Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis.

de Jong, Joep J; Liu, Yang; Robertson, A Gordon; Seiler, Roland; Groeneveld, Clarice S; van der Heijden, Michiel S; Wright, Jonathan L; Douglas, James; Dall'Era, Marc; Crabb, Simon J; van Rhijn, Bas W G; van Kessel, Kim E M; Davicioni, Elai; Castro, Mauro A A; Lotan, Yair; Zwarthoff, Ellen C; Black, Peter C; Boormans, Joost L; Gibb, Ewan A (2019). Long non-coding RNAs identify a subset of luminal muscle-invasive bladder cancer patients with favorable prognosis. Genome medicine, 11(1), p. 60. BioMed Central 10.1186/s13073-019-0669-z

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BACKGROUND

Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease, and gene expression profiling has identified several molecular subtypes with distinct biological and clinicopathological characteristics. While MIBC subtyping has primarily been based on messenger RNA (mRNA), long non-coding RNAs (lncRNAs) may provide additional resolution.

METHODS

LncRNA expression was quantified from microarray data of a MIBC cohort treated with neoadjuvant chemotherapy (NAC) and radical cystectomy (RC) (n = 223). Unsupervised consensus clustering of highly variant lncRNAs identified a four-cluster solution, which was characterized using a panel of MIBC biomarkers, regulon activity profiles, gene signatures, and survival analysis. The four-cluster solution was confirmed in The Cancer Genome Atlas (TCGA) cohort (n = 405). A single-sample genomic classifier (GC) was trained using ridge-penalized logistic regression and validated in two independent cohorts (n = 255 and n = 94).

RESULTS

NAC and TCGA cohorts both contained an lncRNA cluster (LC3) with favorable prognosis that was enriched with tumors of the luminal-papillary (LP) subtype. In both cohorts, patients with LP tumors in LC3 (LPL-C3) were younger and had organ-confined, node-negative disease. The LPL-C3 tumors had enhanced FGFR3, SHH, and wild-type p53 pathway activity. In the TCGA cohort, LPL-C3 tumors were enriched for FGFR3 mutations and depleted for TP53 and RB1 mutations. A GC trained to identify these LPL-C3 patients showed robust performance in two validation cohorts.

CONCLUSIONS

Using lncRNA expression profiles, we identified a biologically distinct subgroup of luminal-papillary MIBC with a favorable prognosis. These data suggest that lncRNAs provide additional information for higher-resolution subtyping, potentially improving precision patient management.

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