Analysis of fibroblasts from patients with cblC and cblG genetic defects of cobalamin metabolism reveals global dysregulation of alternative splicing

Charif Rashka (1) , Sébastien Hergalant (1) , Natacha Dreumont (1) , Abderrahim Oussalah (1, 2) , Jean-Michel Camadro (3) , Virginie Marchand (4) , Ziad Hassan (1) , Matthias Baumgartner (5) , David Rosenblatt (6) , François Feillet (1, 2) , Jean-Louis Guéant (1, 2) , Justine Flayac (1) , David Coelho (1, 2)

1 NGERE - Nutrition-Génétique et Exposition aux Risques Environnementaux
2 MaMEA Nancy-Brabois - Centre de référence des maladies héréditaires du métabolisme
3 IJM (UMR_7592) - Institut Jacques Monod
4 IMoPA - Ingénierie Moléculaire et Physiopathologie Articulaire
5 UZH - Universität Zürich [Zürich] = University of Zurich
6 McGill University = Université McGill [Montréal, Canada]

Vitamin B12 or cobalamin (Cbl) metabolism can be affected by genetic defects leading to defective activity of either methylmalonyl-CoA mutase or methionine synthase or both enzymes. Patients usually present with a wide spectrum of pathologies suggesting that various cellular processes could be affected by modifications in gene expression. We have previously demonstrated that these genetic defects are associated with subcellular mislocalization of RNA binding proteins and subsequent altered nucleo-cytoplasmic shuttling of mRNAs. In order to characterize the possible changes of gene expression in these diseases, we have investigated global gene expression in fibroblasts from patients with cblC and cblG inherited disorders by RNA-seq. The most differentially expressed genes are strongly associated with developmental processes, neurological, ophthalmologic and cardiovascular diseases. These associations are consistent with the clinical presentation of cblC and cblG disorders. Multivariate analysis of transcript processing revealed splicing alterations that led to dramatic changes in cytoskeleton organization, response to stress, methylation of macromolecules and RNA binding. The RNA motifs associated with this differential splicing reflected a potential role of RNA binding proteins such as HuR and HNRNPL. Proteomic analysis confirmed that mRNA processing was significantly disturbed. This study reports a dramatic alteration of gene expression in fibroblasts of patients with cblC and cblG disorders, which resulted partly from disturbed function of RNA binding proteins. These data suggest to evaluate the rescue of the mislocalization of RNA binding proteins as a potential strategy in the treatment of severe cases who are resistant to classical treatments with co-enzyme supplements.

Domains: Life Sciences [q-bio]; Biochemistry, Molecular Biology; Genomics [q-bio.GN]; Life Sciences [q-bio]; Biochemistry, Molecular Biology; Mathematics [math]; Probability [math.PR]; Life Sciences [q-bio]; Biochemistry, Molecular Biology; Molecular Networks [q-bio.MN]; Life Sciences [q-bio]; Food and Nutrition; Computer Science [cs]; Bioinformatics [q-bio.QM]; Life Sciences [q-bio]; Genetics; Human genetics; Life Sciences [q-bio]; Human health and pathology; Tissues and Organs [q-bio.TO]

Charif Rashka, Sébastien Hergalant, Natacha Dreumont, Abderrahim Oussalah, Jean-Michel Camadro, et al.. Analysis of fibroblasts from patients with cblC and cblG genetic defects of cobalamin metabolism reveals global dysregulation of alternative splicing. Human Molecular Genetics, 2020, 29 (12), pp.1969-1985. ⟨10.1093/hmg/ddaa027⟩. ⟨hal-03100129⟩