Suboptimal cell hydration is a significant risk factor for age-related deterioration and disease vulnerability. Herein, we use a Huntington disease cell model to evaluate osmolarity-dependent modulation of (1) aggregation of polyQ-expanded mutant Huntingtin-EGFP reporter protein as a readout for structurally dynamic disease proteins versus (2) induction of HSP70 chaperone to report on stress-induced lability of folded proteins. Cell impermeant alkali-metal salts and polyethylene glycols were added to cell media to osmotically dehydrate cells for crowding, whereas water was added to swell cells for macromolecular dispersion. Cell image and biochemical analyses show that addition of sodium chloride and other alkali-metal salts to cell media promoted aggregation of mHTTExon1-EGFP protein into forming “inclusion bodies” (IBs) in live cells, while concurrently dampened the induction of HSP70 by heat shock. Conversely, a hypo-osmotic medium tempered the compaction of mHTTExon1-EGFP into forming IBs while increasing the induction of HSP70. Cell impermeable PEGs likewise promoted mHTTExon1-EGFP aggregation. These observations underscore the importance of an iso-osmotic cell environment for balanced structure and function of disordered versus folded proteome, that deviations from this ideal carry dire consequences on protein homeostasis conducive to disease protein aggregation and stress vulnerability.

We previously demonstrated that male progeny of cocaine-experienced sires resisted cocaine, expressed as delayed acquisition of cocaine self-administration. Here, we sought to determine whether this phenotype extended to another psychostimulant, methamphetamine (meth). Sires self-administered meth or cocaine or received yoked-saline infusions for 60 days, after which they were mated to naïve females. Some behaviors previously altered in cocaine-sired male rats, including object memory and anxiety-like behavior, were not influenced by paternal meth taking. In contrast to cocaine resistance in cocaine-sired male rats, meth-sired male offspring demonstrated increased susceptibility to meth taking, with no effect in females. Single nuclei RNA- and ATAC-sequencing of the nucleus accumbens was used to identify molecular drivers of phenotypes in cocaine- and meth-sired offspring. Sequencing results revealed unique profiles of gene expression and open chromatin in offspring nucleus accumbens. Differential gene expression in cocaine-resistant, cocaine-sired offspring and meth-susceptible, meth-sired offspring illuminates potential novel treatment targets for psychostimulant use disorders.

Familial Episodic Pain Syndrome (FEPS) is a rare inherited disorder characterized by episodes of severe upper-body pain triggered by different stimuli including cold, stress, or fasting. A gain-of-function point mutation (N855S) in the Transient Receptor Potential Ankyrin 1 (TRPA1) ion channel has been identified in affected individuals, altering its biophysical properties, and leading to sustained nociceptive signaling. While TRPA1 is predominantly studied in sensory neurons, recent findings highlight its key modulatory role for Schwann cells in chronic pain. Here, we investigated the cell-specific contributions of mutant TRPA1 (TRPA1*) in FEPS by developing mouse models with TRPA1* selectively expressed in either Schwann cells or sensory neurons, using CRISPR-based and Cre-loxP strategies. Patch-clamp analyses confirmed that TRPA1* exhibits enhanced current responses to agonists compared to wild-type. Through behavioral assays we revealed that TRPA1* expressed in sensory neurons mediates acute nociception, while TRPA1* in Schwann cells drives mechanical allodynia in response to subthreshold doses of TRPA1 agonists and to physiological pain triggers commonly observed in FEPS patients, including fasting, cold exposure, and restraint stress. Pain responses were associated with the increase in reactive oxygen species (ROS) and accumulation of 4-hydroxynonenal (4-HNE) in TRPA1* sciatic nerves and these effects were reduced by a treatment with an antioxidant. We reveal distinct roles of neuronal and non-neuronal TRPA1 in pain and provide novel in vivo models to investigate the mechanisms of chronic pain in FEPS and related channelopathies. Overall, this study offers new insights into the development of targeted therapies for Schwann cell-TRPA1 to relieve pain in affected individuals.

Spiral ganglion neurons (SGNs) are the primary afferent neurons that convey sound information from the cochlea, but the epigenetic changes that occur during development are unknown. We identified the chromodomain helicase binding protein 4 (CHD4) expression in SGNs. CHD4 is an ATP-dependent chromatin remodeler. We employed the Neurog1 (Ngn1) CreERT2 Chd4 conditional knockout animals to investigate Chd4 function in SGNs. SGNs are classified as type I and II neurons with different innervation patterns. SGNs lacking CHD4 showed abnormal fasciculation of type I neurons along with improper pathfinding of type II fibers. CHD4 binding to chromatin from immortalized multipotent otic progenitor-derived neurons was used to identify candidate target genes in SGNs. Gene ontology analysis of CHD4 target genes revealed cellular processes involved in axon guidance, axonal fasciculation, and the ephrin receptor signaling pathway. Eph/ephrin signaling regulates various biological processes, including axon guidance. We confirmed increased Eph/ephrin transcripts in SGNs from Chd4 conditional knockout cochleae. The results implicate epigenetic changes in circuit wiring by modulating the expression of a subset of axon guidance molecules. The results also provide insights into neurodevelopmental diseases such as Sifrim-Hitz-Weiss syndrome (SIHIWES) and inform strategies for regenerating SGNs.

Spiral ganglion neurons (SGNs) are crucial for hearing, and the loss of SGNs causes hearing loss. Stem cell-based therapies offer a promising approach for SGN regeneration and require understanding the mechanisms governing SGN differentiation. We investigated the chromatin remodeler CHD7 in neuronal differentiation using immortalized multipotent otic progenitor (iMOP) cells. We demonstrated that CHD7 knockdown impaired neuronal differentiation. Genome-wide analysis revealed CHD7 binding at diverse cis-regulatory elements, with notable enrichment at sites marked by the insulator-binding protein CTCF between topologically associating domains (TADs). Insulators marked by the enrichment of CHD7 and CTCF resided near genes critical for neuronal differentiation, including Mir9-2. Targeting these regulatory regions in iMOPs with CRISPR interference (CRISPRi) and activation (CRISPRa) increased miR-9 transcription, irrespective of the method. Blocking the CHD7 and CTCF marked sites suggested that the elements function as insulators to regulate gene expression. The study highlights CHD7 activity at insulators and underscores an unreported mechanism for promoting neuronal differentiation.

Epitranscriptomic modifications play pivotal roles in regulating RNA stability, localization and function. Recently, glycosylation has also emerged as an RNA modification, though its functional implications remain unclear. Here we report that metabolic labelling with a N-azidoacetylgalactosamine-tetraacylated bioorthogonal probe in mammalian cells reveals small, non-coding, glyco-modified RNAs (glycoRNAs) that exhibit unusual stability imparted by their resistance to RNases. These glycoRNAs are primarily found within exosome vesicles as intraluminal cargo, distinct from recently reported cell surface glycoRNAs. Importantly, exosomal glycoRNAs can be transferred to naive cells, highlighting a role in intercellular RNA communication. The inhibition of exosome biogenesis leads to intracellular glycoRNA accumulation, while blocking glycan transfer to proteins reduces glycoRNA sorting into exosomes. These findings suggest a regulatory link between protein and RNA glycosylation in exosome cargo selection. Our studies support a functional role for glycosylation in targeting RNA into exosomes and uncover potential avenues for exosome-based diagnostics and RNA therapeutic applications.

The chromodomain helicase DNA binding protein 7 (CHD7) is a nucleosome repositioner implicated in multiple cellular processes, including neuronal differentiation. We identified CHD7 genome-wide binding sites that regulate neuronal differentiation in an otic stem cell line. We identified CHD7 enrichment at the Sox11 promoter and 3' untranslated region (UTR). Sox11 is a transcription factor essential for neuronal differentiation. CRISPRi of Sox11 promoter or 3'UTR displayed decreased neurite lengths and reduced neuronal marker expression TUBB3 expression. We showed that the Sox11 locus resides at TAD boundaries, and CTCF marks the 3'UTR. We propose that CHD7 modulates chromatin accessibility of the Sox11 promoter and CTCF-marked insulators in the 3'UTR to facilitate neuronal differentiation. CRISPRi of the insulator site alters 3D chromatin organization, affects gene expression and ultimately perturbs cellular processes. Our results implicate a general mechanism of CHD7 in facilitating neuronal differentiation and provide insight into CHD7 dysfunction in CHARGE syndrome, a congenital disorder associated with hearing loss.

Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional control of gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding protein, and SOX2, an SRY-related HMG box pioneer transcription factor, are known to contribute to vestibular and auditory system development, but their genetic interactions in the ear have not been explored. Here, we analyzed inner ear development and the transcriptional regulatory landscapes in mice with variable dosages of Chd7 and/or Sox2. We show that combined haploinsufficiency for Chd7 and Sox2 results in reduced otic cell proliferation, severe malformations of semicircular canals, and shortened cochleae with ectopic hair cells. Examination of mice with conditional, inducible Chd7 loss by Sox2CreER reveals a critical period (~E9.5) of susceptibility in the inner ear to combined Chd7 and Sox2 loss. Data from genome-wide RNA-sequencing and CUT&Tag studies in the otocyst show that CHD7 regulates Sox2 expression and acts early in a gene regulatory network to control expression of key otic patterning genes, including Pax2 and Otx2. CHD7 and SOX2 directly bind independently and cooperatively at transcription start sites and enhancers to regulate otic progenitor cell gene expression. Together, our findings reveal essential roles for Chd7 and Sox2 in early inner ear development and may be applicable for syndromic and other forms of hearing or balance disorders.

Loss of spiral ganglion neurons (SGNs) in the cochlea causes hearing loss. Understanding the mechanisms of cell fate transition accelerates efforts that employ directed differentiation and lineage conversion to repopulate lost SGNs. Proposed strategies to regenerate SGNs rely on altering cell fate by activating transcriptional regulatory networks, but repressing networks for alternative cell lineages is also essential. Epigenomic changes during cell fate transitions suggest that CHD4 represses gene expression by altering the chromatin status. Despite limited direct investigations, human genetic studies implicate CHD4 function in the inner ear. The possibility of CHD4 in suppressing alternative cell fates to promote inner ear regeneration is discussed.

Mitochondrial defects are a hallmark of early pathophysiology in Alzheimer's disease, with pathologically phosphorylated tau reported to induce mitochondrial toxicity. Mitophagy constitutes a key pathway in mitochondrial quality control by which damaged mitochondria are targeted for autophagy. However, few details are known regarding the intersection of mitophagy and pathologies in tauopathy. Here, by applying biochemical and cell biological approaches including time-lapse confocal imaging in live tauopathy neurons, combined with gene rescue experiments via stereotactic injections of adeno-associated virus particles into tauopathy mouse brains, electrophysiological recordings and behavioural tests, we demonstrate for the first time that mitochondrial distribution deficits at presynaptic terminals are an early pathological feature in tauopathy brains. Furthermore, Parkin-mediated mitophagy is extensively activated in tauopathy neurons, which accelerates mitochondrial Rho GTPase 1 (Miro1) turnover and consequently halts Miro1-mediated mitochondrial anterograde movement towards synaptic terminals. As a result, mitochondrial supply at tauopathy synapses is disrupted, impairing synaptic function. Strikingly, increasing Miro1 levels restores the synaptic mitochondrial population by enhancing mitochondrial anterograde movement and thus reverses tauopathy-associated synaptic failure. In tauopathy mouse brains, overexpression of Miro1 markedly elevates synaptic distribution of mitochondria and protects against synaptic damage and neurodegeneration, thereby counteracting impairments in learning and memory as well as synaptic plasticity. Taken together, our study reveals that activation of the Parkin pathway triggers an unexpected effect-depletion of mitochondria from synaptic terminals, a characteristic feature of early tauopathy. We further provide new mechanistic insights into how parkin activation-enhanced Miro1 degradation and impaired mitochondrial anterograde transport drive tauopathy-linked synaptic pathogenesis and establish a foundation for future investigations into new therapeutic strategies to prevent synaptic deterioration in Alzheimer's disease and other tauopathies.

ABSTRACT Homeobox genes act at the top of genetic hierarchies to regulate cell specification and differentiation during embryonic development. We identified the short stature homeobox domain 2 (shox2) transcription factor that is required for vestibular neuron development. shox2 transcripts are initially localized to the otic placode of the developing inner ear where neurosensory progenitors reside. To study shox2 function, we generated CRISPR-mediated mutant shox2 fish. Mutant embryos display behaviors associated with vestibular deficits and showed reduced number of anterior statoacoustic ganglion neurons that innervate the utricle, the vestibular organ in zebrafish. Moreover, a shox2-reporter fish showed labeling of developing statoacoustic ganglion neurons in the anterior macula of the otic vesicle. Single cell RNA-sequencing of cells from the developing otic vesicle of shox2 mutants revealed altered otic progenitor profiles, while single molecule in situ assays showed deregulated levels of transcripts in developing neurons. This study implicates a role for shox2 in development of vestibular but not auditory statoacoustic ganglion neurons.

Synonymous and noncoding single nucleotide polymorphisms (SNPs) in the KCNJ6 gene, encoding G protein-gated inwardly rectifying potassium channel subunit 2 (GIRK2), have been linked with increased electroencephalographic frontal theta event-related oscillations (ERO) in subjects diagnosed with alcohol use disorder (AUD). To identify molecular and cellular mechanisms while retaining the appropriate genetic background, we generated induced excitatory glutamatergic neurons (iN) from iPSCs derived from four AUD-diagnosed subjects with KCNJ6 variants ("Affected: AF") and four control subjects without variants ("Unaffected: UN"). Neurons were analyzed for changes in gene expression, morphology, excitability and physiological properties. Single-cell RNA sequencing suggests that KCNJ6 AF variant neurons have altered patterns of synaptic transmission and cell projection morphogenesis. Results confirm that AF neurons express lower levels of GIRK2, have greater neurite area, and elevated excitability. Interestingly, exposure to intoxicating concentrations of ethanol induces GIRK2 expression and reverses functional effects in AF neurons. Ectopic overexpression of GIRK2 alone mimics the effect of ethanol to normalize induced excitability. We conclude that KCNJ6 variants decrease GIRK2 expression and increase excitability and that this effect can be minimized or reduced with ethanol.

The existence of non-canonical nicotinamide adenine diphosphate (NAD) 5'-end capped RNAs is now well established. Nevertheless, the biological function of this nucleotide metabolite cap remains elusive. Here, we show that the yeast Saccharomyces cerevisiae cytoplasmic 5'-end exoribonuclease Xrn1 is also a NAD cap decapping (deNADding) enzyme that releases intact NAD and subsequently degrades the RNA. The significance of Xrn1 deNADding is evident in a deNADding deficient Xrn1 mutant that predominantly still retains its 5'-monophosphate exonuclease activity. This mutant reveals Xrn1 deNADding is necessary for normal growth on non-fermenting sugar and is involved in modulating mitochondrial NAD-capped RNA levels and may influence intramitochondrial NAD levels. Our findings uncover a contribution of mitochondrial NAD-capped RNAs in overall NAD regulation with the deNADding activity of Xrn1 fulfilling a central role.

Microglia are critical for brain development and play a central role in Alzheimer’s disease (AD) etiology. Down syndrome (DS), also known as trisomy 21, is the most common genetic origin of intellectual disability and the most common risk factor for AD. Surprisingly, little information is available on the impact of trisomy of human chromosome 21 (Hsa21) on microglia in DS brain development and AD in DS (DSAD). Using our new induced pluripotent stem cell (iPSC)-based human microglia-containing cerebral organoid and chimeric mouse brain models, here we report that DS microglia exhibit enhanced synaptic pruning function during brain development. Consequently, electrophysiological recordings demonstrate that DS microglial mouse chimeras show impaired synaptic neurotransmission, as compared to control microglial chimeras. Upon being exposed to human brain tissue-derived soluble pathological tau, DS microglia display dystrophic phenotypes in chimeric mouse brains, recapitulating microglial responses seen in human AD and DSAD brain tissues. Further flow cytometry, single-cell RNA-sequencing, and immunohistological analyses of chimeric mouse brains demonstrate that DS microglia undergo cellular senescence and exhibit elevated type I interferon signaling after being challenged by pathological tau. Mechanistically, we find that shRNA-mediated knockdown of Hsa21encoded type I interferon receptor genes, IFNARs, rescues the defective DS microglial phenotypes both during brain development and in response to pathological tau. Our findings provide first in vivo evidence supporting a paradigm shifting theory that human microglia respond to pathological tau by exhibiting accelerated senescence and dystrophic phenotypes. Our results further suggest that targeting IFNARs may improve microglial functions during DS brain development and prevent human microglial senescence in DS individuals with AD.

Mutations in many synaptic genes are associated with autism spectrum disorders (ASD), suggesting that synaptic dysfunction is a key driver of ASD pathogenesis. Among these mutations, the R451C substitution in the NLGN3 gene that encodes the postsynaptic adhesion molecule Neuroligin-3 is noteworthy because it was the first specific mutation linked to ASDs. In mice, the corresponding Nlgn3 R451C-knockin mutation recapitulates social interaction deficits of ASD patients and produces synaptic abnormalities, but the impact of the NLGN3 R451C mutation on human neurons has not been investigated. Here, we generated human knockin neurons with the NLGN3 R451C and NLGN3 null mutations. Strikingly, analyses of NLGN3 R451C-mutant neurons revealed that the R451C mutation decreased NLGN3 protein levels but enhanced the strength of excitatory synapses without affecting inhibitory synapses; meanwhile NLGN3 knockout neurons showed reduction in excitatory synaptic strengths. Moreover, overexpression of NLGN3 R451C recapitulated the synaptic enhancement in human neurons. Notably, the augmentation of excitatory transmission was confirmed in vivo with human neurons transplanted into mouse forebrain. Using single-cell RNA-seq experiments with co-cultured excitatory and inhibitory NLGN3 R451C-mutant neurons, we identified differentially expressed genes in relatively mature human neurons corresponding to synaptic gene expression networks. Moreover, gene ontology and enrichment analyses revealed convergent gene networks associated with ASDs and other mental disorders. Our findings suggest that the NLGN3 R451C mutation induces a gain-of-function enhancement in excitatory synaptic transmission that may contribute to the pathophysiology of ASD.

PURPOSE OF REVIEW:Sensory hair cells (HCs) of the inner ear are responsible for our ability to hear and balance. Loss of these cells results in hearing loss. Stem cell replacement and in situ regeneration have the potential to replace lost HCs. Newly discovered contributions of transcription factor regulatory networks and epigenetic mechanisms in regulating HC differentiation and regeneration are placed into context of the literature.RECENT FINDINGS:A wealth of new data has helped to define cochlear sensory progenitors in their developmental trajectories. This includes transcription factor networks, epigenetic manipulations, and cochlear HC subtype specification.SUMMARY:Understanding how sensory progenitors differ and how HC subtypes arise will substantially inform efforts in hearing restoration.

Microglia, the brain-resident macrophages, exhibit highly dynamic functions in neurodevelopment and neurodegeneration. Human microglia possess unique features as compared to mouse microglia, but our understanding of human microglial functions is largely limited by an inability to obtain human microglia under homeostatic states. Here, we develop a human pluripotent stem cell (hPSC)-based microglial chimeric mouse brain model by transplanting hPSC-derived primitive macrophage progenitors into neonatal mouse brains. Single-cell RNA-sequencing of the microglial chimeric mouse brains reveals that xenografted hPSC-derived microglia largely retain human microglial identity, as they exhibit signature gene expression patterns consistent with physiological human microglia and recapitulate heterogeneity of adult human microglia. Importantly, the engrafted hPSC-derived microglia exhibit dynamic response to cuprizone-induced demyelination and species-specific transcriptomic differences in the expression of neurological disease-risk genes in microglia. This model will serve as a tool to study the role of human microglia in brain development and degeneration.

Sensorineural hearing loss affects millions of people worldwide and is a growing concern in the aging population. Treatment using aminoglycoside antibiotics for infection and exposure to loud sounds contribute to the degeneration of cochlear hair cells and spiral ganglion neurons. Cell loss impacts cochlear function and causes hearing loss in ∼ 15% of adult Americans (∼36 million). The number of individuals with hearing loss will likely grow with increasing lifespans. Current prosthesis such as hearing aids and cochlear implants can ameliorate hearing loss. However, hearing aids are ineffective if hair cells or spiral ganglion neurons are severely damaged, and cochlear implants are ineffective without properly functioning spiral ganglion neurons. As such, strategies that alleviate hearing loss by preventing degeneration or promoting cell replacement are urgently needed. Despite showing great promise from in vitro studies, the complexity and delicate nature of the inner ear poses a huge challenge for delivering therapeutics. To mitigate risks and complications associated with surgery, new technologies and methodologies have emerged for efficient delivery of therapeutics. We will focus on biomaterials that allow controlled and local drug delivery into the inner ear. The rapid development of microsurgical techniques in conjunction with novel bio- and nanomaterials for sustained drug delivery appears bright for hearing loss treatment.

Stem cell replacement therapy is a potential method for repopulating lost spiral ganglion neurons (SGNs) in the inner ear. Efficacy of cell replacement relies on proper differentiation. Defining the dynamic expression of different transcription factors essential for neuronal differentiation allows us to monitor the progress and determine when the protein functions in differentiating stem cell cultures. Using immortalized multipotent otic progenitors (iMOPs) as a cellular system for SGN differentiation, a method for determining dynamic protein expression from heterogeneous cultures was developed. iMOP-derived neurons were identified and ordered by increasing neurite lengths to create a pseudotime course that reflects the differentiation trajectory. The fluorescence intensities of transcription factors SOX2 and NEUROD1 from individual pseudotemporally ordered cells were measured. Individual cells were grouped by K-means clustering and the mean fluorescence intensity for each cluster determined. Curve fit of the mean fluorescence represented the protein expression dynamics in differentiating cells. The method provides information about protein expression dynamics in differentiating stem cell cultures.