Transcriptomic Analysis of Mecp2 Mutant Mice Reveals Differentially Expressed Genes and Altered Mechanisms in Both Blood and Brain

Abstract

Rett syndrome is a rare neuropsychiatric disorder with a wide symptomatology including impaired communication and movement, cardio-respiratory abnormalities, and seizures. The clinical presentation is typically associated to mutations in the gene coding for the methyl-CpG-binding protein 2 ( MECP2 ), which is a transcription factor. The gene is ubiquitously present in all the cells of the organism with a peak of expression in neurons. For this reason, most of the studies in Rett models have been performed in brain. However, some of the symptoms of Rett are linked to the peripheral expression of MECP2 , suggesting that the effects of the mutations affect gene expression levels in tissues other than the brain. We used RNA sequencing in Mecp2 mutant mice and matched controls, to identify common genes and pathways differentially regulated across different tissues. We performed our study in brain and peripheral blood, and we identified differentially expressed genes (DEGs) and pathways in each tissue. Then, we compared the genes and mechanisms identified in each preparation. We found that some genes and molecular pathways that are differentially expressed in brain are also differentially expressed in blood of Mecp2 mutant mice at a symptomatic—but not presymptomatic—stage. This is the case for the gene Ube2v1 , linked to ubiquitination system, and Serpin1 , involved in complement and coagulation cascades. Analysis of biological functions in the brain shows the enrichment of mechanisms correlated to circadian rhythms, while in the blood are enriched the mechanisms of response to stimulus—including immune response. Some mechanisms are enriched in both preparations, such as lipid metabolism and response to stress. These results suggest that analysis of peripheral blood can reveal ubiquitous altered molecular mechanisms of Rett and have applications in diagnosis and treatments’ assessments.

Genome‐wide transcriptomic and proteomic studies of Rett syndrome mouse models identify common signaling pathways and cellular functions as potential therapeutic targets

“…As Irak1 expression is central to the functioning of this pathway, and the abnormally increased expression of Irak1 is associated with Mecp2 loss of function, significant interest is gathering in the investigation of the possible role of IRAK1 regulation in the NF‐κB pathway and the pathogenesis of Rett syndrome. A dysregulated immune‐inflammatory response implicating the NF‐κB pathway has more recently been observed by Sanfeliu et al () in brains and blood of mice. However, although the authors did not specifically mention Irak1 , the overall findings confirm the immune‐inflammatory response in Rett syndrome mouse models.…”

“…In an attempt to identify region specific gene expression, studies were conducted on individual brain regions and cells isolated from these regions. These included the cortex (Kishi et al, ; Pacheco et al, ; Tudor, Akbarian, Chen, & Jaenisch, ; Urdinguio et al, ), visual cortex (Gabel et al, ; Renthal et al, ), the cerebellum (Ben‐Shachar et al, ; Gabel et al, ; Jordan, Li, Kwan, & Francke, ; Mellen, Ayata, & Heintz, ; Mellen, Ayata, Dewell, Kriaucionis, & Heintz, ; Sanfeliu, Hokamp, Gill, & Tropea, ; Urdinguio et al, ), whole brain (Guo et al, ; Kriaucionis et al, ; Nuber et al, ), the whole hippocampus (Baker et al, ; Tudor et al, ), and the amygdala (Samaco et al, ). Studies were also conducted on cell sources originating from distinct regions of the brain including forebrain (Tudor et al, ), hypothalamus (Chahrour et al, ; Chen et al, ), midbrain (Urdinguio et al, ), and striatum (Zhao, Goffin, Johnson, & Zhou, ), granule cells of the dentate gyrus hippocampal region (Smrt et al, ), embryonic cortical neurons (Bedogni et al, ; Vacca et al, ), and excitatory and inhibitory cortical neurons (Johnson et al, ).…”

“…Other studies used astrocytes (Delepine et al, ; Yasui et al, ) and microglia and peritoneal macrophages (Cronk et al, ), while others used cardiovascular progenitor cells (Hara et al, ) and cortical callosal projection neurons (Kishi et al, ). Studies using cell sources not originating from brain regions include the use of fibroblasts (Orlic‐Milacic et al, ), skeletal muscle (Gold et al, ), and blood (Sanfeliu et al, ). Sample sizes of the studies varied greatly with the highest sample size being 205 (Sanfeliu et al, ) and the others varying between 1 and 100 samples.…”

“…Studies using cell sources not originating from brain regions include the use of fibroblasts (Orlic‐Milacic et al, ), skeletal muscle (Gold et al, ), and blood (Sanfeliu et al, ). Sample sizes of the studies varied greatly with the highest sample size being 205 (Sanfeliu et al, ) and the others varying between 1 and 100 samples. The age of mice used in the studies varied between embryonic, juvenile, and mature with the youngest being E15 (Bedogni et al, ; Vacca et al, ) and the eldest 25 weeks (Tudor et al, ).…”

“…Although MECP2 is expressed in a wide range of tissues, Rett syndrome is principally caused by the deficiency of MeCP2 in the cells of the brain (Chen, Akbarian, Tudor, & Jaenisch, ) and thus apart from four studies (Gold et al, ; Hara et al, ; Orlic‐Milacic et al, ; Sanfeliu et al, ), all transcriptional murine studies were confined to the brain. A handful of studies focused on the transcriptome of the whole brain (Guo et al, ; Kriaucionis et al, ; Nuber et al, ) however these studies revealed only subtle changes in gene expression which can be attributed to the brain being a heterogeneous organ consisting of many distinct functional regions that may individually be affected by the lack of Mecp2.…”