This transformation is associated with poor prognosis and resistance to androgen receptor (AR)-targeted therapies. Diagnosis traditionally relies on tissue biopsy, which is invasive and often not feasible for serial monitoring. We hypothesized that plasma epigenomic profiling using cell-free chromatin immunoprecipitation sequencing (cfChIP-seq) could non-invasively detect the emergence of squamous transformation and provide real-time insights into tumor evolution.
We profiled circulating chromatin in serial plasma samples collected from a patient with mCRPC who was diagnosed with SqCPC following progression on Lutetium-PSMA therapy. cfChIP-seq was performed for H3K27ac and H3K4me3 histone modifications to infer gene regulatory activity at lineage-specific loci. Plasma samples were collected at four timepoints: two before and two after confirmation of squamous histology. Tissue biopsy of a mediastinal lymph node revealed a squamous carcinoma with a TMPRSS2-ERG fusion that confirmed prostatic origin. Genomic comparison of the primary adenocarcinoma and metastatic squamous subclone revealed shared alterations, with the acquisition of biallelic RB1 loss, a known driver of lineage plasticity.
cfChIP-seq revealed dynamic activation of squamous-specific genes (DSC3, SOX2, ETV4, S100A13) and regulatory regions previously identified by ATAC-seq signatures from squamous carcinomas. Activity of squamous genes and regulatory elements was detected in plasma 4 months before histologic diagnosis and declined following initiation of squamous histology-directed chemoimmunotherapy. Signal at housekeeping loci remained stable throughout. Importantly, the signal at squamous-specific sites was independent of the circulating tumor DNA (ctDNA) fraction, suggesting that the cfChIP-seq signal reflects specific epigenomic reprogramming rather than changes in tumor burden alone. Moreover, using this novel liquid biopsy method, we were able to track the evolution of both adenocarcinoma and SqCPC components of the tumor burden.
Our findings demonstrate that cfChIP-seq can detect and track the emergence of histologic transformation in prostate cancer months before it becomes clinically apparent. This case represents the first reported application of liquid biopsy to detect treatment-emergent SqCPC and supports its broader utility in monitoring lineage plasticity in mCRPC. Plasma epigenomic profiling may enable earlier diagnosis, guide subtype-specific therapy, and overcome the limitations of tissue biopsy in advanced prostate cancer.
Written by: Rashad Nawfal, MD,1,2 Karl Semaan, MD, MS,1-4 Jacob E. Berchuck, MD,1,5,6 and Sylvan C. Baca, MD, PhD,2,7,8
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Winship Cancer Institute of Emory University, Atlanta, GA, USA. .
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- The Eli and Edythe L. Broad Institute, Cambridge, MA, USA.