The landscape of BRAF transcript and protein variants in human cancer

Abstract

BackgroundThe BRAF protein kinase is widely studied as a cancer driver and therapeutic target. However, the regulation of its expression is not completely understood.ResultsTaking advantage of the RNA-seq data of more than 4800 patients belonging to 9 different cancer types, we show that BRAF mRNA exists as a pool of 3 isoforms (reference BRAF, BRAF-X1, and BRAF-X2) that differ in the last part of their coding sequences, as well as in the length (BRAF-ref: 76 nt; BRAF-X1 and BRAF-X2: up to 7 kb) and in the sequence of their 3’UTRs. The expression levels of BRAF-ref and BRAF-X1/X2 are inversely correlated, while the most prevalent among the three isoforms varies from cancer type to cancer type. In melanoma cells, the X1 isoform is expressed at the highest level in both therapy-naïve cells and cells with acquired resistance to vemurafenib driven by BRAF gene amplification or expression of the Δ[3–10] splicing variant. In addition to the BRAF-ref protein, the BRAF-X1 protein (the full length as well as the Δ[3–10] variant) is also translated. The expression levels of the BRAF-ref and BRAF-X1 proteins are similar, and together they account for BRAF functional activities. In contrast, the endogenous BRAF-X2 protein is hard to detect because the C-terminal domain is selectively recognized by the ubiquitin-proteasome pathway and targeted for degradation.ConclusionsBy shedding light on the repertoire of BRAF mRNA and protein variants, and on the complex regulation of their expression, our work paves the way to a deeper understanding of a crucially important player in human cancer and to a more informed development of new therapeutic strategies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12943-017-0645-4) contains supplementary material, which is available to authorized users.

Correlation of BRAF Variant V595E, Breed, Histological Grade and Cyclooxygenase-2 Expression in Canine Transitional Cell Carcinomas

“…In humans, only 1% of TCC is caused by BRAF mutation [32], and this mutation appeared to be infrequent in TCC [31]. However, BRAF mutation plays a crucial role in human cancer, and about 7% of all cancer cases carry this mutation [33]. It is frequently mutated in melanomas (50%) [34], papillary thyroid cancers (45%) [35], colon cancers (10%) [36], and in non-small-cell lung cancers (10%) [37].…”

Inducible modulation of miR-204 levels in a zebrafish melanoma model

“…As previously reported ( Marranci et al, 2017 ; Marranci et al, 2019 ), real-time PCR (qRT-PCR) was performed in triplicate, using 2 ul of a 1:4 dilution of cDNA, appropriate primers (0.5 uM each) and SSOADV Universal SYBR Green (Bio-Rad) in 15 ul final reaction volume on a CFX96 Real-Time System (Bio-Rad). The following amplification conditions were used: 30 s 98°C (3 s 98°C, 20 s 60°C, 10 s 72°C)×40 cycles for mRNAs and 30 s 98°C (3 s 98°C, 20 s 58°C, 10 s 72°C)×40 cycles for microRNAs.…”

Precision Medicine in Lung Cancer

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