Fig. 2: Plasma enhancer profiling enables detection of NE-diff across multiple cancers.

a, Schematic demonstrating the measurement of enhancer activity at REs or TFBSs based on H3K27ac cfChIP-seq signal. b, Aggregate H3K27ac cfChIP-seq signal at REs identified by ATAC-seq in prostate tumor tissue¹⁴. Signal in prostate cancer plasma and healthy plasma are colored orange and gray, respectively. Dark lines show the mean signal across all samples in the indicated class. For comparison, signal at ‘common’ REs is shown, which include 10,000 REs with DNAse hypersensitivity across most or all cell types²⁰ (Methods). See also Extended Data Fig. 6. c, Normalized H3K4me3 cfChIP-seq signal in breast cancer patient plasma at the ESR1 gene promoter (n = 19 biologically independent samples). Dark lines indicate the mean signal across all samples in a class (ER⁺ or ER⁻). Box plots show AUC for cfChIP profiles. Wilcoxon test P values are indicated for comparison of ER⁺ versus ER⁻ breast cancer. d, H3K27ac cfChIP-seq signal in breast cancer patient plasma (n = 17 biologically independent samples) at REs with preferentially accessible chromatin in ER⁺ breast cancer⁴. Signal is aggregated across 27,840 REs for each sample. Dark lines indicate the mean signal across all samples in a class (ER⁺ or ER⁻). Box plots show AUC for the aggregate H3K27ac cfChIP profile for each sample. Wilcoxon test P values are indicated for comparison of ER⁺ versus ER⁻ breast cancer. e, H3K27ac cfChIP-seq signal at the AR gene enhancer in patients with castration-resistant prostate cancer. Plasma from patients with metastatic breast cancer is included as a control. f, Aggregated H3K27ac cfChIP-seq signal at ASCL1 binding sites for prostate cancer with and without NE-diff (NEPC and PRAD, respectively; n = 33 biologically independent samples). Box plots indicate AUC for the aggregate H3K27ac profile for each sample. Wilcoxon test P values are indicated for comparison of NEPC versus PRAD. g, ROC curves for distinguishing samples with NE-diff using H3K27ac cfChIP-seq signal at neuroendocrine REs. ‘AUC’ indicates area under the ROC curve for each comparison. For a–c, only plasma samples with estimated ctDNA content >0.03 are included. For all box plots, lower, middle and upper hinges indicate 25th, 50th, and 75th percentiles; whiskers extend to 1.5× the interquartile ranges. All P values indicate two-sided tests. NE, neuroendocrine; PRAD, prostate adenocarcinoma.