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Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes

Breast cancer is a heterogeneous disease classified into four main subtypes with different clinical outcomes, such as patient survival, prognosis, and relapse. Current genetic tests for the differential diagnosis of BC subtypes showed a poor reproducibility. Therefore, an early and correct diagnosis...

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Autores principales: Cava, Claudia, Armaos, Alexandros, Lang, Benjamin, Tartaglia, Gian G., Castiglioni, Isabella
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8758778/
https://www.ncbi.nlm.nih.gov/pubmed/35027621
http://dx.doi.org/10.1038/s41598-021-04664-z
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author Cava, Claudia
Armaos, Alexandros
Lang, Benjamin
Tartaglia, Gian G.
Castiglioni, Isabella
author_facet Cava, Claudia
Armaos, Alexandros
Lang, Benjamin
Tartaglia, Gian G.
Castiglioni, Isabella
author_sort Cava, Claudia
collection PubMed
description Breast cancer is a heterogeneous disease classified into four main subtypes with different clinical outcomes, such as patient survival, prognosis, and relapse. Current genetic tests for the differential diagnosis of BC subtypes showed a poor reproducibility. Therefore, an early and correct diagnosis of molecular subtypes is one of the challenges in the clinic. In the present study, we identified differentially expressed genes, long non-coding RNAs and RNA binding proteins for each BC subtype from a public dataset applying bioinformatics algorithms. In addition, we investigated their interactions and we proposed interacting biomarkers as potential signature specific for each BC subtype. We found a network of only 2 RBPs (RBM20 and PCDH20) and 2 genes (HOXB3 and RASSF7) for luminal A, a network of 21 RBPs and 53 genes for luminal B, a HER2-specific network of 14 RBPs and 30 genes, and a network of 54 RBPs and 302 genes for basal BC. We validated the signature considering their expression levels on an independent dataset evaluating their ability to classify the different molecular subtypes with a machine learning approach. Overall, we achieved good performances of classification with an accuracy >0.80. In addition, we found some interesting novel prognostic biomarkers such as RASSF7 for luminal A, DCTPP1 for luminal B, DHRS11, KLC3, NAGS, and TMEM98 for HER2, and ABHD14A and ADSSL1 for basal. The findings could provide preliminary evidence to identify putative new prognostic biomarkers and therapeutic targets for individual breast cancer subtypes.
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spelling pubmed-87587782022-01-14 Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes Cava, Claudia Armaos, Alexandros Lang, Benjamin Tartaglia, Gian G. Castiglioni, Isabella Sci Rep Article Breast cancer is a heterogeneous disease classified into four main subtypes with different clinical outcomes, such as patient survival, prognosis, and relapse. Current genetic tests for the differential diagnosis of BC subtypes showed a poor reproducibility. Therefore, an early and correct diagnosis of molecular subtypes is one of the challenges in the clinic. In the present study, we identified differentially expressed genes, long non-coding RNAs and RNA binding proteins for each BC subtype from a public dataset applying bioinformatics algorithms. In addition, we investigated their interactions and we proposed interacting biomarkers as potential signature specific for each BC subtype. We found a network of only 2 RBPs (RBM20 and PCDH20) and 2 genes (HOXB3 and RASSF7) for luminal A, a network of 21 RBPs and 53 genes for luminal B, a HER2-specific network of 14 RBPs and 30 genes, and a network of 54 RBPs and 302 genes for basal BC. We validated the signature considering their expression levels on an independent dataset evaluating their ability to classify the different molecular subtypes with a machine learning approach. Overall, we achieved good performances of classification with an accuracy >0.80. In addition, we found some interesting novel prognostic biomarkers such as RASSF7 for luminal A, DCTPP1 for luminal B, DHRS11, KLC3, NAGS, and TMEM98 for HER2, and ABHD14A and ADSSL1 for basal. The findings could provide preliminary evidence to identify putative new prognostic biomarkers and therapeutic targets for individual breast cancer subtypes. Nature Publishing Group UK 2022-01-13 /pmc/articles/PMC8758778/ /pubmed/35027621 http://dx.doi.org/10.1038/s41598-021-04664-z Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Cava, Claudia
Armaos, Alexandros
Lang, Benjamin
Tartaglia, Gian G.
Castiglioni, Isabella
Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes
title Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes
title_full Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes
title_fullStr Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes
title_full_unstemmed Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes
title_short Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes
title_sort identification of long non-coding rnas and rna binding proteins in breast cancer subtypes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8758778/
https://www.ncbi.nlm.nih.gov/pubmed/35027621
http://dx.doi.org/10.1038/s41598-021-04664-z
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