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Inter-tumor heterogeneity might explain divergent clinical evolution of cancers bearing similar pathological features. In the last decade, genomic has highly improved tumor subtypes classification through the identification of oncogenic or tumor suppressor drivers. In addition, epigenetics and long non-coding RNAs (lncRNAs) are emerging as new fields for investigation, which might also account for tumor heterogeneity. There is growing evidence that modifications of lncRNA expression profiles are involved in cancer progression through epigenetic regulation, activation of pro-oncogenic pathways and crosstalks with other RNA subtypes. Consequently, the study of lncRNA expression profile will be a key factor in the future for charting cancer subtype classifications as well as defining prognostic and progression biomarkers.
Cancer subtype classifications based on lncRNA expression profiles
|
Cancer type |
LncRNA database |
Assessment of lncRNA expression |
N |
LncRNA classification |
Molecular alterations |
Prognosis |
|
Glioma |
Refseq, Ensembl |
Microarrays |
284 |
lncR1 lncR2 lncR3 |
Astroglial signature, EGFR amplification Neuronal signature, no recurrent alteration Oligodendroglial signature, IDH1 mutation, |
Overall survival Poor Intermediate Good |
|
Colon |
GEO |
Microarrays |
895 |
High risk Low risk |
N/A N/A |
DFS (150-months DFS) Poor (51,49%) Good (78,09%) |
|
Breast |
GENCODE |
RNA-sequencing |
656 |
C1 C2 C3 C4 |
Basal-like HER2-enriched Luminal A Luminal A + luminal B |
Overall survival Good Poor Good Poor |
|
Renal cell carcinoma |
GENCODE |
RNA-sequencing |
475 |
C1 C2 C3 C4 |
PBRM1 mutations, 9p deletion, BAP 1 mutations PBRM1 mutations Misclassified |
Overall survival (median) Good (7,64 years) Poor (3,33 years) Good (not reached) Good (not reached) |
|
Endometrioid endometrial carcinoma |
GENCODE |
RNA-sequencing |
191 |
Basal-like Luminal-like CTNNB1-enriched |
MSI, POLE, p53 mutations, ESR1, ERBB2 expression CTNNB1 mutations, PTEN loss |
No distinct prognostic groups |
GEO: Gene Expression Omnibus. DFS: disease free survival. EMT: epithelial mesenchymal trnasition. MSI: microsatellite instability, POLE: polymerase epsilon, N/A: not available
