Analysis of the circRNA and T-UCR populations identifies convergent pathways in mouse and human models of Rett syndrome

Abstract

Noncoding RNAs play regulatory roles in physiopathology, but their involvement in neurodevelopmental diseases is poorly understood. Rett syndrome is a severe, progressive neurodevelopmental disorder linked to loss-of-function mutations of the MeCP2 gene for which no cure is yet available. Analysis of the noncoding RNA profile corresponding to the brain-abundant circular RNA (circRNA) and transcribed-ultraconserved region (T-UCR) populations in a mouse model of the disease reveals widespread dysregulation and enrichment in glutamatergic excitatory signaling and microtubule cytoskeleton pathways of the corresponding host genes. Proteomic analysis of hippocampal samples from affected individuals confirms abnormal levels of several cytoskeleton-related proteins together with key alterations in neurotransmission. Importantly, the glutamate receptor GRIA3 gene displays altered biogenesis in affected individuals and in vitro human cells and is influenced by expression of two ultraconserved RNAs. We also describe post-transcriptional regulation of SIRT2 by circRNAs, which modulates acetylation and total protein levels of GluR-1. As a consequence, both regulatory mechanisms converge on the biogenesis of AMPA receptors, with an effect on neuronal differentiation. In both cases, the noncoding RNAs antagonize MeCP2-directed regulation. Our findings indicate that noncoding transcripts may contribute to key alterations in Rett syndrome and are not only useful tools for revealing dysregulated processes but also molecules of biomarker value.

Global Impairment of Immediate-Early Genes Expression in Rett Syndrome Models and Patients Linked to Myelination Defects

“…In concordance with our RNA-seq results, activity-dependent genes have been shown before to be aberrantly expressed in a mouse model of Rett syndrome [ 24 ]. In addition, the examples of cellular receptors whose inputs crosstalk with the expression of IEGs include AMPA receptors [ 25 , 26 ], which we have recently shown to be dysregulated in human cellular models and post-mortem samples of Rett syndrome [ 27 ]. Thus, we reasoned that this class of genes could be of prime interest for the pathophysiology of RTT.…”

“…By contrast, NPAS4 was consistently downregulated in all post-mortem brain regions analyzed ( Figure S4b ), indicating differential dysregulation for individual IEGs in patients, possibly linked to their specific roles in cognitive-related processes. To further prove the impact of MeCP2 regulation on these genes in human models, we used neural progenitor cells depleted of MECP2 by means of CRISPR/Cas9 [ 27 ]. The re-expression of MECP2 in these cells markedly downregulated the levels of FOS , JUNB and EGR2 mRNAs ( Figure 5 e), confirming its regulatory role over IEGs in the human context.…”

Hsa_circ_0000081 promotes the function of gastric cancer through sponging hsa-miR-423-5p to influence 3-phosphoinositide-dependent kinase 1 expression

“…The RPMI (Roswell Park Memorial Institute) 1640 culture medium, containing 10% fetal bovine serum and 1% penicillin and streptomycin (Gibco Life Technologies, USA), was used for all cell lines. All cells were cultured with 5% CO 2 at 37°C [ 19 ].…”

Advances in the pathogenesis of Rett syndrome using cell models

“…71 Long-term culture requires the support of scaffolds, but their components are unclear; Difficult to directed differentiation; Less repeatability than 2D cells in MeCP2-related transcriptional regulation processes could also become therapeutic targets. 83 Symptomatic treatment is one of the important strategies. RTT treatment in clinical and preclinical studies mainly include 2 approaches: one targets genetic and molecular pathology to repair the mutant MECP2 or to regulate downstream molecules targeting related signaling pathways, such as growth factors (IGF-1, BDNF), inhibitors (PTP1B, HDAC6), and other drugs for specific neuron types; the other alleviates the pathologic symptoms with physical stimulation interventions such as deep brain stimulation, 84,85 transcranial magnetic stimulation, etc.…”

“…Another treatment is to reactivate the silent chromosomes that express the normal MECP2 gene in the cells of female patients. In addition, noncoding RNAs participating in MeCP2‐related transcriptional regulation processes could also become therapeutic targets 83 . Symptomatic treatment is one of the important strategies.…”