Wu, Sharon

564 Background: HER2+ ILC is rare (~5% of ILC), with limited data on long-term adjuvant trastuzumab outcomes. We investigated late recurrence and immune landscapes of HER2+ ILC vs invasive ductal carcinoma (IDC) in the phase III NCCTG N9831 trial (NCT00005970) and a real-world cohort. Methods: We evaluated 3304 early-stage HER2+ breast cancer patients (pts) enrolled in N9831 (122 ILC, 3182 IDC). Recurrence-free survival (RFS) and overall survival (OS) were estimated (Kaplan-Meier) and compared using multivariable Cox regression adjusting for age, tumor size, grade, hormone receptor (HR), and nodal status. Findings were validated in a real-world cohort of HER2+ pts (Caris Life Sciences CODEai platform). Immune microenvironments were profiled by WTS deconvolution (Quantiseq). Real-world overall survival was calculated from trastuzumab start to last contact. Results: In N9831, ILC pts were older (median 54 vs 49 y), more ER+ (74.6% vs 51.4%), and had more N3 disease (25.4% vs 12.7%) compared to IDC. ILC pts derived a comparable magnitude of benefit from adjuvant trastuzumab compared to the overall population (HR 0.58 vs 0.67). However, long-term outcomes diverged: while the 5-year RFS was similar (77.1% vs 82.7%), ILC pts experienced a steep decline between years 5-15 (77.1% to 57.7%; ~20% decline) vs IDC (82.7% to 72.7%; ~10% decline) after multivariable Cox analysis (Table). In the real-world early/advanced cohort (n=1328; 26 ILC vs 1302 non-ILC [subset IDC n=595]) treated with trastuzumab-based therapy, ILC pts had worse mOS (33.7 vs 68.6 m, HR 2.01, 95%CI 1.00-4.07, p=0.04) compared to non-ILC. However, there was no statistically significant difference when compared specifically to IDC (HR 1.77, 95% CI 0.87-3.61, p=0.11). ILC had: i) numerically lower tumor mutation burden (TMB)-high (4.2% vs 9.5%, p=0.38); ii) higher infiltration of B cells, Tregs, and M2 macrophages (p<0.05); iii) upregulated MHC class II expression (HLA-DOA, p<0.05); and iv) downregulated proliferative and DNA repair pathways (E2F, G2M, MYC; FDR <0.25) compared to non-ILC. Conclusions: HER2+ ILC carries late recurrence risk despite initial trastuzumab benefit. The unique immune landscape (Treg/M2 macrophage enrichment and lower proliferative signatures) distinguishes HER2+ ILC from IDC, highlighting the need for tailored strategies. Long-term RFS and OS in HER2-positive ILC vs IDC (N9831 trial). Population N 5-year% (95% CI) 10-year% (95% CI) 15-year% (95% CI) ILC 122 RFS 77.13% (69.9, 85.1) OS 84.04% (77.7, 90.9) RFS 70.57% (62.7, 79.4) OS 76.0% (68.7, 84.2) RFS 57.67% (44.2, 75.1) OS 65.22% (56.6, 75.2) IDC 3182 RFS 82.71% (81.4, 84.1) OS 90.18% (89.1, 91.2) RFS 77.45% (75.9, 78.9) OS 81.81% (80.4, 83.2) RFS 72.68% (70.77, 74.6) OS 76.68% (75, 78.4)

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.

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

1098 Background: Leucine-rich repeat-containing protein 15 ( LRRC15) has emerged as a potential biomarker and therapeutic target for various cancers due to its high expression in cancer-associated fibroblasts (CAFs) and role in tumor progression. High LRRC15 expression is associated with poor prognosis in TNBC. This study aims to define the multiomic profile of LRRC15 in TNBC. Methods: 3,038 TNBC samples were analyzed via Next-Generation Sequencing (592, NextSeq; Whole Exome Sequencing, NovaSeq) and Whole Transcriptome Sequencing (NovaSeq; Caris Life Sciences, AZ). Immune cell fractions were estimated using WTS deconvolution (Quantiseq). Stromal cell abundance in the tumor microenvironment (TME) was estimated from RNA expression profiles using MCP Counter. LRRC15 -high (H) and -low (L) tumors were classified by RNA expression above or below the 25th percentile. Real-world overall survival (OS) and treatment-related survival were derived from insurance claims and calculated from tissue collection or treatment initiation to last contact using Kaplan-Meier. Statistical significance was assessed using chi-square and Mann-Whitney U tests with multiple comparison adjustments (q < .05). Results: LRRC15 -H TNBC tumors had higher frequency of PIK3CA (25.9% vs 16.8), PIK3R1 (6.2% vs 1.6%), PTEN (11.3% vs 5.8%), but lower frequency of RB1 (7.8% vs 12.1%) and KMT2D (2% vs 4.4%) compared to LRRC15 -L, all q < 0.05. LRRC15 -H had higher PD-L1 positivity (32.3% vs 24.5%, q < 0.05). Analysis of immune cells showed LRRC15 -H TNBC had higher infiltration of B cells (4.2% vs 3.5%), M1 macrophages (4.3% vs 2%), M2 macrophages (4% vs 2.5%), Tregs (1.9% vs 1.1%), neutrophils (4.9% vs 3.9%), CD8 + T cells (0.4% vs 0.1%), but lower dendritic cells (2.5% vs 3%), all q < 0.05. LRRC15 -H tumors had greater abundance of CAFs (575.6 vs 93.78, 6.14 fold change (FC)) and endothelial cells (7.3 vs 3.7, 1.97 FC), all q < 0.05. LRRC15 -H had higher T-cell inflamed score (71.5 vs -77) and IFNg score (-0.14 vs -1.72), all q < 0.05. LRRC15 -H tumors had higher expression of immune checkpoint genes ( CD274, PDCD1, PDCD1LG2, CTLA4, LAG3, HAVCR2, FOXP3, IDO1, TNFSF14, TIGIT, BTLA, CEACAM1, CD47, CD80, CD86, CD160, CD274 ; FC 1.2-2.5, q < 0.05). LRRC15 -H was associated with better OS (mOS: 24.7 vs 13.6 months; HR 0.61, 95% CI 0.53-0.7, p < 0.001). Post-pembrolizumab survival was longer for LRRC15 -H patients (mOS: 27.2 vs 19.4 months; HR 0.61, 95% CI 0.42-0.89, p = 0.01). Conclusions: LRRC15 -H TNBC exhibited better outcomes with pembrolizumab, likely due to higher immune cell fractions and increased CAFs. These findings highlight TNBC heterogeneity and position LRRC15 as a potential biomarker for tumor stratification, a possible adverse prognostic biomarker and a positive predictive biomarker. Ongoing phase I trials targeting LRRC15 show promise. Combining LRRC15 -targeted therapies with immunotherapy may improve TNBC outcomes, warranting further validation in breast cancer models.

1051 Background: Hispanics or Latinos (HL) and African Americans or Black (AA) have a higher prevalence of advanced-stage breast cancer (BC) at diagnosis compared to Non-Hispanic Whites (NHW). To understand the role of immune system, we evaluated the tumor immune microenvironment (TIME) by race/ethnicity among HL, AA, and NHW BC patients. Methods: 15544BC samples were tested by NGS (592, NextSeq; WES, NovaSeq) and WTS (NovaSeq; Caris Life Sciences, Phoenix, AZ). Race/ethnicity data is self-reported. Immune cell were estimated using WTS deconvolution (Quantiseq). Gene expression profiles were analyzed for T-cell inflammation score (TIS) and interferon-gamma (IFN-gamma) score. Real-world overall survival (OS) was obtained from insurance claims and calculated from date of tumor biopsy to last contact using Kaplan-Meier estimates. Statistical significance was determined by chi-square and Mann-Whitney U test with p -values adjusted for multiple comparisons (q < .05). Results: 7170 NHW (35.3%, N = 2528) biopsied (bx) from primary breast cancer (pBC), 64.7% (N = 4642) metastatic bx (mBC), 1,508 AA (pBC 39.3% N = 592, mBC 60.7% N = 916), and 1,754 HL (pBC 44.1% N = 774, mBC 55.9% N = 980) cases were included. By subtype, there were 1,956 (60.4% NHW, 20.7% NHB, 18.9% HL) TNBC, 3425 HR+/HER2- (72.6% NHW, 11.9% NHB, 15.6% HL), and 694 HER2+ (64.6% NHW, 15.7% NHB, 19.7% HL). Across all cases, AA (20.5%) and HL (20.4%) had greater incidence (%) of PD-L1+ cases versus (vs) NHW (17.4%), all q < .05. TMB-High (³10 mut/Mb) was similar in NHW (11.5%), AA (10.8%), and HL (10.9%). AA tumors had lower median % cell infiltration of M2-like macrophages (M2 Mφ), B cells, and neutrophils vs NHW (Table). HL had a lower fraction of M2 Mφ and higher CD8+ T cells (Table). AA had lower TIS (-8 vs 1, p = .02) while HL had lower IFN-gamma (-0.38 vs. -0.35, q < .05) vs NHW. By subtype, AA had lower neutrophils (4% vs 4.3%) and increased DC fractions (3.1% vs 2.8%) in TNBC vs NHW, all q < .05; no significant changes seen in HL vs NHW. AA had worse mOS than NHW overall (31.8 vs 36.8 months (mo)), HR 1.1, 95% CI 1 – 1.2, p = < .01), in pBC (40.3 vs 49.9 mo, HR 1.3, 95% CI 1.1 – 1.5, p = < .01), but not mBC (27.4 vs 29.1 mo, HR 1, p = 0.2). HL had similar mOS vs NHW overall (37.4 vs 36.8 mo, HR 0.9, p = 0.9) and in mBC (29.1 vs 31 mo, HR 0.96, p = 0.4), but worse mOS in pBC (44.7 vs 50.0 mo, HR 1.1, 95% CI 1 – 1.3, p = .01). Conclusions: Our study shows worse mOS in AA and HL pBC cases vs NHW, possibly from a less inflamed TIME in AA and HL and lower fraction of neutrophils and M2 Mφ despite higher % of PD-L1+. Targeting Mφ and CD8+ T cells and converting cold to hot TIME may lessen race/ethnic disparities, especially in early-stage BC. Immune cell fraction of NHW, AA and HL BC. NHW (median %) AA (median %) HL (median %) q-valueNHW vs AA q-value NHW vs HL B cell 5.2 4.8 5.0 <.05 0.7 DC 2.6 2.7 2.6 0.08 0.4 M1 Mφ 2.5 2.4 2.4 0.4 0.9 M2 Mφ 4.6 3.7 4.2 <.05 <.05 Neutrophils 3.7 3.5 3.4 <.05 <.05 NK cell 2.9 2.9 2.9 0.7 0.6 CD8+ T cell 0.1 0.15 0.26 0.8 <.05 Treg 1.5 1.5 1.6 0.6 <.05

570 Background: Major histocompatibility complex class I (MHC I) plays a critical role in immune surveillance by binding peptides derived from intracellular proteins and presenting them on the cell surface for recognition by CD8+ T cells. Loss or downregulation of MHC I expression has been identified as a key mechanism of immune evasion in cancers. Here, we evaluated MHC I expression and outcomes in all subtypes of breast cancer (BC). Methods: 9,038 BC samples were analyzed via NGS (592-gene panel, NextSeq; WES/WTS, NovaSeq; Caris Life Sciences, Phoenix, AZ), including triple-negative BC (TNBC) 3,038, HER2-positive (HER2+) 1,082, and hormone receptor-positive (HR+HER2-) 4,918. Immune cell fractions were estimated using WTS deconvolution (Quantiseq). MHC I ( HLA-A / HLA-B / HLA-C )-high (H) and -low (L) were classified by RNA expression above or below the 25th percentile. Real-world overall survival (OS) was derived from insurance claims and calculated from tissue collection to last contact using Kaplan-Meier. NanoString IO360 was performed in 114 samples from the FinXX trial (NCT00114816). Statistical significance was assessed using chi-square, Mann-Whitney U, ANOVA, and Cox regression with multiple comparison adjustments (q<.05). Results: TNBC had higher expression of HLA-A and HLA-B (median TPM: 169 and 191) compared to HER2+ (146.6 and 170, q<0.05) and HR+HER2- (141.7 and 157.5, q<0.05). However, there was no significant difference in HLA-C expression across 3 BC subtypes. In TNBC, MHC I-H tumors had higher frequencies of PD-L1 positivity (66.2% vs. 13.1%) as well as higher infiltration of B cells (4.5% vs. 3.2%), M1 macrophages (5% vs. 1.5%), M2 macrophages (4% vs. 2.1%), Tregs (2.8% vs. 0.8%), CD8 + T cells (1.8% vs. 0%), dendritic cells (3.2% vs. 2.8%), higher T-cell inflamed score (137 vs. -144), and IFN g score (0.02 vs. -0.49) compared to MHC I-L TNBC (all q<.05). MHC I-H TNBC was associated with significant improvement in median OS (30.1 vs. 15.2 months, HR 0.55, 95% CI 0.46-0.65, p<0.0001). However, this survival difference was not observed in patients with MHC I-H vs. MHC I-L in HER2+ (HR 1.04, 95% CI 0.74-1.47, p = 0.81) and HR+HER2- (HR 0.87, 95% CI 0.75-1.02, p= 0.09) BC subtypes. We further validated the MHC I expression in the FinXX trial. Similarly, patients with MHC I-H had significant improvement in recurrence-free survival (HR 0.27, 95%CI 0.11-0.66, p = 0.002) and OS (HR 0.23, 95% CI 0.09-0.57, p = 0.0005) compared to MHC I-L. Conclusions: Our findings demonstrate that higher MHC I expression is associated with higher immune infiltration and improved outcomes in TNBC but not in HER2+ or HR+HER2- BC subtypes. These results suggest that MHC I expression plays a critical role in the tumor microenvironment of TNBC. Future studies are needed to evaluate the prognostic value and potential therapeutic target of MHC I in TNBC. Support: Breast Cancer Research Foundation, Bankhead Coley, W81XWH-18-1-0564. Clinical trial information: NCT00114816 .

4166 Background: GN is a front-line therapy for aPDAC. A Phase I/II study demonstrated that GCN has a higher overall response rate and median overall survival (mOS). Our previous study found no difference in outcomes among patients with DNA damage repair gene mutations; however, stromal gene expression correlated with mOS in patients receiving GCN. Here, we further evaluate differences in the outcomes with GCN and GN by site of biopsy. Methods: PDAC samples (n = 4,463) were analyzed by NGS (NextSeq/NovaSeq) or RNA (NovaSeq) (Caris Life Sciences, Phx, AZ). Expression of stromal and related genes ( ACTA2, ADIRF, HAS2, IL-6, MMP-2, MMP-9, SPARC, STAT3, TBGB1, TGFB2, TGFBR3, IDO1, HLA-DRB4, VEGFB) from different biopsy sites [high expression (H) >50% of RNA transcripts per million] was correlated with outcomes to GCN or GN. mOS was obtained from insurance claims and calculated from first treatment to last contact. The hazard ratio (HR) was calculated by the Cox proportional hazards model, and p-values were calculated using the log-rank test. Results: 4325 patients [primary biopsy (PT), n = 1,878; non-liver metastatic biopsy (N-LM), n = 818; Liver biopsy (LM), n = 1,629] received GN while 138 patients (PT, n = 45; N-LM, n = 28; LM, n = 65) received GCN. GCN was associated with longer mOS than GN [∆: 5.2 months (m), HR: 0.76, 95% CI 0.63-0.92, p = 0.01]. GCN was associated with longer mOS compared to GN in LM (∆: 5.6 m, HR: 0.66, 95% CI 0.50-0.87, p = 0.003), but it was not significant in PT (∆: 4.6 m, p = 0.13) and N-LM (∆: 4.4 m, p = 0.35). Median MMP2 (38.5 vs. 163.1 vs. 162.2), VEGFB (14.4 vs. 16.9 vs. 16.2) and TGFBR3 (11.4 vs. 15 vs. 16.4) expression were lower in LM compared to PT and N-LM while TGFB1 (41.6 vs. 34.5 vs. 39.8) and IL6 (1.61 vs. 1.19 vs. 1.41) expression were highest in LM (p < 0.05). In LM, IL6 -H (∆: -11 m, p = 0.037) and TGFB1 -H (∆: -5.9 m, p = 0.10) were associated with worse post-GCN survival compared to GN (p = 0.82 and p = 0.57). Whereas, in N-LM, TGFBR3 -H trended towards longer post-GCN survival (∆: 12 m, p = 0.18), while ADIRF -H trended towards shorter post-GCN survival (∆: -12 m, p = 0.056) compared to GN (p = 0.42 and p = 0.10). While in PT, MMP2 -H (∆: 11.3m, HR: 0.46, p = 0.16), TGFB1 -H (∆: 11.3 m, HR: 0.33, p = 0.09), HLA-DRB4 -H (∆: 12.9 m, HR: 0.44, p = 0.11) and VEGFB -H (∆: 10.7, HR: 0.34, p = 0.09) trended towards longer post-GCN survival compared to GN ( MMP2 -H, ∆: 3.4 m, p = 0.03, TGFB1 -H, p = 0.661, HLA-DRB4 -H, p = 0.67, VEGFB-H , ∆: 1.3 m, p = 0.03). Conclusions: GCN is associated with improved mOS compared to GN, especially in LM.Stromal gene expression in the liver differs from that in N-LM and the pancreas. While high stromal gene expression trends towards worse post-GCN survival in LM, it is associated with improved survival in N-LM and PT. Further validation is needed to understand the impact of stromal gene expression in different tumor sites on survival outcomes and signature development.

Abstract Background: Hispanic American (HA) men with prostate cancer (PC) are more likely to have more aggressive and advanced diseases and greater mortality rates compared to non-Hispanic white (NHW) men. Resistance to the current anticancer therapy is the major hurdle that leads to poor clinical outcomes. Hedgehog, Notch, and Wnt signaling pathways play a crucial role in development, progression, and resistance to the various anticancer therapies. Here, we characterized the enrichment of Hedgehog, Notch, and Wnt signaling pathways and molecular tumors differences between HA and NHW patients. Methods: Our data consist of 88 PC tumors samples (HA=34, NHW=54) obtained from treatment-naive metastatic hormone-sensitive prostate cancer (mHSPC) that were analyzed by next-generation sequencing (592, NextSeq; Whole Exome Sequencing, NovaSeq) and Whole Transcriptome Sequencing (WTS; NovaSeq) (Caris Life Sciences, Phoenix, AZ). Pathway enrichment was determined by Gene Set Enrichment Analysis (GSEA, Broad Institute) by measurable TPM (transcripts per kilobase million). The medical records were reviewed in a deidentified fashion for clinical features. Statistical significance was determined using chi-square and Mann-Whitney U (p&lt;0.05). Results: HA PC had enrichment of Hedgehog signaling (NES: 1.45, FDR=0.04), Notch signaling (NES: 1.41, FDR=0.07), and Wnt/β-catenin signaling (NES: 1.38, FDR=0.11) pathways compared to NHW tumors. HA tumors had higher expression of genes (HES1, Notch1, WNT1, WNT2; FC:1.1-2.5) associated with crosstalk between Hedgehog, Notch, and Wnt/β- catenin signaling pathways (all p&lt;0.05). Moreover, HA tumors had higher expression of stemness (ALDH1A2, ALDH1A1, PROM1; FC: 1.7-3.0), drug efflux (ABCC1, ABCB1; FC: 1.1- 1.5), epithelial to mesenchymal transition (EMT) (TWIST1, MMP2; FC: 1.1-1.5), cell cycle (CCND2; FC: 1.2), inhibition of apoptosis (BIRC2, XIAP; FC: 1.1) and epigenetic (EP300, TET1, TET2; FC: 1.3-1.4) related genes compared to NHW tumors (all p&lt;0.05). HA PC had higher frequency of Hedgehog and Wnt/β-catenin associated SPOP (16% vs 6.6%, p=0.2) and CTNNB1 (12% vs 2.2%, p=0.1) mutation compared to NHW PC. Conclusion: These results demonstrate that tumors from HA patients had enrichment of oncogenic Hedgehog, Notch, and Wnt/β-catenin signaling pathways, higher expression of stemness, drug efflux, EMT, cell cycle, inhibition of apoptosis and epigenetic-related genes, and mutations directly involved in activating the Hedgehog and Wnt/β-catenin signaling pathways. Together, these findings suggest that tumors from HA patients are enriched for gene signatures that promote cancer progression and therapy resistance. Additional research on collaboration and crosstalk between Hedgehog, Notch, and Wnt/β-catenin signaling pathways may help in designing better therapeutic strategies for HA men with mHSPC. Citation Format: Alejandro Recio-Boiles, Sachin Kumar Deshmukh, Ricardo J. Estrada-Mendizabal, Kenneth Barker, Sharon Wu, Joanne Xiu, Milan Radovich, Elisabeth I. Heath, Rana McKay, Juan Chipollini, Cynthia K. Miranti. Defining the role of Hedgehog, Notch, and Wnt signaling pathways in aggressive lethal prostate cancer of Hispanic men [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C100.