HR FBC (N=200), and 290 DEGs between MP LR MaBC (N=38) and MP LR FBC (N=200). Pathway analyses revealed that downregulated genes in MaBC compared to FBC enriched to immune-related functions, including B-cell mediated immunity, whereas upregulated genes were associated with hormone metabolic processes. In all comparisons, expression of MP or BP genes was not significantly different. Conclusions: We found similar MP index distributions between MaBC and FBC. Importantly, differential gene expression between MaBC and FBC provides novel insight into the mechanisms underlying MaBC. Although these data reveal biological distinctions between male and female breast cancer, MP and BP assay performance is preserved across both groups. Further studies are needed to assess clinical outcomes; however, these findings support the use of MP risk of recurrence assay and BP molecular subtyping assay for prognosis and informing treatment decisions in MaBC. Citation Format: Jennifer Crozier, Julie Barone, Kalyan Banda, Beth Lesnikoski, Robert Maganini, Sami Diab, Ian Grady, Thomas Lomis, Charles Cox, Amy Truitt, Benjamin Nota, Andrea Menicucci, Erin Yoder, William Audeh, FLEX Investigators Group. Differential gene expression analysis and clinical utility of MammaPrint and BluePrint in male breast cancer patients [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS14-11.

Background In this phase II clinical trial, we evaluated the efficacy of the nonanthracycline combination of carboplatin and nab-paclitaxel in early stage triple-negative breast cancer (TNBC). Patients and Methods Patients with newly diagnosed stage II-III TNBC (n = 69) were treated with neoadjuvant carboplatin (area under the curve 6) every 28 days for four cycles plus nab-paclitaxel (100 mg/m(2)) weekly for 16 weeks. Pathological complete response (pCR) and residual cancer burden (RCB) were analyzed with germline mutation status, tumor-infiltrating lymphocytes (TILs), TNBC molecular subtype, and GeparSixto immune signature (GSIS). Results Sixty-seven patients were evaluable for safety and response. Fifty-three (79%) patients experienced grade 3/4 adverse events, including grade 3 anemia (43%), neutropenia (39%), leukopenia (15%), thrombocytopenia (12%), fatigue (7%), peripheral neuropathy (7%), neutropenia (16%), and leukopenia (1%). Twenty-four patients (35%) had at least one dose delay, and 50 patients (72%) required dose reduction. Sixty-three (94%) patients completed scheduled treatment. The responses were as follows: 32 of 67 patients (48%) had pCR (RCB 0), 10 of 67 (15%) had RCB I, 19 of 67 (28%) had RCB II, 5 of 67 (7%) had RCB III, and 1 of 67 (2%) progressed and had no surgery. Univariate analysis showed that immune-hot GSIS and DNA repair defect (DRD) were associated with higher pCR with odds ratios of 4.62 (p = .005) and 4.76 (p = .03), respectively, and with RCB 0/I versus RCB II/III with odds ratio 4.80 (p = .01). Immune-hot GSIS was highly correlated with DRD status (p = .03), TIL level (p < .001), and TNBC molecular subtype (p < .001). After adjusting for age, race, stage, and grade, GSIS remained associated with higher pCR and RCB class 0/I versus II/III with odds ratios 7.19 (95% confidence interval [CI], 2.01-25.68; p = .002) and 8.95 (95% CI, 2.09-38.23; p = .003), respectively. Conclusion The combination of carboplatin and nab-paclitaxel for early stage high-risk TNBC showed manageable toxicity and encouraging antitumor activity. Immune-hot GSIS is associated with higher pCR rate and RCB class 0/1. This study provides an additional rationale for using nonanthracycline platinum-based therapy for future neoadjuvant trials in early stage TNBCs. Clinical trial identification number: NCT01525966 Implications for Practice Platinum is an important neoadjuvant chemotherapy agent for treatment of early stage triple-negative breast cancer (TNBC). In this study, carboplatin and nab-paclitaxel were well tolerated and highly effective in TNBC, resulting in pathological complete response of 48%. In univariate and multivariate analyses adjusting for age, race, tumor stage and grade, "immune-hot" GeparSixto immune signature (GSIS) and DNA repair defect (DRD) were associated with higher pathological complete response (pCR) and residual cancer burden class 0/1. The association of immune-hot GSIS with higher pCR holds promise for de-escalating neoadjuvant chemotherapy for patients with early stage TNBC. Although GSIS is not routinely used in clinic, further development of this immune signature into a clinically applicable assay is indicated.

Abstract Background: MammaPrint (MP) is used to identify breast cancer (BC) patients who can safely forego adjuvant chemotherapy. MP combined with the BluePrint (BP) molecular subtyping signature identifies BC subtypes with distinct therapeutic response rates and survival outcomes. In the Neoadjuvant Breast Symphony Trial (NBRST), MP and BP (MP/BP) predicted rates of pathologic complete response to neoadjuvant chemotherapy (NCT) and partial response to neoadjuvant endocrine therapy (NET). Here, we report 5-year overall survival (OS) and distant metastasis-free survival (DMFS) in patients from the NBRST registry according to MP/BP molecular classification. Methods: The NBRST trial (NCT01479101) prospectively enrolled 1072 patients from 2011 to 2014, who received MP and BP testing. Patients were assigned to receive NCT or NET according to NCCN guidelines and consented to 5 years post-surgery follow-up (FU). Clinical outcomes were available for 913 patients from 67 US institutions. Median FU for OS and DMFS was 5 and 4.6 years, respectively. Tumors classified by MP as High Risk (HR) or Low Risk (LR) were further stratified into four molecular subtypes by BP: Luminal A, Luminal B, HER2, and Basal. Differences in OS and DMFS at 3 and 5 years were assessed by Kaplan Meier analysis and log-rank test. Results: MP results from neoadjuvant patients (N=913) classified 16% of tumors as MP LR and 84% as MP HR. MP and BP classified 15.7% (143/913) of tumors as Luminal A, 32.5% (297/913) as Luminal B, 17.1% (156/913) as HER2, and 34.7% (317/913) as Basal. The 5-year OS and DMFS probabilities were significantly lower in HR compared to LR patients (p < 0.001 for OS and DMFS), and lowest in Basal and Luminal B compared to Luminal A and HER2 subtypes (p < 0.001 for OS and DMFS). Most DMFS events in BP Basal tumors occurred within the first 3 years. Of 841 patients that received NCT with or without HER2-targeted therapy, 12.2% (103/841) were LR and 87.8% (738/841) were HR. MP and BP classified 11.9% (100/841) of these patients as Luminal A, 32.6% (274/841) as Luminal B, 8.3% (154/841) as HER2 subtype, and 37.2% (313/841) as Basal. The 5-year OS and DMFS probabilities were lowest in HR, Basal or Luminal B patients (p < 0.001). In 59 patients who received NET alone, 5-year OS and DMFS were significantly worse in HR patients that had Luminal B or HER2 tumors compared to LR Luminal A patients. In the 39 patients with Luminal A tumors, response to NET at the time of surgery was: 46.2% partial response, 41.0% stable disease, 5.1% progressive disease, 2.6% not reported. Five year DMFS in patients with Luminal A tumors treated with NCT or NET was not significantly different (p=0.67).Conclusions: MammaPrint remained prognostic in BC patients undergoing neoadjuvant therapy. Long -term prognosis was excellent in LR groups who received NCT or NET alone. MP and BP can accurately classify patients into specific subtypes with distinct OS and DMFS outcomes at five years, with BP Basals having the worst outcomes, followed by Luminal B, HER2, and Luminal A subtypes. BP Basal patients had the highest frequency of events within the first 3 years post-surgery, suggesting a genomic risk timeline distinct from other BP subtypes and a potential benefit from a secondary therapeutic immediately post-surgery. Additionally, Luminal A patients had a very low risk of progressive disease while on NET alone prior to surgery, with similar DMFS outcomes to Luminal A-types who received NCT. Number of patientsObserved events% at 5 year (95% CI)p-valueAll patients - MammaPrint Risk GroupOS913134p<0.001Low Risk146794.7 (88.4-97.6)High Risk76712781.1 (77.7-84.0)DMFS913182p<0.001Low Risk1461191.2 (84.2-95.2)High Risk76717175.5 (71.9-78.7)All patients - MammaPrint + BluePrint SubtypeOS913134p<0.001Luminal A143794.6 (88.3-97.6)Luminal B2974484.5 (80.0-88.7)Basal3177472.2 (66.2-77.3)HER2156993.4 (87.1-96.7)DMFS913182p<0.001Luminal A1431191.1 (82.1-94.3)Luminal B2976975.2 (68.0-80.4)Basal3178570.4 (64.6-75.5)HER21561787.2 (79.7-92.0)NCT patients - MammaPrint Risk GroupOS841121p<0.001Low Risk103397.4 (90.1-99.4)High Risk73811881.7 (78.3-84.7)DMFS841167p<0.001Low Risk103792.6 (84.1-96.6)High Risk73816076.2 (72.5-79.4)NCT patients - MammaPrint + BluePrint SubtypeOS841121p<0.001Luminal A100395.5 (86.2-98.6)Luminal B2743978.9 (71.7-84.5)Basal3137168.7 (57.9-77.2)HER2154892.8 (85.9-96.4)DMFS841167p<0.001Luminal A100792.4 (83.8-96.5)Luminal B2746375.7 (65.6-76.5)Basal3138171.4 (65.6-76.5)HER21541687.7 (80.2-92.5)NET alone patients - MammaPrintOS597p=0.01Low Risk39293.0 (74.6-98.2)High Risk20580.0 (55.1-92.0)DMFS598p=0.003Low Risk39293.0 (74.6-98.2)High Risk20674.7 (49.4-88.6)NET alone patients - MammaPrint +BluePrint SubtypeOS597p=0.008Luminal A39293.0 (74.6-98.2)Luminal B18483.3 (56.8-94.3)Basal00N/AHER221N/ADMFS598p=0.005Luminal A39293.0 (74.6-98.2)Luminal B18577.4 (50.3-90.9)Basal00N/AHER221N/A Citation Format: Pat Whitworth, James V Pellicane, Jr., Paul Baron, Peter Beitsch, Laura Lee, Michael Rotkis, Angela Mislowsky, Carrie Dul, Charles Nash, Bichlien Nguyen, Mary Murray, Paul Richards, Mark Gittleman, Stephanie Akbari, Shiyu Wang, Erin B Yoder, Andrea Menicucci, Lisa Blumencranz, William Audeh, NBRST Investigators Group. 5-year outcomes in the NBRST trial: Preoperative MammaPrint and BluePrint breast cancer subtype is associated with neoadjuvant treatment response and survival [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD9-01.

591 Background: Although advances in immunotherapy for the treatment of breast cancer have been minimal compared with other cancers, studies demonstrating tumor-infiltrating lymphocytes and immunomodulatory gene activation in the tumor microenvironment suggest the importance of antitumor immune responses in clinical outcomes. A 12-chemokine gene score has been shown to predict the presence of ectopic lymph node-like structures (ELN) in the tumor microenvironment and improved survival in melanoma, colon cancer, and breast cancer patients (Prabhakaran, 2017). Here, we evaluated this signature in an independent dataset of breast cancer patients treated with neoadjuvant chemotherapy. Methods: Tumor specimens used in this retrospective analysis (n = 92) were from breast cancer patients enrolled in either MINT (NCT0151487) or NBRST (NCT01479101) neoadjuvant registry trials from 2011 to 2016. Clinical data were captured with informed consent, and 70-gene signature (70-GS), 80-gene signature (80-GS), and full transcriptome data were generated by Agendia, Inc. Gene expression data were quantile normalized using R limma package. Principal component analysis (PCA) was performed on the normalized dataset using R princomp package. Chemokine score (CS) was defined as the first principal component values resulting from PCA. 70-GS/80-GS and clinical data were evaluated in relation to CS. CS were compared using Mann-Whitney test. Results: Of 92 breast tumors available for analysis, 84% were 70-GS High Risk (HR). Tumors were 39% Luminal-type, 24% HER2-type, and 32% Basal-type by 80-GS. HR tumors had higher CS than 70-GS Low Risk (LR) tumors (p < 0.001). 80-GS Basal-type, HER2-type, and Luminal B tumors had higher CS than Luminal A tumors (p < 0.01 for each comparison). High grade and ER-negative tumors seemed to have a high CS, although not significantly. Tumors from patients who achieved a pathological complete response (pCR) following neoadjuvant chemotherapy had higher CS than patients with residual cancer burden (p = 0.048). Conclusions: The current study demonstrated a significantly higher CS in 70-GS HR tumors and those which achieved pCR following neoadjuvant chemotherapy. Although further study is needed to evaluate the association of high CS with tumor-associated ELN, these results support previous work demonstrating that, although high CS is associated with aggressive clinical features, it also predicts superior clinical outcomes. The current study suggests validation of the 12-chemokine gene score in an independent dataset of breast cancer patients.

3570 Background: Biological heterogeneity of HER2 positive breast cancers has been suggested by a modest benefit of HER2-targeted therapies reported in the APHINITY and ExteNET trials. This highlights the need for improved biomarkers that more precisely identify patients who benefit from HER2-directed agents. The 80-gene molecular subtyping signature (80GS) classifies breast tumors into Luminal, HER2 or Basal type based on the gene expression of downstream signaling pathways. Previous work showed a substantial proportion of tumors identified as HER2 equivocal or HER2 positive by 2013 ASCO/CAP guidelines may be reclassified as non-HER2 type by 80GS. In 2018, ASCO/CAP HER2 IHC/ISH classification guidelines were revised to reduce the frequency of HER2 equivocal cases, for which treatment recommendations have been ambiguous. Here we evaluated concordance between HER2 status by 2018 ASCO/CAP guideline classification and 80GS molecular subtyping. Methods: Pathology reports are provided by physicians for samples that are tested with the 70-gene risk of distant recurrence signature (70GS) and 80GS as part of routine diagnostic care. This analysis includes data sent to Agendia (Irvine, CA) from January 2019 to January 2020. HER2 IHC/ISH results based on ASCO/CAP 2018 guidelines were available for 1453 samples. Results: Of 1453 samples, 1336 (92%) were HER2 negative, 99 (7%) were HER2 positive, and 18 (1.2%) were HER2 equivocal under 2018 guidelines. 80GS reclassified 57 of 99 (58%) HER2 positive tumors as Luminal and 11 of 99 (11%) as Basal; the remaining 31% were confirmed HER2. Furthermore, 55 of 99 (55%) HER2 positive tumors were also ER and PR positive by IHC, with 48 (87%) of these reclassified as Luminal type. Of HER2 negative tumors, 80GS classified 94 of 1336 (7%) as Basal and 2 of 1336 (0.15%) as HER2. Of HER2 equivocal tumors, 16 of 18 (89%) reclassified as Luminal and 2 of 18 (11%) as Basal. Conclusions: In this real-world diagnostic dataset, 2018 ASCO/CAP guidelines resulted in few HER2 equivocal tumors overall, confirming the positive impact of the revised guidelines. However, 80GS reclassified 69% of HER2 positive tumors to non-HER2 molecular subtypes, suggesting these tumors may have suboptimal responses to HER2-directed therapy compared to HER2 enriched. All HER2 equivocal tumors reclassified to non-HER2 subtypes. Molecular classification by 80GS adds further precision in classifying HER2 positive patients and potential to predict responsiveness to HER2-targeted therapies. Further studies are warranted to validate the utility of HER2 status based on 80GS.

Abstract Background: Breast cancer (BC) mortality is higher in African-American women (AA) than in Caucasian women (CA). AA are also diagnosed at a younger age, have more aggressive subtypes and greater incidence of metabolic dysfunction such as obesity and diabetes. These disparities have been attributed to a confluence of socioeconomic, genetic and epigenetic factors. However, the distinctive tumor biology of AA BC is not yet fully elucidated, as AA remain underrepresented in breast cancer studies and databases. Here, we compared clinical and molecular BC features of AA and CA patients for insights into mechanisms associated with these racial disparities. Methods: The FLEX Registry Trial (NCT03053193) is a prospective study evaluating tissue collected from patients with stage I-III BC who have consented to receive MammaPrint(MP)/BluePrint(BP) and clinically annotated full genome (FG) data. FLEX subset analyses investigate new gene associations that may be relevant to BC biology. This sub-study includes 160 AA and 199 CA patients (n=359) enrolled since April 2017. Clinical characteristics used in the analysis include menopausal status, metabolic factors, stage, grade and IHC results. A comprehensive publication search (PubMed) was conducted to validate candidate genes involved in BC in AA, BC genes associated with epigenetic regulation and genes associated with metabolic syndrome. Hierarchical clustering was performed on FG microarray (Agilent) intensity data focusing on the candidate genes (50 probes targeting 37 unique genes). Gene expression was compared between race and MP/BP risk groups. Results: AA were predominately MP High Risk (HR) 67.5%, BP Luminal B 40.2%, BP Basal 22.6%. Interestingly, 40.0% of AA BP Basal were classified by IHC as ER+. CA were MP Low Risk (LR) 54.8%, BP Luminal A 54.8%. Clinically, there were no differences in histology, tumor size, nodal or menopausal status between AA and CA patients. AA had higher grade tumors, higher rates of type 2 diabetes and obesity. Three comparisons were performed: 1) AA and CA, irrespective of MP result, 2) AA and CA HR MP only, and 3) AA only, irrespective of MP result. In comparison 1) 15 unique genes showed significant differences (p<0.05) in gene intensities between AA and CA patients. A heatmap showed four major clusters; cluster 1 included mainly (72.3%) AA patients, and these were predominantly MP HR and BP Basal. In comparison 2) 9 unique genes had significant differences (p<0.05) in gene intensities, 6 of which were common to the first comparison. This showed three major clusters and a significant cluster among AA patients. Finally, comparison 3) found 20 unique genes with significant differences (p<0.05) in gene intensities, 10 of which were common to the previous comparisons. This showed two major clusters with one significant cluster among AA MP HR, BP Basal patients. In total, 11 unique genes showed significant differences in intensities in AA or AA with HR MP including CYP4F8, TWIST1/2, CCND2, FOXA1 and GSTP1. These genes have known functions regulating metabolism and cell cycle. Conclusions: Here we show AA patients were enriched for genes associated with metabolic syndrome and epigenetic regulation of metabolic syndrome. The aberrant function of these genes has been implicated in tumorigenesis, dysregulation of metabolism and drug resistance. Further validation is warranted to fully understand the association of these genes with the unique biology of breast cancer in AA. Citation Format: Raquel Nunes, Lisa E. Blumencranz, Heather M Kling, Sahra Uygun, Sarah Untch, Erin B Yoder, Jennifer A Crozier, William Audeh. Racial disparities in breast cancer: Identifying predisposing clinical and molecular features associated with African American patients [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-10-08.