Table 1.

Molecular differences between HPV+ and HPV HNSCCs: comparison of the various “omics” technologies

MarkerEnriched in (+) or (−) subgroupChromosomal locusGeneticEpigeneticTranscriptomicProteomicReference
Cell cycle
 TP53mu(22, 28, 31, 32, 34)
 E2F1+20q↑↑(19, 22)
 E2F targets (MCMs, CDC2/7, CCNA1, CCNE1)+(41)
 CCND111q13↑↑(17, 22, 28, 41)
 CDKN2A9p21↓↓, mume(7, 17, 28, 32, 41)
 PCNA+(41, 51, 52)
 APP-BP1+16q22↓↓(26, 29)
 miR family “miR15a, miR16, miR195, miR424 and miR497”+a(42)
 RASSF1A3p↓↓(2, 17, 19, 26)
 FHIT3p↓↓(2, 17, 19, 26)
Receptor tyrosine kinases
 EGFR7p12↑↑, mu(22, 28)
 FGFR18p11↑↑(22, 28)
 FGFR2/3+mu(22, 28)
PI3K pathway
 PIK3CA+3q26↑↑, mu(7, 22, 27, 36)
 PIK3R1+mu(22, 36)
MAPK pathway
 KRAS+mu(28)
 HRASmu(22)
TGFβ pathway
 SMAD4+ and −18q21↓↓ and ↑↑(17)
Immune response
 TRAF3+14q32↓↓(22)
 IFN-induced genes (IFIT1, IFITM1-3, IFI6-16, OAS2)+(46)
 IL6+(50)
 IL10+(46)
 IL13+(46)
 Immunoglobulins+(51)
 Lactotransferrins+(51)
 Lymphocyte activation induced (HLA-DRA, HLA-DRB1/3/5, CSK, ICAM1)+(52)
JAK–STAT pathway
 JAK3, STAT5A+me(40)
DNA repair or recombination
 ATM+11q22↓↓(28)
 BRCA1/2+mu(28)
 Testis-specific genes (SYCP2, TCAM1, STAG3)+(7, 41, 46)
 SMG1+me(37)
EMT
 Cadherin family members (CDH8/15, PCDH8-10, PCDHB3)+me(39)
Tissue development and regeneration
 ALDH1A2me(38)
 OSR2me(38)
 GATA4+me(38)
 GRIA1+me(38)
 IRX4+me(38)
Other
 FADD11q13↑↑(22)
 CTTN11q13↑↑(22, 41, 52)
 miR363+(42, 43)
 N/Ab5q↓↓(17, 19, 26)
 N/Ab+7q↑↑(27)
 N/Ab+ and −8p↑↑ and ↓↓(19)
 N/Ab13q↓↓(19)
 N/Ab15q↓↓(26)
 N/AbXp↑↑(26)

NOTE: Chromosomal location for gained or deleted regions is indicated. ↑↑, gain or amplification; ↓↓, loss or deletion; ↑, upregulated; ↓, downregulated; mu, mutated; me, promoter methylated; (+), HPV+; (−), HPV−.

  • amiR15a and miR16 are upregulated in HPV+ oropharyngeal cancer, whereas miR195 and miR497 are downregulated.

  • bNo single molecular markers were mentioned in association with these aberrations.