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Open AccessArticle

Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations

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Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IMBCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and University of Salamanca (USAL), 37007 Salamanca, Spain
2
Human Molecular Genetics Lab, Department of Biology, Universidad del Valle, 477027 Meléndez University City, Cali 25360, Colombia
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School of Systems Engineering and Computation, Universidad del Valle, 477027 Meléndez University City, Cali 25360, Colombia
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Department of Basic Health Sciences, Pontificia Universidad Javeriana Cali, Cali 110321, Colombia
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Department of Biology, University of Cauca, Popayán 190003, Colombia
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Imbanaco Medical Center, Cali 760042, Colombia
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School of Electrical and Electronic Engineering, Universidad del Valle, 477027 Meléndez University City, Cali 25360, Colombia
*
Authors to whom correspondence should be addressed.
Biomolecules 2020, 10(5), 698; https://doi.org/10.3390/biom10050698
Received: 14 January 2020 / Revised: 4 April 2020 / Accepted: 23 April 2020 / Published: 30 April 2020
Cancer is one of the leading causes of mortality worldwide. Breast cancer is the most frequent cancer in women, and in recent years it has become a serious public health problem in Colombia. The development of large-scale omic techniques allows simultaneous analysis of all active genes in tumor cells versus normal cells, providing new ways to discover the drivers of malignant transformations. Whole exome sequencing (WES) was obtained to provide a deep view of the mutational genomic profile in a set of cancer samples from Southwest Colombian women. WES was performed on 52 tumor samples from patients diagnosed with invasive breast cancer, which in most cases (33/52) were ductal luminal breast carcinomas (IDC-LM-BRCA). Global variant call was calculated, and six different algorithms were applied to filter out false positives and identify pathogenic variants. To compare and expand the somatic tumor variants found in the Colombian cohort, exome mutations and genome-wide expression alterations were detected in a larger set of tumor samples of the same breast cancer subtype from TCGA (that included DNA-seq and RNA-seq data). Genes with significant changes in both the mutational and expression profiles were identified, providing a set of genes and mutations associated with the etiology of ductal luminal breast cancer. This set included 19 single mutations identified as tumor driver mutations in 17 genes. Some of the genes (ATM, ERBB3, ESR1, TP53) are well-known cancer genes, while others (CBLB, PRPF8) presented driver mutations that had not been reported before. In the case of the CBLB gene, several mutations were identified in TCGA IDC-LM-BRCA samples associated with overexpression of this gene and repression of tumor suppressive activity of TGF-β pathway. View Full-Text
Keywords: breast cancer; cancer genomics; genetic variant; whole exome sequencing; SNPs; differential expression; RNA-seq; bioinformatics; Limma-Voom; DESeq2 breast cancer; cancer genomics; genetic variant; whole exome sequencing; SNPs; differential expression; RNA-seq; bioinformatics; Limma-Voom; DESeq2
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Cortes-Urrea, C.; Bueno-Gutiérrez, F.; Solarte, M.; Guevara-Burbano, M.; Tobar-Tosse, F.; Vélez-Varela, P.E.; Bonilla, J.C.; Barreto, G.; Velasco-Medina, J.; Moreno, P.A.; De Las Rivas, J. Exomes of Ductal Luminal Breast Cancer Patients from Southwest Colombia: Gene Mutational Profile and Related Expression Alterations. Biomolecules 2020, 10, 698.

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