Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets

Area of Science:

• Genomics
• Molecular Biology
• Neuroscience

Background:

• Common mitochondrial DNA (mtDNA) deletions are structural variants accumulating in aging, metabolically active tissues.
• These deletions are implicated in various disease states.
• Quantifying mtDNA deletions in transcriptomics data presents methodological challenges.

Purpose of the Study:

• To apply and evaluate the Splice-Break2 pipeline for high-throughput quantification of mtDNA deletions in human RNA-Seq datasets.
• To describe methodological considerations for analyzing mtDNA deletions across bulk, single-cell, and spatial transcriptomics.
• To investigate the correlation of common mtDNA deletions with age and tissue type.

Main Methods:

• Utilized the Splice-Break2 pipeline on 1570 human RNA-Seq samples from 14 studies.
• Analyzed bulk, single-cell, and spatial transcriptomics data.
• Correlated deletion abundance with age, tissue type, and specific cell populations.

Main Results:

• The abundance of common mtDNA deletions in RNA-Seq data correlated with levels found in PCR-amplified mtDNA.
• RNA-Seq library preparation significantly impacted deletion detection.
• A significant positive correlation between mtDNA deletions and age was observed in brain and muscle tissues.
• mtDNA deletions were enriched in cortical grey matter layers 3 and 5.
• Remarkable enrichment of common mtDNA deletions was found in brain regions rich in dopaminergic neurons.

Conclusions:

• The Splice-Break2 pipeline provides a viable method for quantifying mtDNA deletions from RNA-Seq data.
• RNA-Seq library preparation is a critical factor influencing mtDNA deletion detection.
• Common mtDNA deletions accumulate with age in specific human tissues and brain regions, particularly those associated with dopaminergic function.