A novel methylated cell-free DNA marker panel to monitor treatment response in metastatic prostate cancer

Figures & data

Figure 1. Flow chart of candidate region selection.

To identify regions associated with clinical progression, DMCs with increased (UP) cfDNA methylation between visits A and B were isolated from our prior sequencing study (green boxes). The proximity of these CpG sites to one another was assessed and regions were defined using the previously established DMRHunter tool. Regions that were differentially methylated in cfDNA from patients who demonstrated a faster TTCP (≤25 weeks) during ARPI treatment were prioritized. Further, DMCs that overlapped with or in close proximity to NE disease-related methylated CpG sites were also examined, and additional regions that were elevated among patients with a faster TTCP were selected as candidates (pink boxes).

cfDNA: Cell-free DNA; DMC: Differentially methylated cytosine; TTCP: Time to clinical progression; NE: Neuroendocrine.

Figure 2. Comparison of overall cfDNA methylation levels of each region between study visits.

Boxplots show the median, first and third quartile methylation levels (copies/ml) for (A) Region 1, (B) Region 2, (C) Region 3, (D) Region 5, (E) Region 6, (F) Region 7, (G) Region 8, (H) Region 10, and (I) Region 11. Kruskal–Wallis analysis was performed to compare all visits, with pairwise comparisons for significantly altered methylated regions (*p < 0.05). n = 39 patients for visit A, n = 40 patients for visit B, n = 36 patients for visit C.

cfDNA: Cell-free DNA.

Figure 3. Correlation analysis of visit A cfDNA methylation levels with time to clinical progression.

The total methylated copies/ml at visit A was correlated with TTCP (weeks) for (A) Region 1, (B) Region 2, (C) Region 3, (D) Region 5, (E) Region 6, (F) Region 7, (G) Region 8, (H) Region 10, and (I) Region 11. Spearman rho and p-values are shown for all nine regions assessed.

cfDNA: Cell-free DNA; TTCP: Time to clinical progression.

Figure 4. Correlation analysis of visit B cfDNA methylation levels with time to clinical progression.

The total methylated copies/ml at visit B was correlated with TTCP (weeks) for (A) Region 1, (B) Region 2, (C) Region 3, (D) Region 5, (E) Region 6, (F) Region 7, (G) Region 8, (H) Region 10, and (I) Region 11. Spearman rho and p-values are shown.

cfDNA: Cell-free DNA; TTCP: Time to clinical progression.

Table 1. Cox proportional hazards models examining the relationship between cfDNA methylation levels of each region and time to clinical progression.

Region	Visit	HR	95% CI	p-value	C-index
R1	A	1.34	0.94–1.91	0.10	0.64
	B	2.25	1.23–4.11	0.01^†	0.68
	C	0.54	0.20–1.51	0.24	0.58
R2	A	1.28	0.92–1.77	0.15	0.62
	B	2.22	1.28–3.87	0.005^†	0.70
	C	0.45	0.17–1.22	0.12	0.62
R3	A	1.27	0.91–1.76	0.16	0.63
	B	2.64	1.44–4.82	0.002^†	0.73
	C	0.62	0.22–1.72	0.36	0.57
R5	A	1.22	0.88–1.69	0.24	0.64
	B	1.84	1.19–2.86	0.006^†	0.69
	C	0.70	0.30–1.62	0.40	0.56
R6	A	1.34	0.94–1.91	0.10	0.64
	B	2.39	1.32–4.31	0.004^†	0.71
	C	0.53	0.16–1.77	0.30	0.57
R7	A	1.30	0.96–1.74	0.09	0.56
	B	1.36	1.00–1.85	0.051	0.56
	C	0.93	0.67–1.29	0.66	0.58
R8	A	1.30	0.95–1.80	0.10	0.66
	B	2.23	1.28–3.86	0.004^†	0.72
	C	0.63	0.24–1.70	0.37	0.58
R10	A	1.43	0.96–2.12	0.08	0.65
	B	2.47	1.37–4.44	0.003^†	0.70
	C	0.52	0.18–1.52	0.23	0.59
R11	A	1.28	0.92–1.79	0.15	0.64
	B	2.69	1.50–4.83	0.001^†	0.75
	C	0.64	0.22–1.92	0.43	0.59

† p < 0.05.

cfDNA: Cell-free DNA; CI: Confidence interval; HR: Hazard ratio; TTCP: Time to clinical progression.

Table 2. Multivariable modeling to examine association between methylation of all regions analyzed with time to clinical progression.

Cox models with weighted scores
Covariate	HR (95%CI)	p-value	C-index
Score A	1.14 (0.94–1.39)	0.19	0.65
Score B	1.16 (1.05–1.28)	0.004^†	0.72
Score C	1.19 (0.91–1.56)	0.19	0.60

† p < 0.05.

HR: Hazard ratio; TTCP: Time to clinical progression.