Variations in mitochondrial genome as potential prognostic markers in sickle cell disease

Alterations in the mitochondrial genome integrity, including changes in mitochondrial DNA copy number (mtDNA-CN) and accumulation of mtDNA mutations, are associated with aging and diverse disorders, often linked to underlying systemic inflammation and metabolic stress. In sickle cell disease (SCD), inflammation drives the pathology, resulting in organ damage and early mortality. The prognostic role of mitochondrial genomic variation in SCD is largely unexplored. This study investigated whole blood derived mtDNA alterations, including mtDNACN and mtDNA mutations, in adults with SCD, sickle trait, and healthy controls, and examined their associations with age and mortality in SCD. We also assessed mtDNA heteroplasmy distribution across tissues in a humanized mouse model of SCD. Elevated mtDNA-CN and mtDNA heteroplasmy burden were observed with increasing genotype severity across all cohorts (HbAA, HbAS < HbSB+ < HbSC < SCA (HbSS and HbSβ0)). In sickle cell anemia (SCA) patients, mtDNA mutation burden- including mtDNA heteroplasmy and mtDNA deletions increased with age, whereas mtDNA-CN level declined, indicating progressive deterioration of mtDNA integrity with age. In SCD patients, specific mtDNA variants showed strong positive correlations with mortality risk, lower mtDNA-CN correlated with higher NIH risk scores, and nuclear variants CYB5R3 T117S and PIEZO1 E756del influenced mtDNA mutation burden without affecting NIH risk score. Consistent patterns of mutational load were observed across specific regions in mitochondrial genome in both humans and mice, suggesting potential mtDNA mutational hotspots. We conclude that variations in the mitochondrial genome are potential prognostic markers for SCD.