Abstract Background: Metastatic castration-resistant prostate cancer (mCRPC) exhibits high mortality due to the emergence of therapy resistance phenotypes. We recently tested a novel combination therapy in patients with mCRPC who had progressed on androgen receptor (AR) -targeted therapies, targeting PD-L1 and PARP1 with durvalumab and olaparib, respectively. While a subset of patients exhibited partial responses, most patients experienced disease progression within a year. The goal of the current study is to perform comprehensive profiling of circulating tumor DNA (ctDNA) and buffy coat to assess the molecular characteristics of progressive vs. responsive prostate tumors. Methods: We obtained plasma cell-free DNA (cfDNA), a mixture of ctDNA and other tissue-derived DNA, from 38 individuals treated with the PD-L1/PARP1-targeted combination therapy (NCT02484404) at baseline, after two months of treatment, and upon disease progression. Whole-genome sequencing (WGS, median coverage: 139×) was performed using cfDNA and buffy coat DNA as germline control. Germline and somatic mutations including small mutations and structural rearrangements were individually curated to determine cfDNA tumor fraction. To infer epigenetic regulation, whole-genome 5-hydroxymethylcytosine and 5-methylcytosine (5hmC and 5mC, respectively) sequencing was performed using the Biomodal evoC platform. T/B cell receptor repertoire was inferred from buffy coat sequencing using MiXCR. Results: A negative association between baseline cfDNA tumor fraction and progression-free survival (PFS) was observed. BRCA2 alterations were associated with durable responses, whereas oncogenic mutations in TP53 and MAPK signaling pathway were associated with intrinsic resistance or rapid progression. Using cfDNA methylation sequencing, we identified disease-specific AR signaling genes depleted for promoter/early intronic 5mCs and enriched for 5hmCs in ctDNA-positive plasma. Similarly, AR-associated transcription factor binding sites were depleted for 5mCs and enriched for 5hmCs. Given the association between 5mC depletion and gene expression from matched tissues, we inferred gene expression and evaluated genes that correlate with drug response. Longer PFS was associated with greater activities of interferon signaling and inflammation at baseline, consistent with greater diversity of inferred T cell clonotypes. Comparing pre- and post-treatment plasma samples, distinct genetic programs were identified from patients with longer vs shorter PFS, suggesting different mechanisms of adaptive vs intrinsic treatment resistance. Conclusions: Baseline genomic deficiencies associated with DNA damage repair were differentially correlated with PD-L1/PARP1-targeted therapy response. Epigenetic alterations associated with inflammatory genes and baseline T lymphocyte clonal complexity inform better therapy outcomes. Time-course evaluation of global patterns of 5hmCs and 5mCs identified distinct epigenetic mechanisms associated with therapy response or failure. Citation Format: Chennan Li, Anna Baj, Clara C. Y. Seo, Nicholas T. Terrigino, John B. Bright, S. Thomas Hennigan, Isaiah M. King, Scott Wilkinson, Shana Y. Trostel, William D. Figg, William L. Dahut, Jung-Min Lee, David Y. Takeda, Fatima Karzai, Adam G. Sowalsky. Mechanisms of resistance to PD-L1/PARP1-targeted therapy in metastatic castration-resistant prostate cancer inferred by liquid biopsy abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Innovations in Prostate Cancer Research and Treatment; 2026 Jan 20-22; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86 (2Suppl): Abstract nr A038.
Li et al. (Tue,) studied this question.