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© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.

Abstract

Simple Summary

Breast cancer (BC) is the most common invasive tumor in women and the second leading cause of cancer-related death. Therefore, identification of druggable targets to improve current therapies and overcome resistance is a major goal. In this work, we performed an in silico analysis of transcriptomic datasets in breast cancer, and focused on those involved in DNA damage, as were clearly upregulated using gene set enrichment analyses (GSEA), particular the following pathways: ATM/ATR, BARD1 and Fanconi Anemia. BHLHE40, RFWD2, BRIP1, PRKDC, NBN, RNF8, FANCD2, RAD1, BLM, DCLRE1C, UBE2T, CSTF1, MCM7, RFC4, YWHAB, YWHAZ, CDC6, CCNE1, and FANCI genes were amplified/overexpressed in BC, and correlated with detrimental prognosis. Finally, we selected the best transcriptomic signature of genes within this function that associated with clinical outcome to identify functional genomic correlates of outcome.

Abstract

Among the described druggable vulnerabilities, acting on the DNA repair mechanism has gained momentum, with the approval of PARP inhibitors in several indications, including breast cancer. However, beyond the mere presence of BRCA1/BRCA2 mutations, the identification of additional biomarkers that would help to select tumors with an extreme dependence on DNA repair machinery would help to stratify therapeutic decisions. Gene set enrichment analyses (GSEA) using public datasets evaluating expression values between normal breast tissue and breast cancer identified a set of upregulated genes. Genes included in different pathways, such as ATM/ATR, BARD1, and Fanconi Anemia, which are involved in the DNA damage response, were selected and confirmed using molecular alterations data contained at cBioportal. Nineteen genes from these gene sets were identified to be amplified and upregulated in breast cancer but only five of them NBN, PRKDC, RFWD2, UBE2T, and YWHAZ meet criteria in all breast cancer molecular subtypes. Correlation of the selected genes with prognosis (relapse free survival, RFS, and overall survival, OS) was performed using the KM Plotter Online Tool. In last place, we selected the best signature of genes within this process whose upregulation can be indicative of a more aggressive phenotype and linked with worse outcome. In summary, we identify genomic correlates within DNA damage pathway associated with prognosis in breast cancer.

Details

Title
Genomic Correlates of DNA Damage in Breast Cancer Subtypes
Author
Esther Cabañas Morafraile 1 ; Pérez-Peña, Javier 2 ; Fuentes-Antrás, Jesús 1 ; Manzano, Aránzazu 1 ; Pérez-Segura, Pedro 1 ; Pandiella, Atanasio 2 ; Galán-Moya, Eva M 3   VIAFID ORCID Logo  ; Ocaña, Alberto 4   VIAFID ORCID Logo 

 Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC) and Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28040 Madrid, Spain; [email protected] (E.C.M.); [email protected] (J.F.-A.); [email protected] (A.M.); [email protected] (P.P.-S.) 
 Instituto de Biología Molecular y Celular del Cáncer del CSIC, IBSAL and CIBERONC, 37007 Salamanca, Spain; [email protected] (J.P.-P.); [email protected] (A.P.) 
 Translational Oncology Laboratory, Centro Regional de Investigaciones Biomédicas (CRIB) and Nursery School, Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; [email protected] 
 Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC) and Centro de Investigación Biomédica en Red en Oncología (CIBERONC), 28040 Madrid, Spain; [email protected] (E.C.M.); [email protected] (J.F.-A.); [email protected] (A.M.); [email protected] (P.P.-S.); Translational Oncology Laboratory, Centro Regional de Investigaciones Biomédicas (CRIB) and Nursery School, Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; [email protected] 
First page
2117
Publication year
2021
Publication date
2021
Publisher
MDPI AG
e-ISSN
20726694
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2528255036
Copyright
© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.