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

Mitochondria, often dubbed the powerhouses of the cell, play a crucial role in energy production and various cellular processes. Within these tiny organelles lies another vital component: mitochondrial DNA (mtDNA). Recently, scientists have been delving into the realm of mtDNA deletions—large structural changes within the mitochondrial genome—seeking to understand their implications in aging and disease.

In a groundbreaking study, researchers at the Keck School of Medicine of USC applied the Splice-Break2 pipeline, a powerful tool designed for high-throughput quantification of mtDNA deletions, to human RNA sequencing (RNA-Seq) datasets. Their aim? To unravel the methodological intricacies of evaluating common mtDNA deletions across different types of datasets, including bulk, single-cell, and spatial transcriptomics.

MtDNA deletions captured by RNA-Seq

Fig. 2

a The Top 30 most frequent mtDNA deletions evaluated in this study and previously described13. Multiple sequence alignment (MSA) plot of RNA-Seq reads from a dataset of 30 brain samples20 containing the (b) 6335–13999 deletion, (c) 7816–14807 deletion, and (d) 8471–13449 deletion.

What did they uncover? Let’s delve into the key findings:

  1. Correlation with PCR-amplified mtDNA: The study revealed that the abundance of certain common deletions detected in PCR-amplified mtDNA aligns closely with levels observed in RNA-Seq data, highlighting the reliability of RNA-Seq in quantifying mtDNA deletions.
  2. Impact of library preparation: Interestingly, the method used for RNA-Seq library preparation had a significant impact on deletion detection, emphasizing the importance of methodological considerations in experimental design.
  3. Age-related changes: Analysis of a diverse set of samples spanning 14 RNA-Seq studies unveiled a significant positive correlation between mtDNA deletions and age in brain and muscle tissues, shedding light on the role of these deletions in the aging process.
  4. Spatial distribution: The study also uncovered intriguing spatial patterns of mtDNA deletions, with notable enrichment observed in cortical grey matter, particularly in layers 3 and 5.
  5. Neuronal implications: Perhaps most fascinatingly, regions of the brain housing dopaminergic neurons—such as the substantia nigra, ventral tegmental area, and caudate nucleus—showed remarkable enrichment of common mtDNA deletions, hinting at potential implications for neurodegenerative diseases.

Overall, this study provides a comprehensive exploration of mtDNA deletions using RNA-Seq datasets, offering valuable insights into their dynamics, distribution, and potential implications for aging and disease. By unraveling the mysteries of mitochondrial DNA, researchers are paving the way for a deeper understanding of cellular function and disease pathology.

Omidsalar AA, McCullough CG, Xu L, Boedijono S, Gerke D, Webb MG, Manojlovic Z, Sequeira A, Lew MF, Santorelli M, Serrano GE, Beach TG, Limon A, Vawter MP, Hjelm BE. (2024) Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets. Commun Biol 7(1):200. [article]

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