Multi-omic PREdictors of Diagnosis, prognosis and monitoring of Inherited errors of Cobalamin meTaboliSm – PREDICTS

Cobalamin (Cbl, or vitamin B12) is the cofactor for methionine synthase (MS encoded by MTR) and methylmalonyl-CoA mutase (MUT encoded by MMUT), whose genetic defects lead to increased homocysteine (Hcy) and methylmalonic acid (MMA), respectively. Inherited errors of Cbl metabolism (IECM) are produced by mutations in genes of Cbl transport and cellular availability (among them cblC type with combined deficit in MS and MMUT), in MTR (cbG type with increased Hcy) and MMUT (with increased MMA). They produce age-dependent megaloblastic/macrocytic anaemia and neurological manifestations, with lethargy, hypotonia, mental retardation, seizures and metabolic decompensation in the first years of life and peripheral neurological, ataxia, cognitive and ophthalmological outcomes in later life. Lethal decompensations are reported in the first year. Some of the IECM pathological mechanisms have been dissected by our groups in recent years, including in collaborative works, but the overall scenarios that lead to the severity, high clinical variability and limited therapy response are far away from being understood. Impaired MS activity produces cellular stress, disruption of tricarboxylic acid (TCA) cycle and respiratory chain, organ-specific epigenetic instability, decreased sirtuins, altered nucleo-cytoplasmic shuttling of mRNAs and RNA binding proteins and subsequent altered energy metabolism, neuroplasticity, and brain development. Deficient MUT produces a disruption of TCA, accumulation of organic acids and ultrastructural mitochondrial alterations and mitophagy in brain, liver, kidney and heart. One emerging hypothesis is that genomic-epigenomic alterations and age-dependent cumulative post-translational modifications (PTM) by increased organic acids may impair other metabolic pathways than those directly linked to Cbl.
Taken together, these data led us to hypothesize that the great variability of age-related manifestations and limited treatment efficacy in IECM are related to interdependent multi-omic changes that include genomic, epigenomic and PTM mechanisms resulting in dysfunction of key proteins that disrupt Cbl-dependent and other metabolic pathways.
Our objective is to elucidate whether multi-layered omic changes and underlying mechanisms enable the prediction of age-dependent severe neurological, ophtalmological and organ-specific metabolic decompensation as well as identification of diagnostic deadlocks and innovative therapeutic targets in cases with limited treatment efficacy. Three specific objectives will be addressed: (i) to identify multi-omic hallmarks and biomarkers in a retrospective cohort of patients, (ii) to identify cell and organ specificity of hallmarks and biomarkers in differentiated cells derived from iPSC and animal models (iii) modeling interacting metabolic disruptions and biomarkers to be used in monitoring the personalized treatment and metabolic recovery of patients.
The project will be based on selection of cases with cblC, epi-cblC, MUT and cblG clinical and metabolic contrasted presentations according to age, severity and limited influence of conventional treatments in WP1. We will assess clinical versus multi-omic (genomic, epigenomic, PTM-proteomic and metabolomic) relationships in blood, fibroblasts, already prepared iPSC and differentiated cells (WP1 and WP2) and animal models (WP3), using such a wide variety of models to ensure all findings are robust and disease relevant. By implementing an integrated bioinformatics and systems biology approach (WP4), we will map perturbations across the entire metabolic network, enabling identification of therapeutically targetable entry points and pathways.
The project will produce biomarker panels for diagnostic deadlocks, stratified diagnosis and management of severe IECM cases and will identify innovative treatment targets, including those related to sirtuins, PTM-related mechanisms and recovery of disrupted urea/TCA.