Mitochondrial Control Region Alterations and Breast Cancer Risk: A Study in South Indian Population

<div><p>Background</p><p>Mitochondrial displacement loop (D-loop) is the hot spot for mitochondrial DNA (mtDNA) alterations which influence the generation of cellular reactive oxygen species (ROS). Association of D-loop alterations with breast cancer has been reported in few ethnic groups; however none of the reports were documented from Indian subcontinent.</p><p>Methodology</p><p>We screened the entire mitochondrial D-loop region (1124 bp) of breast cancer patients (n = 213) and controls (n = 207) of south Indian origin by PCR-sequencing analysis. Haplotype frequencies for significant loci, the standardized disequilibrium coefficient (D′) for pair-wise linkage disequilibrium (LD) were assessed by Haploview Software.</p><p>Principal Findings</p><p>We identified 7 novel mutations and 170 reported polymorphisms in the D-loop region of patients and/or controls. Polymorphisms were predominantly located in hypervariable region I (60%) than in II (30%) of D-loop region. The frequencies of <i>310‘C’</i> insertion (<i>P</i> = 0.018), <i>T16189C</i> (<i>P</i> = 0.0019) variants and <i>310‘C’ins/16189C</i> (<i>P</i> = 0.00019) haplotype were significantly higher in cases than in controls. Furthermore, strong LD was observed between nucleotide position 310 and 16189 in controls (D′ = 0.49) as compared to patients (D′ = 0.14).</p><p>Conclusions</p><p>Mitochondrial D-loop alterations may constitute inherent risk factors for breast cancer development. The analysis of genetic alterations in the D-loop region might help to identify patients at high risk for bad progression, thereby helping to refine therapeutic decisions in breast cancer.</p></div

Graphical representation of minor allele frequencies of significant D-loop SNPs in breast cancer patients with different clinical parameters:

<p>(A) breast cancer stage; (B) menopausal status; (C) estrogen receptor status; (D) progesterone receptor status; (E) human epidermal growth factor receptor 2 status. Asterisk (*) indicates the significant difference (<i>P</i><0.05, as determined by the Student’s t-test) between patient groups with different clinical parameters. Percentage values were used for statistical analysis.</p

Novel mutations detected in mitochondrial D-loop region of breast cancer patients.

<p>rCRS: Revised Cambridge Reference Sequence.</p><p>IUPAC: International Union of Pure and Applied Chemistry.</p

Novel mutations observed in D-loop region of breast cancer patients:

<p>(A) 12 ‘C’ insertion; (B) A37G transition; (C) A238G transition; (D) C463T transition; (E) C566G transversion; (F) T16445C transition; (G) G16485A transition.</p

Linkage disequilibrium (LD) analysis of significant D-loop SNPs in cases and controls:

<p>Haploview plots are presented along the single nucleotide polymorphisms studied. The pair-wise linkage disequilibrium values (D′ = 0–100) of all significant SNPs are given in each diamond. A value of 100 represents maximum possible linkage disequilibrium.</p