Hypomethylation at H19DMR in penile squamous cell carcinoma is not related to HPV infection

Figures & data

Table 1. Clinical and pathological aspects of penile squamous cell carcinoma participants.

Variables	N (%)
Age (years)
Mean (range)	63.8 years (23–94)
<40	4/30 (13.3)
40–60	9/30 (30)
>60	17/30 (56.7)
p16^INK4a
No	18/30 (60)
Yes	12/30 (40)
hrHPV
No	14/30 (46.6)
Yes	16/30 (53.2)
Staging
pTis + pTa + pT1(a.b)	7/30 (23.3)
pT2	12/30 (40)
pT3	11/30 (36.7)
Sistemic metastasis
No	22/26 (84.6)
Yes	4/26 (15.4)
Lymph node metastasis
No	13/27 (48.1)
Yes	14/27 (51.9)
Locoregional recurrence
No	19/27 (70.3)
Yes	7/27 (29.7)
PLI
Mild and Moderate	18/30 (60)
Intense	12/30 (40)
IPI
Mild and Moderate	16/30 (53.3)
Intense	14/30 (46.7)

pTis: carcinoma in situ; pTa: non-invasive carcinoma; pT1a: subepithelial invasion without lymphovascular invasion, perineural invasion or grade 3; pT1b: subepithelial invasion with lymphovascular invasion, perineural invasion or grade 3; pT2: invasion of corpus spongiosum; pT3: invasion of corpus cavernosum; PLI: peritumoral lymphocyte infiltrate; IPI: intratumoral polymorphonuclear infiltrate.

Figure 1. Bisulfite sequencing of H19DMR in penile squamous cell carcinoma. Each row represents a sample (S) and its HPV status (positive samples were considered as p16^INK4a+ or hrHPV+). The number of reads is specified for each sample. The SNPs position are specified by the red arrow.

Figure 2. Average of methylated, unmethylated and partially methylated reads in HPV positive (HPV+) and negative (HPV-) of penile squamous cell carcinoma. Positive samples were considered as p16^INK4a+ or hrHPV+.

Figure 3. Percentage of methylation for each CpG site in HPV positive (HPV+) and negative (HPV-) of penile squamous cell carcinoma. The CTCF binding site is indicated by the grey arrow. Positive samples were considered as p16^INK4a+ or hrHPV+.

Table 2. Correlation between clinical data of penile squamous cell carcinoma participants and methylation level at H19DMR.

	Methylation level (%)
Variables (n)	0–30	31–60	P-value
Age (23–94 years)
≤60 (12/30)	7	5	0.164
>60 (18/30)	6	12
p16^INK4a
Positive (12/30)	8	10	0.590
Negative (18/30)	5	7
hrHPV
Positive (16/30)	5	9	0.338
Negative (14/30)	8	8
LNM
Positive (14/27)	6	7	0.584
Negative (13/27)	6	8
LR
Positive (7/26)	8	11	0.655
Negative (17/26)	3	4
SM
Positive (4/26)	8	14	0.187
Negative (22/26)	3	1
PLI
Mild/Moderate (18/30)	7	11	0.409
Intense (12/30)	6	6
IPI
Mild/Moderate (16/30)	4	12	0.035
Intense (14/30)	9	5
Staging
pTis + pTa + pT1(a.b)	3	4	0.652
pT2	4	8
pT3	6	5

p-value for Fisher Exact Probability Test. In bold and italics, p < 0.05. LNM: Lymph Node Metastasis; LR: Locoregional Recurrence; SM: Sistemic Metastasis; PLI: Peritumoral Lymphocytic Infiltrate; IPI: Intratumoral Polymorphonuclear Infiltrate. pTis carcinoma in situ, pTa non-invasive carcinoma, pT1a subepithelial invasion without lymphovascular invasion, perineural invasion or grade 3, pT1b subepithelial invasion with lymphovascular invasion, perineural invasion or grade 3, pT2 invasion of corpus spongiosum, pT3 invasion of corpus cavernosum.

Figure 4. Kaplan – Meier curve for survival probability (n = 27). (a) methylation levels; (b) rs2107425 genotype; (c) s2071094 genotype.

Table 3. Correlation between SNPs genotype (rs2107425 and rs2071094) and H19DMR methylation pattern.

SNP	Methylation level (%)		p value
	0–30	31–60
rs2107425
(n = 30)	C/C = 0.46	C/C = 0.30
	C/T = 0.31	C/T = 0.40	0.721
	T/T = 0.23	T/T = 0.30
rs2071094
(n = 30)	G/G = 0.28	G/G = 0.35
	G/T = 0.42	G/T = 0.35	0.441
	T/T = 0.3	T/T = 0.3

Data availability statement

Data is available with the authors.