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 | Â | Markers | Sensitivity/specificity (%)/AUC |
|---|---|---|---|
Epigenomics | Candidate from previous study, Q-MSP analysis (HNSCC) [29] | DAPK, DCC, MINT-31, TIMP-3, p16, MGMT, CCNA1 | NR |
| Â | 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 |
| Â | Â | MINT31, CCNA1, p16 | 24.0/97.1/0.61 |
| Â | Candidate from previous study, Q-MSP discovery and validation (HNSCC) [25] | KIF1A, EDNRB | 77.4/93.1/NR |
| Â | Candidate from previous study, Q-MSP assessment (HNSCC) [26] | EDNRB | 65/51/0.61 |
| Â | 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 |
| Â | Â | 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 |
| Â | Â | ERBB4_P255_F, IL11_P11_R, PTCH2_P37_F, TMEFF1_P234_F, TNFSF10_E53_F, TWIST1_P44_R | 62/100/NR |
| Â | 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 |
| Â | qRTPCR and ELISA validation of previously reported candidates [67] | IL-8, SAT, H3F3A, S100P | 71/89/0.81 |
| Â | Â | IL-8, IL-1B, SAT, OAZ1 | 79/77/0.86 |
| Â | Â | IL-8, IL-1B, SAT, DUSP1 | 80/77/0.85 |
| Â | Â | IL-8, IL-1B, S100P, OAZ1 | 64/86/0.78 |
| Â | Â | IL-8, SAT, OAZ1, S100P | 87/56/0.75 |
| Â | Discovery and validation by RT-preamp-qPCR (OSCC) [6] | miR-200a | NR/NR/0.65 |
| Â | Â | miR-125a | NR/NR/0.62 |
| Â | 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 |
| Â | 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 | Â |
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 | Â | Â |
Metabolomics | ULC/Q-TOF-MS (OSCC) [8] | Valine, lactic acid | 86.5/82.4/0.89 |
| Â | Discovery by CE-TOF-MS-based metabolomics [7] | Taurine, piperidine and a peak at 120.0801 m/z | NR/NR/0.87 |