Prostate cancer phenotypes determined from circulating tumor DNA associate with outcomes to 177 Lu-PSMA-617 therapy

Background: Metastatic castration-resistant prostate cancer (mCRPC) is a lethal disease with a major unmet clinical need to identify therapeutics that extend survival and biomarkers that predict treatment responses. The prostate-specific membrane antigen (PSMA) radioligand, 177 Lu-PSMA-617 ( 177 Lu-PSMA) is documented to increase overall survival (OS), but responses are highly variable. Analysis of cell-free DNA (cfDNA) from liquid biopsies offers a non-invasive window to profile tumor genomics and phenotypes, and identify markers predictive of 177 Lu-PSMA outcomes. Methods: We interrogated a real-world prospective cohort of 140 patients with mCRPC meeting clinical guidelines for 177 Lu-PSMA treatment. We analyzed pre-treatment and on-treatment circulating tumor DNA (ctDNA) by whole genome sequencing to quantitate ctDNA abundance and assess tumor-derived genomic features such as copy number alterations, somatic mutations, and structural rearrangements. We also employed a novel computational tool termed Proteus that uses ctDNA fragmentomic profiles to determine the expression of individual genes as well as expression programs that comprise a spectrum of relevant tumor phenotypes including mCRPC lineage subtypes, proliferation scores, and hypoxia signatures that may plausibly influence responses to 177 Lu-PSMA. Tumor phenotype characteristics were integrated with PSMA-PET and SPECT imaging findings and evaluated for associations with clinical outcomes. Results: Pre-treatment ctDNA fraction was strongly associated of OS (multivariate HR=2.19, P =0.002), independent of prostate-specific antigen (PSA) response, and correlated positively with PSMA- and FDG-PET total tumor volume (R=0.59 and R=0.69, respectively). Poor responders were characterized by higher baseline ctDNA fraction, genomic instability, and overall tumor mutational burden. Deleterious alterations in the DNA repair gene ATM were associated with improved OS, whereas MYC amplifications were associated with poorer survival. Tumor phenotype features derived from ctDNA including cell cycle proliferation score, neuroendocrine differentiation, and complex copy number variation on chromosome 8 independently associated with clinical outcomes. Conclusions: Our findings demonstrate that baseline ctDNA analysis provides prognostic information for mCRPC patients undergoing 177 Lu-PSMA therapy. ctDNA fraction and quantity, alongside specific genomic alterations and tumor phenotype features represent promising, non-invasively acquired biomarkers to guide patient selection, improve therapeutic monitoring, and further dissect genomic mechanisms of resistance to 177 Lu-PSMA.