Preservation of ALYREF Phase Separation Mitigates Doxorubicin‐Induced Cardiomyocyte DNA Damage and Cardiotoxicity

Binding of Doxorubicin to ALYREF disrupts its phase‐separated condensate and induces DNA damage and apoptosis in cardiomyocytes Abstract The clinical utility of the anticancer agent doxorubicin (DOX) is limited by its dose‐dependent cardiotoxicity. ALYREF, a nuclear protein that preserves genomic stability through interactions with intranuclear components or as an m⁵C‐binding regulator of mRNA maturation and export, has not been previously implicated in DOX‐induced cardiotoxicity (DIC). Here, the role and underlying mechanisms of ALYREF in the pathogenesis of DIC are investigated. The findings demonstrate that ALYREF expression is markedly reduced in a murine model of DIC. Myocardial‐specific overexpression of ALYREF attenuates DOX‐induced DNA damage and cardiomyocyte apoptosis, whereas cardiac‐specific knockout of ALYREF (ALYREF CKO) exacerbates DOX‐induced cardiac dysfunction. Mechanistically, it is identified that nuclear DOX directly binds to the aspartate residue (D171) within the intrinsically disordered regions (IDRs) of ALYREF, disrupting its liquid–liquid phase separation (LLPS) and promoting its ubiquitin‐mediated degradation. The condensate state of ALYREF is essential for maintaining the integrity of the NORAD‐activated ribonucleoprotein complex 1 (NARC1). Consequently, disruption of ALYREF LLPS leads to dissociation of the NARC1 complex, resulting in DNA damage and apoptosis in CMs. Collectively, these findings reveal a previously unrecognized mechanism by which DIC via interference with ALYREF condensates, offering new insight into the molecular basis of DIC. Binding of Doxorubicin to ALYREF disrupts its phase-separated condensate and induces DNA damage and apoptosis in cardiomyocytes Abstract The clinical utility of the anticancer agent doxorubicin (DOX) is limited by its dose-dependent cardiotoxicity. ALYREF, a nuclear protein that preserves genomic stability through interactions with intranuclear components or as an m⁵C-binding regulator of mRNA maturation and export, has not been previously implicated in DOX-induced cardiotoxicity (DIC). Here, the role and underlying mechanisms of ALYREF in the pathogenesis of DIC are investigated. The findings demonstrate that ALYREF expression is markedly reduced in a murine model of DIC. Myocardial-specific overexpression of ALYREF attenuates DOX-induced DNA damage and cardiomyocyte apoptosis, whereas cardiac-specific knockout of ALYREF (ALYREF CKO) exacerbates DOX-induced cardiac dysfunction. Mechanistically, it is identified that nuclear DOX directly binds to the aspartate residue (D171) within the intrinsically disordered regions (IDRs) of ALYREF, disrupting its liquid–liquid phase separation (LLPS) and promoting its ubiquitin-mediated degradation. The condensate state of ALYREF is essential for maintaining the integrity of the NORAD-activated ribonucleoprotein complex 1 (NARC1). Consequently, disruption of ALYREF LLPS leads to dissociation of the NARC1 complex, resulting in DNA damage and apoptosis in CMs. Collectively, these findings reveal a previously unrecognized mechanism by which DIC via interference with ALYREF condensates, offering new insight into the molecular basis of DIC. Advanced Science, Volume 12, Issue 43, November 20, 2025.