Analysis of Serum mtDNA Fragmentation Patterns and Heteroplasmy to Predict Outcomes in Acute Respiratory Failure

BackgroundSerum mitochondrial DNA (mtDNA) fragments act as proinflammatory damage-associated molecular patterns (DAMPs), and have been linked to outcomes in critical illness. However, their prognostic value remains uncertain, possibly due to confounding nuclear mitochondrial insertions (NUMTs) which obscure both quantitation and variant detection. MethodsUsing a targeted deep sequencing and bioinformatics workflow, we created filtering strategies to minimize NUMT-related artifacts. To evaluate the method, we performed a secondary analysis of serum samples collected from NCT00976833, a study of acute respiratory failure patients. By modeling DNA insert size distributions, we excluded likely NUMT-derived DNA fragments based on their size, improving the accuracy of mtDNA DAMP fragmentomic analysis. To improve variant detection, we introduced a novel "read mismatch percentage" metric to identify NUMT-induced chimeric read pairs, enabling identification of mtDNA variants. ResultsMean NUMT-depleted, but not raw, mtDNA insert size was lower in non-survivors. Short DNA inserts (<150 bp) displayed little NUMT contamination, and their abundance and size correlated with mortality more strongly than total mtDNA abundance. Sequence variants were called and some associated with survival and post-acute quality of life. Variant m.1,719G>A, found in small humanin-like 3 (MT-SHLP3), associated with survival. Other variants associated with overall poor outcome (non-survival or poor QoL). Two noncoding variants previously associated with low VO2 max and coronary artery disease (m.295C>T and m.462C>T) also associated with poor outcome in the present study. Two MT-ND5 variants m.13,708G>A (a missense variant previously implicated in kidney dysfunction) and m.12,612A>G (a synonymous variant previously associated with coronary artery disease) also associated with poor overall outcome. ConclusionsOur results addressed limitations of standard qPCR-based methods for the study of mtDNA DAMPs. Beyond addressing confounding NUMT, the method identified fragmentomic and variant associations overlooked by qPCR. Cell-free DNA fragmentomic and variant information are well-established biomarkers for cancer, and this method could facilitate similar patient-specific biomarkers in the context of critical illness. The method is composed of commercially available reagents and open source software, which could additionally promote adoption and reproducibility.