Plasma epigenomic profiling reveals treatment-emergent squamous transformation in prostate cancer

Abstract

Squamous transformation of prostate adenocarcinoma is a rare resistance mechanism in patients with advanced prostate cancer that impacts both prognosis and treatment. Herein, we profile circulating chromatin in serial plasma samples collected from a patient with metastatic prostate cancer that experienced squamous transformation. We detect dynamic changes in gene regulation from circulating chromatin reflecting the emergence of squamous differentiation, enabling non-invasive diagnosis and monitoring of this resistance phenotype, with potential therapeutic implications.

Fig. 1. Radiographic and molecular characterization of treatment-emergent squamous cell carcinoma.

a Clinical course of the patient. ADT: Androgen deprivation therapy, mCRPC: metastatic castration resistant prostate cancer, FDG: Fluorodeoxyglucose, PSMA: Prostate specific membrane antigen, ICI: Immune checkpoint inhibitor, SBRT: Stereotactic body radiation therapy. b Comparative PSMA-PET and FDG-PET imaging (I) PSMA-PET scan with low uptake in the same two hilar lymph nodes. (II) FDG-PET scan with high metabolic activity in two left hilar lymph nodes. (III) PSMA-PET scan with avid uptake at the same T10 metastasis. (IV) FDG-PET scan with avid uptake at the T10 metastasis. c Histologic and immunohistochemical findings of mediastinal lymph nodes biopsies (I) Hematoxylin and eosin (H&E) stain showing squamous morphology. (II) Positive staining for p40. (III) Negative staining for NKX3-1. (IV) Weak staining for ERG. (V) H&E stain highlighting focal tumor clusters without squamous differentiation, (VI) which show NKX3-1 positivity. (VII) H&E stain of radical prostatectomy specimen (with treatment effect): Residual intraductal (left; with surrounding basal cells) and invasive (middle/right; without basal cells) carcinoma was present (b represents a higher magnification of boxed area in a). The tumor cells had pale cytoplasm and small round nuclei with prominent nucleoli. c Focally, in less than 5% of the tumor, squamous differentiation (sqd) was seen in the intraductal carcinoma; squamous differentiation was not seen in the invasive component. d Genomic profiling of the patient’s primary tumor from the radical prostatectomy specimen and a metastatic lesion from an enlarged mediastinal lymph node with low PSMA expression on PSMA PET scan (tumor purity 30% and 50%, respectively).

Fig. 2. Longitudinal monitoring of squamous differentiation from patient plasma.

a Overview of the experimental workflow to detect and monitor squamous transformation from circulating chromatin. b Normalized signal from H3K4me3 cell-free ChIP-seq profiles at representative SCC-associated (DSC3, SOX2, ETV4, S100A13) and PRAD-associated (NKX3-1) loci in baseline and post-squamous transformation plasma samples. c Genomic Regions Enrichment of Annotations Tool analysis (GREAT) of TCGA squamous ATAC peaks (n = 7353). d Longitudinal tracking of the squamous (purple) and adenocarcinoma (blue) plasma epigenomic scores. H3K4me3 signal at housekeeping genes activity (red) and ctDNA fraction (green) included for comparison. All values were rescaled based on the mean signal in healthy plasma at each set of sites. e Correlation of the aggregated H3K27ac signal across adenocarcinoma and squamous sites with the estimated ctDNA fraction in plasma samples from patients with prostate adenocarcinoma.