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Authors: Margaux Haering, Andrea Del Bondio, Helene Puccio, Bianca Habermann

Summary

Mitochondria are essential eukaryotic organelles, primarily recognized for their roles in ATP production, cellular metabolism and signalling. It is widely accepted that their structure, composition and function differ across cell types. However, little is known about mitochondrial variability within the same cell type. A comprehensive understanding of mitochondrial function and dynamics requires investigation at both, the individual cell type and single-cell resolution. Based on our mitoXplorer 2.0 web tool, we introduce mitoXplorer 3.0 with new features adapted for analysing single-cell sequencing data, focusing only on mitochondria. We developed a formatting script, scXplorer, which generates mitoXplorer 3.0 compatible files for data upload. The script generates pseudo-bulk transcriptomes of cell types from scRNA-seq data, enabling differential expression analysis and subsequent mitochondria-centric analysis with mitoXplorer classical interfaces. It also creates a single-cell expression matrix only containing mitochondria-associated genes (mito-genes), which can be analysed for cell-to-cell variability with novel, interactive interfaces created for mitoXplorer 3.0: these new interfaces help to identify sub-clusters of cell types based only on mito-genes and offer in-depth mitochondria-centric analysis of subpopulations. We demonstrate the usability and predictive power of mitoXplorer 3.0 through analysis of single-cell transcriptome data from a Spinocerebellar Ataxia Type 1 study. Our analysis identified several mitochondrial processes and genes significantly affected in SCA1 Purkinje cells, potentially contributing to mitochondrial dysfunction and subsequent Purkinje cell degeneration in this disease. MitoXplorer 3.0 is freely available at https://mitoxplorer3.ibdm.univ-amu.fr .

Link to HAL – hal-05408974

Link to DOI – 10.1016/j.jmb.2025.169004