Biology subjects

Caporali, L.

Publications and source records attributed to Caporali, L..

3 recordsLinked to original sources

bioRxiv2026

Cell free-mtDNA release drives pyroptosis and inflammation in cell models carrying the mitochondrial m.3243A>G pathogenic variant

Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) syndrome is primarily caused by the heteroplasmic m.3243A>G/MT-TL1 pathogenic variant. Patients exhibit elevated circulating cell-free mtDNA (cf-mtDNA) in plasma, which acts as a damage-associated molecular pattern. Using patient-derived fibroblasts and neuronal progenitors, as well as transmitochondrial cytoplasmic hybrids (cybrids), we show that mutant cells release higher levels of cf-mtDNA than wild-type controls, demonstrating that the m.3243A>G pathogenic variant drives mtDNA release. Mechanistically, increased mitochondrial oxidative stress promotes mtDNA oxidation and fragmentation, leading to Ca2+ overload and subsequent mtDNA extrusion. This, in turn, triggers inflammasome activation and pyroptosis, resulting in the secretion of pro-inflammatory cytokines and the activation of innate immune pathways. Pharmacological inhibition of the Mitochondrial Calcium Uniporter (MCU) or Voltage-Dependent Anion Channel (VDAC) reduced mtDNA release, confirming their involvement. Overall, our findings reveal a previously unrecognized mechanism in MELAS linking mitochondrial dysfunction to innate immune activation, with potential implications for therapeutic intervention.

cell biology↗

bioRxiv2025

nAPOGEE: A machine-learning platform for clinically actionable pathogenicity assessment of all mitochondrial noncoding variants

Mitochondrial noncoding variants, particularly those in tRNA and rRNA genes, pose significant challenges for clinical interpretation due to heteroplasmy, broad phenotypic heterogeneity where symptoms can overlap with other conditions, and the limited availability of well-established genotype-phenotype correlations. Despite their central role in mitochondrial translation, these variants have remained largely unexplored by the existing variant-effect predictors. Here, we present nAPOGEE, a novel machine-learning framework specifically designed to assess the pathogenicity of all possible single-nucleotide variants in human mitochondrial noncoding RNAs. nAPOGEE integrates two specialized predictors: tAPOGEE, which outperforms existing tools for tRNAs, and rAPOGEE, the first dedicated classifier for mitochondrial rRNA variants. Using curated training datasets, phylogenetic conservation metrics, secondary structure modeling, RNA-specific embeddings, and thermodynamic features, nAPOGEE provides biologically interpretable predictions and posterior probabilities aligned with the ACMG/AMP guidelines. Applied to both curated variant sets and population-scale data, nAPOGEE revealed consistent spatial correlation of the predicted pathogenicity, reflecting underlying structural and evolutionary constraints. This study addresses a longstanding gap in mitochondrial genomics and offers a clinically applicable tool for variant prioritization, reclassification, and research into mitochondrial disease mechanisms.

bioinformatics↗

bioRxiv2023

A computational study to assess the pathogenicity of single or combinations of missense variants on respiratory Complex I

Variants found in the respiratory complex I (CI) subunit genes encoded by mitochondrial DNA can cause severe genetic diseases. However, it is difficult to establish a priori whether a single or a combination of CI variants may impact oxidative phosphorylation. Here we propose a computational approach based on coarse-grained molecular dynamics simulations. One of the primary CI variants (m.14484T>C/MT-ND6) associated with the Leber hereditary optic neuropathy was used as a test case. This variant was investigated alone or in combination with two additional rare CI variants whose role remains uncertain. We found that the primary variant stiffens CI dynamics in the crucial E-channel region and that one of the other variants, located in the vicinity of the primary one, further worsens the stiffening. This approach may be extended to other variants candidate to exert a pathogenic impact on CI function, or to investigate the interaction of multiple variants. TeaserMolecular dynamics is able to predict the functional impact of variants hitting respiratory complex I mitochondrial genes.

biophysics↗