Integration of multi-omics layers empowers precision diagnosis through unveiling pathogenic mechanisms on maple syrup urine disease.

Autores de IIS La Fe

• Patricia Correcher Medina

  Autor

Participantes ajenos a IIS La Fe

• Tejedor, Juan Ramon
• Soriano-Sexto, Alejandro
• Beccari, Leonardo
• Castejon-Fernandez, Natalia
• Sainz-Ledo, Lidia
• Alba-Linares, Juan Jose
• Urdinguio, Rocio G
• Ugarte, Magdalena
• Fernandez, Agustin F
• Rodriguez-Pombo, Pilar
• Fraga, Mario F
• Perez, Belen

Grupos

• Nutrición y Metabolopatías

  Investigador Principal

  Patricia Correcher Medina

• Perinatología

  

  Leader

  Máximo Vento Torres

Abstract

Maple syrup urine disease (MSUD) is a rare inherited metabolic disorder characterized by deficient activity of the branched-chain alpha-ketoacid dehydrogenase (BCKDH) 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 completely elucidated. 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 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-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. Furthermore, the integration of multi-omics layers facilitated the identification of a strong epigenetic repression in the DBT 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 DBT promoter, thereby unveiling alternative modes of disease inheritance. 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.

© 2024 The Author(s). Journal of Inherited Metabolic Disease published by John Wiley & Sons Ltd on behalf of SSIEM.

Keywords

• data integration; epigenomics; maple syrup urine disease; molecular diagnostics; transcriptomics