Gene co-expression networks shed light into diseases of brain iron accumulation

Abstract

Aberrant brain iron deposition is observed in both common and rare neurodegenerative disorders, including those categorized as Neurodegeneration with Brain Iron Accumulation (NBIA), which are characterized by focal iron accumulation in the basal ganglia. Two NBIA genes are directly involved in iron metabolism, but whether other NBIA-related genes also regulate iron homeostasis in the human brain, and whether aberrant iron deposition contributes to neurodegenerative processes remains largely unknown. This study aims to expand our understanding of these iron overload diseases and identify relationships between known NBIA genes and their main interacting partners by using a systems biology approach. We used whole-transcriptome gene expression data from human brain samples originating from 101 neuropathologically normal individuals (10 brain regions) to generate weighted gene co-expression networks and cluster the 10 known NBIA genes in an unsupervised manner. We investigated NBIA-enriched networks for relevant cell types and pathways, and whether they are disrupted by iron loading in NBIA diseased tissue and in an in vivo mouse model. We identified two basal ganglia gene co-expression modules significantly enriched for NBIA genes, which resemble neuronal and oligodendrocytic signatures. These NBIA gene networks are enriched for iron-related genes, and implicate synapse and lipid metabolism related pathways. Our data also indicates that these networks are disrupted by excessive brain iron loading. We identified multiple cell types in the origin of NBIA disorders. We also found unforeseen links between NBIA networks and iron-related processes, and demonstrate convergent pathways connecting NBIAs and phenotypically overlapping diseases. Our results are of further relevance for these diseases by providing candidates for new causative genes and possible points for therapeutic intervention.

Keywords: Human brain; Iron metabolism; NBIA; WGCNA; Whole-transcriptome analysis.

Fig. 1

Expression patterns of NBIA genes in pathologically confirmed normal human brains. The following brain regions were studied: cerebellum (CRBL), frontal cortex (FCTX), hippocampus (HIPP), medulla (MEDU), occipital cortex (OCTX), putamen (PUTM), substantia nigra (SNIG), temporal cortex (TCTX), thalamus (THAL), and white matter (WHMT, highlighted in red). A) Example of brain expression patterns of an NBIA gene (FA2H) which presents the highest expression levels in the white matter. B) Example of brain expression patterns of an NBIA gene (PANK2) which presents the lowest expression levels in the white matter.

Fig. 2

Network representation of the putamen NBIA-enriched modules generated using VisANT (http://visant.bu.edu) (Hu et al., 2004). A) Brown module, showing genes connected with a topological overlap measure (TOM) > 0.08. B) Green module, showing genes connected with a TOM > 0.18. NBIA genes are highlighted in red and iron-related genes are in purple. Given the TOM cut-offs used, not all NBIA and iron-related genes could be included. The biggest circles represent the top hub genes in each module, which stands for the most interconnected genes in the module. Note the connections of NBIA genes and iron-related genes with the same hub genes.

Fig. 3

Expression patterns of NBIA genes and neuronal or oligodendrocyte markers (A–C), using data from the Allen Brain Atlas (http://mouse.brain-map.org) (Lein et al., 2007), and patterns of iron accumulation in the brain of wild-type and Hfe^−/− xTfr2^mut mice (D). A) Genes in the neuronal-enriched module (putamen brown module, 1600014C10Rik is the mouse ortholog for C19orf12); B) Genes in the oligodendrocyte-enriched module (putamen green module, data for FTL was not available); C) NBIA genes in other co-expression modules; D) 3,3′-diaminobenzidine-4HCl (DAB)-enhanced Perls' staining shows iron loading in the caudate-putamen and corpus callosum of the Hfe^−/− xTfr2^mut mice compared with matched wild-type mice. CC — corpus callosum; CP — caudate-putamen.