scholarly journals Short somatic alterations at the site of copy number variation in breast cancer

2020 ◽  
Vol 112 (1) ◽  
pp. 444-453
Author(s):  
Fumi Murakami ◽  
Yumi Tsuboi ◽  
Yuka Takahashi ◽  
Yoshiya Horimoto ◽  
Kaoru Mogushi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Number Variation ◽  
Somatic Alterations

scholarly journals Human rDNA Copy Number Is Unstable in Metastatic Breast Cancers

2019 ◽  
Author(s):  
Virginia Valori ◽  
Katalin Tus ◽  
Christina Laukaitis ◽  
David T. Harris ◽  
Lauren LeBeau ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genome Instability ◽  
Gene Clusters ◽  
Genome Rearrangements ◽  
Epigenetic Silencing ◽  
Healthy Tissue ◽  
Gene Promoters ◽  
Number Variation

AbstractEpigenetic silencing, including the formation of heterochromatin, silent chromosome territories, and repressed gene promoters, acts to stabilize patterns of gene regulation and the physical structure of the genome. Reduction of epigenetic silencing can result in genome rearrangements, particularly at intrinsically unstable regions of the genome such as transposons, satellite repeats, and repetitive gene clusters including the rRNA gene clusters (rDNA). It is thus expected that mutational or environmental conditions that compromise heterochromatin function might cause genome instability, and diseases associated with decreased epigenetic stability might exhibit genome changes as part of their etiology. We find support of this hypothesis in invasive ductal breast carcinoma, in which reduced epigenetic silencing has been previously described, by using a facile method to quantify rDNA copy number in biopsied breast tumors and pair-matched healthy tissue. We found that rDNA and satellite DNA sequences had significant copy number variation – both losses and gains of copies – compared to healthy tissue, arguing that these genome rearrangements are common in developing breast cancer. Thus, any proposed etiology onset or progression of breast cancer should consider alterations to the epigenome, but must also accommodate concomitant changes to genome sequence at heterochromatic loci.Authors’ StatementOne of the common hallmarks of cancer is genome instability, including hypermutation and changes to chromosome structure. Using tumor tissues obtained from women with invasive ductal carcinoma, we find that a sensitive area of the genome – the ribosomal DNA gene repeat cluster – shows hypervariability in copy number. The patterns we observe as not consistent with an adaptive loss leading to increased tumor growth, but rather we conclude that copy number variation at repeat DNA is a general consequence of reduced heterochromatin function in cancer progression.

Abstract 4720: Genome-wide copy number variation and breast cancer risk: Preliminary report

2010 ◽  
Author(s):  
Kyoung-Mu Lee ◽  
Miey Park ◽  
Sang-Hoon Moon ◽  
Hyung-Chol Kim ◽  
Ji-Young Lee ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Breast Cancer Risk ◽  
Cancer Risk ◽  
Copy Number Variation ◽  
Copy Number ◽  
Preliminary Report ◽  
Genome Wide ◽  
Number Variation

scholarly journals Comprehensive Analysis of Metabolic Genes in Breast Cancer Based on Multi-Omics Data

2021 ◽  
Vol 27 ◽  
Author(s):  
Yu Hua ◽  
Lihong Gao ◽  
Xiaobo Li
Keyword(s):  
Breast Cancer ◽  
Dna Methylation ◽  
Arachidonic Acid ◽  
Copy Number Variation ◽  
Immune Cells ◽  
Copy Number ◽  
Clinical Parameters ◽  
Omics Data ◽  
Metabolic Genes ◽  
Number Variation

Background: Reprogramming of cell metabolism is one of the most important hallmarks of breast cancer. This study aimed to comprehensively analyze metabolic genes in the initiation, progression, and prognosis of breast cancer.Materials and Methods: Data from The Cancer Genome Atlas (TCGA) in breast cancer were downloaded including RNA-seq, copy number variation, mutation, and DNA methylation. A gene co-expression network was constructed by the weighted correlation network analysis (WGCNA) package in R. Association of metabolic genes with tumor-related immune cells and clinical parameters were also investigated.Results: We summarized 3,620 metabolic genes and observed mutations in 2,964 genes, of which the most frequently mutated were PIK3CA (51%), TNN (26%), and KMT2C (15%). Four genes (AKT1, ERBB2, KMT2C, and USP34) were associated with survival of breast cancer. Significant association was detected in the tumor mutation burden (TMB) of metabolic genes with T stage (p = 0.045) and N stage (p = 0.004). Copy number variations were significantly associated with recurrence and prognosis of breast cancer. The co-expression network for differentially expressed metabolic genes by WGCNA suggested that the modules were associated with glycerophospholipid, arachidonic acid, carbon, glycolysis/gluconeogenesis, and pyrimidine/purine metabolism. Glycerophospholipid metabolism correlated with most of the immune cells, while arachidonic acid metabolism demonstrated a significant correlation with endothelial cells. Methylation and miRNA jointly regulated 14 metabolic genes while mutation and methylation jointly regulated PIK3R1.Conclusion: Based on multi-omics data of somatic mutation, copy number variation, mRNA expression, miRNA expression, and DNA methylation, we identified a series of differentially expressed metabolic genes. Metabolic genes are associated with tumor-related immune cells and clinical parameters, which might be therapy targets in future clinical application.

Genome-wide analysis of DNA copy number variation in breast cancer using DNA microarrays

10.1038/14385 ◽  
1999 ◽  
Vol 23 (S3) ◽  
pp. 69-69 ◽  
Author(s):  
Jonathan R. Pollack ◽  
Charles M. Perou ◽  
Therese Sorlie ◽  
Ash A. Alizadeh ◽  
Christian Rees ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Dna Microarrays ◽  
Dna Copy Number ◽  
Genome Wide Analysis ◽  
Dna Copy Number Variation ◽  
Genome Wide ◽  
Number Variation

scholarly journals Germline DNA copy number variation in familial and early-onset breast cancer

2012 ◽  
Vol 14 (1) ◽  
Author(s):  
Ana CV Krepischi ◽  
Maria Isabel W Achatz ◽  
Erika MM Santos ◽  
Silvia S Costa ◽  
Bianca CG Lisboa ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number Variation ◽  
Early Onset ◽  
Copy Number ◽  
Early Onset Breast Cancer ◽  
Dna Copy Number ◽  
Dna Copy Number Variation ◽  
Number Variation

scholarly journals Feasibility of analyzing DNA copy number variation in breast cancer tumor specimens from 1950 to 2010: how old is too old?

2018 ◽  
Vol 29 (3) ◽  
pp. 305-314 ◽  
Author(s):  
Nancy Krieger ◽  
Sheida Nabavi ◽  
Pamela D. Waterman ◽  
Ninah S. Achacoso ◽  
Luana Acton ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Copy Number Variation ◽  
Copy Number ◽  
Dna Copy Number ◽  
Dna Copy Number Variation ◽  
Number Variation ◽  
Cancer Tumor
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