Table 1.
The application of m6A modification in prognostic risk models of different kinds of lung cancer.
| Type of lung cancer | Risk signature | Prognostic factors and biomarkers | Expression in lung tumour | Prognostic | Enriched pathways or biological processes | Ref. |
|---|---|---|---|---|---|---|
| LUAD | regulator | HNRNPC | ↑ | low OS | pyrimidine metabolism, purine metabolism, spliceosome, cell cycle, RNA degradation, RNA polymerase, basal transcription factors, DNA replication, mismatch repair, nucleotide excision repair | [143] |
| IGF2BP3 | ↑ | low OS | G2M checkpoint, E2F targets, mitotic spindle, spermatogenesis, MTORC1 signalling, MYC targets V1, MYC targets V2, glycolysis, epithelial-mesenchymal transition, DNA repair | [144] | ||
| IGF2BP1 | ↑ | poor prognosis | cell cycle-related pathway (positive correlation): organelle fission, spindle organisation, DNA recombination immune regulation (negative correlation): leucocyte activation involved in inflammatory response, mast cell-mediated immunity, cilium or flagellum-dependent cell motility | [145] | ||
|
YTHDC1, YTHDC2 YTHDF1, YTHDF2, YTHDF3 |
↓ ↑ |
low YTHDC2, YTHDF1, YTHDF2 better OS | antigen processing and presentation, hemidesmosome assembly, formation of primary germ layer, appendage development | [146] | ||
| HNRNPA2B1, HNRNPC, KIAA1429, RBM15, METTL3 | ↑ | poor prognosis | cell cycle, DNA replication, RNA degradation, RNA polymerase, nucleotide excision repair, basal transcription factors | [147] | ||
| METTL14, METTL3, ZC3H13, YTHDF1, HNRNPC, RBM15 | ↑ | poor prognosis | cell cycle, RNA degradation, p53 signalling pathway, homologous recombination, mismatch repair | [149] | ||
|
LUAD LUSC |
regulator |
LUAD: IGF2BP1, IGF2BP2, HNRNPC, KIAA1429, HNRNPA2B1 LUSC: CBLL1, HNRNPC, METTL3 |
poor prognosis | [148] | ||
| SCLC | regulator |
G3BP1, METTL5 ALKBH5, IGF2BP3, RBM15B |
↑ | high score: low OS | [150] | |
| LUSC | regulator gene | FTO, METTL3 | ↑ | high‐risk group: low OS | [151] | |
| WTAP, YTHDC1, YTHDF1 | ↑ | high‐risk group: low OS | [152] | |||
| LUAD | regulator gene | KIAA1429, RBM15, HNRNPC | ↑ | poor prognosis | extracellular matrix structural constituent conferring tensile strength, receptor regulator activity, receptor-ligand activity, protein digestion and absorption, cell cycle, neuroactive ligand-receptor interaction signalling pathways | [153] |
| IGF2BP3, HNRNPA2B1, HNRNPC | ↑ | high-risk group: low OS | G2M checkpoint, E2F targets, MTORC1 signalling, MYC targets, DNA repair | [154] | ||
| IGF2BP1, HNRNPC, HNRNPA2B1 | ↑ | poor prognosis | cell cycle, genetic material (purine and pyrimidine) metabolism, DNA replication, translation process (RNA polymerase and RNA degradation) | [155] | ||
|
ZCRB1 ADH1C, YTHDC2 |
↑ ↓ |
poor prognosis | nuclear division, organelle fission, regulation of mRNA metabolic process, regulation of chromosome organisation | [156] | ||
| HNRNPC, IGFBP3, IGF2BP1 | ↑ | high-risk group: low OS | humoral immune response, defence response to bacterium, hormone metabolic process, apical part of the cell, apical plasma membrane, secretory granule lumen, receptor-ligand activity, enzyme inhibitor activity | [157] | ||
| METTL3, IGF2BP2, HNRNPC, HNRNPA2B1 | ↑ | high-risk score: poor prognosis | [158] | |||
| IGF2BP1, IGF2BP2, HNRNPA2B1, METTL3, HNRNPC | ↑ | high-risk group: low OS | cell division, cell proliferation, cell cycle, p53 signalling pathway | [159] | ||
| CLEC3B, TENM3, IGF2BP1, E2F7, ANLN, ANKRD18B, FBN2 | high-risk score: poor prognosis | immune-related biological processes (humoral immune response and regulation of adaptive immune response), cell cycle | [49] | |||
| HNRNPC, METTL3, KIAA1429, YTHDC2, ALKBH5, YTHDF1 | ↑ | high-risk score: poor prognosis | RNA modification, regulation of mRNA metabolic process, mRNA methylation, mRNA modification, regulation of mRNA stability, regulation of RNA stability, RNA methylation, regulation of mRNA catabolic process, mRNA processing, positive regulation of translational initiation | [160] | ||
|
LUSC; LUAD |
regulator gene |
METTL3, YTHDC1, HNRNPC; YTHDC2, METTL3, RBM15, HNRNPC, YTHDF2, YTHDF1, ZC3H13, KIAA1429 |
ZC3H13: ↓ Others: ↑ |
high‐risk score: low OS |
SMAD protein signal transduction, regulation of mitogen-activated protein kinase cascade, positive regulation of cell growth/division. viral carcinogenesis, regulation of actin cytoskeleton, PPAR signalling pathway, PI3K-Akt signalling pathway |
[162] |
| NSCLC | regulator gene | FTO, YTHDC2 | ↓ | poor prognosis | oxidative phosphorylation, ribosome, translation, 3-UTR-mediated translational regulation, metabolism of mRNA, influenza life cycle | [163] |
| LUAD | m6A-related RNA | RFXAP, KHDRBS2, MAPRE3, TXN, EGFR, MGST3, USP1, ARHGEF4, CDHR5, ADAMTS6 |
EGFR: ↑ Others: ↓ |
high-risk score: low OS | RNA biosynthetic processes and developmental process | [164] |
| NSCLC | m6A-related-AS |
LUAD: DGKZ|15540|AP, PMP22|39340|AP (risky) ABCC6|34219|AT, KIAA0586|27718|ES, LDB1|12935|AP, RPS25|19054|ES, S100A14|7729|AP (protective) LUSC: AKR1E2|10639|ES, SSH1|24258|ES (risky) ALPK1|70369|ES, FAM63A|7531|AP, CHMP1A|38102|ES, TSTD2|87013|AT, KIAA1598|13239|AP, ASXL3|45046|AT, VPS37A|82796|ES, TOX2|59455|ES, ZNF544|52429|ES, NOL8|86863|ES, FAM124B|57772|AT, PTCHD4|76446|AT (protective) |
high-risk group: low OS |
LUAD: the GPCR signalling pathway, DNA metabolic process, DNA repair, cellular response to DNA damage stimulus, carbon oxygen lyase activity, cell adhesion molecule binding pathways LUSC: the TGF-beta signalling pathway, peptidyl-serine modification, regulation of actin cytoskeleton, intracellular signalling by second messengers, early endosome pathway |
[166] | |
| LUAD | m6A-related lncRNA | AP001178.1, AL121772.2, AL360270.2, AL358115.1, AF131215.5, AC010999.2, TRAF3IP2-AS1, AC026355.2, ADPGK-AS1, LINC02656, AC012409.4 | high-risk group: low OS | Spliceosomal tri-snRNP complex assembly, formation of quadruple SL/U4/U5/U6 snRNP, mRNA trans-splicing via spliceosome, Golgi lumen, endopeptidase inhibitor activity, peptidase inhibitor activity, etc. | [167] | |
| ADPGK-AS1, AC103591.3, AC018529.1, AC010175.1, AC016747.2, AC007613.1, AC026355.2, ABALON, AC034102.8, AC073316.3, AL031667.3, AC005884.1, TSPOAP1-AS1 |
ABALON: ↑ Others: ↓ |
high-risk group: low OS | the spliceosome, mRNA surveillance, ribosome biogenesis in eukaryotes, viral carcinogenesis, nucleocytoplasmic transport pathway | [168] | ||
|
DLGAP1-AS2, COLCA1, LINC00968, MGC32805, TRG-AS1, FENDRR, RPARP-AS1, TBX5-AS1, CRNDE, TMPO-AS1, ARHGEF26-AS1 |
Upregulated TMPO-AS1 and DLGAP1-AS2: poor OS | high-risk group: low OS | cilium movement, neuronal activity ligand-receptor interaction, NABA matrisome associated | [169] | ||
| NSCLC | Co-expressed mRNAs and ncRNAs |
mRNAs: CPED1, CD302, SCN1A, NEIL3, PTPRM, CCDC68, MTURN, ANLN, LIFR, GPRIN1, DDX11, RNASE1, IGF2BP1, HMGA2, MT-ND6, and LRP8 ncRNAs: SH3BP5-AS1, AL122010.1, AL021368.3, AL162586.1, AC020978.2, AC135050.3, and AC138028.6 |
high-risk group: low OS | G2M checkpoint, mTORC1 signalling, MYC targets V1, E2F targets, PI3K-AKT-mTOR signalling, hypoxia, glycolysis, DNA repair | [170] |