Xiu, Joanne

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.

PURPOSE Homologous recombination deficiency (HRD) is a key determinant of sensitivity to DNA-damaging agents; however, its genomic characterization in colorectal cancer (CRC) remains limited. This study investigated whether low RNA expression of homologous recombination (HR) genes identifies patients with metastatic CRC who derive survival benefit from oxaliplatin- or irinotecan-based therapy. METHODS A total of 22,957 metastatic CRC samples were subjected to DNA and RNA sequencing (Caris Life Sciences, Dallas, TX). Patients with microsatellite instability–high or pathogenic HR gene mutations were excluded to define a HR-proficient cohort. Overall survival (OS) was compared between patients with low (bottom 25%) versus high (top 25%) RNA expression of HR genes after oxaliplatin or irinotecan exposure. Validation was performed in the PARADIGM phase III trial cohort (n = 262) of first-line modified fluorouracil, leucovorin, and oxaliplatin-treated patients with available RNAseq data. RESULTS In the discovery cohort, low expression of core HR genes correlated with significantly longer OS after oxaliplatin or irinotecan exposure, specifically RAD51 (43.0 v 36.3 months; P < .005) and BLM (42.9 v 34.2 months; P < .005). Similar associations were observed for RAD51 (28.1 v 22.9 months; P = .02) and BLM (29.1 v 23.2 months; P < .005) in irinotecan-treated patients. In the PARADIGM validation cohort, low BLM expression was associated with improved OS (41.5 v 22.4 months; HR = 0.52; P = .002), whereas RAD51 showed a favorable but nonsignificant trend. These findings remained significant after adjustment for treatment arm, tumor sidedness, and metastatic burden. CONCLUSION Low BLM RNA expression is associated with improved survival after treatment with DNA-damaging agents, whereas low RAD51 expression shows a favorable but nonsignificant trend. These findings are exploratory and suggest that RNA-based HR gene expression may warrant further investigation as a potential prognostic biomarker in metastatic CRC.

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 &gt;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&lt;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&lt;0.05. Moderate correlations were observed between PD-L1 CPS and each chemokine (r = 0.41, p&lt;.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&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.

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&lt;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&lt;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&lt;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&lt;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&lt;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&lt;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: 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 &lt;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&lt;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&lt;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&lt;0.05. In lymph node bx, AA had lower median % of M2 Mɸ (3.4% vs 4.4%, q&lt;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&lt;0.001) and HL (42.4 m vs 48.5 m, HR 1.2, 95% CI 1.1-1.4, p&lt;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&lt;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&lt;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&lt;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&lt;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&lt;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 &lt; 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&lt;0.05. ILC had higher expression of androgen receptor (91.2% vs 83.5%, q&lt;0.05) and higher MAPK activation score (-0.81 vs -1.19, q&lt;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&lt;0.25). ILC tumors had higher infiltration of B cells, dendritic cells, neutrophils, NK cells and M2 macrophages, but lower M1 macrophages, all q&lt;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&lt;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.

1114 Background: While treatment and management of TNBC has improved, there is a need for novel prognostic biomarkers to better inform outcomes and guide therapeutic options. ILF2 is a poorly characterized protein with pleiotropic functions that is highly expressed in TNBC. Here we evaluated the associations of ILF2 with 1) genomic and transcriptomic data, 2) tumor microenvironment (TME), and 3) clinical outcomes in TNBC. Methods: 15,544 breast cancer (BC) samples, including 3,038 TNBC, were tested by NGS (592, NextSeq; WES, NovaSeq) and WTS (NovaSeq; Caris Life Sciences, Phoenix, AZ). ILF2 -high (H) and ILF2 -low(L) TNBC were defined by respective quartiles. Immune cell fractions were estimated by WTS deconvolution (Quantiseq). Real world overall survival (OS) was obtained from insurance claims and calculated from tissue collection to last contact using Kaplan-Meier estimates. Statistical significance was determined by chi-square, Fisher’s exact, and Mann-Whitney U test with p-values adjustments (q < .05). Results: ILF2 expression (median Log2(TPM+1) was higher (all q < .05) in key subgroups: ductal compared to lobular carcinoma (6.4 vs 6.0); primary compared to metastatic BC (6.4 vs 6.3); African American compared to White (6.4 vs 6.3); basal compared to luminal A, luminal B, HER2 PAM50 subtypes (6.9 vs 5.8, 6.3, 6.3); and TNBC compared to HR+HER2+, HR-HER2+, HR+HER2- subtypes (6.7 vs 6.3, 6.4, 6.2). Biopsied tissues from primary TNBC (pTNBC) and metastatic TNBC (mTNBC) patients were stratified into ILF2- H and ILF2- L groups. In both mTNBC and pTNBC, ILF2- H groups had 1) higher percentage of young patients (age < 50) (pTNBC: 35.5% vs 19.8%; mTNBC: 28.1% vs 17.3%; all q < .05); 2) higher mutation frequency of TP53 (pTNBC: 94.5% vs 79.6%; mTNBC: 92.4% vs 74.4%), but lower frequencies for PIK3CA ( pTNBC: 5.1% vs 23.4% , mTNBC: 8.8% vs 27.4%), CDH1 ( pTNBC: 0.8% vs 6.1%; mTNBC: 2.8% vs 12.2%; all q < .05); 3) higher infiltration of NK cells (pTNBC: 3% vs 2.6%; mTNBC: 2.8% vs 2.6%), but lower infiltration of M2 Mφ (pTNBC: 2.5% vs 3.3%; mTNBC: 2.6% vs 3.2%) and Tregs (pTNBC: 1.5% vs 1.9%; mTNBC: 1.4% vs 1.7%; all q < .05); 4) higher expression levels of immune checkpoint ( CD274, PDCD1LG2, CTLA4, LAG3, HAVCR2, FOXP3, IDO1, CD276 , FC: 1.2-3.1; all q < .05), stem cell genes (C D44, NANOG, POU5F1, KLF4, ALDH1A1 , FC: 1.4-2.4; all q < .05), and drug efflux genes ( ABCC3, ABCC11, ABCC2, ABCB1, ABCG2, ABCC1 , FC: 1.1-4.5; all q < .05) compared to ILF2- L group. In pTNBC, ILF2- H had significantly shorter OS vs ILF2- L group (22.3 vs 28.9 months, HR 1.2 [95% CI 1-1.5], p = .03), but no significant differences were observed between mTNBC ILF2 groups (HR 1.1 [95% CI 0.93-1.3], p = .2). Conclusions: ILF2 -H TNBC patients showed differential genomic and transcriptomic alterations that relate to therapy resistance, immune suppressive TME, and shorter OS. Further studies are warranted to validate the effects of ILF2 upregulation on therapeutic efficacy.

1107 Background: Chronic stress-mediated β2-adrenergic receptor (β2-AR) signaling promotes tumor growth via immunosuppression in the tumor microenvironment (TME) in preclinical models. Blockade of β2-AR has shown higher survival benefit in patients with TNBC in observational studies compared to other breast cancer (BC) subtypes. However, the molecular and immunological features associated with ADRB2 (gene for β2-AR) gene expression in TNBC are unknown, prompting this investigation. Methods: 3,038 TNBC samples were analyzed via NGS (592-gene panel, NextSeq; WES/WTS, NovaSeq; Caris Life Sciences, Phoenix, AZ). Immune cell fractions were calculated by deconvolution of WTS: Quantiseq. TNBC ADRB2 -high(H) and ADRB2 -low(L) RNA expression were classified as above or below the 50 th percentile, respectively. Real-world overall survival (OS) was obtained from insurance claims and calculated from tissue collection to last contact using Kaplan-Meier estimates. Statistical significance was assessed using chi-square and Mann-Whitney U tests with multiple comparison adjustments (q < 0.05). Results: ADRB2 gene expression was lowest in TNBC (median (TPM: 1.6) compared to N = 453 HR-HER2+ (1.9), N = 629 HR+HER2+ (2.0) and N = 4,918 HR+HER2- (2.2) BC (all q < 0.05). African American or Black patients (N = 670) had lower expression of ADRB2 compared to European American or White (N = 1,412) TNBC patients (1.3 vs 1.7, q < 0.05). ADRB2 -H TNBC had higher mutation frequency of PIK3CA (21% vs 15.4%), CDH1 (7% vs 3.5%), NF1 (8% vs 4%), AKT1 (3.5% vs 2.1%), but lower frequency of TP53 (81.6% vs 87.5%), NOTCH1 (2.5% vs 4.5%) and NOTCH3 (4.4% vs 11.7%) compared to ADRB2 -L, all q < 0.05. ADRB2 -H had greater PD-L1 (22C3) positivity (39.1% vs 30.2%, q < 0.05), higher % of B cells (4.5 vs 3.4), M1 Mφ (3.4 vs 2.8), M2 Mφ (3.9 vs 2.2), Tregs (2.2 vs 1.3), NK cells (3.1 vs 2.6), DC (3.1 vs 2.9), CD8 + T cells (0.9 vs 0.2), all q < 0.05. ADRB2 -H TNBC had higher T-cell inflamed score (95 vs -80), IFN γ score (-0.23 vs -0.37), MAPK activation score (-0.46 vs -1.7), all q < 0.05; and higher expression of immune checkpoint genes ( CD274, PDCD1, PDCD1LG2, CTLA4, LAG3, HAVCR2, FOXP3, IDO1, TNFSF14, TIGIT, BTLA, CEACAM1, CD47, CD274 ; fold change: 1.6-3.7, all q < 0.05). ADRB2 -H tumors had higher expression of genes related to inflammatory response, IFNγ response, IL6-JAK-STAT3 signaling (normalized enrichment score (NES): 1.9 – 2.1), while ADRB2 -L had enrichment of MYC targets V1, MYC targets V2, E2F targets and G2M checkpoint (NES: 2.5 – 4.2), all FDR < 0.01. ADRB2 -H TNBC had better OS (mOS: 23.6 vs 18.6 months; HR 0.81, 95% CI 0.73-0.89, p < 0.0001) compared to ADRB2 -L. Conclusions: High ADRB2 expression in TNBC is associated with better survival and an immune enriched TME, elevated immune checkpoints and other targetable vulnerabilities. Future studies are needed to investigate ADRB2 as a potential stress biomarker and therapeutic target.

1106 Background: TNBC, although an aggressive breast cancer (BC) subtype, is highly immunogenic and the only BC subtype where the ICI pembrolizumab is approved. However, predictive biomarkers for pembrolizumab benefit are limited. The chemokines CXCL9 and CXCL10 attract CD8 + T cells into the tumor microenvironment (TME) and are associated with chemotherapy benefit, but little is known about their role in prediciting pembrolizumab benefit in TNBC. We investigated the association of CXCL9 , CXCL10 and their cognate receptor CXCR3 with TME and ICI efficacy. Methods: 3,038 TNBC samples were analyzed via NGS (592-gene panel, NextSeq; WES/WTS, NovaSeq; Caris Life Sciences, Phoenix, AZ). Tumor mutational burden (TMB) totaled somatic mutations per tumor (high > 10 mt/MB). Immune cell fractions were estimated using WTS deconvolution (Quantiseq). CXCL9 / CXCL10 / CXCR3 -high (H) and -low (L) tumors were classified by RNA expression above or below the 50th percentile. Real-world overall survival (OS) was derived from insurance claims and calculated from start of pembrolizumab to last contact using Kaplan-Meier. Statistical significance was assessed using chi-square and Mann-Whitney U with multiple comparison adjustments (q < .05). Results: TNBC expressed higher levels of CXCL9 and CXCL10 (median (TPM): 5.3 and 14.7) compared to N = 1,082 HER2+ (4.8 and 10.3, p < 0.05) and N = 4,918 HR+HER2- (2.7 and 7, q < .05) BC. CXCR3 expression was higher in TNBC compared to HR+HER2- (1.9 vs 1.7, q < .05), but no difference when compared to HER2+ (1.9 vs 2, q = 0.97) BC. CXCL9 / CXCL10 / CXCR3 -H TNBC had higher median OS post pembrolizumab [ CXCL9 -H vs -L: 26.5 vs 15.7 months (mo), HR: 0.65 (95% CI 0.5-0.84); CXCL10 -H vs -L: 26.0 vs 20.6 mo, HR 0.74 (0.57-0.95); CXCR3 -H vs -L: 32.6 vs 18.3 mo, HR 0.68 (0.52-0.88), all p < 0.05 ]. CXCL9 -H, CXCL10 -H and CXCR3 -H had higher PD-L1 positivity (22C3), TMB high, higher T cell inflamed score, TP53 mutations, elevated B and CD8 + T cells infiltration, but not neutrophils, and higher expression of immune checkpoint genes (Table). Conclusions: High CXCL9 / CXCL10 / CXCR3 expression is associated with longer survival in patients with TNBC post pembrolizumab, and characterized by an immune-enriched TME. Further investigation is needed to evaluate this chemokine axis in TNBC and its potential as a therapeutic target to enhance ICI efficacy. TME characteristics by CXCL9, CXCL10 and CXCR3 expression. CXCL9 CXCL10 CXCR3 High Low q-value High Low q-value High Low q-value PD-L1 % 54 14 <.05 54 14.7 <.05 49 19 <.05 TMB high % 14.3 8 <.05 12.6 9.7 <.05 12.4 9.8 <.05 B cell (median %) 4.4 3.5 <.05 4.3 3.6 <.05 5 3.4 <.05 CD8+T cell (median %) 1.2 0 <.05 1 0 <.05 1.3 0 <.05 Neutrophil (median %) 4.2 4.5 <.05 4.2 4.4 <.05 4.2 4.3 0.2 T cell inflamed score 100 -84 <.05 98 -84 <.05 108 -100 <.05 CTLA4 (median TPM) 3.2 0.7 <.05 3 0.8 <.05 3.4 0.7 <.05 LAG3 (median TPM) 6.6 2.1 <.05 6.9 2 <.05 6.8 2 <.05 TP53 mutation % 88 81 <.05 90.5 78.6 <.05 86 83 0.08