Dataset Information

Differential Expression of BARD1 Isoforms in Melanoma.

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 (?, ?, ?, ?, and ?) contributing to a large proportion of the expressed transcripts. In addition, we identified four novel splice events, namely, ?(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.

SUBMITTER: McDougall LI

PROVIDER: S-EPMC7927127 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Publications

Differential Expression of BARD1 Isoforms in Melanoma.

McDougall Lorissa I LI Powell Ryan M RM Ratajska Magdalena M Lynch-Sutherland Chi F CF Hossain Sultana Mehbuba SM Wiggins George A R GAR Harazin-Lechowska Agnieszka A Cybulska-Stopa Bożena B Motwani Jyoti J Macaulay Erin C EC Reid Glen G Walker Logan C LC Ryś Janusz J Eccles Michael R MR

Genes 20210223 2

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 ...[more]

PMID: 33672422

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Project description:As more small RNA sequencing libraries are becoming available, it clearly emerges that microRNAs (miRNAs) are highly heterogeneous both in length and sequence. In comparison to canonical miRNAs, miRNA isoforms (termed as "isomiRs") might exhibit different biological properties, such as a different target repertoire, or enhanced/reduced stability. Nonetheless, this layer of information has remained largely unexplored due to the scarcity of small RNA NGS-datasets and the absence of proper analytical tools. Here, we present a workflow for the characterization and analysis of miRNAs and their variants in next-generation sequencing datasets. IsomiRs can originate from an alternative dicing event ("templated" forms) or from the addition of nucleotides through an enzymatic activity or target-dependent mechanisms ("non-templated" forms). Our pipeline allows distinguishing canonical miRNAs from templated and non-templated isomiRs by alignment to a custom database, which comprises all possible 3'-, 5'-, and trimmed variants. Functionally equivalent isomiRs can be grouped together according to the type of modification (e.g., uridylation, adenylation, trimming …) to assess which miRNAs are more intensively modified in a given biological context. When applied to the analysis of primary epithelial breast cancer cells, our methodology provided a 40% increase in the number of detected miRNA species and allowed to easily identify and classify more than 1000 variants. Most modifications were compatible with templated IsomiRs, as a consequence of imprecise Drosha or Dicer cleavage. However, some non-templated variants were consistently found either in the normal or in the cancer cells, with the 3'-end adenylation and uridylation as the most frequent events, suggesting that miRNA post-transcriptional modification frequently occurs. In conclusion, our analytical tool permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms.

Dataset Information

Differential Expression of BARD1 Isoforms in Melanoma.

Publications

Differential Expression of <i>BARD1</i> Isoforms in Melanoma.

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