Mitochondrial Genome Analysis of Primary Open Angle Glaucoma Patients

<div><p>Primary open angle glaucoma (POAG) is a multi-factorial optic disc neuropathy characterized by accelerating damage of the retinal ganglion cells and atrophy of the optic nerve head. The vulnerability of the optic nerve damage leading to POAG has been postulated to result from oxidative stress and mitochondrial dysfunction. In this study, we investigated the possible involvement of the mitochondrial genomic variants in 101 patients and 71 controls by direct sequencing of the entire mitochondrial genome. The number of variable positions in the mtDNA with respect to the revised Cambridge Reference Sequence (rCRS), have been designated “Segregating Sites”. The segregating sites present only in the patients or controls have been designated “Unique Segregating Sites (USS)”. The population mutation rate (<i>θ = 4N_eμ</i>) as estimated by Watterson’s θ (θ_w), considering only the USS, was significantly higher among the patients (p = 9.8×10⁻¹⁵) compared to controls. The difference in θ_w and the number of USS were more pronounced when restricted to the coding region (p<1.31×10⁻²¹ and p = 0.006607, respectively). Further analysis of the region revealed non-synonymous variations were significantly higher in Complex I among the patients (p = 0.0053). Similar trends were retained when USS was considered only within complex I (frequency 0.49 vs 0.31 with p<0.0001 and mutation rate p-value <1.49×10⁻⁴³) and <i>ND5</i> within its gene cluster (frequency 0.47 vs 0.23 with p<0.0001 and mutation rate p-value <4.42×10⁻⁴⁷). <i>ND5</i> is involved in the proton pumping mechanism. Incidentally, glaucomatous trabecular meshwork cells have been reported to be more sensitive to inhibition of complex I activity. Thus mutations in <i>ND5</i>, expected to inhibit complex I activity, could lead to generation of oxidative stress and favor glaucomatous condition.</p></div

Distribution of non-synonymous unique segregating sites (USS) in Complex I genes.

<p>The frequency of non-synonymous USS was significantly higher (p<0.0001) in patients compared to controls in the case of the <i>ND5</i> gene. However, the frequency of USS was higher for controls in <i>ND1</i> and <i>ND2</i>.</p

SNPs associated with POAG.

<p>CHISQ: Chi-Square; MAF: Minor Allele Frequency; OR: Odds Ratio.</p

Distribution of unique segregating sites (USS) in the RNA genes.

<p>The frequency of USS was significantly higher (p = 0. 0045) in patients compared to controls in the <i>12S rRNA</i> gene.</p

Distribution of segregating sites in different regions of mtDNA.

<p>The frequency of segregating sites was marginally higher for coding regions in the patients relative to the controls (0.69 vs 0.62, p = 0.0347). No significant difference was observed in the RNA and the control region.</p

Number of unique segregating sites in patients and controls.

*<p>Unique segregating sites: Referred to the unique sites in patients or controls.</p

Distribution of non-synonymous unique segregating sites (USS) in the mtDNA complexes.

<p>The frequency of non-synonymous USS was significantly higher (p<0.0001) in patients compared to controls in the case of Complex I. Marginally higher segregating sites were observed in controls for Complex IV and Complex V.</p

Non synonymous changes identified only in POAG patients.

*<p>AA: Amino Acid.</p

Haplogroup frequencies in patients and controls <i>(Chi-squared test for homogeneity p-value is 0.205).</i>

<p>Haplogroup frequencies in patients and controls <i>(Chi-squared test for homogeneity p-value is 0.205).</i></p

Frequencies of mutations showing escalating trend with the progression of the liver diseases from no liver fibrosis (nLF) or liver fibrosis (LF) to liver cirrhosis (LC) and hepatocellular carcinoma (HCC).

<p>Significant mutations were indicated in bold (p≤0.05) and marginal significant values were represented in italics.</p><p>Frequencies of mutations showing escalating trend with the progression of the liver diseases from no liver fibrosis (nLF) or liver fibrosis (LF) to liver cirrhosis (LC) and hepatocellular carcinoma (HCC).</p