Differential Expression of <i>BARD1</i> Isoforms in Melanoma
Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/2/320 |
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| author | Lorissa I. McDougall Ryan M. Powell Magdalena Ratajska Chi F. Lynch-Sutherland Sultana Mehbuba Hossain George A. R. Wiggins Agnieszka Harazin-Lechowska Bożena Cybulska-Stopa Jyoti Motwani Erin C. Macaulay Glen Reid Logan C. Walker Janusz Ryś Michael R. Eccles |
| author_facet | Lorissa I. McDougall Ryan M. Powell Magdalena Ratajska Chi F. Lynch-Sutherland Sultana Mehbuba Hossain George A. R. Wiggins Agnieszka Harazin-Lechowska Bożena Cybulska-Stopa Jyoti Motwani Erin C. Macaulay Glen Reid Logan C. Walker Janusz Ryś Michael R. Eccles |
| author_sort | Lorissa I. McDougall |
| collection | DOAJ |
| description | Melanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of <i>BARD1</i> splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six <i>BARD1</i> mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ε, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified <i>BARD1</i> splice variants in melanoma are warranted. |
| first_indexed | 2024-03-09T00:35:27Z |
| format | Article |
| id | doaj.art-61d7cbb9ba684ae8b87d221159744bbc |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T00:35:27Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-61d7cbb9ba684ae8b87d221159744bbc2023-12-11T18:10:25ZengMDPI AGGenes2073-44252021-02-0112232010.3390/genes12020320Differential Expression of <i>BARD1</i> Isoforms in MelanomaLorissa I. McDougall0Ryan M. Powell1Magdalena Ratajska2Chi F. Lynch-Sutherland3Sultana Mehbuba Hossain4George A. R. Wiggins5Agnieszka Harazin-Lechowska6Bożena Cybulska-Stopa7Jyoti Motwani8Erin C. Macaulay9Glen Reid10Logan C. Walker11Janusz Ryś12Michael R. Eccles13Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandDepartment of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandDepartment of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandDepartment of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandDepartment of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandDepartment of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New ZealandDepartment of Tumour Pathology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, PolandDepartment of Clinical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, PolandDepartment of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandDepartment of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandDepartment of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandDepartment of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New ZealandDepartment of Tumour Pathology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, PolandDepartment of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New ZealandMelanoma comprises <5% of cutaneous malignancies, yet it causes a significant proportion of skin cancer-related deaths worldwide. While new therapies for melanoma have been developed, not all patients respond well. Thus, further research is required to better predict patient outcomes. Using long-range nanopore sequencing, RT-qPCR, and RNA sequencing analyses, we examined the transcription of <i>BARD1</i> splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six <i>BARD1</i> mRNA variants were identified in total, with several previously characterised isoforms (γ, φ, δ, ε, and η) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, Δ(E3_E9), ▼(i8), IVS10+131▼46, and IVS10▼176, occurring in various combinations in multiple transcripts. We found that short-read RNA-Seq analyses were limited in their ability to predict isoforms containing multiple non-contiguous splicing events, as compared to long-range nanopore sequencing. These studies suggest that further investigations into the functional significance of the identified <i>BARD1</i> splice variants in melanoma are warranted.https://www.mdpi.com/2073-4425/12/2/320melanoma<i>BARD1</i>nanopore sequencingRNA-Seq |
| spellingShingle | Lorissa I. McDougall Ryan M. Powell Magdalena Ratajska Chi F. Lynch-Sutherland Sultana Mehbuba Hossain George A. R. Wiggins Agnieszka Harazin-Lechowska Bożena Cybulska-Stopa Jyoti Motwani Erin C. Macaulay Glen Reid Logan C. Walker Janusz Ryś Michael R. Eccles Differential Expression of <i>BARD1</i> Isoforms in Melanoma Genes melanoma <i>BARD1</i> nanopore sequencing RNA-Seq |
| title | Differential Expression of <i>BARD1</i> Isoforms in Melanoma |
| title_full | Differential Expression of <i>BARD1</i> Isoforms in Melanoma |
| title_fullStr | Differential Expression of <i>BARD1</i> Isoforms in Melanoma |
| title_full_unstemmed | Differential Expression of <i>BARD1</i> Isoforms in Melanoma |
| title_short | Differential Expression of <i>BARD1</i> Isoforms in Melanoma |
| title_sort | differential expression of i bard1 i isoforms in melanoma |
| topic | melanoma <i>BARD1</i> nanopore sequencing RNA-Seq |
| url | https://www.mdpi.com/2073-4425/12/2/320 |
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