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Table 1 Promising oral, and head and neck cancer salivary biomarkers discovered using epigenomics, transcriptomics, proteomics and metabolomics

From: Salivary biomarker development using genomic, proteomic and metabolomic approaches

Approach   Markers Sensitivity/specificity (%)/AUC
Epigenomics Candidate from previous study, Q-MSP analysis (HNSCC) [29] DAPK, DCC, MINT-31, TIMP-3, p16, MGMT, CCNA1 NR
  Candidate gene selection based on a previous study, Q-MSP discovery and validation (HNSCC) [23] MINT31, CCNA1, DCC, DAPK, p16 34.1/91.8/0.63
   MINT31, CCNA1, p16 24.0/97.1/0.61
  Candidate from previous study, Q-MSP discovery and validation (HNSCC) [25] KIF1A, EDNRB 77.4/93.1/NR
  Candidate from previous study, Q-MSP assessment (HNSCC) [26] EDNRB 65/51/0.61
  Discovery by methylation array (OSCC) [27] GABRB3_E42_F, IL11_P11_R, INSR_P1063_R, NOTCH3_E403_F, NTRK3_E131_F, PXN_P308_F 77/83/NR
   ADCYAP1_P455_R, CEBPA_P706_F, EPHA5_E158_R, FGF3_E198_R, HLF_E192_F, IL11_P11_R, INSR_P1063_R, NOTCH3_E403_F 69/96/NR
   ERBB4_P255_F, IL11_P11_R, PTCH2_P37_F, TMEFF1_P234_F, TNFSF10_E53_F, TWIST1_P44_R 62/100/NR
  Discovery with HumanMethylation27 DNA assay, validation with Q-MSP [30] HOXA9, NID2 50/90/0.77
Transcriptomics Microarray discovery and qPCR validation (OSCC) [4] IL8, IL1B, OAZ1, SAT 91/91/0.95
  qRTPCR and ELISA validation of previously reported candidates [67] IL-8, SAT, H3F3A, S100P 71/89/0.81
   IL-8, IL-1B, SAT, OAZ1 79/77/0.86
   IL-8, IL-1B, SAT, DUSP1 80/77/0.85
   IL-8, IL-1B, S100P, OAZ1 64/86/0.78
   IL-8, SAT, OAZ1, S100P 87/56/0.75
  Discovery and validation by RT-preamp-qPCR (OSCC) [6] miR-200a NR/NR/0.65
   miR-125a NR/NR/0.62
  Candidate gene selection based on previous study, qRT-PCR quantification [57] miR-31 80/68/0.82
Proteomics Discovery by C4 RP-LC and capillary reversed-phase LC with quadruple time-of-flight MS and validation by ELISA and immunoblotting (OSCC) [15] M2BP, profilin, CD59, MRP14, catalase 90/83/0.93
  ELISA assessment and qPCR confirmation [65] IL-8 86/97/0.98
Combination of proteomic/transcriptomics Reproducibility study of validated biomarkers using ELISA and qRT-PCR (OSCC) [46] Proteins: IL-1B, IL-8 and M2BP  
mRNAs: IL-8, IL-1B, SAT1, S100P 0.89/0.78/0.86, 0.67/0.96/0.85, 0.82/0.84/0.88 for OSCC total/T1-T2/T3-T4 respectively   
Metabolomics ULC/Q-TOF-MS (OSCC) [8] Valine, lactic acid 86.5/82.4/0.89
  Discovery by CE-TOF-MS-based metabolomics [7] Taurine, piperidine and a peak at 120.0801 m/z NR/NR/0.87
  1. AUC, area under curve; CE-TOF-MS, capillary electrophoresis time-of-flight mass spectrometry; ELISA, enzyme-linked immunosorbent assay; HNSCC, head and neck squamous cell carcinoma; LC, liquid chromatography; MS, mass spectrometry; NR, not reported; OSCC, oral squamous cell carcinoma; Q-MSP, quantitative methylation-sensitive PCR; qPCR, quantitative PCR; qRT-PCR, quantitative reverse transcription PCR; RT-preamp-qPCR, reverse transcription preamplification quantitative PCR; ULC/Q-TOF-MS, ultraperformance liquid chromatography coupled with quadruple/time-of-flight mass spectrometry; C4 RP-LC, C4 reversed-phase liquid chromatography.