Abstract 7152: High-dimensional, single-cell analysis and transcriptional profiling reveal novel correlatives of response to PARP inhibition plus PD-1 blockade in triple-negative breast cancer
Authors: Alexander P. Gottlieb, Gregory J. Baker, Jia-Ren Lin, Ricardo Pastorello, Yu-An Chen, Tuulia Vallius, Janae Davis, Clarence Yapp, Sarah E. Church, Eric Miller, Anniina Farkkila, Shaveta Vinayak, Melinda L. Telli, Sara M. Tolaney, Filipa Lynce, Joan S. Brugge, Alan D'Andrea, Geoffrey Shapiro, Sandro Santagata, Peter K. Sorger, Elizabeth A. Mittendorf, Jennifer L. Guerriero
Journal: Cancer Research (2025)

Abstract Background: TOPACIO was a phase I/II study evaluating the PARP inhibitor (PARPi) niraparib in combination with the anti-PD-1 antibody pembrolizumab in patients with locally advanced or metastatic triple-negative breast cancer (TNBC, n=55), irrespective of BRCA status. In the efficacy-evaluable population (n=47) the objective response rate (ORR) was 21% and disease control rate (DCR) 49%. Although activity was greater in BRCA-MUT patients (7/15, ORR=47% and 12/15, DCR=80%), durable clinical benefit was seen in patients with BRCA-WT tumors (3/27, ORR=11% and 9/27, DCR=33%). Patients with PD-L1+ tumors (28/47, 60%) achieved higher ORR (9/28, 32%) than those with PD-L1neg tumors (1/13, 8%). It remains unstudied whether tumor gene expression or immune composition in baseline biospecimens is predictive of treatment response. We conducted exploratory biomarker analyses to uncover gene expression patterns and immune states associated with treatment response. Methods: Transcriptional profiling of baseline samples was performed using the BC360 (n=41) and PanCancer IO360 (n=42) panels (Nanostring) and multigene signatures were used to measure tumor and immune activities. Transcriptional analysis was paired with high-dimensional, single-cell cyclic immunofluorescence (CyCIF) of samples with adequate tissue for analysis (n=22) to characterize the immune microenvironment at single-cell resolution. Results: BRCA-MUT tumors showed increased downstream interferon signaling and immune infiltration relative to BRCA-WT tumors (p &amp;lt; 0.05). Downstream interferon and immunoproteasome scores were elevated in objective responders (p &amp;lt; 0.05). Genes involved in WNT signaling (TANKS1, TANKS2, PARP4, and NETO2) associated with long-term response, defined by those still on therapy and responding at data cut off. Low NETO2 gene expression strongly associated with better ORR (p = 0.01). CyCIF analysis performed on whole tissue sections accounting for 2.97x106 single cells revealed that in BRCA-WT patients, baseline infiltration of immune cells - cells expressing CD45, CD3 (T cells), CD20 (B cells) or CD68/CD163 (macrophages) positively correlated with favorable PFS (R=0.81, p=0.0004, Spearman’s correlation). Further, increasing fractions of CD8+ and PD-1+ CD4+ T cells strongly associated with favorable PFS (R &amp;gt; 0.71, p &amp;lt; 0.0041). In BRCA-MUT patients, baseline immune composition did not correlate with clinical outcome. Conclusions: NETO2 expression, WNT pathway, and interferon signaling associate with response to niraparib plus pembrolizumab. While BRCA-MUT tumors showed higher baseline immune cell abundance compared to BRCA-WT, immune and T cell infiltration was predictive of PFS duration only in BRCA-WT patients, suggesting divergent mechanisms of response to PARPi and ICB dependent on BRCA status. Citation Format: Alexander P. Gottlieb, Gregory J. Baker, Jia-Ren Lin, Ricardo Pastorello, Yu-An Chen, Tuulia Vallius, Janae Davis, Clarence Yapp, Sarah E. Church, Eric Miller, Anniina Farkkila, Shaveta Vinayak, Melinda L. Telli, Sara M. Tolaney, Filipa Lynce, Joan S. Brugge, Alan D'Andrea, Geoffrey Shapiro, Sandro Santagata, Peter K. Sorger, Elizabeth A. Mittendorf, Jennifer L. Guerriero. High-dimensional, single-cell analysis and transcriptional profiling reveal novel correlatives of response to PARP inhibition plus PD-1 blockade in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7152.