Oncotarget

Research Papers:

Development of diagnostic SCAR markers for genomic DNA amplifications in breast carcinoma by DNA cloning of high-GC RAMP-PCR fragments

Shangyi Fu, Jingliang Cheng, Chunli Wei, Luquan Yang, Xiuli Xiao, Dianzheng Zhang, M. David Stewart and Junjiang Fu _

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Oncotarget. 2017; 8:43866-43877. https://doi.org/10.18632/oncotarget.16704

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Abstract

Shangyi Fu2,*, Jingliang Cheng1,*, Chunli Wei1,*, Luquan Yang1, Xiuli Xiao3, Dianzheng Zhang4, M. David Stewart2,5,6 and Junjiang Fu1,7

1Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan 646000, China

2Honors College, University of Houston, Houston, TX 77204, USA

3Department of Pathology, Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, Sichuan 646000, China

4Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, PA 19131, USA

5Department of Biology & Biochemistry, University of Houston, Houston, TX 77204, USA

6Texas Heart Institute at St. Luke's Episcopal Hospital, Houston, TX 77030, USA

7Judicial Authentication Center, Southwest Medical University, Luzhou, Sichuan 646000, China

*These authors have contributed equally to this work

Correspondence to:

Junjiang Fu, email: [email protected], [email protected]

Dianzheng Zhang, email: [email protected]

Keywords: high-GC primer, RAMP, random amplified polymorphic DNA (RAPD), sequence-characterized amplified region (SCAR), genomic instability

Received: February 24, 2017     Accepted: March 19, 2017     Published: March 30, 2017

ABSTRACT

Cancer is genetically heterogeneous regarding to molecular genetic characteristics and pathogenic pathways. A wide spectrum of biomarkers, including DNA markers, is used in determining genomic instability, molecular subtype determination and disease prognosis, and estimating sensitivity to different drugs in clinical practice. In a previous study, we developed highly effective DNA markers using improved random amplified polymorphic DNA (RAPD) with high-GC primers, which is a valuable approach for the genetic authentication of medicinal plants. In this study, we applied this effective DNA marker technique to generate genetic fingerprints that detect genomic alterations in human breast cancer tissues and then developed sequence-characterized amplified region (SCAR) markers. Three SCAR markers (BC10-1, BC13-4 and BC31-2) had high levels of genomic DNA amplification in breast cancer. The PHKG2 and RNF40 genes are either overlapping or close to the sequences of SCAR marker BC13-4, while SCAR marker BC10-1 is in the intron and overlap the DPEP1 gene, suggesting that alterations in the expression of these genes could contribute to cancer progression. Screening of breast cancer cell lines showed that the mRNA expression levels for the PHKG2 and DPEP1 were lower in non-tumorigenic mammary epithelial cell MCF10A, but elevated in other cell lines. The DPEP1 mRNA level in invasive ductal carcinoma specimens was significantly higher than that of the adjacent normal tissues in women. Taken together, high-GC RAMP-PCR provides greater efficacy in measuring genomic DNA amplifications, deletion or copy number variations. Furthermore, SCAR markers BC10-1 and BC13-4 might be useful diagnostic markers for breast cancer carcinomas.


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