ABSTRACT
Friedreich's ataxia (FRDA), the most common inherited ataxia, is caused by recessive mutations that reduce the levels of frataxin (FXN), a mitochondrial iron binding protein. We developed an inducible mouse model of Fxn deficiency that enabled us to control the onset and progression of disease phenotypes by the modulation of Fxn levels. Systemic knockdown of Fxn in adult mice led to multiple phenotypes paralleling those observed in human patients across multiple organ systems. By reversing knockdown after clinical features appear, we were able to determine to what extent observed phenotypes represent reversible cellular dysfunction. Remarkably, upon restoration of near wild-type FXN levels, we observed significant recovery of function, associated pathology and transcriptomic dysregulation even after substantial motor dysfunction and pathology were observed. This model will be of broad utility in therapeutic development and in refining our understanding of the relative contribution of reversible cellular dysfunction at different stages in disease.
Subject(s)
Disease Models, Animal , Friedreich Ataxia/pathology , Gene Expression Regulation , Iron-Binding Proteins/biosynthesis , Phenotype , Animals , Gene Knockdown Techniques , Humans , Iron-Binding Proteins/genetics , Mice , FrataxinABSTRACT
The regenerative capacity of the injured CNS in adult mammals is severely limited, yet axons in the peripheral nervous system (PNS) regrow, albeit to a limited extent, after injury. We reasoned that coordinate regulation of gene expression in injured neurons involving multiple pathways was central to PNS regenerative capacity. To provide a framework for revealing pathways involved in PNS axon regrowth after injury, we applied a comprehensive systems biology approach, starting with gene expression profiling of dorsal root ganglia (DRGs) combined with multi-level bioinformatic analyses and experimental validation of network predictions. We used this rubric to identify a drug that accelerates DRG neurite outgrowth in vitro and optic nerve outgrowth in vivo by inducing elements of the identified network. The work provides a functional genomics foundation for understanding neural repair and proof of the power of such approaches in tackling complex problems in nervous system biology.
Subject(s)
Axons/physiology , Ganglia, Spinal/cytology , Nerve Regeneration/physiology , Neurons/cytology , Peripheral Nervous System Diseases/physiopathology , Animals , Animals, Newborn , Antigens, Neoplasm/genetics , Antigens, Neoplasm/metabolism , Cell Adhesion Molecules/genetics , Cell Adhesion Molecules/metabolism , Cells, Cultured , Chromatin Immunoprecipitation , Disease Models, Animal , Gene Expression Regulation/genetics , Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) , Ion Channels , Membrane Glycoproteins/genetics , Membrane Glycoproteins/metabolism , Membrane Proteins/genetics , Membrane Proteins/metabolism , Mice , Mice, Inbred C57BL , Microfilament Proteins , Nerve Regeneration/genetics , Nitrogenous Group Transferases/genetics , Nitrogenous Group Transferases/metabolism , PTEN Phosphohydrolase/genetics , PTEN Phosphohydrolase/metabolism , cdc42 GTP-Binding Protein/genetics , cdc42 GTP-Binding Protein/metabolismABSTRACT
OBJECTIVE: Gene expression studies in peripheral tissues from patients with neurodegenerative disorders can provide insights into disease pathogenesis, and identify potential biomarkers, an important goal of translational research in neurodegeneration. Friedreich Ataxia (FRDA) is a chronic neurodegenerative disease caused by reduced transcription of frataxin, a ubiquitously expressed protein. We studied in vitro lymphocytes from FRDA patients and carriers to identify a peripheral gene expression phenotype. Peripheral biomarkers related to disease status would be extremely valuable for assessing drug efficacy and could provide new pathophysiological insights. METHODS: We characterized the gene expression profiles in peripheral blood mononuclear cells (PBMCs) from FRDA patients, compared with controls and related carriers. Cells were studied both before and after in vitro treatment with compounds that increase frataxin levels. Quantitative real-time polymerase chain reaction and additional microarrays were used to confirm a core set of genes in multiple independent series. RESULTS: We identified a subset of genes changed in cells from patients with pathological frataxin deficiency, and a core set of these genes were confirmed in independent series. Changes in gene expression were related to the mitochondria, lipid metabolism, cell cycle, and DNA repair, consistent with FRDA's known pathophysiology. We evaluated the in vitro effect of multiple compounds (histone deacetylase inhibitors) on this putative biomarker set, and found that this biochemical phenotype was ameliorated in accordance with drug efficacy. INTERPRETATION: Frataxin downregulation is associated with robust changes in gene expression in PBMCs, providing pathogenetic insights and a core subset of genes that, if verified in vivo, could be used as a peripheral biomarker.
Subject(s)
Friedreich Ataxia/metabolism , Iron-Binding Proteins/drug effects , Leukocytes, Mononuclear/metabolism , Adult , Cell Culture Techniques , Female , Friedreich Ataxia/genetics , Gene Expression , Humans , Iron-Binding Proteins/genetics , Leukocytes, Mononuclear/cytology , Male , Phenotype , Real-Time Polymerase Chain Reaction , FrataxinABSTRACT
Progranulin (GRN) mutations cause frontotemporal dementia (FTD), but GRN's function in the CNS remains largely unknown. To identify the pathways downstream of GRN, we used weighted gene coexpression network analysis (WGCNA) to develop a systems-level view of transcriptional alterations in a human neural progenitor model of GRN-deficiency. This highlighted key pathways such as apoptosis and ubiquitination in GRN deficient human neurons, while revealing an unexpected major role for the Wnt signaling pathway, which was confirmed by analysis of gene expression data from postmortem FTD brain. Furthermore, we observed that the Wnt receptor Fzd2 was one of only a few genes upregulated at 6 weeks in a GRN knockout mouse, and that FZD2 reduction caused increased apoptosis, while its upregulation promoted neuronal survival in vitro. Together, these in vitro and in vivo data point to an adaptive role for altered Wnt signaling in GRN deficiency-mediated FTD, representing a potential therapeutic target.
