Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and...

Area of Science:

• Genomics
• Mitochondrial Biology
• Neuroscience

Background:

• Mitochondrial DNA (mtDNA) deletions are associated with various disorders, particularly those affecting high-energy-demand tissues like muscle and brain.
• The 16.6 kb mitochondrial genome is susceptible to deletions that can lead to cellular dysfunction.

Purpose of the Study:

• To develop and validate a comprehensive pipeline (Splice-Break) for detecting and quantifying mitochondrial DNA deletions.
• To catalogue the frequency and abundance of mtDNA deletions in human postmortem brain and blood samples.

Main Methods:

• Mitochondria-targeted PCR, next-generation sequencing, and a bioinformatics pipeline utilizing MapSplice for deletion breakpoint detection.
• Post-hoc filtering, annotation, and validation steps were employed to ensure accuracy.
• Analysis of 93 postmortem samples from brain and blood tissues.

Main Results:

• A catalogue of 4489 putative mtDNA deletions was generated.
• The common 4977 bp deletion was not the most frequent or abundant; brain tissue had significantly more deletions than blood.
• Deletion burden increased with age, and the highest levels were found in major depressive disorder brain samples, exceeding those in Kearns-Sayre Syndrome muscle.

Conclusions:

• The Splice-Break pipeline offers high-resolution detection and quantification of mtDNA deletions.
• mtDNA deletions are prevalent in healthy and diseased tissues, with varying abundance and tissue-specific patterns.
• Age and specific neurological conditions like major depressive disorder are associated with increased mtDNA deletion burdens.