Non-coding RNA in the wiring and remodeling of neural circuits

Non-coding RNAs as a Critical Player in the Regulation of Inflammasome in Inflammatory Bowel Diseases; Emphasize on lncRNAs

Inflammatory bowel disease (IBD) is an idiopathic disease caused by a dysregulated immune response to host intestinal microflora. A hyperactive inflammatory and immunological response in the gut has been shown to be one of the disease's long-term causes despite the complexity of the clinical pathology of IBD. The innate immune system activator known as human gut inflammasome is thought to be a significant underlying cause of pathology and is closely linked to the development of IBD. It is essential to comprehend the function of inflammasome activation in IBD to treat it effectively. Systemic inflammasome regulation may be a proper therapeutic and clinical strategy to manage IBD symptoms since inflammasomes may have a significant function in IBD. Non-coding RNAs (ncRNAs) are a type of RNA transcript that is incapable of encoding proteins or peptides. In IBD, inflammation develops and worsens as a result of its imbalance. Culminating evidence has been shown that ncRNAs, and particularly long non-coding RNAs (lncRNAs), may play a role in the regulation of NLR family pyrin domain containing 3 (NLRP3) inflammasome activation in IBD. The relationship between IBD and the gut inflammasome, as well as current developments in IBD research and treatment approaches, have been the main topics of this review. We have covered inflammasomes and their constituents, results from in vivo research, inflammasome inhibitors, and advancements in inflammasome-targeted therapeutics for IBD.

MicroRNA mechanisms instructing Purkinje cell specification

MicroRNAs (miRNAs) are critical for brain development; however, if, when, and how miRNAs drive neuronal subtype specification remains poorly understood. To address this, we engineered technologies with vastly improved spatiotemporal resolution that allow the dissection of cell-type-specific miRNA-target networks. Fast and reversible miRNA loss of function showed that miRNAs are necessary for Purkinje cell (PC) differentiation, which previously appeared to be miRNA independent, and identified distinct critical miRNA windows for dendritogenesis and climbing fiber synaptogenesis, structural features defining PC identity. Using new mouse models that enable miRNA-target network mapping in rare cell types, we uncovered PC-specific post-transcriptional programs. Manipulation of these programs revealed that the PC-enriched miR-206 and targets Shank3, Prag1, En2, and Vash1, which are uniquely repressed in PCs, are critical regulators of PC-specific dendritogenesis and synaptogenesis, with miR-206 knockdown and target overexpression partially phenocopying miRNA loss of function. Our results suggest that gene expression regulation by miRNAs, beyond transcription, is critical for neuronal subtype specification.

Noncoding RNA gives agency to the molecular and cellular substrates of learning and memory

In the past decade, there has been a virtual explosion in the appreciation and study of noncoding RNA (ncRNA) in the brain. Rapidly emerging evidence suggests that many classes of ncRNA coordinate processes related to learning and memory, achieved via their precise subcellular localisation and interactions with DNA, mRNA and RNA binding proteins. Here we discuss these mechanisms using examples of recently discovered and well-studied ncRNAs, including long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs), which are directly involved in regulating experience-dependent neural plasticity.

A case of Meckel's diverticulum complicated with intestinal duplication: a case report

BACKGROUND

Meckel's diverticulum and intestinal duplication malformations are two isolated digestive tract malformations in children. It is uncommon to see cases of both digestive tract malformations occurring at the same time. This report presents a rare case of Meckel's diverticulum complicated with intestinal duplication, highlighting the importance of intraoperative exploration.

CASE PRESENTATION

A 5-year-old Han Chinese boy presented with abdominal pain and vomiting. The patient had tenderness in the right lower quadrant of the abdomen. Preoperative imaging suggested Meckel's diverticulum, but intraoperative exploration revealed both Meckel's diverticulum and intestinal duplication. Surgical resection and anastomosis were performed, and histopathology confirmed the diagnosis. The patient was discharged 7 days after surgery.

CONCLUSION

Meckel's diverticulum combined with intestinal duplication malformations is rare, and intraoperative exploration is essential in the diagnosis and treatment of surgical disease.

Transcriptome profiling of serum exosomes by RNA-Seq reveals lipid metabolic changes as a potential biomarker for evaluation of roxadustat treatment of chronic kidney diseases

The incidence of chronic kidney disease (CKD) is increasing globally; however, effective preventive and therapeutic strategies are currently limited. Roxadustat is being clinically used to treat renal anemia in CKD patients to reduce anemia-related complications and improve patients' life quality. Exosomes are small vesicles carrying important information that contribute to cell-to-cell communication and are present in various body fluids. However, little is known about the role of serum exosomes and their association with CKD after roxadustat treatment. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential as sensitive nucleic acid biomarkers in various human diseases. In this study, we aimed to identify the changed mRNAs-lncRNAs after roxadustat treatment as novel biomarkers for assessing the efficiency of the treatment. Through our study using RNA-seq data, we identified 957 mRNAs (626 upregulated and 331 downregulated after roxadustat treatment) and 914 lncRNAs (444 upregulated and 470 downregulated) derived from exosomes that were significantly changed, which was highly correlated to lipid metabolism. Our analysis through whole transcriptome profiling of exosome RNAs encompasses an identified differentially expressed mRNA-lncRNA regulatory axis in a larger patient cohort for the validation of suitable biomarkers for assessing CKD after roxadustat treatment.

MicroRNA-138-5p suppresses excitatory synaptic strength at the cerebellar input layer

MicroRNAs are small, highly conserved non-coding RNAs that negatively regulate mRNA translation and stability. In the brain, miRNAs contribute to neuronal development, synaptogenesis, and synaptic plasticity. MicroRNA 138-5p (miR-138-5p) controls inhibitory synaptic transmission in the hippocampus and is highly expressed in cerebellar excitatory neurons. However, its specific role in cerebellar synaptic transmission remains unknown. Here, we investigated excitatory transmission in the cerebellum of mice expressing a sponge construct that sequesters endogenous miR-138-5p. Mossy fibre stimulation-evoked EPSCs in granule cells were ∼40% larger in miR-138-5p sponge mice compared to controls. Furthermore, we observed larger miniature EPSC amplitudes, suggesting an increased number of functional postsynaptic AMPA receptors. High-frequency train stimulation revealed enhanced short-term depression following miR-138-5p downregulation. Together with computational modelling, this suggests a negative regulation of presynaptic release probability. Overall, our results demonstrate that miR-138-5p suppresses synaptic strength through pre- and postsynaptic mechanisms, providing a potentially powerful mechanism for tuning excitatory synaptic input into the cerebellum. KEY POINTS: MicroRNAs are powerful regulators of mRNA translation and control key cell biological processes including synaptic transmission, but their role in regulating synaptic function in the cerebellum has remained elusive. In this study, we investigated how microRNA-138-5p (miR-138-5p) modulates excitatory transmission at adult murine cerebellar mossy fibre to granule cell synapses. Downregulation of miR-138-5p enhances excitatory synaptic strength at the cerebellar input layer and increases short-term depression. miR-138-5p exerts its regulatory function through both pre- and postsynaptic mechanisms by negatively regulating release probability at mossy fibre boutons, as well as functional AMPA receptor numbers in granule cells. These findings provide insights into the role of miR-138-5p in the cerebellum and expand our understanding of microRNA-dependent control of excitatory synaptic transmission and short-term plasticity.

Deregulated mRNA and microRNA Expression Patterns in the Prefrontal Cortex of the BTBR Mouse Model of Autism

Autism spectrum disorder (ASD) is a neurodevelopmental condition caused by both genetic and environmental factors. Since no single gene variant accounts for more than 1% of the cases, the converging actions of ASD-related genes and other factors, including microRNAs (miRNAs), may contribute to ASD pathogenesis. To date, few studies have simultaneously investigated the mRNA and miRNA profiles in an ASD-relevant model. The BTBR mouse strain displays a range of behaviors with ASD-like features but little is known about the protein-coding and noncoding gene expression landscape that may underlie the ASD-like phenotype. Here we performed parallel mRNA and miRNA profiling using the prefrontal cortex (PFC) of BTBR and C57BL/6 J (B6) mice. This identified 1063 differentially expressed genes and 48 differentially expressed miRNAs. Integration of mRNA and miRNA data identified a strong inverse relationship between upregulated (DEGs) and downregulated miRNAs, and vice versa. Pathway analysis, taking account of the inverse relationship between differentially expressed miRNAs and their target mRNAs highlighted significant shared enrichment in immune signaling, myelination, and neurodevelopmental processes. Notably, miRNA changes were predicted to affect synapse-related functions but we did not find enrichment of protein-coding genes linked to cellular components or biological processes related to synapses in the PFC of BTBR mice, indicating processes may evade miRNA control. In contrast, other miRNAs were predicted to have extensive relationships with DEGs suggesting their role as potential hub coordinators of gene expression. Profiling findings were confirmed via qRT-PCR for representative protein-coding transcripts and miRNAs. Our study underscores the complex interplay between gene expression and miRNA regulation within immune and inflammatory pathways in the BTBR model, offering insights into the neurodevelopmental mechanisms of ASD. These results support the value of the BTBR mouse model and identify strategies that could adjust molecular pathways for therapeutic applications in ASD research.

In vivo AGO-APP identifies a module of microRNAs cooperatively preserving neural progenitors

MicroRNAs are essential regulators of gene expression. Their function is particularly important during neurogenesis, when the production of large numbers of neurons from a limited number of neural stem cells depends on the precise control of determination, proliferation and differentiation. However, microRNAs can target many mRNAs and vice-versa, raising the question of how specificity is achieved to elicit a precise regulatory response. Here we introduce in vivo AGO-APP, a novel approach to purify Argonaute-bound, and therefore active microRNAs from specific cell types. Using AGO-APP in the larval Drosophila central nervous system, we identify a module of microRNAs predicted to redundantly target all iconic genes known to control the transition from neuroblasts to neurons. While microRNA overexpression generally validated predictions, knockdown of individual microRNAs did not induce detectable phenotypes. In contrast, neuroblasts were induced to differentiate precociously when several microRNAs were knocked down simultaneously. Our data supports the concept that at physiological expression levels, the cooperative action of miRNAs allows efficient targeting of entire gene networks.

A functional screen uncovers circular RNAs regulating excitatory synaptogenesis in hippocampal neurons

Circular RNAs (circRNAs) are an expanding class of largely unexplored RNAs which are prominently enriched in the mammalian brain. Here, we systematically interrogate their role in excitatory synaptogenesis of rat hippocampal neurons using RNA interference. Thereby, we identify seven circRNAs as negative regulators of excitatory synapse formation, many of which contain high-affinity microRNA binding sites. Knockdown of one of these candidates, circRERE, promotes the formation of electrophysiologically silent synapses. Mechanistically, circRERE knockdown results in a preferential upregulation of synaptic mRNAs containing binding sites for miR-128-3p. Overexpression of circRERE stabilizes miR-128-3p and rescues exaggerated synapse formation upon circRERE knockdown in a miR-128-3p binding site-specific manner. Overall, our results uncover circRERE-mediated stabilization of miR-128-3p as a means to restrict the formation of silent excitatory synaptic co-clusters and more generally implicate circRNA-dependent microRNA regulation in the control of synapse development and function.

Dynamic regulation of cortical interneuron wiring

Inhibitory interneurons play crucial roles in modulating the circuits and activity patterns of the cerebral cortex. In particular, interneurons must adapt to changes in cortical activity and environmental information to drive appropriate responses. In this review, we focus on the latest progress in our understanding of the processes that regulate interneuron wiring adaptability. We discuss newly identified types of regulatory processes, from structural synaptic changes to long-range neuromodulation, and provide an update on the activity-dependent molecular underpinnings at the transcriptional and post-transcriptional levels.

Mechanisms for Orofacial Pain: Roles of Immunomodulation, Metabolic Reprogramming, Oxidative Stress and Epigenetic Regulation

Background and Objectives: Orofacial pain corresponds to pain sensitization originating from the facial and oral regions, often accompanied by diagnostic complexity due to a multitude of contributory factors, leading to significant patient distress and impairment. Here, we have reviewed current mechanistic pathways and biochemical aspects of complex orofacial pain pathology, highlighting recent advancements in understanding its multifactorial regulation and signaling and thus providing a holistic approach to challenging it. Materials and Methods: Studies were identified from an online search of the PubMed database without any search time range. Results: We have discussed neuron-glia interactions and glial cell activation in terms of immunomodulatory effects, metabolism reprogramming effects and epigenetic modulatory effects, in response to orofacial pain sensitization comprising different originating factors. We have highlighted the fundamental role of oxidative stress affecting significant cellular pathways as well as cellular machinery, which renders pain pathology intricate and multidimensional. Emerging research on the epigenetic modulation of pain regulatory genes in response to molecular and cellular environmental factors is also discussed, alongside updates on novel diagnostic and treatment approaches. Conclusions: This review deliberates the integrative perspectives and implications of modulation in the immune system, glucose metabolism, lipid metabolism and redox homeostasis accompanied by mitochondrial dysfunction as well as epigenetic regulation accommodating the effect of dysregulated non-coding RNAs for an interdisciplinary understanding of pain pathology at the molecular level, aiming to improve patient outcomes with precise diagnosis offering improved pain management and treatment.

CDR1as Deficiency Prevents Photoreceptor Degeneration by Regulating miR-7a-5p/α-syn/Parthanatos Pathway in Retinal Detachment

Retinal detachment (RD) is the separation of the neural retina from the retinal pigment epithelium, with photoreceptor degeneration being a major cause of irreversible vision loss. Herein, ischemia and hypoxia after RD decreased the level of miR-7a-5p (miR-7) and promoted the expression of its main target, α-synuclein (α-syn), which activated the parthanatos pathway and led to photoreceptor damage. Circular RNA CDR1as is an antisense transcript of cerebellar degeneration-associated protein 1, which functions as a "sponge" for miR-7, thereby regulating the abundance and activity of miR-7. In this study, CDR1as expression was elevated after RD. Adeno-associated virus serotype 9 vector containing the shRNA-CDR1as sequence was used to inhibit CDR1as expression via subretinal injection. Hematoxylin and eosin staining and transmission electron microscopy revealed that the morphology and outer nuclear layer thickness of the retina were preserved and photoreceptor cell death was decreased after experimental RD in mice. Mechanistically, CDR1as deficiency significantly increased the expression of miR-7, then decreased the expression of α-syn, poly (ADP-ribose) polymerase 1, apoptosis-inducing factor, and migration inhibitory factor. Furthermore, visual function was improved as shown by Morris water maze experiments in the mouse model of RD. These findings suggest a surprisingly neuroprotective role for CDR1as deficiency, which is probably mediated by enhancing miR-7 activity and inhibiting α-syn/poly (ADP-ribose) polymerase 1/apoptosis-inducing factor pathway, thereby preventing photoreceptor degeneration.

miRNA-mediated control of gephyrin synthesis drives sustained inhibitory synaptic plasticity

Activity-dependent protein synthesis is crucial for long-lasting forms of synaptic plasticity. However, our understanding of translational mechanisms controlling GABAergic synapses is limited. One distinct form of inhibitory long-term potentiation (iLTP) enhances postsynaptic clusters of GABAARs and the primary inhibitory scaffold, gephyrin, to promote sustained synaptic strengthening. While we previously found that persistent iLTP requires mRNA translation, the mechanisms controlling plasticity-induced gephyrin translation remain unknown. We identify miR153 as a novel regulator of Gphn mRNA translation which controls gephyrin protein levels and synaptic clustering, ultimately impacting inhibitory synaptic structure and function. iLTP induction downregulates miR153, reversing its translational suppression of Gphn mRNA and promoting de novo gephyrin protein synthesis and synaptic clustering during iLTP. Finally, we find that reduced miR153 expression during iLTP is driven by an excitation-transcription coupling pathway involving calcineurin, NFAT and HDACs, which also controls the miRNA-dependent upregulation of GABAARs. Together, we delineate a miRNA-dependent post-transcriptional mechanism that controls the expression of the key synaptic scaffold, gephyrin, and may converge with parallel miRNA pathways to coordinate gene upregulation to maintain inhibitory synaptic plasticity.

Modelling cell type-specific lncRNA regulatory network in autism with Cycle

BACKGROUND

Autism spectrum disorder (ASD) is a class of complex neurodevelopment disorders with high genetic heterogeneity. Long non-coding RNAs (lncRNAs) are vital regulators that perform specific functions within diverse cell types and play pivotal roles in neurological diseases including ASD. Therefore, exploring lncRNA regulation would contribute to deciphering ASD molecular mechanisms. Existing computational methods utilize bulk transcriptomics data to identify lncRNA regulation in all of samples, which could reveal the commonalities of lncRNA regulation in ASD, but ignore the specificity of lncRNA regulation across various cell types.

RESULTS

Here, we present Cycle (Cell type-specific lncRNA regulatory network) to construct the landscape of cell type-specific lncRNA regulation in ASD. We have found that each ASD cell type is unique in lncRNA regulation, and more than one-third and all cell type-specific lncRNA regulatory networks are characterized as scale-free and small-world, respectively. Across 17 ASD cell types, we have discovered 19 rewired and 11 stable modules, along with eight rewired and three stable hubs within the constructed cell type-specific lncRNA regulatory networks. Enrichment analysis reveals that the discovered rewired and stable modules and hubs are closely related to ASD. Furthermore, more similar ASD cell types tend to be connected with higher strength in the constructed cell similarity network. Finally, the comparison results demonstrate that Cycle is a potential method for uncovering cell type-specific lncRNA regulation.

CONCLUSION

Overall, these results illustrate that Cycle is a promising method to model the landscape of cell type-specific lncRNA regulation, and provides insights into understanding the heterogeneity of lncRNA regulation between various ASD cell types.

CyCoNP lncRNA establishes cis and trans RNA-RNA interactions to supervise neuron physiology

The combination of morphogenetic and transcription factors together with the synergic aid of noncoding RNAs and their cognate RNA binding proteins contribute to shape motor neurons (MN) identity. Here, we extend the noncoding perspective of human MN, by detailing the molecular and biological activity of CyCoNP (as Cytoplasmic Coordinator of Neural Progenitors) a highly expressed and MN-enriched human lncRNA. Through in silico prediction, in vivo RNA purification and loss of function experiments followed by RNA-sequencing, we found that CyCoNP sustains a specific neuron differentiation program, required for the physiology of both neuroblastoma cells and hiPSC-derived MN, which mainly involves miR-4492 and NCAM1 mRNA. We propose a novel lncRNA-mediated 'dual mode' of action, in which CyCoNP acts in trans as a classical RNA sponge by sequestering miR-4492 from its pro-neuronal targets, including NCAM1 mRNA, and at the same time it plays an additional role in cis by interacting with NCAM1 mRNA and regulating the availability and localization of the miR-4492 in its proximity. These data highlight novel insights into the noncoding RNA-mediated control of human neuron physiology and point out the importance of lncRNA-mediated interactions for the spatial distribution of regulatory molecules.

Non-Coding RNA Involved in the Pathogenesis of Atherosclerosis-A Narrative Review

Atherosclerosis is a highly prevalent condition associated with lipid accumulation in the intima layer of arterial blood vessels. The development of atherosclerotic plaques is associated with the incidence of major cardiovascular events, such as acute coronary syndrome or ischemic stroke. Due to the significant prevalence of atherosclerosis and its subclinical progression, it is associated with severe and potentially lethal complications. The pathogenesis of atherosclerosis is complex and not entirely known. The identification of novel non-invasive diagnostic markers and treatment methods that could suppress the progression of this condition is highly required. Non-coding RNA (ncRNA) involves several subclasses of RNA molecules. microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) differently regulate gene expression. Importantly, these molecules are frequently dysregulated under pathological conditions, which is associated with enhanced or suppressed expression of their target genes. In this review, we aim to discuss the involvement of ncRNA in crucial mechanisms implicated in the pathogenesis of atherosclerosis. We summarize current evidence on the potential use of these molecules as diagnostic and therapeutic targets.

Gas5 regulates early-life stress-induced anxiety and spatial memory

Early-life stress (ES) induced by maternal separation (MS) remains a proven causality of anxiety and memory deficits at later stages of life. Emerging studies have shown that MS-induced gene expression in the hippocampus is operated at the level of transcription. However, the extent of involvement of non-coding RNAs in MS-induced behavioural deficits remains unexplored. Here, we have investigated the role of synapse-enriched long non-coding RNAs (lncRNAs) in anxiety and memory upon MS. We observed that MS led to an enhancement of expression of the lncRNA growth arrest specific 5 (Gas5) in the hippocampus; accompanied by increased levels of anxiety and deficits in spatial memory. Gas5 knockdown in early life was able to reduce anxiety and partially rescue the spatial memory deficits of maternally separated adult mice. However, the reversal of MS-induced anxiety and memory deficits is not attributed to Gas5 activity during neuronal development as Gas5 RNAi did not influence spine development. Gene Ontology analysis revealed that Gas5 exerts its function by regulating RNA metabolism and translation. Our study highlights the importance of MS-regulated lncRNA in anxiety and spatial memory.

Role of Extracellular Vesicle-Derived Noncoding RNAs in Diabetic Kidney Disease

Background

Diabetic kidney disease (DKD), a metabolism-related syndrome characterized by abnormal glomerular filtration rate, proteinuria, and renal microangiopathy, is one of the most common forms of chronic kidney disease, whereas extracellular vesicles (EVs) have been recently evidenced as a novel cell communication player in DKD occurrence and progress via releasing various bioactive molecules, including proteins, lipids, and especially RNA, among which noncoding RNAs (including miRNAs, lncRNAs, and circRNAs) are the major regulators. However, the functional relevance of EV-derived ncRNAs in DKD is to be elucidated.

Summary

Studies have reported that EV-derived ncRNAs regulate gene expression via a diverse range of regulatory mechanisms, contributing to diverse phenotypes related to DKD progression. Furthermore, there are already many potential clinical diagnostic and therapeutic studies based on these ncRNAs, which can be expected to have potential applications in clinical practice for EV-derived ncRNAs.

Key Messages

In the current review, we summarized the mechanistic role of EVs in DKD according to biological function classifications, including inflammation and oxidative stress, epithelial-mesenchymal transition, cell death, and extracellular matrix deposition. In addition, we comprehensively discussed the potential applications of EV-derived ncRNAs as diagnostic biomarkers and therapeutic targets in DKD.

Long non-coding RNAs with essential roles in neurodegenerative disorders

ABSTRACT

Recently, with the advent of high-resolution and high-throughput sequencing technologies, an increasing number of long non-coding RNAs (lncRNAs) have been found to be involved in the regulation of neuronal function in the central nervous system with specific spatiotemporal patterns, across different neurodegenerative diseases. However, the underlying mechanisms of lncRNAs during neurodegeneration remain poorly understood. This review provides an overview of the current knowledge of the biology of lncRNAs and focuses on introducing the latest identified roles, regulatory mechanisms, and research status of lncRNAs in Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Finally, this review discusses the potential values of lncRNAs as diagnostic biomarkers and therapeutic targets for neurodegenerative diseases, hoping to provide broader implications for developing effective treatments.

Epigenetic regulation in adult neural stem cells

Neural stem cells (NSCs) exhibit self-renewing and multipotential properties. Adult NSCs are located in two neurogenic regions of adult brain: the ventricular-subventricular zone (V-SVZ) of the lateral ventricle and the subgranular zone of the dentate gyrus in the hippocampus. Maintenance and differentiation of adult NSCs are regulated by both intrinsic and extrinsic signals that may be integrated through expression of some key factors in the adult NSCs. A number of transcription factors have been shown to play essential roles in transcriptional regulation of NSC cell fate transitions in the adult brain. Epigenetic regulators have also emerged as key players in regulation of NSCs, neural progenitor cells and their differentiated progeny via epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling and RNA-mediated transcriptional regulation. This minireview is primarily focused on epigenetic regulations of adult NSCs during adult neurogenesis, in conjunction with transcriptional regulation in these processes.

Exploring the memory: existing activity-dependent tools to tag and manipulate engram cells

The theory of engrams, proposed several years ago, is highly crucial to understanding the progress of memory. Although it significantly contributes to identifying new treatments for cognitive disorders, it is limited by a lack of technology. Several scientists have attempted to validate this theory but failed. With the increasing availability of activity-dependent tools, several researchers have found traces of engram cells. Activity-dependent tools are based on the mechanisms underlying neuronal activity and use a combination of emerging molecular biological and genetic technology. Scientists have used these tools to tag and manipulate engram neurons and identified numerous internal connections between engram neurons and memory. In this review, we provide the background, principles, and selected examples of applications of existing activity-dependent tools. Using a combination of traditional definitions and concepts of engram cells, we discuss the applications and limitations of these tools and propose certain developmental directions to further explore the functions of engram cells.

miRNA-mediated control of gephyrin synthesis drives sustained inhibitory synaptic plasticity

Activity-dependent protein synthesis is crucial for many long-lasting forms of synaptic plasticity. However, our understanding of the translational mechanisms controlling inhibitory synapses is limited. One distinct form of inhibitory long-term potentiation (iLTP) enhances postsynaptic clusters of GABAARs and the primary inhibitory scaffold, gephyrin, to promote sustained synaptic strengthening. While we previously found that persistent iLTP requires mRNA translation, the precise mechanisms controlling gephyrin translation during this process remain unknown. Here, we identify miR153 as a novel regulator of Gphn mRNA translation which controls gephyrin protein levels and synaptic clustering, ultimately impacting GABAergic synaptic structure and function. We find that iLTP induction downregulates miR153, reversing its translational suppression of Gphn mRNA and allowing for increased de novo gephyrin protein synthesis and synaptic clustering during iLTP. Finally, we find that reduced miR153 expression during iLTP is driven by an excitation-transcription coupling pathway involving calcineurin, NFAT and HDACs, which also controls the miRNA-dependent upregulation of GABAARs. Overall, this work delineates a miRNA-dependent post-transcriptional mechanism that controls the expression of the key synaptic scaffold, gephyrin, and may converge with parallel miRNA pathways to coordinate gene upregulation to maintain inhibitory synaptic plasticity.

Silc1 long noncoding RNA is an immediate-early gene promoting efficient memory formation

Long noncoding RNAs (lncRNAs) are expressed in many brain circuits and types of neurons; nevertheless, their functional significance for normal brain functions remains elusive. Here, we study the functions in the central nervous system of Silc1, an lncRNA we have shown previously to be important for neuronal regeneration in the peripheral nervous system. We found that Silc1 is rapidly and strongly induced in the hippocampus upon exposure to novelty and is required for efficient spatial learning. Silc1 production is important for induction of Sox11 (its cis-regulated target gene) throughout the CA1-CA3 regions and proper expression of key Sox11 target genes. Consistent with its role in neuronal plasticity, Silc1 levels decline during aging and in models of Alzheimer's disease. Overall, we describe a plasticity pathway in which Silc1 acts as an immediate-early gene to activate Sox11 and induce a neuronal growth-associated transcriptional program important for learning.

MicroRNAs are necessary for the emergence of Purkinje cell identity

Brain computations are dictated by the unique morphology and connectivity of neuronal subtypes, features established by closely timed developmental events. MicroRNAs (miRNAs) are critical for brain development, but current technologies lack the spatiotemporal resolution to determine how miRNAs instruct the steps leading to subtype identity. Here, we developed new tools to tackle this major gap. Fast and reversible miRNA loss-of-function revealed that miRNAs are necessary for cerebellar Purkinje cell (PC) differentiation, which previously appeared miRNA-independent, and resolved distinct miRNA critical windows in PC dendritogenesis and climbing fiber synaptogenesis, key determinants of PC identity. To identify underlying mechanisms, we generated a mouse model, which enables precise mapping of miRNAs and their targets in rare cell types. With PC-specific maps, we found that the PC-enriched miR-206 drives exuberant dendritogenesis and modulates synaptogenesis. Our results showcase vastly improved approaches for dissecting miRNA function and reveal that many critical miRNA mechanisms remain largely unexplored.

Highlights

Fast miRNA loss-of-function with T6B impairs postnatal Purkinje cell developmentReversible T6B reveals critical miRNA windows for dendritogenesis and synaptogenesisConditional Spy3-Ago2 mouse line enables miRNA-target network mapping in rare cellsPurkinje cell-enriched miR-206 regulates its unique dendritic and synaptic morphology.

Brain cell-specific origin of circulating microRNA biomarkers in experimental temporal lobe epilepsy

The diagnosis of epilepsy is complex and challenging and would benefit from the availability of molecular biomarkers, ideally measurable in a biofluid such as blood. Experimental and human epilepsy are associated with altered brain and blood levels of various microRNAs (miRNAs). Evidence is lacking, however, as to whether any of the circulating pool of miRNAs originates from the brain. To explore the link between circulating miRNAs and the pathophysiology of epilepsy, we first sequenced argonaute 2 (Ago2)-bound miRNAs in plasma samples collected from mice subject to status epilepticus induced by intraamygdala microinjection of kainic acid. This identified time-dependent changes in plasma levels of miRNAs with known neuronal and microglial-cell origins. To explore whether the circulating miRNAs had originated from the brain, we generated mice expressing FLAG-Ago2 in neurons or microglia using tamoxifen-inducible Thy1 or Cx3cr1 promoters, respectively. FLAG immunoprecipitates from the plasma of these mice after seizures contained miRNAs, including let-7i-5p and miR-19b-3p. Taken together, these studies confirm that a portion of the circulating pool of miRNAs in experimental epilepsy originates from the brain, increasing support for miRNAs as mechanistic biomarkers of epilepsy.

An miRNA with a major impact on stress

miRNAs regulate mRNAs, including those important for synapse function in the brain. Mucha and colleagues recently identified a novel miRNA-mRNA interaction in the basolateral amygdala that acts as a homeostatic counter to stress-induced anxiety and synaptic changes, suggesting miRNAs as potential avenues for therapeutic intervention in anxiety disorders.

Integrative transcriptomic profiling of mRNA, miRNA, circRNA, and lncRNA in alveolar macrophages isolated from PRRSV-infected porcine

Introduction

The porcine reproductive and respiratory syndrome virus (PRRSV) continues to pose a significant threat to the global swine industry, attributed largely to its immunosuppressive properties and the chronic nature of its infection. The absence of effective vaccines and therapeutics amplifies the urgency to deepen our comprehension of PRRSV's intricate pathogenic mechanisms. Previous transcriptomic studies, although informative, are partially constrained by their predominant reliance on in vitro models or lack of long-term infections. Moreover, the role of circular RNAs (circRNAs) during PRRSV invasion is yet to be elucidated.

Methods

In this study, we employed an in vivo approach, exposing piglets to a PRRSV challenge over varied durations of 3, 7, or 21 days. Subsequently, porcine alveolar macrophages were isolated for a comprehensive transcriptomic investigation, examining the expression patterns of mRNAs, miRNAs, circRNAs, and long non-coding RNAs (lncRNAs).

Results

Differentially expressed RNAs from all four categories were identified, underscoring the dynamic interplay among these RNA species during PRRSV infection. Functional enrichment analyses indicate that these differentially expressed RNAs, as well as their target genes, play a pivotal role in immune related pathways. For the first time, we integrated circRNAs into the lncRNA-miRNA-mRNA relationship, constructing a competitive endogenous RNA (ceRNA) network. Our findings highlight the immune-related genes, CTLA4 and SAMHD1, as well as their associated miRNAs, lncRNAs, and circRNAs, suggesting potential therapeutic targets for PRRS. Importantly, we corroborated the expression patterns of selected RNAs through RT-qPCR, ensuring consistency with our transcriptomic sequencing data.

Discussion

This study sheds lights on the intricate RNA interplay during PRRSV infection and provides a solid foundation for future therapeutic strategizing.