Transcriptomic profiling of TK2 deficient human skeletal muscle suggests a role for the p53 signalling pathway and identifies growth and differentiation factor-15 as a potential novel biomarker for mitochondrial myopathies
1 Bioinformatics Core Facility, IDIBAPS, Hospital Clinic, Barcelona, Spain
2 Neuromuscular Unit, Neurology Department, Fundación Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
3 Pathology Department, Hospital Sant Joan de Déu, Barcelona, Spain
4 Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
5 Department of Child, Adolescent, and Developmental Neurology, Children’s Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
6 U.O.S. Diagnostica Malattie Neuromuscolari, Fondazione Ospedale Maggiore Mangiagalli e Regina Elena, IRCCS, Milan, Italy
7 Laboratory for Neuropathology, Ghent University Hospital, Ghent, Belgium
8 Institute of Neuropathology, Hospital de Bellvitge, Barcelona, Spain
9 Neuropaediatrics Department, Vall d’Hebron Hospital, Barcelona, Spain
10 Biochemistry and Molecular Biology Department, University of Zaragoza, Zaragoza, Spain
11 Center for Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
12 Clinical Biochemistry Department, Hospital Sant Joan de Déu, Barcelona, Spain
13 Orthopaedic Surgery & Traumatology Department, Hospital Sant Joan de Déu, Barcelona, Spain
BMC Genomics 2014, 15:91 doi:10.1186/1471-2164-15-91Published: 1 February 2014
Mutations in the gene encoding thymidine kinase 2 (TK2) result in the myopathic form of mitochondrial DNA depletion syndrome which is a mitochondrial encephalomyopathy presenting in children. In order to unveil some of the mechanisms involved in this pathology and to identify potential biomarkers and therapeutic targets we have investigated the gene expression profile of human skeletal muscle deficient for TK2 using cDNA microarrays.
We have analysed the whole transcriptome of skeletal muscle from patients with TK2 mutations and compared it to normal muscle and to muscle from patients with other mitochondrial myopathies. We have identified a set of over 700 genes which are differentially expressed in TK2 deficient muscle. Bioinformatics analysis reveals important changes in muscle metabolism, in particular, in glucose and glycogen utilisation, and activation of the starvation response which affects aminoacid and lipid metabolism. We have identified those transcriptional regulators which are likely to be responsible for the observed changes in gene expression.
Our data point towards the tumor suppressor p53 as the regulator at the centre of a network of genes which are responsible for a coordinated response to TK2 mutations which involves inflammation, activation of muscle cell death by apoptosis and induction of growth and differentiation factor 15 (GDF-15) in muscle and serum. We propose that GDF-15 may represent a potential novel biomarker for mitochondrial dysfunction although further studies are required.