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.
Highlights
Melanoma develops following the malignant transformation of pigment-producing melanocytes and is the fifth most common form of cancer in adults [1]
The results show that previously identified BARD1 mRNAs encoding isoforms, as well as novel splice isoforms, can be detected using both long-range nanopore sequencing, in addition to short-read and targeted approaches, including RNA-Seq and RT-qPCR in both melanoma cell lines and tissue samples
Using long-range PCR and nanopore sequencing, we identified a set of mRNAs corresponding to 76 different BARD1 splice variants in total (Table S3), with six variant transcripts being expressed predominately (Figure 1A)
Summary
Melanoma develops following the malignant transformation of pigment-producing melanocytes and is the fifth most common form of cancer in adults [1]. While melanoma is responsible for the majority of skin cancer-related deaths, it accounts for
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