Altered transcriptional and epigenetic regulation affects brain cells proliferation and differentiation in the ultra-rare genetic demyelinating disease AGC1 deficiency: a study on in vitro models

AGC1 deficiency is a rare demyelinating disease caused by mutations in the SLC25A12 gene, which encodes for the mitochondrial glutamate-aspartate carrier 1 (AGC1/Alarar), highly expressed in the central nervous system. In neurons, impairment in AGC1 activity leads to reduction in N-acetyl-aspartate, the main lipid precursor for myelin synthesis (Profilo et al., 2017); in oligodendrocytes progenitors cells, AGC1 down regulation has been related to early arrest proliferation and premature differentiation (Petralla et al., 2019). Additionally, in vivo AGC1 deficiency models i.e., heterozygous mice for AGC1 knock-out and neurospheres from their subventricular zone, respectively, showed a global decrease in cells proliferation and a switch in neural stem cells (NSCs) commitment, with specific reduction in OPCs number and increase in neural and astrocytic pools (Petralla et al., 2019). Therefore, the present study aims to investigate the transcriptional and epigenetic regulation underlying the alterations observed in OPCs and NSCs biological mechanisms, in either AGC1 deficiency models of Oli-neu cells (murine immortalized oligodendrocytes precursors cells), partially silenced by a shRNA for SLC25A12 gene, and SVZ-derived neurospheres from AGC1+/- mice. Western blot and immunofluorescence analysis revealed significant variations in the expression of transcription factors involved in brain cells’ proliferation and differentiation, in association with altered histone post-translational modifications, as well as histone acetylases (HATs) and deacetylases (HDACs) activity/expression, suggesting an improper transcriptional and epigenetic regulation affecting both AGC1 deficiency in vitro models. Furthermore, given the large role of acetylation in controlling in specific time-windows OPC maturation (Hernandez and Casaccia; 2015), pharmacological HATs/HDACs inhibitions were performed, confirming the involvement of chromatin remodelling enzymes in the altered proliferation and early differentiation observed in the AGC1 deficiency models of siAGC1 Oli-neu cells and AGC1+/- mice-derived neurospheres.

Development of an innovative strategy to enhance the efficacy of gene therapy for CDKL5 deficiency disorder

CDKL5 (cyclin-dependent kinase-like 5) deficiency disorder (CDD) is a severe X-linked neurodevelopmental disease caused by mutations in the CDKL5 gene, characterized by early-onset epileptic seizures, intellectual disability, motor and visual impairment and respiratory dysregulation. Although pharmacological treatments are used to control seizures, there is currently no cure to ameliorate symptoms for CDD. Albeit delivery of a wild-type copy of the mutated gene to cells represents the most curative approach for a monogenic disease, proof-of-concept studies highlight significant efficacy caveats for brain gene therapy. The major one regards the low efficiency of gene delivery to the CNS by viral vectors. We used a secretable Igk-TATk-CDKL5 protein to enhance the efficiency of a gene therapy for CDD. In view of the properties of the Igk-chain leader sequence, the TATk-CDKL5 protein produced by infected cells is secreted via constitutive secretory pathways. Importantly, due to the transduction property of the TATk peptide, the secreted CDKL5 protein is internalized by cells. We compared the effects of a CDKL5 gene therapy with an IgK-TATk-CDKL5 gene therapy in a Cdkl5 KO mouse model to validate whether the Igk-TATk-CDKL5 approach significantly improve the therapeutic efficacy. We found that, although AAVPHP.B_Igk-TATk-CDKL5 and AAVPHP.B_CDKL5 vectors had similar brain infection efficiency, the AAVPHP.B_Igk-TATk-CDKL5 vector led to a higher CDKL5 protein replacement and Cdkl5 KO mice treated with the AAVPHP.B_Igk-TATk-CDKL5 vector showed a behavioral and neuroanatomical improvement in comparison with Cdkl5 KO mice treated with the AAVPHP.B_CDKL5 vector.

Cardiac functional and structural abnormalities in a mouse model of CDKL5 deficiency disorder

CDKL5 (cyclin-dependent kinase-like 5) deficiency disorder (CDD) is a rare and severe neurodevelopmental disease that mostly affects girls who are heterozygous for mutations in the X-linked CDKL5 gene. The lack of CDKL5 protein expression or function leads to the appearance of numerous clinical features, including early-onset seizures, marked hypotonia, autistic features, and severe neurodevelopmental impairment. Mouse models of CDD, Cdkl5 KO mice, exhibit several behavioral phenotypes that mimic CDD features, such as impaired learning and memory, social interaction, and motor coordination. CDD symptomatology, along with the high CDKL5 expression levels in the brain, underscores the critical role that CDKL5 plays in proper brain development and function. Nevertheless, the improvement of the clinical overview of CDD in the past few years has defined a more detailed phenotypic spectrum; this includes very common alterations in peripheral organ and tissue function, such as gastrointestinal problems, irregular breathing, hypotonia, and scoliosis, suggesting that CDKL5 deficiency compromises not only CNS function but also that of other organs/tissues. Here we report, for the first time, that a mouse model of CDD, the heterozygous Cdkl5 KO (Cdkl5 +/-) female mouse, exhibits cardiac functional and structural abnormalities. The mice also showed QTc prolongation and increased heart rate. These changes correlate with a marked decrease in parasympathetic activity to the heart and in the expression of the Scn5a and Hcn4 voltage-gated channels. Moreover, the Cdkl5 +/- heart shows typical signs of heart aging, including increased fibrosis, mitochondrial dysfunctions, and increased ROS production. Overall, our study not only contributes to the understanding of the role of CDKL5 in heart structure/function but also documents a novel preclinical phenotype for future therapeutic investigation.

Role of neuroinflammation in the pathophysiology of CDKL5 deficiency disorder

Cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder (CDD), a rare neurodevelopmental disease caused by mutations in the X-linked CDKL5 gene, is characterized by early-onset epilepsy, intellectual disability, and autistic features. To date, little is known about the etiology of CDD and no therapies are available. When overactivated in response to neuronal damage and genetic or environmental factors, microglia – the brain macrophages – cause damage to neighboring neurons by producing neurotoxic factors and pro-inflammatory molecules. Importantly, overactivated microglia have been described in several neurodegenerative and neurodevelopmental disorders, suggesting that active neuroinflammation may account for the compromised neuronal survival and/or brain development observed in these pathologies. Recent evidence shows a subclinical chronic inflammatory status in plasma from CDD patients. However, it is unknown whether a similar inflammatory status is present in the brain of CDD patients and, if so, whether it plays a causative or exacerbating role in the pathophysiology of CDD. Here, we show evidence of a chronic microglia overactivation status in the brain of Cdkl5 KO mice, characterized by alterations in microglial cell number/morphology and increased pro-inflammatory gene expression. We found that the neuroinflammatory process is already present in the postnatal period in Cdkl5 KO mice and worsens during aging. Remarkably, by restoring microglia alterations, treatment with luteolin, a natural anti-inflammatory flavonoid, promotes neuronal survival in the brain of Cdkl5 KO mice since it counteracts hippocampal neuron cell death and protects neurons from NMDA-induced excitotoxic damage. In addition, through the restoration of microglia alterations, luteolin treatment also increases hippocampal neurogenesis and restores dendritic spine maturation and dendritic arborization of hippocampal and cortical pyramidal neurons in Cdkl5 KO mice, leading to improved behavioral performance. These findings highlight new insights into the CDD pathophysiology and provide the first evidence that therapeutic approaches aimed at counteracting neuroinflammation could be beneficial in CDD.

Resetting SETD2/H3K36ME3 deficiency in advanced systemic mastocytosis

Systemic Mastocytosis (SM) is a hematological disorder characterized by abnormal proliferation of mast cells in various organs, ranging from indolent variants to advanced entities with poor prognosis. The KIT D816V gene mutation drives mast cell growth, but its presence alone is not fully transforming. The SETD2 gene, responsible for maintaining genomic integrity, is often impaired in advanced SM (advSM), leading to reduced expression of histone marker H3K36Me3. Proteasome inhibitors are effective in restoring SETD2 function and suppressing mast cell growth, offering an alternative therapy for patients resistant to tyrosine kinase inhibitors. Aberrant expression of Plk1 and Aurora kinase A correlates with SETD2 loss and can be targeted with inhibitors like alisertib and volasertib, leading to reduced cell growth and apoptosis. Additionally, inhibition of Wee1 enhances apoptosis and reduces colony growth in SM cells. Molecular diagnostic techniques like droplet digital polymerase chain reaction (ddPCR) offer a less invasive and reliable method for detecting the D816V mutation in peripheral blood, and efforts to standardize molecular assays across laboratories show promising reproducibility. Overall, this research provides new insights into the mechanisms of advanced SM, identifies potential therapeutic targets, and validates molecular diagnostic tools for SM diagnosis.

Dissecting and resetting SETD2/H3K36ME3 deficiency in chronic myeloid leukemia

Chronic myeloid leukemia (CML) is characterized by the presence of the BCR::ABL1 fusion gene, leading to a constitutively active tyrosine kinase that drives the disease. Genomic instability is a hallmark of CML, contributing to disease progression and treatment resistance. A study identified SETD2, a histone methyltransferase, as frequently dysfunctional in advanced-phase CML, resulting in reduced trimethylation of Histone H3 at lysine 36 (H3K36Me3). This loss is associated with poor prognosis and increased genetic instability. Investigations revealed that SETD2 dysfunction is caused by post-translational modifications mediated by Aurora kinase A and MDM2, leading to proteasome-mediated degradation. Aurora kinase A phosphorylates SETD2, while MDM2 ubiquitinates it, targeting it for degradation. Inhibition of MDM2 and Aurora kinase A restored SETD2 expression and activity, suggesting potential therapeutic targets. Loss of SETD2 and H3K36Me3 impairs DNA repair mechanisms, favoring error-prone repair pathways over faithful ones, exacerbating genetic instability. Reintroduction of SETD2 into deficient cells restored DNA repair pathways, preserving genomic integrity. Analysis of CD34+ progenitor cells from CML patients showed reduced SETD2 levels compared to healthy individuals, correlating with decreased clonogenic capacity. Notably, SETD2 loss is not detectable at diagnosis but emerges during disease progression, indicating its role as an early indicator of CML advancement. Therapeutically, inhibitors targeting Aurora kinase A, MDM2, and the proteasome showed efficacy in cells expressing SETD2, particularly in those with low SETD2 levels. Proteasome inhibitors induced apoptosis and DNA damage in SETD2-deficient cells, highlighting their potential for CML treatment. In conclusion, SETD2 acts as a tumor suppressor in CML, with its dysfunction contributing to genetic instability and disease progression. Targeting the mechanisms of SETD2 loss presents promising therapeutic avenues for controlling CML proliferation and restoring genomic integrity.

Decoding Agc1 deficiency: bioinformatics approaches to unveil the functional implications of Slc25a12 on the transcriptome and epigenome

In the brain, mutations in SLC25A12 gene encoding AGC1 cause an ultra-rare genetic disease reported as a developmental and epileptic encephalopathy associated with global cerebral hypomyelination. Symptoms of the disease include diffused hypomyelination, arrested psychomotor development, severe hypotonia, seizures and are common to other neurological and developmental disorders. Amongst the biological components believed to be most affected by AGC1 deficiency are oligodendrocytes, glial cells responsible for myelination. Recent studies (Poeta et al, 2022) have also shown how altered levels of transcription factors and epigenetic modifications greatly affect proliferation and differentiation in oligodendrocyte precursor cells (OPCs). In this study we explore the transcriptomic landscape of Agc1 in two different system models: OPCs silenced for Agc1 and iPSCs from human patients differentiated to neural progenitors. Analyses range from differential expression analysis, alternative splicing, master regulator analysis. ATAC-seq results on OPCs were integrated with results from RNA-Seq to assess the activity of a TF based on the accessibility data from its putative targets, which allows to integrate RNA-Seq data to infer their role as either activators or repressors. All the findings for this model were also integrated with early data from iPSCs RNA-seq results, looking for possible commonalities between the two different system models, among which we find a downregulation in genes encoding for SREBP, a transcription factor regulating fatty acids biosynthesis, a key process for myelination which could explain the hypomyelinated state of patients. We also find that in both systems cells tend to form more neurites, likely losing their ability to differentiate, considering their progenitor state. We also report several alterations in the chromatin state of cells lacking Agc1, which confirms the hypothesis for which Agc1 is not a disease restricted only to metabolic alterations in the cells, but there is a profound shift of the regulatory state of these cells.