Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells
Alternative mRNA splicing is common in cancers. In BRAF V600E-mutated malignant melanoma, a frequent mechanism of acquired resistance to BRAF inhibitors involves alternative splicing (AS) of BRAF. The resulting shortened BRAF protein constitutively dimerizes and conveys drug resistance. Here, we hav...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-07-01
|
| Series: | Biomolecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-273X/12/7/993 |
| _version_ | 1797440596406697984 |
|---|---|
| author | Honey Bokharaie Walter Kolch Aleksandar Krstic |
| author_facet | Honey Bokharaie Walter Kolch Aleksandar Krstic |
| author_sort | Honey Bokharaie |
| collection | DOAJ |
| description | Alternative mRNA splicing is common in cancers. In BRAF V600E-mutated malignant melanoma, a frequent mechanism of acquired resistance to BRAF inhibitors involves alternative splicing (AS) of BRAF. The resulting shortened BRAF protein constitutively dimerizes and conveys drug resistance. Here, we have analysed AS in SK-MEL-239 melanoma cells and a BRAF inhibitor (vemurafenib)-resistant derivative that expresses an AS, shortened BRAF V600E transcript. Transcriptome analysis showed differential expression of spliceosome components between the two cell lines. As there is no consensus approach to analysing AS events, we used and compared four common AS softwares based on different principles, DEXSeq, rMATS, ASpli, and LeafCutter. Two of them correctly identified the BRAF V600E AS in the vemurafenib-resistant cells. Only 12 AS events were identified by all four softwares. Testing the AS predictions experimentally showed that these overlapping predictions are highly accurate. Interestingly, they identified AS caused alterations in the expression of melanin synthesis and cell migration genes in the vemurafenib-resistant cells. This analysis shows that combining different AS analysis approaches produces reliable results and meaningful, biologically testable hypotheses. |
| first_indexed | 2024-03-09T12:10:27Z |
| format | Article |
| id | doaj.art-381a8ffd10824a5b9aa2769e4a473d84 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T12:10:27Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-381a8ffd10824a5b9aa2769e4a473d842023-11-30T22:52:38ZengMDPI AGBiomolecules2218-273X2022-07-0112799310.3390/biom12070993Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma CellsHoney Bokharaie0Walter Kolch1Aleksandar Krstic2Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin 4, IrelandSystems Biology Ireland, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin 4, IrelandSystems Biology Ireland, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin 4, IrelandAlternative mRNA splicing is common in cancers. In BRAF V600E-mutated malignant melanoma, a frequent mechanism of acquired resistance to BRAF inhibitors involves alternative splicing (AS) of BRAF. The resulting shortened BRAF protein constitutively dimerizes and conveys drug resistance. Here, we have analysed AS in SK-MEL-239 melanoma cells and a BRAF inhibitor (vemurafenib)-resistant derivative that expresses an AS, shortened BRAF V600E transcript. Transcriptome analysis showed differential expression of spliceosome components between the two cell lines. As there is no consensus approach to analysing AS events, we used and compared four common AS softwares based on different principles, DEXSeq, rMATS, ASpli, and LeafCutter. Two of them correctly identified the BRAF V600E AS in the vemurafenib-resistant cells. Only 12 AS events were identified by all four softwares. Testing the AS predictions experimentally showed that these overlapping predictions are highly accurate. Interestingly, they identified AS caused alterations in the expression of melanin synthesis and cell migration genes in the vemurafenib-resistant cells. This analysis shows that combining different AS analysis approaches produces reliable results and meaningful, biologically testable hypotheses.https://www.mdpi.com/2218-273X/12/7/993alternative splicing (AS)BRAF (v-Raf murine sarcoma viral oncogene homolog B)malignant melanomavemurafenibdrug resistancecancer |
| spellingShingle | Honey Bokharaie Walter Kolch Aleksandar Krstic Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells Biomolecules alternative splicing (AS) BRAF (v-Raf murine sarcoma viral oncogene homolog B) malignant melanoma vemurafenib drug resistance cancer |
| title | Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells |
| title_full | Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells |
| title_fullStr | Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells |
| title_full_unstemmed | Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells |
| title_short | Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells |
| title_sort | analysis of alternative mrna splicing in vemurafenib resistant melanoma cells |
| topic | alternative splicing (AS) BRAF (v-Raf murine sarcoma viral oncogene homolog B) malignant melanoma vemurafenib drug resistance cancer |
| url | https://www.mdpi.com/2218-273X/12/7/993 |
| work_keys_str_mv | AT honeybokharaie analysisofalternativemrnasplicinginvemurafenibresistantmelanomacells AT walterkolch analysisofalternativemrnasplicinginvemurafenibresistantmelanomacells AT aleksandarkrstic analysisofalternativemrnasplicinginvemurafenibresistantmelanomacells |