Table 1.

Genes hypermethylated in OPSCC

Pathway	Gene	Name	Hypermethylated in	Region analyzed	Reference
Apoptosis	DAPK	Death-associated protein kinase 1	HPV-negative/positive	Promoter region	[39]
	RASSF1	Ras association domain-containing protein 1	HPV-negative	− 244 from TSSa	[50]
				Promoter region	[45, 51]
	STAT5	Signal transducer and activator of transcription 5	HPV-negative	+ 42 from TSS	[50]
Cell cycle	CCNA1	Cyclin A1	HPV-positive	Promoter region	[51]
				+ 7 from TSS	[50]
	CDKN2A	Cyclin-dependent kinase inhibitor-2A	HPV-negative	Promoter region	[43–45, 51]
			HPV-positive	Three loci within the CpG island of CDKN2A gene	[165]
	CHFRb	Checkpoint with forkhead and ring finger domains	HPV-negative	Promoter region	[39]
	TP73	Tumor protein p73	HPV-negative/positive	Promoter region	[39]
Cell fate determination	APC	Adenomatous polyposis coli	HPV-negative/positive	Promoter region	[39]
DNA repair	MGMT	O6-methylguanine-DNA methyltransferases	HPV-negative	− 272 from TSS	[50, 51]
Protein glycosylation	TUSC3	Tumor suppressor candidate 3	HPV-positive	+ 29 from TSS	[50]
Inflammation	JAK3	Janus kinase 3	HPV-positive	+ 64 from TSS	[50]
Invasion and metastasis	CADM1	Cell Adhesion Molecule 1	HPV-positive	Promoter region	[39]
	CDH11	Cadherin 11	HPV-positive	− 354 from TSS	[50]
	CDH13a	Cadherin 13	HPV-negative/positive	Promoter region	[39]
	IGSF4	Immunoglobulin superfamily member 4	HPV-positive	Promoter region	[166]
	SPDEF	SAM pointed domain-containing Ets transcription factor	HPV-negative	+ 116 from TSS	[50]
	TIMP3	TIMP metallopeptidase inhibitor 3	HPV-positive	Promoter region	[39, 51]
	SYBL1	Synaptobrevin-like 1	HPV-positive	− 349 from TSS	[50]
Signaling	ESR1	Estrogen receptor 2	HPV-negative/positive	Promoter region	[39]
	ESR2	Estrogen receptor 2	HPV-negative	+ 66 from TSS	[50]
	GALR1	Galanin receptor type 1/2	HPV-positive	Two loci within the CpG island of the GALR1 gene	[165]
	GRB7	Growth factor receptor-bound protein 7	HPV-positive	− 160 from TSS	[50]
	RARβa	Retinoic acid receptor β	HPV-negative/positive	Promoter region	[39]
Transcription	RUNX1T1	RUNX1 translocation partner 1	HPV-positive	+ 145 from TSS	[50]
	TCF21	Transcription factor 21	HPV-positive	Promoter region	[167]
WNT signaling	SFRP1	Soluble frizzled receptor protein 1	Drinkers	Promoter region	[56]
	SFRP4	Soluble frizzled receptor protein 4	HPV-positive	Promoter region	[56]
	WIF1	WNT inhibitory factor 1	NA	Promoter region	[54]

NA not applicable

^a TSS transcription start site

^bHypermethylation of these genes is associated with development of radioresistance in other tumor types