Coelho, P. Barreto

1024 Background: Invasive lobular carcinoma (ILC) is a distinct breast cancer (BC) subtype with dissemination patterns differing from invasive breast carcinoma of no special type (IBC-NST). While genomic differences between ILC and IBC-NST have been described, the extent to which molecular and immune profiles vary by metastatic organ and histology is poorly characterized. Methods: We conducted a retrospective analysis to evaluate organ- and histology-specific molecular features of metastatic BC (mBC). Patients with metastatic IBC-NST or pure ILC underwent NGS (592, NextSeq; WES/WTS, NovaSeq; Caris Life Sciences). Tumor mutational burden (high ≥10 mut/Mb), PD-L1 expression (22C3), and immune cell fractions (RNAseq deconvolution, quanTIseq) were assessed. Analyses were restricted to sites with ≥10 biopsies per histology. Comparisons used chi-square or Mann–Whitney U tests with multiple testing correction (q < 0.05). Results: A total of 2645 mBC biopsies (605 ILC; 2040 IBC-NST) were analyzed (Table). In ILC, ERBB2 mut frequency differed by metastatic site (q<0.01), with higher prevalence in liver (32.7%) and lower in gastrointestinal (GI) lesions (3.7%). In IBC-NST, ESR1 and GATA3 mut and FGFR1 amplification were enriched in liver metastases, whereas PD-L1 expression was highest in skin (20.7%) and lowest in liver (5.0%). No organ-specific differences were observed for PIK3CA, AKT, PTEN, BRCA1/2 or RB1 . Across metastatic sites, both ILC and IBC-NST showed differences in B cells, macrophages (M1/M2), neutrophils, NK cells, dendritic cells, CD8+ T cells, and Tregs (all q < 0.05); CD4+ T-cell differences were observed only in IBC-NST (q = 0.002). In organ-specific ILC vs IBC-NST comparisons, CDH1 mut were more frequent in ILC across sites, along with higher PIK3CA mut in skin (ILC 51.3% vs IBC-NST 34.4%) and higher ERBB2 mut in liver (32.7% vs 3.3%), whereas a higher TP53 mut frequency was observed in IBC-NST in skin (28.5% vs 52.3%) and lymph nodes (LND) (23.5% vs 55.5%) (all q < 0.01). Conclusions: mBC exhibits marked organ-specific molecular and immune heterogeneity that differs by histology. These findings support histology- and site-aware interpretation of metastatic biopsies and may inform biomarker assessment and treatment decisions in advanced disease. BC-NST ILC Skin LND Bone Breast Liver Perit. CNS q-value Skin LND Bone Breast GI Liver GYN Perit. CNS q-value N (specimens) 785 401 109 361 220 15 44 - 172 84 62 56 56 54 43 37 11 - ERBB2 mut (%) 3.2 3.1 3.2 2.3 3.3 7.1 2.5 1.0 7.1 7.4 16.4 15.4 3.7 32.7 2.4 5.7 11.1 <0.01 ESR1 mut (%) 9.4 5.2 8.3 16.0 28.2 7.1 2.4 0.0 7.8 7.2 8.9 9.8 16.7 26.0 4.9 20.0 0.0 0.9 FGFR1 amp (%) 10.1 6.6 5.6 12.8 16.5 0.0 9.7 0.02 4.4 3.4 6.7 6.1 2.4 5.6 7.7 18.5 0.0 1.0 IHC-PD-L1 (%) 20.7 - 5.3 16.0 5.0 11.1 10.3 0.02 8.9 - 5.0 5.7 6.1 0.0 0.0 0.0 14.3 1.0 TMB-High (%) 10.7 10.1 8.8 8.8 8.5 14.3 21.4 0.8 27.6 11.0 19.6 28.0 11.3 19.6 9.8 32.4 22.2 0.8 Perit: peritoneum; CNS: central nervous system; GYN: genital tract.

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&lt;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&lt;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&lt;0.05). Immune profiling revealed reduced infiltration of M2 macrophages (4.3% vs. 6%, p&lt;0.05) and neutrophil (2.2% vs. 6.9%, p&lt;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&lt;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&lt;0.05) and lymph node (6% vs. 4.5%, p&lt;0.05). Neutrophil infiltration was elevated in bone versus liver (6.9% vs. 2%, p&lt;0.05) but T regulatory cells were lower in bone compared to lymph nodes (1% vs. 2.4%, p&lt;0.05). Bone showed reduced expression of CD47 (median TPM 50.6 vs. 109.9, p&lt;0.05) compared to skin. Further bone had lower IFN-gamma scores (-0.41 vs. -0.17, p&lt;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.