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Despite its profound metabolic implications, the molecular alterations underlying this metabolic impairment had not yet been completely elucidated. We performed a comprehensive multi\u2010omics integration analysis, including genomic, epigenomic, and transcriptomic data from fibroblasts derived from a cohort of MSUD patients and unaffected controls to genetically characterize an MSUD case and to unravel the MSUD pathophysiology. 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\u2010related signatures. Subsequent data integration revealed the impact of AP1\u2010related 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. Furthermore, the integration of multi\u2010omics layers facilitated the identification of a strong epigenetic repression in the <jats:italic>DBT<\/jats:italic> promoter in a patient wherein no BCKDH pathogenic variants had been detected. A Circular Chromatin Conformation Capture assay indicated a disturbance of the interactions of <jats:italic>DBT<\/jats:italic> promoter, thereby unveiling alternative modes of disease inheritance. Integration of multi\u2010omics 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.<\/jats:p>","DOI":"10.1002\/jimd.12829","type":"journal-article","created":{"date-parts":[[2024,12,11]],"date-time":"2024-12-11T04:40:12Z","timestamp":1733892012000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Integration of multi\u2010omics layers empowers precision diagnosis through unveiling pathogenic mechanisms on maple syrup urine disease"],"prefix":"10.1002","volume":"48","author":[{"given":"Juan Ram\u00f3n","family":"Tejedor","sequence":"first","affiliation":[{"name":"Nanomaterials and Nanotechnology Research Centre (CINN\u2010CSIC) Spanish National Research Council (CSIC)  Principality of Asturias Spain"},{"name":"Health Research Institute of Asturias (ISPA) Foundation for Biomedical 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