Fig. 5. SAMOSA-Tag of PDXs nominates global chromatin dysregulation in prostate cancer metastasis.

a, Overview of the approach for SAMOSA-Tag of PDXs generated from primary and metastatic castration-resistant prostate tumors sampled from a single patient. Live human cells were enriched from tumors explanted from PDX mice using FACS. Six replicate SAMOSA-Tag reactions were performed using approximately 30,000 nuclei each isolated from primary and metastatic PDXs. b, Clustered chromatin fiber types detected in primary and metastatic PDXs falling in one of 17 prostate-specific chromHMM states. Unsupervised Leiden clustering identified seven fiber types—five regular clusters in NRL ranging from 171 to 208 bp and two irregular clusters. c, Heatmap of log₂ fold change in fiber type usage across chromHMM states (∆) in metastatic versus primary PDXs. Effect sizes were the coefficients of case status (primary versus metastatic), which was the predictor variable in a logistic regression model with domain-specific fiber usage as the response variable. Statistically significant differences were identified using a Wald’s test of coefficients; two-tailed P values were adjusted for multiple testing using Storey’s q⁴⁹, with a significance threshold of q ≤ 0.05. Red indicates fiber types enriched in metastasis, while blue indicates fiber types enriched in primary tumors. The gray dots mark non-significant (NS) results. Chromatin state abbreviations: EnhA1 and EnhA2, active enhancers; EnhBiv, bivalent enhancer; EnhG1 and EnhG2, genic enhancers; EnhWk, weak enhancer; ReprPC, repressed polycomb; ReprPCWk, weak repressed polycomb; TssA, active TSS; TssBiv, bivalent/poised TSS; TssFlnk, flanking TSS; TssFlnkD, downstream flanking TSS; TssFlnkU, upstream flanking TSS; Tx, strong transcription; TxWk, weak transcription; ZNF/Rpts, zinc-finger genes and repeats. d, Speculative model of changes in single-molecule chromatin accessibility during prostate cancer progression based on PDX SAMOSA-Tag. Highly accessible, irregular chromatin fibers devoid of phased nucleosomes were enriched in metastatic cells, which was suggestive of deranged activity of BAF remodelers, the prime candidates for generating nucleosome-free, irregular, single-molecule accessibility patterns.