Wu, S.

Abstract Background: Tertiary lymphoid structures (TLS), which are organized ectopic lymphoid aggregates resembling secondary lymphoid organs, have been associated with improved outcomes across various cancer types. However, limited data exist on the prognostic relevance of TLS in HER2+ BC pts treated with trastuzumab. In our prior work, we demonstrated that the presence of functional TLS, defined by lymphoid aggregates with elevated expression of BCL6 or IL21R, correlated with improved outcomes in the NCCTG N9831 trial. In this study, we evaluated TLS-related gene and outcomes in the real-world database. Methods: 1344 HER2+ (HR-HER2+: 560; HR+HER2+: 784) BC samples were analyzed via NGS (592-gene panel, NextSeq; WES/WTS, NovaSeq; Caris Life Sciences). Above (high) or below (low) the 50th percentile expression levels of TLS-related genes were used to calculate overall survival (OS). IL21R-high (H) and -low (L) tumors were classified by RNA expression above or below the 50th percentile. Real-world OS was derived from insurance claims and calculated from date of biopsy to last contact using Kaplan-Meier. Statistical significance was assessed using chi-square and Mann-Whitney U with multiple comparison adjustments (q < 0.05). Results: Among pts with HR-HER2+ BC, high expression of IL21R, CXCL9, CD38, and CXCL10 were associated with improved OS (Table). In contrast, among pts with HR+HER2+ BC, high expression of CXCR3, PDCD1, TBX21, CD200 and IL21R, were associated with improved OS. In both HR-HER2+ and HR+HER2+, IL21R-H groups had 1) higher infiltration of B cells (HR-HER2+: 4.4% vs 2.9%; HR+HER2+: 5.6% vs 4.2%), M1 MΦ (HR-HER2+: 3.9% vs 2.6%; HR+HER2+: 3% vs 2.1%), M2 MΦ (HR-HER2+: 4% vs 3.2%; HR+HER2+: 5.7% vs 4.4%), NK cells (HR-HER2+: 2.8% vs 2.5%; HR+HER2+: 2.7% vs 2.4%), CD8+ T cell (HR-HER2+: 0.9% vs 0%; HR+HER2+: 0.7% vs 0%), Tregs (HR-HER2+: 2.9% vs 1.4%; HR+HER2+: 2.8% vs 1.5%), all q<.05; 2) higher T cell inflamed score (HR-HER2+: 87.5 vs -95; HR+HER2+: 71 vs -86), IFNy score (HR-HER2+: -0.19 vs -0.48; HR+HER2+: -0.27 vs -0.49), all q<.05; 3) higher expression levels of MHC class I genes (HLA-A, HLA-B, HLA-C, HLA-E, FC: 1.6-2.3; all q<.05), MHC class II genes (HLA-DQA1, HLA-DOA, HLA-DPA1, HLA-DMA, FC: 2.2-3.2; all q<.05) compared to IL21R-L group. Conclusion: Consistent with our prior findings, overexpression of TLS-related genes was associated with improved outcomes in HER2+ BC in real-world data. Notably, the prognostic impact of TLS-related genes differed by hormone receptor (HR) status. Among these, IL21R emerged as the only gene significantly associated with clinical outcomes across both datasets and HR subgroups. Higher IL21R expression is associated with more B cell, M1 MΦ, CD8 T cell and NK cells. These findings underscore the potential importance of the IL21/IL21R axis in HER2+ BC and warrant further investigation to validate its role and therapeutic relevance. Citation Format: S. Chumsri, S. Deshmukh, Y. Liu, S. Wu, J. Xiu, N. Norton, S. Shipra Gandhi, E. Torres, M. Lustberg, E. Perez, A. Nassar, G. Sledge, E. Thompson, K. Knutson. Tertiary lymphoid structure (TLS)-related gene expression and outcomes in HER2-Positive (HER2+) breast cancer (BC) in the Real-World Database [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-09-08.

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive yet immunogenic subtype of breast cancer (BC) and the only one with FDA-approved immune checkpoint inhibitor (ICI) - pembrolizumab. Currently, PD-L1 (22C3) is the companion biomarker for predicting pembrolizumab benefit, but its utility is limited by spatial/temporal heterogeneity, assay variability, and modest correlation with treatment response. Chemokines such as CXCL9, CXCL10, and CCL5 recruit CD8+ T cells into the tumor microenvironment and have been associated with improved response to ICI, but their predictive value alongside PD-L1 remains unclear. Here, we examined the relationship between these chemokines, PD-L1, and pembrolizumab efficacy in TNBC. Methods: We analyzed 3662 TNBC tumors profiled by NGS (592, NextSeq; WES/WTS, NovaSeq; Caris Life Sciences). Immune cells were estimated using WTS deconvolution (Quantiseq). PD-L1 positivity was defined as >10% CPS (PharmDx 22C3). CXCL9/CXCL10/CCL5-high (H) and -low (L) TNBC were classified by RNA expression above or below 50th percentile. Real-world median overall survival (mOS) was derived from insurance claims and calculated from start of pembrolizumab to last contact using Kaplan-Meier. Statistical significance was assessed by chi-square and Mann-Whitney U with multiple comparison adjustments (q<0.05). Results: TNBC expressed higher levels of CXCL9, CXCL10, and CCL5 (N = 3662, median TPM: 5.3, 14.8, and 15.1) compared to HER2+ (N = 1344; 4.8, 10.1, 10.6) and HR+HER2- BC (N = 6097; 2.7, 6.6, 9.4), all q<0.05. Moderate correlations were observed between PD-L1 CPS and each chemokine (r = 0.41, p<.01). PD-L1-positive tumors had better mOS (24.3 months (m) vs 18.6 m, HR 0.75, 95% CI 0.6-0.92, p=0.007) compared to PD-L1-negative TNBC post-pembrolizumab. Among PD-L1-negative tumors, those with CXCL9-H had better mOS (26.9 m vs 15.8 m for CXCL9-L, HR 0.61, 95% CI 0.45-0.82, p=0.001) post-pembrolizumab. Among PD-L1-positive tumors, CXCL10-H and CCL5-H was associated with improved mOS (CXCL10-H: 25.7 m vs. 20.7 m for CXC10-L, p = 0.03; CCL5-H: 26.7 vs. 18.5 m for CCL5-L, p = 0.03) post-pembrolizumab. PD-L1 negative CXCL9-H, PD-L1 positive CXCL10-H and PD-L1 positive CCL5-H groups showed higher infiltration of CD8+ T cell, B cells, M1/M2 macrophages, Tregs. They also exhibited higher T cell inflamed score, IFNy score and MAPK activation score vs. CXCL9-L, CXCL10-L and CCL5-L groups (Table). Conclusions: In TNBC, a chemokine signature comprising CXCL9, CXCL10 and CCL5 refines PD-L1 based prediction of pembrolizumab benefit. Specifically, high CXCL10 or CCL5 expression in PD-L1-positive tumors, and high CXCL9 expression in PD-L1-negative tumors, were associated with improved survival post pembrolizumab and immune-rich microenvironment. These findings support the use of chemokine profiling to complement PD-L1 and enhance patient selection for ICI therapy in TNBC. Citation Format: S. Gandhi, S. Deshmukh, S. Wu, J. Xiu, G. Sledge Jr., D. Trapani, J. Leone, S. Chumsri, M. Lustberg, C. Hong, S. Yao, K. Takabe, M. Ernstoff, M. Opyrchal, P. Chalasani, C. Paulos, G. Lesinski, A. Madabhushi, S. Badve, K. Kalinsky, P. Kalinski. Chemokine signatures improve PD-L1-based prediction of pembrolizumab response in triple-negative breast cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-08-14.

Abstract Background: Male breast cancer (MaBC) is a rare malignancy, accounting for approximately 1% of all breast cancer cases. Our previous studies suggest that MaBC is biologically distinct from female breast cancer (FeBC), exhibiting a unique mutational profile and immune-genomic microenvironment. While the impact of these molecular alterations on site-specific metastases has been explored in FeBC, it remains poorly understood in MaBC. This gap limits accurate risk stratification and prediction of disease trajectory in male patients. In this study, we investigated site-specific genomic and immune alterations across metastatic sites in MaBC. Methods: 238 MaBC samples were tested by NGS (592, NextSeq; WES, NovaSeq) and WTS (NovaSeq; Caris Life Sciences, Phoenix, AZ). We performed analysis in hormone receptor-positive (HR+) and HER2-negative (HER2-) subtypes which are most common in male. HR+HER2- was defined as estrogen receptor (ER) or progesterone receptor (PR) positive and HER2 IHC 1+ or 2+ with negative chromogenic in situ hybridization (CISH) assay. Immune cells were estimated using WTS deconvolution (Quantiseq). Gene expression profiles were analyzed for T-cell inflamed score, interferon-gamma (IFN-gamma) score and MAPK Activation Score. We classified patients by site of biopsy/specimen site. Statistical significance was assessed with chi-square and Mann-Whitney U tests, p<0.05 is considered statistically significant. Results: Our cohort included 86 HR+HER2- MaBC samples biopsied from primary breast cancer (pBC) (n=39), bone (n=15), liver (n=8), lung (n=8), lymph nodes (n=7), and skin (n=9) mets. We report here only the data on statistically significant differences, but the overall landscape has been depicted across all defined-sites investigated. pBC showed a significantly lower prevalence of PIK3CA mutations (23.6% vs. 53.3%, p<0.05) compared to bone mets. ESR1 mutations were absent in pBC but present in 25% of liver and 25% of lung mets (all comparisons p<0.05). Immune profiling revealed reduced infiltration of M2 macrophages (4.3% vs. 6%, p<0.05) and neutrophil (2.2% vs. 6.9%, p<0.05) in pBC relative to bone Mets. Further, CD4+ T cells were lower in pBC compared to lymph nodes (0% vs. 2.4%, p<0.05). pBC had lower expression of immune checkpoint genes (PDCD1LG2, HAVCR2 and CD47) compared to other mets. pBC exhibited lower MAPK pathway activation score (-1.6 vs. 0.17, p=0.03) and a trend toward lower T cell-inflamed gene expression scores (-65 vs. 8, p=0.06) compared to bone mets. Bone mets had higher infiltration of M2 macrophage compared to lung (6% vs. 4.4%, p<0.05) and lymph node (6% vs. 4.5%, p<0.05). Neutrophil infiltration was elevated in bone versus liver (6.9% vs. 2%, p<0.05) but T regulatory cells were lower in bone compared to lymph nodes (1% vs. 2.4%, p<0.05). Bone showed reduced expression of CD47 (median TPM 50.6 vs. 109.9, p<0.05) compared to skin. Further bone had lower IFN-gamma scores (-0.41 vs. -0.17, p<0.05) compared to lymph node. Data on prior number and types of cancer treatment to give a context to the findings will be presented at the meeting. Conclusions: Our study highlights that each MaBC metastatic site harbors a unique genomic and immune landscape that can influence tumor behavior and potentially impact patient prognosis. Better understanding of metastatic site-specific molecular features in larger cohorts can help in the future research efforts and guiding treatment decisions. Citation Format: D. Trapani, S. Deshmukh, S. Wu, J. Xiu, N. Lin, G. Curigliano, P. Spanheimer, P. Advani, P. Barreto Coelho, M. Lustberg, G. Sledge Jr, S. Tolaney, J. Leone. Site specific Genomic and Immune Landscapes Underpinning in metastatic Male Breast Cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-08-04.

Abstract Background: Triple-negative breast cancer (TNBC) is highly aggressive subtype with poor prognosis and there is an urgent need to develop novel therapies. Deregulated cellular energetics is a known hallmark of cancer. Stearoyl-CoA desaturase-1 (SCD1), is a key enzyme in fatty acid (FA) synthesis, converting saturated to monounsaturated FA. It is upregulated in TNBC, and its expression correlates with poor survival. Hence, targeting SCD1 is a novel strategy for cancer therapy. We have developed an SCD1 inhibitor, MTI-301 and shown anti-tumor activity in murine TNBC cell lines with MTI-301 alone and in combination with paclitaxel. Here, we study the efficacy of MTI-301 in TNBC mouse model and, molecular and immunological association of SCD1 in TNBC. Methods: MTI-301 activity (10 mg/kg oral gavage daily) was evaluated in E0771 immunocompetent TNBC mouse models alone and with immune checkpoint inhibitors (ICI) and paclitaxel (anti-PD-L1 Ab 200ug/mouse; IP and 25 mg/kg IP both given 2/week). Immune markers such as CD4+ T cell and CD8+ T cell in mice tumor tissue were assessed by immunohistochemistry (IHC). Tumor volume was measured by calipers 2/week and compared between groups by ANOVA test. Molecular and immune characterization was performed in 1,581 invasive ductal (ID) TNBC patient (pt) samples tested by NGS (592-gene panel, NextSeq; WES/WTS, NovaSeq; Caris Life Sciences, Phoenix, AZ). ID-TNBC SCD1-high(H) and SCD1-low(L) RNA expression were classified as above or below the 50 percentiles, respectively. Immune cell fractions were calculated by deconvolution of WTS: Quantiseq. Pathway enrichment was determined by GSEA (Broad Inst). Statistical significance was determined using chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q<0.05). Results: Compared to vehicle control, MTI-301 showed significant reduction in mean tumor volume and was associated with macrophage phagocytosis and intratumor infiltration of CD4 and CD8 T cells. We have also showed that MTI-301 + anti-PD1 Ab + paclitaxel has significant antitumor activity compared to either agent alone. IHC analysis is ongoing. In real-word pt data, SCD1-H TNBC (N=791) had higher immune cell infiltration of M2 MΦ (2.95% vs. 2.58%) and neutrophils (4.5% vs. 4.1%) compared to SCD1-L (N=790), all q<0.05. SCD1-H had decreased IFNγ score (-0.29 vs -0.24), but increased MAPK activation score (-0.57 vs -1.77), all q<0.05. SCD1-H had higher levels of metabolic regulator genes (IL10, IL10RA, SOCS3, HIF1A, DUSP6, FC: 1.4-1.8), immune checkpoint genes (PDCD1, CTLA4, LAG3, TIGIT, VISTA, CD244, CD160, BTLA, HAVCR2, FC: 1.3-1.6), stem cell related genes (CD44, ALDH1A1, ALDH1A2, ALDH1A3, KLF4, NANOG, FC: 1.4-1.6) and markers of exhausted T cells (CXCL13, CD38, CD101, ENTPD1, CD69, CD103, KLRG1, PRF1, GZMB, FC: 1.2-1.7), all q<0.05. SCD1-H had enrichment of pathways related to oxidative phosphorylation, FA metabolism, PI3K/AKT/MTOR, EMT, DNA repair, TGF beta, P53 and inflammatory response (NES: 1.7-3.8, all FDR<0.25). SCD1-H had higher frequency of PIK3CA (18.1% vs 8.8%), PTEN (10.7% vs 5.2%), PIK3R1 (6.4% vs 2.3%), AKT1 (3.3% vs 1.3%) and NF1 (8.3% vs 2.7%) mutation compared to SCD1-L, all q<0.05. Conclusion: SCD1 high TNBC tumors are associated with immune suppressive TME, FA metabolism, and dysregulated PI3K pathway, positioning SCD1 as a metabolic driver of therapy resistance and immune evasion and support its targeting to enhance chemo-ICI efficacy. SCD1 inhibitor, MTI-301 significantly reduced tumor growth and enhanced effector immune cell infiltration in TNBC murine models with combinatorial activity with chemo-ICI, indicating that pharmacologic modulation of SCD1 is a promising strategy for cancer therapy. We will be conducting Phase I clinical trial with MTI-301 in pts with advanced tumors including TNBC (NCT NCT06911008). Citation Format: P. P. Advani, S. K. Deshmukh, R. Whetten, M. Redig, M. Pawlush, S. Wu, J. Xiu, J. P. Leone, S. Gandhi, M. Lustberg, G. Sledge Jr, J. Copland. Metabolic and immune reprogramming via SCD1 inhibition enhances chemo-immunotherapy response in TNBC [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS2-12-07.

Abstract Background: Antibody-drug conjugates (ADCs) are increasingly used in the treatment of breast cancer due to their superior efficacy compared to conventional chemotherapy. The management of male breast cancer is largely extrapolated from clinical data in females and evidence regarding the efficacy of ADCs in men remains limited. This study aimed to compare survival outcomes between male and female breast cancer patients treated with ADCs across the spectrum of human epidermal growth factor receptor 2 (HER2) expression. Methods: We included total of 2,954 (Male: 34, Female: 2,920 breast cancer samples) from patients who underwent treatment with ADCs. We excluded patients with triple-negative breast cancer status due to the rarity of this subtype in males and the worse prognosis of triple-negative breast cancer, so that the cohorts would be more homogeneous without overrepresentation of triple-negative breast cancer in females. We categorized patients by HER2 status as: HER2-null (if there was 0% stain on HER2 IHC), HER2-ultra low (if HER2 IHC was 0 but with stain 1-10%), HER2-low (if HER2 IHC was 1+ or 2+ with a negative chromogenic in situ hybridization [CISH] assay), and HER2-positive (if HER2 IHC was 3+ or 2+ with a positive CISH assay). Real-world median overall survival was derived from insurance claims and calculated from the start of first ADC with either trastuzumab deruxtecan (T-DXd) or trastuzumab emtansine (T-DM1) or sacituzumab govitecan (SG) to last contact using Kaplan-Meier. Statistical significance was assessed using chi-square and Mann-Whitney U. Results: The distribution of sex by HER2 expression group was: HER2-null: 8 males vs 612 females; HER2-ultra low 6 males vs 467 females; HER2-low 11 males vs 903 females; HER2-positive 9 males vs 938 females. Median survival from treatment initiation with either T-DXd or SG in the HER2-null cohort was 21.31 months in males vs 15.72 months in females (HR 0.82, 95% CI 0.33 - 2.01, p=0.67); in the HER2-ultra low cohort was 17.73 months in males vs 14.47 months in females (HR 0.84, 95% CI 0.26 - 2.63, p=0.76); in the HER2-low cohort was 11.08 months in males vs 18.62 months in females (HR 1.53, 95% CI 0.63 - 3.7; p=0.34). In the HER2-positive cohort, 5/9 males (55.5%) and 544/938 females (58%) were treated with T-DXd. Median survival from treatment initiation with either T-DXd or T-DM1 in the HER2-positive cohort was 36.55 months in males vs 46.52 months in females (HR 1.77, 95% CI 0.84 - 3.74, p=0.12). Conclusions: In this study, survival appears to be comparable between males and females with breast cancer across the spectrum of HER2 expression when both are treated with ADCs, although the survival in the HER2-positive cohort appears numerically lower in males, consistent with data on HER2-positive MaBC. An important limitation is the small sample size of the male breast cancer cohorts, and the lack of a categorization of HER2 in HR+ vs HR-, for the small MaBC sample size. However, to our knowledge this is the first analysis evaluating outcomes of men treated with ADCs across the spectrum of HER2 expression. Citation Format: D. Trapani, S. Deshmukh, S. Wu, J. Xiu, N. Lin, G. Curigliano, P. Spanheimer, S. Gandhi, S. Chumsri, S. Graff, M. Lustberg, G. Sledge Jr, S. Tolaney, J. Leone. Comparative efficacy of antibody drug conjugates (ADCs) in male versus female breast cancer across the spectrum of HER2 expression [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS4-01-13.

Abstract Background: Hispanic/Latinx (HL) and African American (AA) breast cancer (BC) patients (pts) have increased prevalence of high-risk features such as incidence of BC at age <50 and estrogen receptor negativity. We previously showed that AA and HL had a lower fraction of neutrophils and M2 macrophages (Mɸ) despite higher percentage of PD-L1 positive cases. This study aims to further characterize differences in the tumor immune microenvironment between racial and ethnic groups, with a focus on how these differences vary by site of biopsy. Methods: We analyzed 19,459 BC samples tested by NGS (592, NextSeq; WES, NovaSeq) and WTS (NovaSeq; Caris Life Sciences). Race/ethnicity data were self-reported by pts. Immune cell proportions were estimated using WTS deconvolution (Quantiseq). Gene expression was analyzed for T-cell inflammed score (TIS), MAPK Activation Score (MPAS) and interferon-gamma (IFNy) score. Real-world overall survival (OS) data were derived from insurance claims, calculated from tissue collection or treatment initiation to last contact, and analyzed using Kaplan-Meier. Statistical significance was assessed by chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q<0.05). Results: There were 9674 Non-Hispanic Whites (NHW) (primary BC, defined as biopsy (bx) from breast) pBC: n=3,537, 36.6%; (metastatic BC, defined as biopsy outside of the breast) mBC: n=6,137 63.4%, 1800 AA (pBC: n=750, 42%, mBC: n=1,050, 58%), and 1795 HL (pBC: n=842, 47%; mBC n=953, 53%) samples. There were 2364 TNBC (66% NHW, 19% NHB, 15% HL), 4318 HR+/HER2- (76% NHW, 11.6% NHB, 12.4% HL), and 893 HER2+ (68% NHW, 15% NHB, 17% HL). In pBC overall, AA had lower median cell fraction (%) of B cells (4.8% vs 5.3%), M2 Mɸ (3.4% vs 4.4%), but higher median cell fraction of dendritic cells (DC) (2.8% vs 2.6%) compared to NHW while HL had lower median cell fraction of M2 Mɸ (3.9% vs 4.4%) and higher median cell fraction of CD8+ T cell (0.4% vs 0.2%), all q<0.05. In pBC, HL had higher IFNy score (-0.3 vs -0.34), while AA had lower MPAS (-1.2 vs -0.96), all q<0.05. In lymph node bx, AA had lower median % of M2 Mɸ (3.4% vs 4.4%, q<0.05). No significant differences were seen in the liver bx by race but notably there were lower median cell fractions of CD4+, CD8+, and regulatory T cells (0.0 across NHW, AA, HL) across all race/ethnicities vs. other biopsy sites. By subtype, TNBC primary bx yielded much of the significant changes with AA having lower median cell fraction of M2 Mɸ (2.49% vs 3.04%, q= 0.01) compared to NHW. In primary bx, AA (35.6 m vs 48.5 m, HR 1.4, 95% CI 1.2-1.5, p<0.001) and HL (42.4 m vs 48.5 m, HR 1.2, 95% CI 1.1-1.4, p<0.001) had worse median OS versus NHW. In lymph node bx, AA also had worse OS (29.2 m vs 37.2 m, HR 1.2, 95% CI 1-1.5, p=0.03) compared to NHW. In liver bx, there was worse mOS overall but no difference by race (NHW 18.65m, AA 18.79m, HL 20.6m, p =0.73). In HR+/HER2- liver bx AA had worse OS (14.2 m vs 20.9 m, HR 1.3, 95% CI 1-1.7, p=0.03) versus NHW. In HER2+ primary bx, HL had worse OS (43.2m vs 66.9m, HR 1.7, 95% CI 1.1-2.6, p=0.009). There was a trend towards worse mOS in TNBC AA patients receiving pembrolizumab (18.42m vs HL 23.69m vs NHW 35.30m; p=0.16) and HER2+ AA patients receiving trastuzumab deruxtecan (AA: 16.06m vs HL: 26.81m vs NHW: not reached; p = 0.05). Conclusions: We found race and biopsy site specific differences in the breast cancer immune microenvironment. AA pts had lower M2 Mɸ in primary and lymph node bx while NHW pts showed higher CD8+ T cell in primary tumors. Liver biopsies exhibited low T cell infiltration across all groups. AA pts had worse mOS in primary and lymph node bx compared to NHW but not in liver bx of which we saw worse mOS in all races. These results highlight the need to consider both race and bx site in treatment decisions. Citation Format: R. Hsu, S. Deshmukh, N. Gyabaah-Kessie, E. Rallos, B. Al-Zubeidy, E. Gonzalez, A. G. Baugh, S. Carrel, M. Li, D. Zavala, A. Martynova, P. Jayachandran, D. Stewart, D. Spicer, S. Wu, J. Xiu, G. W. Sledge Jr., R. L. Mahtani, A. C. Sandoval Leon, S. Gandhi, S. Chumsri, M. Lustberg, M. C. Stern, E. T. Roussos Torres. Immune microenvironment and survival differences among Hispanic and African American breast cancer cases by biopsy site [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PS3-12-06.

Abstract Background: Invasive lobular carcinoma (ILC) is the second most common breast cancer (BC) subtype, accounting for up to 15% of cases. Although several biologic differences between ILC and invasive carcinoma of no special type (NST) have been described, most data are derived from primary tumors. In contrast, the biology of metastatic ILC remains poorly defined. This study aimed to investigate the unique genomic, transcriptomic, and immune landscapes of metastatic ILC using a multi-omic approach. Methods: This real-world study included patients with confirmed NST or pure ILC who had a biopsy of a metastatic lesion or a breast lesion in the setting of known metastatic disease. Tumors underwent whole exome sequencing (NGS 592, NextSeq; WES, NovaSeq), whole transcriptome sequencing (WTS, NovaSeq) (Caris Life Sciences, Phoenix, AZ). Demographic and baseline molecular features were compared across histologic subtypes. Tumor mutational burden (TMB; high ≥10 mut/MB) was assessed by NGS. Immune cell populations were estimated by RNAseq deconvolution (quanTIseq). Pathway enrichment analysis was determined by GSEA. Overall survival (OS) was defined from the date of biopsy to death from any cause using Kaplan-Meier estimates. Statistical tests included chi-square and Mann-Whitney U with multiple testing correction (q<0.05). Results: Among 2,651 metastatic BC samples (ILC n = 608; NST n = 2,043), patients with ILC were older (median 67 vs 63 yrs) and more likely white (81.5% ILC vs 73.1% NST), all p<0.05. By IHC, ILC were more frequently HR+/HER2- (83.6% vs 55.9%), less commonly triple-negative (11.9% vs 29.8%) or HER2+ (4.6% vs 14.3%), all p<0.05. PAM50 subtypes differed between ILC and NST: luminal A (Lum A) (31.1% vs 13.7%) and luminal B (Lum B) (44.9% vs 43.8%) intrinsic subtypes were enriched in ILC, while NST was more frequently basal (1.2% vs 22.4%) and HER2-enriched (19.8% vs 22.2%), all p<0.05. Within luminal BC, Lum B was more common than Lum A in both histologies, but Lum A was proportionally more frequent in ILC (ILC: 40.3% Lum A vs 59.7% Lum B; NST: 23.4% Lum A vs 76.6% Lum B), p<0.0001. Comparative multi-omic analysis focused on the 922 HR+/HER2- tumors (ILC n = 275; NST n = 647). Compared to NST, ILC had higher frequency of CDH1 (87.3% vs 6.1%), PIK3CA (52.7% vs 38.5%), FOXA1 (9.0% vs 3.4%), ERBB2 (7.1% vs 2.0%), ARID1A, and NF1 (both q < 0.05) mutations and TMB high (17.7% vs 9.9%), but lower frequency of TP53 (15.7% vs 33.3%), ESR1 (10.9% vs 18.1%) and GATA3 (2.3% vs 14.9%) mutations along with FGFR1 amplifications (15.3% vs 6.7%), all q<0.05. ILC had higher expression of androgen receptor (91.2% vs 83.5%, q<0.05) and higher MAPK activation score (-0.81 vs -1.19, q<0.05), consistent with a luminal, hormone-driven phenotype. NST tumors demonstrated enrichment of pathways involved in the cell cycle and metabolic activity, including E2F targets, G2M checkpoint, MYC targets, mTORC1 signaling, glycolysis, and unfolded protein response (NES: 1.5-2.7, FDR<0.25). ILC tumors had higher infiltration of B cells, dendritic cells, neutrophils, NK cells and M2 macrophages, but lower M1 macrophages, all q<0.05. ILC had differential expression of immune checkpoint genes (upregulation: CD274 (PD-L1), PDCD1 (PD-1), TNFSF14, CEACAM1, CD160, fold change (FC): 1.2-1.5; down: HAVCR2 (TIM-3): FC: 1.2), all q<0.05. Median OS (mOS) was similar between luminal ILC and NST (33.8 vs 35.4 months (mo); HR 1.0, 95% CI 0.91-1.3). No mOS difference was seen between Lum A ILC and NST (47.4 vs 50.5 mo; HR 1.0, 0.84-1.43), while Lum B ILC had worse mOS than NST (27.4 vs 35.3 mo; HR 1.3, 1.1-1.6). Conclusions: This study represents the largest cohort to date with multi-omic characterization of metastatic ILC, revealing distinct genomic, transcriptomic, and immune features compared to NST. These findings highlight the unique biology of ILC and may inform future subtype-specific therapeutic strategies. Citation Format: G. Nader-Marta, S. Kumar Deshmukh, K. Fanucci, P. Tarantino, S. Schnitt, A. Lee, S. Oesterreich, S. Wu, J. Xiu, P. Advani, M. Lustberg, N. Lin, S. Tolaney, E. Mayer, O. Metzger, G. Sledge Jr., R. Jeselsohn. The Genomic, Transcriptomic, and Immune Hallmarks of Metastatic Lobular Breast Cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PD9-07.