Integration of Multi-Omics layers empowers precision diagnosis through unveilling pathogenic mechanisms of Maple Syrup Urine Disease

Purpose: Maple syrup urine disease (MSUD) is a rare inherited metabolic disorder characterized by deficient activity of the branched-chain alpha-ketoacid dehydrogenase (BCKD) complex, required to metabolize the amino acids leucine, isoleucine and valine. Despite its profound metabolic implications, the molecular alterations underlying this metabolic impairment had not yet been elucidated. Methods: We performed a comprehensive multi-omics integration analysis, including genomic, epigenomic and transcriptomic data from fibroblasts derived from a cohort of MSUD patients and unaffected controls to genetically characterize a MSUD case and to unravel the MSUD pathophysiology. Results: The integration of multi-omics layers facilitated the identification of a strong epigenetic repression in the DBT promoter in a patient wherein no BCKD pathogenic variants had been detected, thereby unveiling alternative modes of disease inheritance and confirming its diagnosis potential. Furthermore, MSUD patients exhibit a defined episignature that reshapes the global DNA methylation landscape, resulting in the stimulation of HOX cluster genes and the restriction of cell cycle gene-related signatures. Subsequent data integration revealed the impact of AP1-related and CEBPB transcription factors on the observed molecular reorganization, with MEIS1 emerging as a potential downstream candidate affected by robust epigenetic repression in MSUD patients. Conclusion: Integration of multi-omics data unveiled underlying molecular networks rewired in MSUD patients and represents a powerful approach with diagnostic potential for rare genetic disorders with unknown genetic bases.