4.6 Article

Identification of Recurrent Chromosome Breaks Underlying Structural Rearrangements in Mammary Cancer Cell Lines

期刊

GENES
卷 13, 期 7, 页码 -

出版社

MDPI
DOI: 10.3390/genes13071228

关键词

breast cancer; spontaneous chromosome breaks; double-strand breaks (DSBs); CNV; 16q loss; structural rearrangements; genome instability; MCF-7; MCF-10A; Break-seq; SHCBP1; ORC6

资金

  1. National Institute of Health [GM118799-01A1]
  2. Upstate Medical University Intramural Carol Baldwin Cancer Research Fund
  3. SUNY EMPIRE innovative program scholar grant
  4. Upstate Medical University Cancer Center grant
  5. Upstate Foundation Turn4ACure Fund

向作者/读者索取更多资源

This study investigates the correlation between chromosomal structural rearrangement breakpoints and DNA double-strand breaks (DSBs) in breast cancer cells. The researchers found that these events mostly occur in the pericentromeric region of chromosome 16q. Recurrent DSBs were also detected in both cancer and control cells. The study identifies potential oncogenes that may contribute to breast cancer progression.
Cancer genomes are characterized by the accumulation of small-scale somatic mutations as well as large-scale chromosomal deletions, amplifications, and complex structural rearrangements. This characteristic is at least partially dependent on the ability of cancer cells to undergo recurrent chromosome breakage. In order to address the extent to which chromosomal structural rearrangement breakpoints correlate with recurrent DNA double-strand breaks (DSBs), we simultaneously mapped chromosome structural variation breakpoints (using whole-genome DNA-seq) and spontaneous DSB formation (using Break-seq) in the estrogen receptor (ER)-positive breast cancer cell line MCF-7 and a non-cancer control breast epithelium cell line MCF-10A. We identified concurrent DSBs and structural variation breakpoints almost exclusively in the pericentromeric region of chromosome 16q in MCF-7 cells. We fine-tuned the identification of copy number variation breakpoints on 16q. In addition, we detected recurrent DSBs that occurred in both MCF-7 and MCF-10A. We propose a model for DSB-driven chromosome rearrangements that lead to the translocation of 16q, likely with 10q, and the eventual 16q loss that does not involve the pericentromere of 16q. We present evidence from RNA-seq data that select genes, including SHCBP1, ORC6, and MYLK3, which are immediately downstream from the 16q pericentromere, show heightened expression in MCF-7 cell line compared to the control. Data published by The Cancer Genome Atlas show that all three genes have increased expression in breast tumor samples. We found that SHCBP1 and ORC6 are both strong poor prognosis and treatment outcome markers in the ER-positive breast cancer cohort. We suggest that these genes are potential oncogenes for breast cancer progression. The search for tumor suppressor loss that accompanies the 16q loss ought to be augmented by the identification of potential oncogenes that gained expression during chromosomal rearrangements.

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