Cell type-specific DNA methylome signatures reveal epigenetic mechanisms for neuronal diversity and neurodevelopmental disorder.

DNA methylation plays a critical function in establishing and maintaining cell identity in brain. Disruption of DNA methylation-related processes leads to diverse neurological disorders. However, the role of DNA methylation characteristics in neuronal diversity remains underexplored. Here, we report detailed context-specific DNA methylation maps for GABAergic, glutamatergic (Glu) and Purkinje neurons, together with matched transcriptome profiles. Genome-wide mCH levels are distinguishable, while the mCG levels are similar among the three cell types. Substantial CG-differentially methylated regions (DMRs) are also seen, with Glu neurons experiencing substantial hypomethylation events. The relationship between mCG levels and gene expression displays cell type-specific patterns, while genic CH methylation exhibits a negative effect on transcriptional abundance. We found that cell type-specific CG-DMRs are informative in terms of represented neuronal function. Furthermore, we observed that the identified Glu-specific hypo-DMRs have a high level of consistency with the chromatin accessibility of excitatory neurons and the regions enriched for histone modifications (H3K27ac and H3K4me1) of active enhancers, suggesting their regulatory potential. Hypomethylation regions specific to each cell type are predicted to bind neuron type-specific transcription factors. Finally, we show that the DNA methylation changes in a mouse model of Rett syndrome, a neurodevelopmental disorder caused by the de novo mutations in MECP2, are cell type- and brain region-specific. Our results suggest that cell type-specific DNA methylation signatures are associated with the functional characteristics of the neuronal subtypes. The presented results emphasize the importance of DNA methylation-mediated epigenetic regulation in neuronal diversity and disease.

Identification of PSMB5 as a genetic modifier of fragile X-associated tremor/ataxia syndrome.

Fragile X­associated tremor/ataxia syndrome (FXTAS) is a debilitating late-onset neurodegenerative disease in premutation carriers of the expanded CGG repeat in FMR1 that presents with a spectrum of neurological manifestations, such as gait ataxia, intention tremor, and parkinsonism [P. J. Hagerman, R. J. Hagerman, Ann. N. Y. Acad. Sci. 1338, 58­70 (2015); S. Jacquemont et al., JAMA 291, 460­469 (2004)]. Here, we performed whole-genome sequencing (WGS) on male premutation carriers (CGG55­200) and prioritized candidate variants to screen for candidate genetic modifiers using a Drosophila model of FXTAS. We found 18 genes that genetically modulate CGG-associated neurotoxicity in Drosophila, such as Prosbeta5 (PSMB5), pAbp (PABPC1L), e(y)1 (TAF9), and CG14231 (OSGEPL1). Among them, knockdown of Prosbeta5 (PSMB5) suppressed CGG-associated neurodegeneration in the fly as well as in N2A cells. Interestingly, an expression quantitative trait locus variant in PSMB5, PSMB5rs11543947-A, was found to be associated with decreased expression of PSMB5 and delayed onset of FXTAS in human FMR1 premutation carriers. Finally, we demonstrate evidence that PSMB5 knockdown results in suppression of CGG neurotoxicity via both the RAN translation and RNA-mediated toxicity mechanisms, thereby presenting a therapeutic strategy for FXTAS.

Intracellular crotonyl-CoA stimulates transcription through p300-catalyzed histone crotonylation.

Acetylation of histones at DNA regulatory elements plays a critical role in transcriptional activation. Histones are also modified by other acyl moieties, including crotonyl, yet the mechanisms that govern acetylation versus crotonylation and the functional consequences of this "choice" remain unclear. We show that the coactivator p300 has both crotonyltransferase and acetyltransferase activities, and that p300-catalyzed histone crotonylation directly stimulates transcription to a greater degree than histone acetylation. Levels of histone crotonylation are regulated by the cellular concentration of crotonyl-CoA, which can be altered through genetic and environmental perturbations. In a cell-based model of transcriptional activation, increasing or decreasing the cellular concentration of crotonyl-CoA leads to enhanced or diminished gene expression, respectively, which correlates with the levels of histone crotonylation flanking the regulatory elements of activated genes. Our findings support a general principle wherein differential histone acylation (i.e., acetylation versus crotonylation) couples cellular metabolism to the regulation of gene expression.

Expansion of Human-Specific GGC Repeat in Neuronal Intranuclear Inclusion Disease-Related Disorders.

Neuronal intranuclear inclusion disease (NIID) is a slowly progressing neurodegenerative disease characterized by eosinophilic intranuclear inclusions in the nervous system and multiple visceral organs. The clinical manifestation of NIID varies widely, and both familial and sporadic cases have been reported. Here we have performed genetic linkage analysis and mapped the disease locus to 1p13.3-q23.1; however, whole-exome sequencing revealed no potential disease-causing mutations. We then performed long-read genome sequencing and identified a large GGC repeat expansion within human-specific NOTCH2NLC. Expanded GGC repeats as the cause of NIID was further confirmed in an additional three NIID-affected families as well as five sporadic NIID-affected case subjects. Moreover, given the clinical heterogeneity of NIID, we examined the size of the GGC repeat among 456 families with a variety of neurological conditions with the known pathogenic genes excluded. Surprisingly, GGC repeat expansion was observed in two Alzheimer disease (AD)-affected families and three parkinsonism-affected families, implicating that the GGC repeat expansions in NOTCH2NLC could also contribute to the pathogenesis of both AD and PD. Therefore, we suggest defining a term NIID-related disorders (NIIDRD), which will include NIID and other related neurodegenerative diseases caused by the expanded GGC repeat within human-specific NOTCH2NLC.

Metabolic pathways modulate the neuronal toxicity associated with fragile X-associated tremor/ataxia syndrome.

Fragile X-associated tremor/ataxia syndrome (FXTAS) is an adult-onset neurodegenerative disorder that affects premutation carriers (55-200 CGG repeats) of the fragile X mental retardation 1 (FMR1) gene. Much remains unknown regarding the metabolic alterations associated with FXTAS, especially in the brain, and the most affected region, the cerebellum. Investigating the metabolic changes in FXTAS will aid in the identification of biomarkers as well as in understanding the pathogenesis of disease. To identify the metabolic alterations associated with FXTAS, we took advantage of our FXTAS mouse model that expresses 90 CGG repeats in cerebellar Purkinje neurons and exhibits the key phenotypic features of FXTAS. We performed untargeted global metabolic profiling of age-matched control and FXTAS mice cerebella at 16-20 weeks and 55 weeks. Out of 506 metabolites measured in cerebellum, we identified 186 metabolites that demonstrate significant perturbations due to the (CGG)90 repeat (P<0.05) and found that these differences increase dramatically with age. To identify key metabolic changes in FXTAS pathogenesis, we performed a genetic screen using a Drosophila model of FXTAS. Out of 28 genes that we tested in the fly, 8 genes showed significant enhanced neuronal toxicity associated with CGG repeats, such as Schlank (ceramide synthase), Sk2 (sphingosine kinase) and Ras (IMP dehydrogenase). By combining metabolic profiling with a Drosophila genetic screen to identify genetic modifiers of FXTAS, we demonstrate an effective method for functional validation of high-throughput metabolic data and show that sphingolipid and purine metabolism are significantly perturbed in FXTAS pathogenesis.

Cannabinoids in dermatologic surgery.

Though known as a medicinal herb for centuries, the recent legalization of cannabinoids across many states has ushered in a new era where cannabinoids have become a popular treatment option among clinicians and patients alike. Cannabinoids have demonstrated efficacy in wound healing, reducing inflammation, ameliorating pain, and have shown potential as an antitumor agent. As a result, cannabinoids have been rapidly woven into the fabric of modern medicine. However, the utility of cannabinoids in dermatologic surgery has not been explored to date. In this article, we review the current literature to discuss the potential impact of cannabinoid use in dermatologic surgery.

Tools to study the severity of itch in 8- to 17-year-old children: Validation of TweenItchyQoL and ItchyQuant.

BACKGROUND/OBJECTIVES: Validated pruritus-specific quality of life and self-reported severity instruments exist primarily for adults. Clinical trials to develop therapeutics for children with chronic pruritus are hampered by the paucity of appropriate outcome measures. To address this gap, we aimed to develop validated instruments to measure itch-specific quality of life and self-reported severity in children. METHODS: We conducted in-depth, open-ended interviews of itchy children and generated concepts to develop TweenItchyQoL. We administered TweenItchyQoL, ItchyQuant, a cartoon-annotated self-reported pruritus severity numeric rating scale (NRS), and a non-cartoon NRS to 175 itchy children aged 8-17 years. We analyzed the data for feasibility, preference, reliability, construct validity, and responsiveness. RESULTS: Average completion time was 4.8 minutes for TweenItchyQoL and 33 seconds for ItchyQuant. The majority of patients either preferred ItchyQuant or found no difference between ItchyQuant and the NRS. Cronbach's alpha for TweenItchyQoL total and subscales ranged from 0.84 to 0.95. Test-retest reliability coefficients were ≥0.7 for TweenItchyQoL and 0.4 for ItchyQuant. A 3-dimensional bifactor model was most appropriate (RMSEA = 0.048) on the confirmatory factor analyses. As a function of those reporting worsening, improvement, or no change at their final visit, TweenItchyQoL and ItchyQuant scores in those cohorts changed as expected. CONCLUSIONS: This new set of validated and feasible instruments shows promise to quantify itch severity and QoL impact in older children.

Pruritus assessment tools for 6 to 7-year-old children: KidsItchyQoL and ItchyQuant.

BACKGROUND/OBJECTIVES: Measures of pruritus severity and quality of life (QoL) are necessary for the development of therapeutics for children with chronic pruritus. In children, questionnaires need to be developed for specific age groups given the differences in cognitive levels. In this study, we aimed to develop tools to assess QoL and pruritus severity in children 6 to 7-years-old with chronic pruritus. METHODS: Based on open interviews with children, we developed a cartoon-annotated QoL instrument, KidsItchyQoL, and validated an existing pruritus severity instrument, ItchyQuant, that measures pruritus impact and severity for the preceding week. Both instruments were administered to 100 children aged 6-7 years with chronic pruritus. The data were analyzed for reliability, reproducibility, construct validity, and responsiveness. RESULTS: We found the 14-item KidsItchyQoL to be reliable (Cronbach's α = 0.846) and reproducible (intraclass correlation coefficient (ICC) = 0.66) as was the ItchyQuant (ICC = 0.47). With respect to construct validity, examination of eigenvalues of the inter-item polychoric correlation matrix suggested three dominant factors. A subsequent confirmatory factor analysis suggested that a 3-dimensional simple structure model with correlated factors provided a reasonable data representation. The responsiveness of KidsItchyQoL and ItchyQuant (P = .005, GLM procedure) were demonstrated with scores changing as expected with the self-reported change of itch severity. CONCLUSIONS: These results demonstrate promise for a new set of reliable research tools to assess QoL and pruritus severity in children 6 to 7 years of age.

Targeted Histone Peptides: Insights into the Spatial Regulation of the Methyltransferase PRC2 by using a Surrogate of Heterotypic Chromatin.

Eukaryotic genomes are dynamically regulated through a host of epigenetic stimuli. The substrate for these epigenetic transactions, chromatin, is a polymer of nucleosome building blocks. In native chromatin, each nucleosome can differ from its neighbors as a result of covalent modifications to both the DNA and the histone packaging proteins. The heterotypic nature of chromatin presents a formidable obstacle to biochemical studies seeking to understand the role of context on epigenetic regulation. A chemical approach to the production of heterotypic chromatin that can be used in such studies is introduced. This method involves the attachment of a user-defined modified histone peptide to a designated nucleosome within the polymer by using a peptide nucleic acid (PNA) targeting compound. This strategy was applied to dissect the effect of chromatin context on the activity of the histone methyltransferase PRC2. The results show that PRC2 can be stimulated to produce histone H3 methylation from a defined nucleation site.

Cutaneous findings in myotonic dystrophy.

Myotonic dystrophy types 1 and 2 are a group of complex genetic disorders resulting from the expansion of (CTG)n nucleotide repeats in the DMPK gene. In addition to the hallmark manifestations of myotonia and skeletal muscle atrophy, myotonic dystrophy also affects a myriad of other organs including the heart, lungs, as well as the skin. The most common cutaneous manifestations of myotonic dystrophy are early male frontal alopecia and adult-onset pilomatricomas. Myotonic dystrophy also increases the risk of developing malignant skin diseases such as basal cell carcinoma and melanoma. To aid in the diagnosis and treatment of myotonic dystrophy related skin conditions, it is important for the dermatologist to become cognizant of the common and rare cutaneous manifestations of this genetic disorder. We performed a PubMed search using the key terms "myotonic dystrophy" AND "cutaneous" OR "skin" OR "dermatologic" AND "manifestation" OR "finding." The resulting publications were manually reviewed for additional relevant publications, and subsequent additional searches were performed as needed, especially regarding the molecular mechanisms of pathogenesis. In this review, we aim to provide an overview of myotonic dystrophy types 1 and 2 and summarize their cutaneous manifestations as well as potential mechanisms of pathogenesis.

Metabolic Alterations in FMR1 Premutation Carriers.

FMR1 gene premutation carriers are at risk of developing Fragile X-associated tremor/ataxia syndrome (FXTAS) and Fragile X-associated primary ovarian insufficiency (FXPOI) in adulthood. Currently the development of biomarkers and effective treatments in FMR1 premutations is still in its infancy. Recent metabolic studies have shown novel findings in asymptomatic FMR1 premutation carriers and FXTAS, which provide promising insight through identification of potential biomarkers and therapeutic pathways. Here we review the latest advancements of the metabolic alterations found in asymptomatic FMR1 premutation carriers and FXTAS, along with our perspective for future studies in this emerging field.

Application of Drosophila Model Toward Understanding the Molecular Basis of Fragile X Syndrome.

Drosophila melanogaster is an ideal model to study Fragile X syndrome (FXS) as it presents us with a toolbox to identify genetic modifiers and to investigate the molecular mechanisms of FXS. Here we describe some of the methods that have been used to study FXS, ranging from reverse genetic screening using the GAL4-UAS system, to mushroom body staining and courtship behavioral assays to examine the learning and memory deficits associated with FXS.

Fragile X-Associated Tremor/Ataxia Syndrome: From Molecular Pathogenesis to Development of Therapeutics.

Fragile X-associated tremor/ataxia syndrome (FXTAS) is a neurodegenerative disorder caused by a premutation CGG repeat expansion (55-200 repeats) within the 5' UTR of the fragile X gene (FMR1). FXTAS is characterized by intension tremor, cerebellar ataxia, progressive neurodegeneration, parkinsonism and cognitive decline. The development of transgenic mouse and Drosophila melanogaster models carrying an expanded CGG repeat has yielded valuable insight into the pathophysiology of FXTAS. To date, we know of two main molecular mechanisms of this disorder: (1) a toxic gain of function of the expanded CGG-repeat FMR1 mRNA, which results in the binding/sequestration of the CGG-binding proteins; and (2) CGG repeat-associated non-AUG-initiated (RAN) translation, which generates a polyglycine peptide toxic to cells. Besides these CGG-mediated mechanisms, recent studies have shed light on additional mechanisms of pathogenesis, such as the antisense transcript ASFMR1, mitochondrial dysfunction, DNA damage from R-loop formation and 5-hydroxymethylcytosine (5hmC)-mediated epigenetic modulation. Here we summarize the recent progress towards understanding the etiology of FXTAS and provide an overview of potential treatment strategies.

CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntington's disease.

Huntington's disease is a neurodegenerative disorder caused by a polyglutamine repeat in the Huntingtin gene (HTT). Although suppressing the expression of mutant HTT (mHTT) has been explored as a therapeutic strategy to treat Huntington's disease, considerable efforts have gone into developing allele-specific suppression of mHTT expression, given that loss of Htt in mice can lead to embryonic lethality. It remains unknown whether depletion of HTT in the adult brain, regardless of its allele, could be a safe therapy. Here, we report that permanent suppression of endogenous mHTT expression in the striatum of mHTT-expressing mice (HD140Q-knockin mice) using CRISPR/Cas9-mediated inactivation effectively depleted HTT aggregates and attenuated early neuropathology. The reduction of mHTT expression in striatal neuronal cells in adult HD140Q-knockin mice did not affect viability, but alleviated motor deficits. Our studies suggest that non-allele-specific CRISPR/Cas9-mediated gene editing could be used to efficiently and permanently eliminate polyglutamine expansion-mediated neuronal toxicity in the adult brain.