A multimodal analysis of genomic and RNA splicing features in myeloid malignancies.
Fiche publication
Date publication
mars 2023
Journal
iScience
Auteurs
Membres identifiés du Cancéropôle Est :
Dr PAGLIUCA Simona
Tous les auteurs :
Durmaz A, Gurnari C, Hershberger CE, Pagliuca S, Daniels N, Awada H, Awada H, Adema V, Mori M, Ponvilawan B, Kubota Y, Kewan T, Bahaj WS, Barnard J, Scott J, Padgett RA, Haferlach T, Maciejewski JP, Visconte V
Lien Pubmed
Résumé
RNA splicing dysfunctions are more widespread than what is believed by only estimating the effects resulting by splicing factor mutations (SF) in myeloid neoplasia (MN). The genetic complexity of MN is amenable to machine learning (ML) strategies. We applied an integrative ML approach to identify co-varying features by combining genomic lesions (mutations, deletions, and copy number), exon-inclusion ratio as measure of RNA splicing (percent spliced in, PSI), and gene expression (GE) of 1,258 MN and 63 normal controls. We identified 15 clusters based on mutations, GE, and PSI. Different PSI levels were present at various extents regardless of SF suggesting that changes in RNA splicing were not strictly related to SF. Combination of PSI and GE further distinguished the features and identified PSI similarities and differences, common pathways, and expression signatures across clusters. Thus, multimodal features can resolve the complex architecture of MN and help identifying convergent molecular and transcriptomic pathways amenable to therapies.
Mots clés
Bioinformatics, Cancer, Omics
Référence
iScience. 2023 03 17;26(3):106238