Promoter hypermethylation using 24-gene array in early head and neck cancer

Figures & data

Table 1. Gene promoter hypermethylation early oral (166) and oropharyngeal (51) cancers

		Promoter hypermethylation (%)
Gene	Chromosome	OSCC	OPSCC	P value	adjusted P value*
RARB	3p24.2	31	35	0.540	0.741
CHFR	12q24.33	20	26	0.391	0.796
CDH13	16q23.3	13	59	< 0.001	< 0.001
DAPK1	9q21.33	12	20	0.171	0.781
APC	5q22.2	10	6	0.574	0.239
CADM1	11q23.3	5	2	0.689	0.575
TP73	1p36.32	3	14	0.003	0.019
CDKN2A	9p21.3	3	0	0.594	0.999
CDKN2B	9p31.3	3	2	1.000	0.497
ESR1	6q25.1	2	6	0.359	0.659
TIMP3	22q12.3	2	8	0.055	0.175
RASSF1A	3p21.31	2	2	1.000	0.786
PTEN	10q23.3	1	0	1.000	1.000
CASP8	2q33.3	1	0	1.000	0.999
FHIT	3p21.31	1	0	1.000	1.000
MLH1	3p22.2	0	0	N.A.	N.A.
CD44	11p13	0	0	N.A.	N.A.
GSTP1	11q13.2	0	0	N.A.	N.A.
HIC1	17p13.3	0	0	N.A.	N.A.
BRCA1	17q21.31	0	0	N.A.	N.A.
BRCA2	13q12.3	0	0	N.A.	N.A.
VHL	3p25.3	0	0	N.A.	N.A.
ATM	11q22.3	0	0	N.A.	N.A.
CDKN1B	12p13.1	0	0	N.A.	N.A.
Number of hypermethylated TSG, medial (range)		1 (0 - 6)	2 (0 - 5)	0.001	0.010

* adjusted for differences in smoking, alcohol consumption, cT and cN classification.

Figure 1. Promoter hypermethylation and disease specific survival in early OSCC samples. Log Rank test: P = 0.007; Cox regression analysis: hazard ratio 0.18 (95% confidence interval: 0.04 - 0.75), P = 0.002. *(patients/events): < 2 meth. genes 29 events in 123 patients; ≥ 2 meth. genes 2 events in 43 patients.

Table 2. Cox regression analysis of disease specific survival in early OSCC

Variable	HR (95% CI)	P value
Univariate
≥ 2 hypermethylated genes	0.18 (0.04–0.75)	0.018
Multivariate model
≥ 2 hypermethylated genes	0.17 (0.04–0.70)	0.014
pN classification	4.16 (2.01–8.61)	< 0.001

Table 3. Characteristics of early OSCC and OPSCC

Patient or tumor characteristics	Oral Cavity (%)	Oropharynx (%)	P value
No. of cases	166	51
Age Average (range)	61 (23–90)	60 (43–86)	0.420
Sex Male Female	100 (60) 66 (40)	31 (61) 20 (39)	0.945
Smoking No Yes	82 (49) 84 (51)	7 (14) 44 (86)	< 0.001
Alcohol No Yes	78 (47) 88 (53)	9 (18) 42 (82)	< 0.001
Clinical T-classification T1 T2	82 (49) 84 (51)	9 (18) 42 (82)	< 0.001
Clinical N-classification N0 N1–3 Missing	146 (88) 20 (12) 0 (0)	20 (39) 29 (57) 2 (4)	< 0.001
Sublocation Tongue Floor of mouth	103 (62) 63 (38)	NA
Pathologic N-classification N0 N1–3	111 (67) 55 (33)	NA
Vaso-invasion No Yes	151 (91) 15 (9)	NA
Perineural growth No Yes	118 (71) 48 (29)	NA
Invasive pattern tumor front Cohesive Non-cohesive	54 (33) 111 (67)	NA
Infiltration depth 0 – 4 mm > 4 mm	51 (31) 115 (69)	NA
Differentiation grade Good/moderate Poor/undifferentiated Missing	147 (87) 13 (8) 6 (4)	NA
Treatment primary tumor^1 Surgery Surgery and adjuvant radiotherapy Radiotherapy None	130 (78) 36 (22) 0 (0) 0 (0)	1 (2) 3 (6) 46 (92) 1 (0)	< 0.001

¹ Four patients with oropharyngeal cancer received treatment with palliative instead of curative intent (three radiotherapy and one no therapy).

Figure 2. Promoter hypermethylation in early OSCC and OPSCC samples. Only genes with hypermethylation in at least one sample are illustrated.

Figure 3. Promoter hypermethylation and overall survival in patients with early OSCC and OPSCC. ≥ 2 hypermethylated genes is an effect modifier in oral and oropharyngeal SCC, P = 0.012. Log Rank test: OSCC (P = 0.054); OPSCC (P = 0.080). *(patients/events): OSCC < 2 meth. genes 36 events in 122 patients; ≥ 2 meth. genes 6 events in 43 patients; OPSCC < 2 meth. genes 4 events in 22 patients; ≥ 2 meth. genes 11 events in 25 patients. One OSCC patient out of analysis due to missing data.

Table 4. Baseline characteristics in OSCC and OPSCC in methylated subgroups

	Oral Cavity			Oropharynx
Patient or tumor characteristics	< 2 TSG	≥ 2 TSG	P value	< 2 TSG	≥ 2 TSG	P value
Age Average (range)	62 (23–90)	59 (41–86)	0.880	58 (43–76)	61 (47–78)	0.087
Sex Male Female	59% 41%	65% 35%	0.448	59% 41%	64% 36%	0.730
Smoking No Yes	51% 49%	44% 56%	0.427	14% 86%	16% 84%	0.820
Alcohol No Yes	50% 50%	40% 60%	0.255	14% 86%	24% 76%	0.368
Clinical T-classification T1 T2	54% 46%	37% 63%	0.063	14% 86%	16% 84%	0.820
Clinical N-classification N0 N1–3 Nx	89% 11%	86% 14%	0.656	41% 59%	44% 48% 8%	0.358
Treatment primary tumor Surgery Surgery and radiotherapy Radiotherapy	79% 21% 0%	77% 23% 0%	0.772	0% 0% 100%	4% 12% 84%	0.146

Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin 2011; 61:69 - 90; http://dx.doi.org/10.3322/caac.20107; PMID: 21296855

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