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Volume 12
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10.3390/genes12020320
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Brief Report

Differential Expression of BARD1 Isoforms in Melanoma

by
Lorissa I. McDougall
1,†,
Ryan M. Powell
1,†,
Magdalena Ratajska
1,2,
Chi F. Lynch-Sutherland
1,
Sultana Mehbuba Hossain
1,
George A. R. Wiggins
3,
Agnieszka Harazin-Lechowska
4,
Bożena Cybulska-Stopa
5,
Jyoti Motwani
1,
Erin C. Macaulay
1,
Glen Reid
1,
Logan C. Walker
3,
Janusz Ryś
4 and
Michael R. Eccles
1,6,*
1
Department of Pathology, Otago Medical School, Dunedin Campus, University of Otago, Dunedin 9010, New Zealand
2
Department of Biology and Medical Genetics, Medical University of Gdansk, 80-211 Gdansk, Poland
3
Department of Pathology and Biomedical Science, University of Otago, Christchurch 8011, New Zealand
4
Department of Tumour Pathology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, Poland
5
Department of Clinical Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, Cracow Branch, 8011 Cracow, Poland
6
Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1010, New Zealand
*
Author to whom correspondence should be addressed.
†
Authors contributed equally to this work.
Genes 2021, 12(2), 320; https://doi.org/10.3390/genes12020320
Submission received: 24 December 2020 / Revised: 12 February 2021 / Accepted: 20 February 2021 / Published: 23 February 2021
(This article belongs to the Special Issue BARD1 in Cancer)
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Abstract

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 BARD1 splice isoforms in melanoma cell lines and patient tissue samples. Seventy-six BARD1 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 BARD1 splice variants in melanoma are warranted.
Keywords: melanoma; BARD1; nanopore sequencing; RNA-Seq melanoma; BARD1; nanopore sequencing; RNA-Seq

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MDPI and ACS Style

McDougall, L.I.; Powell, R.M.; Ratajska, M.; Lynch-Sutherland, C.F.; Hossain, S.M.; Wiggins, G.A.R.; Harazin-Lechowska, A.; Cybulska-Stopa, B.; Motwani, J.; Macaulay, E.C.; et al. Differential Expression of BARD1 Isoforms in Melanoma. Genes 2021, 12, 320. https://doi.org/10.3390/genes12020320

AMA Style

McDougall LI, Powell RM, Ratajska M, Lynch-Sutherland CF, Hossain SM, Wiggins GAR, Harazin-Lechowska A, Cybulska-Stopa B, Motwani J, Macaulay EC, et al. Differential Expression of BARD1 Isoforms in Melanoma. Genes. 2021; 12(2):320. https://doi.org/10.3390/genes12020320

Chicago/Turabian Style

McDougall, Lorissa I., 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, and et al. 2021. "Differential Expression of BARD1 Isoforms in Melanoma" Genes 12, no. 2: 320. https://doi.org/10.3390/genes12020320

APA Style

McDougall, L. I., Powell, R. M., Ratajska, M., Lynch-Sutherland, C. F., Hossain, S. M., Wiggins, G. A. R., Harazin-Lechowska, A., Cybulska-Stopa, B., Motwani, J., Macaulay, E. C., Reid, G., Walker, L. C., Ryś, J., & Eccles, M. R. (2021). Differential Expression of BARD1 Isoforms in Melanoma. Genes, 12(2), 320. https://doi.org/10.3390/genes12020320

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