Cell phenotype underlies prostate cancer presentation and treatment resistance and can be regulated by epigenomic features. However, the osteotropic tendency of prostate cancer limits access to metastatic tissue, meaning most prior insights into prostate cancer chromatin biology are from preclinical models that do not fully represent disease complexity. Noninvasive chromatin immunoprecipitation of histones in plasma cell–free DNA (cfDNA) in humans may enable the capture of disparate prostate cancer phenotypes. In this study, we analyzed activating promoter- and enhancer-associated H3K4me2 from cfDNA in metastatic prostate cancer enriched for divergent patterns of metastasis and diverse clinical presentation. H3K4me2 density across prostate cancer genes, accessible chromatin, and lineage-defining transcription factor–binding sites correlated strongly with ctDNA fraction—demonstrating capture of prostate cancer–specific biology and informing the development of a statistical framework to adjust for ctDNA fraction. Chromatin hallmarks mirrored synchronously measured clinicogenomic features: bone- versus liver-predominant disease, serum PSA, biopsy-confirmed histopathologic subtype, and RB1 deletions convergently indicated phenotype segregation along an axis of differential androgen receptor activity and neuroendocrine identity. Detection of lineage switching after sequential progression on systemic therapy in select patients indicates potential use for individualized resistance monitoring. Epigenomic footprints of metastasis-induced normal tissue destruction were evident in bulk cfDNA from two patients. Finally, a public epigenomic resource was generated using a distinct chromatin marker that has not been widely investigated in prostate cancer. These results provide insights into the adaptive molecular landscape of aggressive prostate cancer and endorse plasma cfDNA chromatin profiling as a biomarker source and biological discovery tool. Significance: Plasma cell–free chromatin immunoprecipitation sequencing enables phenotypic dissection of lethal prostate cancer and is a practical tool for biomarker discovery while overcoming prior limitations of access to relevant tissue and reliance on model systems.

Triple-negative breast cancer (TNBC) is the breast cancer subtype with the poorest prognosis and lacks actionable molecular targets for treatment. Maternal embryonic leucine zipper kinase (MELK) is highly expressed in TNBC and has been implicated in poor clinical outcomes, though its mechanistic role in the aggressive biology of TNBC is poorly understood. Here, we demonstrate a role of MELK in TNBC progression and metastasis. Analysis of publicly available datasets revealed that high MELK expression correlates with worse overall survival, recurrence-free survival, and distant metastasis-free survival, and MELK is co-expressed with metastasis-related genes. Functional studies demonstrated that MELK inhibition, using genomic or pharmacologic inhibition, reduces mammosphere formation, migration, and invasion in high-MELK-expressing TNBC cell lines. Conversely, MELK overexpression in low-MELK-expressing cell lines significantly increased invasive capacity in vitro and metastatic potential in vivo, as evidenced by enhanced metastasis to the liver and lungs in a chorioallantoic membrane assay. These findings highlight MELK as a key regulator of TNBC aggressiveness and support its potential as a therapeutic target to mitigate metastasis and improve patient outcomes.

Supplementary Figures 1-12 with embedded captions.

Supplementary Figures 1-12 with embedded captions.

Supplementary Tables 1-11 from Plasma Cell–Free DNA Chromatin Immunoprecipitation Profiling Depicts Phenotypic and Clinical Heterogeneity in Advanced Prostate Cancer

PURPOSE: MammaPrint (MP), a 70-gene expression profile assay, informs treatment decisions in early-stage breast cancer by classifying patients into high or low risk of recurrence categories. However, racial disparities in breast cancer outcomes necessitate an evaluation of MP's prognostic utility across diverse populations. This study explores differences in MP scores and associated outcomes among women of various racial backgrounds. MATERIALS AND METHODS: We retrospectively analyzed women with early-stage breast cancer who underwent MP testing (2013-2023) at University Hospitals Seidman Cancer Center. Patients were stratified by self-reported race and MP scores (high v low risk). Clinical outcomes, including recurrence-free survival (RFS) and overall survival (OS), were compared using Kaplan-Meier and Cox proportional hazards models. RESULTS: Among 1,349 women, 15.7% were African American (AA), 83.4% White, 0.6% Asian, and 0.3% from other racial groups. Overall, 64.7% had low-risk and 35.3% had high-risk scores. AA women had a significantly higher proportion of high-risk MP scores compared with White women (49.1% v 32.7%). Although the 5-year RFS rates were comparable between AA and White women (76.5% v 77.2%), the 5-year OS rates were slightly lower for AA women compared with White women (77.8% v 78.2%). MP remained prognostic for RFS at 3, 5, and 10 years regardless of race. Multivariable analysis revealed no significant differences in OS (hazard ratio [HR], 0.94 [95% CI, 0.47 to 1.89]; P = .866) or RFS (HR, 0.83 [95% CI, 0.43 to 1.59]; P = .572) between AA and White women after adjusting for MP risk groups and other clinical factors. High-risk MP scores were associated with worse OS (HR, 3.06 [95% CI, 1.64 to 5.70]; P < .001) and RFS (HR, 2.68 [95% CI, 1.55 to 4.62]; P < .001) compared with low-risk scores. Other factors associated with worse RFS and OS were tumor size, nodal involvement, and age. Interaction models indicated no difference is OS or RFS in AA women and White women with either low-risk or high-risk MP, respectively. CONCLUSION: Despite AA women exhibiting a higher proportion of high-risk MP scores, survival outcomes were comparable with those of White women. These findings underscore MP's consistent prognostic performance across racial groups but further highlight the need to address additional clinical and social determinants influencing breast cancer outcomes beyond genomic risk alone.