Related Experiment Video
Updated: May 25, 2026
Identification and Quantification of Deranged Metabolites in Critically Ill Patients Using NMR-Based Metabolomics
Published on: November 29, 2024
An improved analytic workflow for serum mtDNA DAMP abundance, fragmentation and heteroplasmic variants: a
Grant T Daly1, Emily M Hartsell1, Viktor M Pastukh1
1Department of Pharmacology, University of South Alabama Whiddon College of Medicine, Mobile, 36688, USA.
Abstract:
Serum mitochondrial DNA (mtDNA) fragments act as proinflammatory damage-associated molecular patterns (DAMPs), and have been linked to outcomes in critical illness. However, the prognostic value of mtDNA DAMPs remains uncertain, possibly due to confounding nuclear mitochondrial insertions (NUMTs), which obscure both quantitation and variant detection. We developed a deep sequencing and bioinformatics workflow to minimize NUMT-related artifacts. By modeling insert size distributions in ICU patients with acute respiratory failure, we excluded likely NUMT-derived fragments, improving the accuracy of mtDNA DAMP fragmentomic analysis. Short inserts (<150 bp) had low NUMT contamination, and their abundance and size correlated with mortality more strongly than total mtDNA abundance. To improve variant detection, we introduced a novel "read mismatch percentage" to identify NUMT-induced chimeras, enabling identification of mtDNA variants linked to survival and post-acute quality of life. This workflow supports the need for further studies on serum mtDNA variants to predict acute and long-term outcomes in critical illness.
Insights
Serum mitochondrial DNA (mtDNA) fragments, or damage-associated molecular patterns (DAMPs), can predict critical illness outcomes. New methods improve accuracy by minimizing confounding nuclear mitochondrial insertions (NUMTs).
Area of Science:
- Biochemistry
- Genetics
- Critical Care Medicine
Background:
- Serum mitochondrial DNA (mtDNA) fragments function as damage-associated molecular patterns (DAMPs) and are associated with critical illness outcomes.
- The prognostic significance of mtDNA DAMPs is uncertain due to confounding nuclear mitochondrial insertions (NUMTs) affecting quantitation and variant detection.
Purpose of the Study:
- To develop and validate a deep sequencing and bioinformatics workflow to accurately quantify serum mtDNA DAMPs and detect variants by minimizing NUMT-related artifacts.
- To assess the correlation of short mtDNA fragments and variants with mortality and quality of life in intensive care unit (ICU) patients.
Main Methods:
- Developed a deep sequencing and bioinformatics workflow to distinguish mtDNA fragments from NUMT-derived artifacts.
- Modeled insert size distributions in ICU patients with acute respiratory failure to exclude NUMT contamination.
- Introduced a "read mismatch percentage" metric to identify NUMT-induced chimeras for improved variant detection.
Main Results:
- Short mtDNA inserts (<150 bp) showed low NUMT contamination and correlated more strongly with mortality than total mtDNA abundance.
- The workflow successfully improved the accuracy of mtDNA DAMP fragmentomic analysis.
- Identified specific mtDNA variants associated with patient survival and post-acute quality of life.
Conclusions:
- The developed workflow enhances the accuracy of serum mtDNA fragmentomic and variant analysis in critical illness.
- Short mtDNA fragments and specific mtDNA variants show prognostic value for acute and long-term outcomes in critical illness.
- Further research on serum mtDNA variants is warranted for predicting patient outcomes in critical care settings.
