Cargando…

A framework for mutational signature analysis based on DNA shape parameters

The mutation risk of a DNA locus depends on its oligonucleotide context. In turn, mutability of oligonucleotides varies across individuals, due to exposure to mutagenic agents or due to variable efficiency and/or accuracy of DNA repair. Such variability is captured by mutational signatures, a mathem...

Descripción completa

Detalles Bibliográficos
Autores principales: Karolak, Aleksandra, Levatić, Jurica, Supek, Fran
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8752002/
https://www.ncbi.nlm.nih.gov/pubmed/35015788
http://dx.doi.org/10.1371/journal.pone.0262495
_version_ 1784631801510100992
author Karolak, Aleksandra
Levatić, Jurica
Supek, Fran
author_facet Karolak, Aleksandra
Levatić, Jurica
Supek, Fran
author_sort Karolak, Aleksandra
collection PubMed
description The mutation risk of a DNA locus depends on its oligonucleotide context. In turn, mutability of oligonucleotides varies across individuals, due to exposure to mutagenic agents or due to variable efficiency and/or accuracy of DNA repair. Such variability is captured by mutational signatures, a mathematical construct obtained by a deconvolution of mutation frequency spectra across individuals. There is a need to enhance methods for inferring mutational signatures to make better use of sparse mutation data (e.g., resulting from exome sequencing of cancers), to facilitate insight into underlying biological mechanisms, and to provide more accurate mutation rate baselines for inferring positive and negative selection. We propose a conceptualization of mutational signatures that represents oligonucleotides via descriptors of DNA conformation: base pair, base pair step, and minor groove width parameters. We demonstrate how such DNA structural parameters can accurately predict mutation occurrence due to DNA repair failures or due to exposure to diverse mutagens such as radiation, chemical exposure, and the APOBEC cytosine deaminase enzymes. Furthermore, the mutation frequency of DNA oligomers classed by structural features can accurately capture systematic variability in mutagenesis of >1,000 tumors originating from diverse human tissues. A nonnegative matrix factorization was applied to mutation spectra stratified by DNA structural features, thereby extracting novel mutational signatures. Moreover, many of the known trinucleotide signatures were associated with an additional spectrum in the DNA structural descriptor space, which may aid interpretation and provide mechanistic insight. Overall, we suggest that the power of DNA sequence motif-based mutational signature analysis can be enhanced by drawing on DNA shape features.
format Online
Article
Text
id pubmed-8752002
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-87520022022-01-12 A framework for mutational signature analysis based on DNA shape parameters Karolak, Aleksandra Levatić, Jurica Supek, Fran PLoS One Research Article The mutation risk of a DNA locus depends on its oligonucleotide context. In turn, mutability of oligonucleotides varies across individuals, due to exposure to mutagenic agents or due to variable efficiency and/or accuracy of DNA repair. Such variability is captured by mutational signatures, a mathematical construct obtained by a deconvolution of mutation frequency spectra across individuals. There is a need to enhance methods for inferring mutational signatures to make better use of sparse mutation data (e.g., resulting from exome sequencing of cancers), to facilitate insight into underlying biological mechanisms, and to provide more accurate mutation rate baselines for inferring positive and negative selection. We propose a conceptualization of mutational signatures that represents oligonucleotides via descriptors of DNA conformation: base pair, base pair step, and minor groove width parameters. We demonstrate how such DNA structural parameters can accurately predict mutation occurrence due to DNA repair failures or due to exposure to diverse mutagens such as radiation, chemical exposure, and the APOBEC cytosine deaminase enzymes. Furthermore, the mutation frequency of DNA oligomers classed by structural features can accurately capture systematic variability in mutagenesis of >1,000 tumors originating from diverse human tissues. A nonnegative matrix factorization was applied to mutation spectra stratified by DNA structural features, thereby extracting novel mutational signatures. Moreover, many of the known trinucleotide signatures were associated with an additional spectrum in the DNA structural descriptor space, which may aid interpretation and provide mechanistic insight. Overall, we suggest that the power of DNA sequence motif-based mutational signature analysis can be enhanced by drawing on DNA shape features. Public Library of Science 2022-01-11 /pmc/articles/PMC8752002/ /pubmed/35015788 http://dx.doi.org/10.1371/journal.pone.0262495 Text en © 2022 Karolak et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Karolak, Aleksandra
Levatić, Jurica
Supek, Fran
A framework for mutational signature analysis based on DNA shape parameters
title A framework for mutational signature analysis based on DNA shape parameters
title_full A framework for mutational signature analysis based on DNA shape parameters
title_fullStr A framework for mutational signature analysis based on DNA shape parameters
title_full_unstemmed A framework for mutational signature analysis based on DNA shape parameters
title_short A framework for mutational signature analysis based on DNA shape parameters
title_sort framework for mutational signature analysis based on dna shape parameters
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8752002/
https://www.ncbi.nlm.nih.gov/pubmed/35015788
http://dx.doi.org/10.1371/journal.pone.0262495
work_keys_str_mv AT karolakaleksandra aframeworkformutationalsignatureanalysisbasedondnashapeparameters
AT levaticjurica aframeworkformutationalsignatureanalysisbasedondnashapeparameters
AT supekfran aframeworkformutationalsignatureanalysisbasedondnashapeparameters
AT karolakaleksandra frameworkformutationalsignatureanalysisbasedondnashapeparameters
AT levaticjurica frameworkformutationalsignatureanalysisbasedondnashapeparameters
AT supekfran frameworkformutationalsignatureanalysisbasedondnashapeparameters