The lncRNA Neat1 promotes activation of inflammasomes in macrophages

Alternative transcription increases isoform complexity in Long Non-Coding RNAs and alters their functions in cancer

Transcriptional start and end variance, a less-explored aspect of lncRNA biology, is a critical determinant of isoform diversity in human RNA. While alternative splicing (AS) has been extensively studied as a mechanism of isoform generation, differences in transcriptional start and termination site usage-whether from distinct promoters or varying initiation events at the same core promoter-contribute more to isoform diversity than alternative splicing. In the context of long non-coding RNAs (lncRNAs), even subtle alterations to transcriptional start and end sites can induce significant changes in the structural and functional capacities of individual lncRNA isoforms. This review highlights the underappreciated realm of transcriptional start and end variance in lncRNAs, exploring its pivotal role in shaping the diversity of lncRNA transcripts. In cancer, where lncRNAs are increasingly recognised as key players in tumorigenesis, understanding the ramifications of transcriptional start and end variance is crucial. With single nucleotide alterations capable of influencing the folding energy, shape, stability, and function of a lncRNA molecules, significant changes to transcriptional regulation may lead to aberrant isoforms with implications for cancer initiation, progression, and potentially, its treatment. As lncRNAs emerge as therapeutic targets, particularly with the advancement of antisense oligonucleotide (ASO) technologies, it becomes crucial to understand the regulatory landscape of transcriptional variation among lncRNA isoforms, to ensure selective targeting of oncogenic transcripts while sparing those with normal physiological functions. By highlighting the significance of transcriptional start and end site variation as major contributors to lncRNA diversity, the potential exploitation for precision therapeutic interventions in the field of non-coding RNA cancer research can be expanded.

METTL14-mediated lncRNA NEAT1 promotes asthma progression by regulating the miR-302a-3p/March5 axis

Asthma is a chronic inflammatory airway disease with airway remodeling as its main pathological basis. LncRNA NEAT1 has been reported to be up-regulated in asthma, but its upstream and downstream regulatory mechanisms are unclear. This study explored the role and functional mechanism of lncRNA NEAT1 in asthma. Airway smooth muscle cells (ASMCs) isolated from the bronchial tissues of asthmatic patients and healthy volunteers were employed and transfected with an overexpression lentivirus and short hairpin lentivirus. Real-time quantitative PCR (qRT-PCR) and western blotting were used to determine the expression levels of genes. The proliferation and migration of ASMCs were evaluated, and the levels of pro-inflammatory cytokines, inflammasomes, and ROS were determined. Mitophagy was observed by transmission electron microscopy (TEM). An asthma model was established to further confirm the effects of lncRNA NEAT1 on asthma. Our results showed that lncRNA NEAT1 was highly expressed in asthma patient-derived ASMCs. LncRNA NEAT1 enhanced ASMC proliferation and migration, promoted inflammation, and inhibited mitophagy. Treatment with a mitophagy inducer reversed the effects of lncRNA NEAT1. The regulatory axis of lncRNA NEAT1/miR-302a-3p/March5 was confirmed, and lncRNA NEAT1 was found to influence ASMC function via the miR-302a-3p/March5 axis. Moreover, METTL14 was found to enhance lncRNA NEAT1 m6A modification and promote its expression, and thereby participate in the functional regulation of ASMCs. The role of lncRNA NEAT1 was also confirmed in an asthma mouse model, where it alleviated asthma pathology in lncRNA NEAT1 knockdown mice. Collectively, our present study confirmed that METTL14 mediated m6A modification of lncRNA NEAT1 and improved lncRNA NEAT1 expression, which further inhibited mitophagy and promoted asthma progression by regulating the miR-302a-3p/March5 axis. Our study elucidated the mechanism by which lncRNA NEAT1 affects airway remodeling. It also provides valuable insights into the pathogenesis of asthma, and suggests lncRNA NEAT1 as a possible biomarker for asthma.

RNA-associated Nuclear Condensates: Where the Nucleus Keeps Its RNAs in Check

Noncoding RNAs (ncRNAs) are emerging regulators of cellular processes and stress response by controlling chromatin architecture and gene expression. Recent studies have revealed that these ncRNAs functions are closely associated with RNA-mediated nuclear condensates, membrane-less compartments formed by liquid-liquid phase separation (LLPS) that provide a specialized subnuclear environment for genome organization as well as transcriptional and post-transcriptional regulation. Disruption of RNA-mediated nuclear condensates is increasingly linked to human diseases, including neurodegenerative disease and cancer, emphasizing their essential role in maintaining cellular homeostasis. Advances in high-resolution microscopy and high-throughput sequencing have elucidated subcompartmental structures and genetic components of nuclear condensates by identifying associated RNA molecules and providing the details of RNA-protein interactions at a single-nucleotide resolution. We now understand that ncRNAs act as scaffolds that recruit RNA-binding proteins (RBPs) with intrinsically disordered domains to trigger the nucleation event for LLPS, resulting in the formation of nuclear condensates. In this review, we summarize how RNAs and RBPs contribute to RNA-mediated nuclear condensate formation via LLPS and support their regulatory functions.

Single-cell analysis reveals fibroblast heterogeneity and myofibroblast conversion in ligamentum flavum hypertrophy

BACKGROUND CONTEXT

The ligamentum flavum (LF) is a crucial structure in maintaining spinal stability; however, hypertrophy of the LF is a significant contributor to lumbar spinal canal stenosis (LSCS). The mechanisms linking LF hypertrophy to the exacerbation of LSCS remain incompletely understood.

PURPOSE

This study aimed to investigate the cellular proportions and signaling pathways observed in the hypertrophied LF.

STUDY DESIGN

LF tissues were obtained from 3 patients undergoing lumbar decompressive surgery. These patients had been diagnosed with LSCS prior to surgery and had an LF thickness exceeding 3.5 mm.

METHODS

Single-cell RNA sequencing was performed following LF tissue dissociation, and data were processed for quality control, dimensional reduction, and clustering. Differential gene expression and gene ontology analyses revealed key molecular pathways driving LF hypertrophy. Cell-cell communication analysis was analyzed to elucidate interactions among various cell types within the LF tissues.

RESULTS

Fibroblasts accounted for 75% of the total cells, followed by endothelial cells, T cells, macrophages, and B cells. Among heterogeneous types of fibroblasts, we identified that a subset of fibroblasts trans-differentiated into myofibroblasts. Two types of macrophages that exhibited phenotypic plasticity akin to M1 and M2 states were observed. We also identified novel signaling pathways involved in fibroblast and immune cell interaction in the hypertrophied LF, such as GAS and GRN, as well as known signaling pathways, such as TGF-β, PDGF, CXCL, and ANGPTL.

CONCLUSION

Our study shows the changing cellular composition and pathogenic signaling pathways involved during the process of chronic inflammation highlighting the transdifferentiation process from fibroblasts to myofibroblasts in the hypertrophied LF.

CLINICAL SIGNIFICANCE

The identification of pathways such as GAS, GRN, TGF-β, ANGPTL, and CXCL, which appear to potentially contribute to LF hypertrophy, could significantly enhance our understanding of the pathogenesis of LSCS.

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.

A Comprehensive Review of Long Non-Coding RNAs in the Cancer-Immunity Cycle: Mechanisms and Therapeutic Implications

Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators of the dynamic interplay between cancer progression and immune responses. This review explored their influence on key processes of the cancer-immunity cycle, such as immune cell differentiation, antigen presentation, and tumor immunogenicity. By modulating tumor escape from the immune response, therapeutic resistance, and tumor-stroma interactions, lncRNAs actively shape the tumor microenvironment. Due to their growing knowledge in the area of immune suppression, directly intervening in the induction of regulatory T cells (Tregs), M2 macrophages, and regulating immune checkpoint pathways such as PD-L1, CTLA-4, and others, lncRNAs can be considered promising therapeutic targets. Advances in single-cell technologies and immunotherapy have significantly expanded our understanding of lncRNA-driven regulatory networks, paving the way for novel precision medicine approaches. Ultimately, we discussed how targeting lncRNAs could enhance cancer immunotherapy, offering new avenues for biomarker discovery and therapeutic intervention.

Defining the transcriptional routes controlling lncRNA NEAT1 expression: implications in cellular stress response, inflammation, and differentiation

NEAT1 (Nuclear Enriched Abundant Transcript 1) is a long non-coding RNA playing a critical role in both physiological and pathological settings by directly modulating a variety of biological events, including transcriptional regulation, RNA processing, and chromatin remodeling. Multiple evidence demonstrated that different transcription factors and signaling pathways modulate biological processes by tightly regulating NEAT1 expression. These regulatory mechanisms act at different levels, allowing cells to rapidly modulate NEAT1 expression and dynamically respond to sudden changes in cellular conditions. In this review, we summarize and discuss the transcriptional routes controlling NEAT1 expression, emphasizing recent evidence showing the pivotal role of NEAT1 in regulating important biological processes, such as cellular stress response, inflammation, and cell differentiation.

Involvement of lncRNAs NEAT1 and ZBTB11-AS1 in Active and Persistent HIV-1 Infection in C20 Human Microglial Cell Line

HIV-1 infection in microglia induces HIV-associated neurocognitive disorder (HAND). Recent evidence suggests that microglia can be infected with HIV-1 in the active, persistent, or latent replication stages. The molecular mechanisms governing these stages of infection are still the subject of continuous study. In this study, we analyzed the relationship between HIV-1 infection and two lncRNAs, NEAT1 and ZBTB11-AS1, on different days post-infection. We found that on days 1 and 4 post-infection, HIV-1 was actively replicating; meanwhile, by day 21, HIV-1 had entered a persistent stage. We also noted that the expression levels of NEAT1 and ZBTB11-AS1 varied during these different stages of HIV-1 infection in microglia, as did their subcellular localization. We performed an interaction network analysis and identified DDX3X and ZC3HAV1 as hypothetically related to NEAT1 and ZBTB11-AS1 in the C20 human microglial cell line. Additionally, we determined that IL-6, a cytokine regulated by DDX3X and ZC3HAV1, exhibits changes in protein expression levels during both active and persistent HIV-1 infection.

Interplay between NETosis and the lncRNA-microRNA regulatory axis in the immunopathogenesis of cancer

Neutrophil extracellular traps (NETs), web-like complex structures secreted by neutrophils, have emerged as key players in the modulation of immune responses and the immunopathogenesis of immune disorders. Initially described for their antimicrobial function, NETs now play a part in the fundamental processes of cancer biology, including cancer initiation, metastatic dissemination, and immune evasion strategies. NETs hijack anti-tumor immunity by entrapping circulating cancer cells, fostering the growth of tumors, and reorganizing the tumor microenvironment such that it is pro-malignancy. Emerging evidence emphasizes the role of NETosis coupled with non-coding RNAs-long non-coding RNAs (lncRNAs) and microRNAs (miRNAs)-as key regulators of gene expression and controllers of processes vital for cancer growth, such as immune response and programmed cell death processes like apoptosis, necroptosis, pyroptosis, and ferroptosis. Aberrantly expressed non-coding RNAs have been attributed to immune dysregulation and excessive NET production, promoting tumor growth. NETs are also associated with a myriad of pathological conditions, such as autoimmune disorders, cystic fibrosis, sepsis, and thrombotic disorders. New therapeutic approaches-such as DNase therapy and PAD4 inhibitors-target NET production and their degradation to modify immune function and the efficiency of immunotherapies. Further clarification of the intricate interactions of NETosis, lncRNAs, and miRNAs has the potential to establish new strategies for the suppression of the growth of tumors and preventing immune evasion. This review seeks to elucidate the interactions between NETosis and the regulatory networks involving non-coding RNAs that significantly contribute to the immunopathogenesis of cancer.

Secretory IgA binding to FCRL3 triggers shared inflammatory cytokine secretion by human regulatory T cells and effector T cells

Several human lymphocyte subsets express the novel secretory IgA receptor FCRL3 (Fc receptor-like 3). Secretory IgA binding to FCRL3 diminishes the inhibitory capacity of regulatory T cells and promotes a T helper 17-like phenotype. Here, we report that in CD4+ regulatory T cells and CD8+ terminal effector T cells secretory IgA induced a shared inflammatory gene signature that included PTGS2 encoding COX2, and the prototypic inflammatory cytokine genes IL1A, IL1B, and IL8. Secretory IgA in regulatory T cells also elevated gene transcripts required for lineage identity and function. Secretory IgA promoted interleukin (IL)-1β, IL-6, IL-8, IL-10, interferon γ, and tumor necrosis factor α protein secretion by both T cell types. Moreover, secretory IgA promoted NLRP3 inflammasome activation in regulatory T cells. Pharmacologic COX2 and NLRP3 inhibitors partially rescued the inhibitory competence of regulatory T cells, suggesting respective mechanistic roles. We propose that secretory IgA provokes a coordinated inflammatory response in regulatory and effector T cells to facilitate mucosal pathogen clearance.

Emerging Role of Long, Non-Coding RNA Nuclear-Enriched Abundant Transcript 1 in Stress- and Immune-Related Diseases

Long, non-coding RNAs (lncRNAs) are a class of RNAs exceeding 200 nucleotides in length, lacking the ability to be translated into proteins. Over the past few decades, an increasing number of publications have established lncRNAs as potent regulators in a broad spectrum of diseases. They modulate the expression of critical genes by affecting transcription, post-transcription, translation, and protein modification. This regulation frequently involves the interaction of lncRNAs with various molecules, such as proteins, RNA, and DNA. lncRNAs are involved in diseases where stress is a significant factor. In recent years, lncRNAs have been identified as regulators of both innate and adaptive immune responses, playing significant roles in the onset and progression of diseases. Additionally, lncRNAs hold potential as biomarkers or therapeutic targets for numerous stress- and immune-related diseases. lncRNA nuclear-enriched abundant transcript 1 (NEAT1) is a notable example. This review consolidates the latest findings about the role of lncRNA NEAT1 in stress response and immune cell function in non-cancer diseases. It summarizes studies on NEAT1 regulating stress response, both innate and adaptive immunity, and its potential as a biomarker and therapeutic target for stress- and immune-related diseases.

Therapeutic connections between pyroptosis and paclitaxel in anti-tumor effects: an updated review

As a form of inflammation-associated cell death, pyroptosis has gained widespread attention in recent years. Accumulating evidence indicates that pyroptosis regulates tumor growth and is associated with autoimmune disorders and inflammatory response. Paclitaxel, a traditional Chinese medicine, usually induces death of cancer cells as a chemotherapeutic agent. Previous studies have revealed that paclitaxel can exert an anti-tumor effect through a variety of cell death mechanisms, of which pyroptosis plays a pivotal role in inhibiting tumor growth and enhancing anti-tumor immunity. In this review, we summarize the current advances in therapeutic connections between pyroptosis and paclitaxel in anti-tumor effects.

The Role of tRNA Fragments on Neurogenesis Alteration by H₂O₂-induced Oxidative Stress

Transfer RNAs (tRNAs) are small non-coding RNA molecules transcribed from tRNA genes. tRNAs cleaved into a diverse population tRNA fragments (tRFs) ranging in length from 18 to 40 nucleotides, they interact with RNA binding proteins and influence the stability and translation. Stress is one of the reasons for tRFs cleavage. In our study, we modeled oxidative stress conditions with hydrogen peroxide (H2O2) exposure and dealt with one of the frequently expressed tRF in the hippocampus region of the brain, which is tRF-Glu-CTC. For this purpose, neural stem cells (NSCs) were exposed to H2O2, and tRF-Glu-CTC levels were increased in various H2O2 concentrations. A decrease was seen in microtubule-associated protein 2 (MAP2) marker expression. To understand the H2O2 oxidative stress condition on the expression of tRNA fragments, 72 hpf zebrafish embryos exposed to different H2O2 concentrations, an increase in the level of tRF-Glu-CTC was observed in all concentrations of H2O2 compared to control. Subsequently, neurogenesis markers were figured out via Calb2a (calbindin 2a) in situ hybridization (ISH) and HuC/D immunofluorescence staining (IF) staining experiments. Under H2O2 exposure, a decline was observed in Calb2a and HuC/D markers. To understand the inhibitory role of tRF-Glu-CTC on neurogenesis, NSCs were transfected via tRF-Glu-CTC inhibitor, and neurogenesis markers (ßIII-tubulin, MAP2, and GFAP) were determined with qRT-PCR and IF staining. tRF-Glu-CTC inhibitor reversed the diminished neuronal markers expression under the exposure of H2O2. Gene Ontology (GO) enrichment analysis showed us that targets of tRF-Glu-CTC are generally related to neuronal function and synaptic processes.

scRNA-seq uncovers the transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages

Microsporidia are single-celled intracellular parasites that cause opportunistic diseases in humans. Encephalitozoon intestinalis is a prevalent human-infecting species that invades the small intestine. Macrophages are potential reservoirs of infection, and dissemination to other organ systems is also observed. The macrophage response to infection and the developmental trajectory of the parasite are not well studied. Here we use single cell RNA sequencing to investigate transcriptional changes in both the parasite and the host during E. intestinalis infection of human macrophages in vitro. The parasite undergoes large transcriptional changes throughout the life cycle, providing a blueprint for parasite development. While a small population of infected macrophages mount a response, most remain transcriptionally unchanged, suggesting that the majority of parasites may avoid host detection. The stealthy microsporidian lifestyle likely allows these parasites to harness macrophages for replication. Together, our data provide insights into the host response in primary human macrophages and the E. intestinalis developmental program.

RNA-Seq analysis reveals the long noncoding RNAs associated with immunity in wild Myotis myotis bats

BACKGROUND

Bats possess a uniquely adapted immune system that enables them to live with viral infections without the expected maladies. The molecular basis and regulation of bats' immune response is still not fully understood. Long non-coding RNAs (lncRNAs) represent an emerging class of molecules with critical regulatory roles in multiple biological processes, including immunity. We hypothesise that lncRNA-based regulation in bats may enable them to limit disease and live with viral pathogens.

RESULTS

We developed a lncRNA prediction pipeline to annotate the long non-coding transcriptome across multiple bat tissues and at the population level. Characterisation of our lncRNA dataset based on 100 blood transcriptomes from wild Myotis myotis bats revealed lower and more tissue-specific expression compared with coding genes, reduced GC content and shorter length distributions, consistent with lncRNA profiles observed in other species. Using WGCNA network analyses and gene ontology, we identified two mRNA-lncRNA co-expression modules in Myotis myotis associated with distinct immune response: one linked to T-cell activation and vial processes, and the other to inflammation. From these immune-related lncRNAs, we selected four candidates with high translational potential for regulating viral infections and inflammation. These include a newly identified lncRNA, BatLnc1, with potential antiviral functions; the M. myotis ortholog of TUG1, implicated in viral-host interactions; and well-known lncRNAs MALAT1 and NEAT1, recognised for their roles in inflammatory regulation.

CONCLUSIONS

We conducted the first ab initio prediction of lncRNAs in a non-model bat species, the wild-caught M. myotis. Our network analysis revealed significant variation in immune status among a subset of individuals, potentially due to pathogenic conditions. From these variations, we identified lncRNAs most likely associated with immune response in bats. This initial exploration lays the groundwork for future experimental validations of lncRNA functions, offering promising insights into their role in bat immunity.

Long non-coding RNA transcripts in Mycobacterium tuberculosis-host interactions

Tuberculosis (TB) persists as a significant health threat, affecting millions of people all over the world. Despite years of control measures, the elimination of TB has become a difficult task as morbidity and mortality rates remain unaffected for several years. Developing new diagnostics and therapeutics is paramount to keeping TB under control. However, it largely depends upon understanding the pathogenic mechanisms of Mycobacterium tuberculosis (Mtb), the causative agent of TB. Mtb is an intracellular pathogen capable of subverting the defensive functions of the immune cells, and it can survive and multiply within humans' mononuclear phagocytes. Emerging evidence indicates that long non-coding RNAs (lncRNAs), a class of RNA molecules with limited coding potential, are critical players in this intricate game as they regulate gene expression at transcriptional and post-transcriptional levels and also by chromatin modification. Moreover, they have been shown to regulate cellular processes by controlling the function of other molecules, such as DNA, RNA, and protein, through binding with them. Recent studies have shown that lncRNAs are differentially regulated in the tissues of TB patients and cells infected in vitro with Mtb. Some dysregulated lncRNAs are associated with essential roles in modulating immune response, apoptosis, and autophagy in the host cells, adding a new dimension to TB pathogenesis. In this article, we provide a comprehensive review of the recent literature in this field and the impact of lncRNAs in unraveling pathogenic mechanisms in TB. We also discuss how the studies involving lncRNAs provide insight into TB pathogenesis, especially Mtb-host interactions.

Interleukin-12 signaling drives Alzheimer's disease pathology through disrupting neuronal and oligodendrocyte homeostasis

Neuroinflammation including interleukin (IL)-12/IL-23-signaling is central to Alzheimer's disease (AD) pathology. Inhibition of p40, a subunit of IL-12/IL-23, attenuates pathology in AD-like mice; however, its signaling mechanism and expression pattern remained elusive. Here we show that IL-12 receptors are predominantly expressed in neurons and oligodendrocytes in AD-like APPPS1 mice and in patients with AD, whereas IL-23 receptor transcripts are barely detectable. Consistently, deletion of the IL-12 receptor in neuroectodermal cells ameliorated AD pathology in APPPS1 mice, whereas removal of IL-23 receptors had no effect. Genetic ablation of IL-12 signaling alone reverted the loss of mature oligodendrocytes, restored myelin homeostasis, rescued the amyloid-β-dependent reduction of parvalbumin-positive interneurons and restored phagocytosis-related changes in microglia of APPPS1 mice. Furthermore, IL-12 protein expression was increased in human AD brains compared to healthy age-matched controls, and human oligodendrocyte-like cells responded profoundly to IL-12 stimulation. We conclude that oligodendroglial and neuronal IL-12 signaling, but not IL-23 signaling, are key in orchestrating AD-related neuroimmune crosstalk and that IL-12 represents an attractive therapeutic target in AD.

A comparison of the expression patterns and diagnostic capability of the ncRNAs NEAT1 and miR-34a in non-obstructive azoospermia and severe oligospermia

Infertility is a major global health problem, affecting 8-12% of couples worldwide, with male causes contributing to approximately 50% of cases. Notably, around 15% of infertile men are azoospermic. Consequently, there is a critical necessity to find noninvasive biomarkers to help in diagnosing and assessing the susceptibility of patients with various infertility disorders. This study is designed to determine the roles of NEAT1 and miR-34a as diagnostic and susceptibility biomarkers for non-obstructive azoospermia and severe oligospermia. The interactions between these non-coding RNA (ncRNAs) were explored, along with their correlations to hormonal profiles and clinical parameters like sperm count and motility. The potential of serum NEAT1 and miR-34a as diagnostic biomarkers for these conditions was explored. The study included 100 participants: 40 non-obstructive azoospermia patients, 40 severe oligospermia patients, and 20 healthy controls. Quantitative real-time PCR and transcriptomics-based bioinformatics tools were employed to explore the co-expression networks and molecular interactions of NEAT1, miR-34a, SIRT1, and their associated hormonal and genetic pathways. Results indicated that NEAT1 was significantly downregulated in severe oligospermia patients, while its levels in non-obstructive azoospermia patients did not differ significantly from healthy controls. Furthermore, serum miR-34a expression was considerably upregulated in both patient groups compared to controls. This study highlights the promise of serum NEAT1 and miR-34a as diagnostic markers for non-obstructive azoospermia and severe oligospermia. These findings provide valuable insights into male infertility and indicate potential avenues for personalized treatment strategies.

Decoding CKD-induced muscle atrophy through the critical role of lncRNA GAS5 and pyroptosis

Skeletal muscle atrophy is a prevalent complication of chronic kidney disease (CKD) and serves as an indicator of adverse prognosis and poor quality of life; however, the underlying mechanisms remain ambiguous. Emerging evidence has shown that long non-coding RNAs (lncRNAs) are involved in the pathogenesis of skeletal muscle atrophy. Using RNA sequencing (RNA-seq), we discerned elevated GAS5 expression in the muscles of CKD mice and verified these findings by real-time qPCR. Transmission electron microscopy confirmed morphological signs of pyroptosis, a potentially causal cellular death form. Additionally, elevated levels of pyroptosis markers, such as NLRP3, cleaved caspase-1, and GSDMD-N, were observed in CKD mouse models and lipopolysaccharide (LPS)/ATP-stimulated C2C12 myotubes. Intriguingly, the knockdown of GAS5 reduced these markers, alleviating pyroptosis and enhancing myofiber size, both in vitro and in vivo. Furthermore, we pinpointed an interaction between GAS5 and the mitochondrial translation elongation factor (TUFM) through RNA pull-down and mass spectrometry. This interaction amplified NLRP3 activity, contributing to pyroptosis and muscle atrophy. Notably, overexpressing TUFM counterbalanced this effect. Fundamentally, the interaction between GAS5 and TUFM appears to compromise the anti-pyroptosis capacity of TUFM. Consequently, this amplifies the activation of the NLRP3 pathway, which may underpin the crucial mechanism driving pyroptosis-mediated muscle atrophy. Our findings provide new evidence for GAS5's role in regulating cellular pyroptosis in CKD-induced skeletal muscle atrophy.

Macrophage-derived lncRNAs in cancer: regulators of tumor progression and therapeutic targets

Macrophages are key tumor microenvironment (TME) regulators, exhibiting remarkable plasticity that enables them to either suppress or promote cancer progression. Emerging evidence highlights the critical role of macrophage-derived long non-coding RNAs (lncRNAs) in shaping tumor immunity, influencing macrophage polarization, immune evasion, angiogenesis, metastasis, and therapy resistance. This review comprehensively elucidates the functional roles of M1- and M2-associated lncRNAs, detailing their molecular mechanisms and impact on cancer pathogenesis. In summary, elucidating the roles of lncRNAs derived from macrophages in cancer progression offers new avenues for therapeutic strategies, significantly improving patient outcomes in the fight against the disease. Further research into the functional significance of these lncRNAs and the development of targeted therapies is essential to harness their potential fully in clinical applications. We further explore their potential as biomarkers for cancer prognosis and therapeutic targets for modulating macrophage activity to enhance anti-cancer immunity. Targeting macrophage-derived lncRNAs represents a promising avenue for precision oncology, offering novel strategies to reshape the TME and improve cancer treatment outcomes.

Mechanism of action of lncRNA-NEAT1 in immune diseases

NEAT1, a long non-coding RNA (lncRNA), is involved in assembling nuclear paraspeckles that have been found to impact various immune-related diseases, such as autoimmune diseases, allergic diseases, cancer immunity, sepsis, etc. In immune-related diseases, lncRNA-NEAT1 affects the activation, proliferation, and differentiation process of immune cells by interacting with transcription factors and miRNA (MicroRNA) to regulate an expression level in immune-related genes. It can also regulate the apoptosis and autophagy processes of immune cells by regulating inflammatory responses, interacting with apoptosis-related proteins, or regulating the expression of autophagy-related genes, thereby regulating the development of immune-related diseases. In recent years, a large number of researchers have found that the abnormal expression of lncRNA-NEAT1 has a great impact on the onset and progression of immune diseases, such as innate immunity after viral infection and the humoral immunity of T lymphocytes. In this paper, the specific mechanism of action and the function of lncRNA-NEAT1 in different immune-related diseases are sorted out and analyzed, to furnish a theoretical foundation for the study of the mechanism of action of immune cells.

Cell death-associated lncRNAs in cancer immunopathogenesis: An exploration of molecular mechanisms and signaling pathways

Cancer remains one of the foremost causes of mortality worldwide, highlighting the urgent need for novel therapeutic targets due to the insufficient efficacy and adverse side effects associated with existing cancer treatments. Long non-coding RNAs (lncRNAs), defined as RNA transcripts longer than 200 nucleotides, have emerged as pivotal regulators in the initiation and progression of various malignancies. In oncology, programmed cell death (PCD) serves as the primary mechanism for tumor cell elimination, comprising processes such as apoptosis, pyroptosis, autophagy, and ferroptosis. Recent studies have elucidated a substantial relationship between lncRNAs and these PCD pathways, indicating that lncRNAs can modulate the apoptotic and non-apoptotic death mechanisms. This regulation may influence not only the dynamics of cancer progression but also the therapeutic response to clinical interventions. This review delves into the intricate role of lncRNAs within the context of PCD in cancer, unveiling the underlying pathogenic mechanisms while proposing innovative strategies for cancer therapy. Additionally, it discusses the potential therapeutic implications of targeting lncRNAs in PCD and related signaling pathways, aiming to enhance treatment outcomes for patients facing cancer.

Integrative Genomics Approach Identifies Glial Transcriptomic Dysregulation and Risk in the Cortex of Individuals With Alcohol Use Disorder

BACKGROUND

Alcohol use disorder (AUD) is a prevalent neuropsychiatric disorder that is a major global health concern, affecting millions of people worldwide. Previous studies of AUD used underpowered single-cell analysis or bulk homogenates of postmortem brain tissue, which obscure gene expression changes in specific cell types. Therefore, we sought to conduct the largest-to-date single-nucleus RNA sequencing (snRNA-seq) postmortem brain study in AUD to elucidate transcriptomic pathology with cell type-specific resolution.

METHODS

Here, we performed snRNA-seq and high-dimensional network analysis of 73 postmortem samples from individuals with AUD (n = 36, nnuclei = 248,873) and neurotypical control individuals (n = 37, nnuclei = 210,573) in the dorsolateral prefrontal cortex from both male and female donors. Additionally, we performed analysis for cell type-specific enrichment of aggregate genetic risk for AUD as well as integration of the AUD proteome for secondary validation.

RESULTS

We identified 32 distinct cell clusters and found widespread cell type-specific transcriptomic changes across the cortex in AUD, particularly affecting glial populations. We found the greatest dysregulation in novel microglial and astrocytic subtypes that accounted for the majority of differential gene expression and coexpression modules linked to AUD. Differential gene expression was secondarily validated by integration of a publicly available AUD proteome. Finally, analysis for aggregate genetic risk for AUD identified subtypes of glia as potential key players not only affected by but also causally linked to the progression of AUD.

CONCLUSIONS

These results highlight the importance of cell type-specific molecular changes in AUD and offer opportunities to identify novel targets for treatment on the single-nucleus level.

Monocytic myeloid-derived suppressor cells contribute to the exacerbation of bone destruction in periodontitis

BACKGROUND

Periodontitis (PD) is a chronic infectious and inflammatory disease characterized by alveolar bone loss. The distinctive activity of immune cells critically exacerbates bone resorption in PD. Myeloid-derived suppressor cells (MDSCs) are known to contribute to various chronic inflammatory conditions, but their role in the pathogenesis and progression of PD remains poorly understood.

METHODS

We used single-cell transcriptomic analysis with human gingival samples and animal models of experimental periodontitis to examine the role of M-MDSCs in PD. We also explored the therapeutic effect of depleting MDSCs on PD in vivo. Additionally, the mechanisms of long non-coding RNA Neat1 and the pathway of NF-κB-dependent "canonical NLRP3 inflammasome activation" in MDSCs were investigated in PD.

RESULTS

In this study, we revealed that monocytic (M)-MDSCs were significantly increased in inflamed gingiva of PD patients compared to healthy individuals. Expansion of M-MDSCs was also observed in the mouse model of ligature-induced periodontitis, and depletion of MDSCs in PD mice could ameliorate alveolar bone loss and reduce periodontal inflammation. Mechanistically, we found that long non-coding RNA Neat1 was significantly upregulated in M-MDSCs, which achieved this proinflammatory effect by activating NF-κB signaling in PD. Furthermore, the pathway of NF-κB-dependent "canonical NLRP3 inflammasome activation" was confirmed in the PD mouse model, accompanied by increased secretion of proinflammatory cytokines that drive alveolar bone loss, including IL-1β, IL-6 and TNF-α.

CONCLUSIONS

In conclusion, this study highlights the pivotal proinflammatory role of M-MDSCs in PD and suggests that targeting these cells may represent a novel immunotherapeutic approach. Future research could focus on strategies to specifically target MDSCs for the treatment of periodontitis.

Long non-coding RNAs: Emerging regulators of invasion and metastasis in pancreatic cancer

BACKGROUND

The invasion and metastasis of pancreatic cancer (PC) are key factors contributing to disease progression and poor prognosis. This process is primarily driven by EMT, which has been the focus of recent studies highlighting the role of long non-coding RNAs (lncRNAs) as crucial regulators of EMT. However, the mechanisms by which lncRNAs influence invasive metastasis are multifaceted, extending beyond EMT regulation alone.

AIM OF REVIEW

This review primarily aims to characterize lncRNAs affecting invasion and metastasis in pancreatic cancer. We summarize the regulatory roles of lncRNAs across multiple molecular pathways and highlight their translational potential, considering the implications for clinical applications in diagnostics and therapeutics.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The review focuses on three principal scientific themes. First, we primarily summarize lncRNAs orchestrate various signaling pathways, such as TGF-β/Smad, Wnt/β-catenin, and Notch, to regulate molecular changes associated with EMT, thereby enhancing cellular motility and invasivenes. Second, we summarize the effects of lncRNAs on autophagy and ferroptosis and discuss the role of exosomal lncRNAs in the tumor microenvironment to regulate the behavior of neighboring cells and promote cancer cell invasion. Third, we emphasize the effects of RNA modifications (such as m6A and m5C methylation) on stabilizing lncRNAs and enhancing their capacity to mediate invasive metastasis in PC. Lastly, we discuss the translational potential of these findings, emphasizing the inherent challenges in using lncRNAs as clinical biomarkers and therapeutic targets, while proposing prospective research strategies.

The role of lncRNA NEAT1 in acute graft-versus-host disease: Regulation of macrophage polarization and inflammatory cytokine secretion via JNK/NLRP3 pathway

BACKGROUND

Acute graft-versus-host disease (aGVHD) is a complication of allogeneic hematopoietic stem cell transplantation (allo-HSCT). The role of macrophages as proficient antigen-presenting cells in aGVHD is a prominent area of investigation in contemporary research. The association between long noncoding RNA nuclear enriched abundant transcript 1 (lncRNA NEAT1) and the macrophage function is of significant interest. However, the role of lncRNA NEAT1 in aGVHD needs to be further explored.

METHODS

Peripheral blood mononuclear cells (PBMCs) were collected from patients with or without aGVHD (non-aGVHD) after allo-HSCT. RAW264.7 cells and bone marrow-derived macrophages (BMDMs) were transduced with NEAT1 lentiviral vector or transfected with NEAT1 small interfering RNA to change the expression level of lncRNA NEAT1. Finally, an aGVHD mouse model was established to evaluate the role of JNK inhibitor or NLRP3 inhibitor in aGVHD.

RESULTS

Compared with non-aGVHD patients, lncRNA NEAT1 was significantly up-regulated in the PBMCs of aGVHD patients. ROC and AUC analysis confirmed that the expression of lncRNA NEAT1 was correlated with the occurrence of aGVHD. The overexpression of lncRNA NEAT1 in RAW264.7 could significantly promote the proliferation, migration, and differentiation into M1 macrophages. Knockdown of lncRNA NEAT1 could significantly decrease the proportion of M1 macrophages, regulate pro-inflammatory cytokines secretion, and affect the JNK/NLRP3 pathway in lipopolysaccharides (LPS)-induced BMDMs. Correspondingly, JNK and NLRP3 inhibitors reduced LPS-induced pro-inflammatory responses in macrophages. Furthermore, JNK and NLRP3 inhibitors regulated macrophage polarization and improved symptoms in aGVHD mice.

CONCLUSIONS

The aforementioned data suggest that lncRNA NEAT1 potentially plays a significant role in macrophage polarization and the secretion of inflammatory cytokines through its modulation of the JNK/NLRP3 pathway. Consequently, this study establishes a foundation for the development of novel therapeutic approaches targeting aGVHD.

The Role of Long Non-Coding RNA in Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a chronic autoimmune disease that leads to joint damage and physical dysfunction. The pathogenesis of RA is highly complex, involving genetic, epigenetic, immune, and metabolic factors, among others. Over the years, research has highlighted the importance of non-coding RNAs (ncRNAs) in regulating gene expression. Given their dysregulation in numerous conditions, ncRNAs are thought to play a role in pathological processes. In RA, aberrant levels of circulating long ncRNAs (lncRNAs) are commonly observed in peripheral blood, along with their dysregulated expression in peripheral blood mononuclear cells and synovial tissue. This review discusses the involvement of lncRNAs in inflammation and the aggressive characteristics of fibroblast-like synoviocytes, a key cellular population driving RA progression.

An updated review on abnormal epigenetic modifications in the pathogenesis of systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease. The inconsistent prevalence of SLE between monozygotic twins suggests that environmental factors affect the occurrence of this disease. Abnormal epigenetic regulation is strongly associated with the pathogenesis of SLE. Epigenetic mechanisms may be involved in the development of lupus through DNA methylation, histone modification, noncoding RNAs, and other modifications. This review aims to show numerous studies as a treasure map to better understand the effects of aberrant epigenetic modification in the onset and development of SLE, which will benefit the current basic research and provide potential diagnostic biomarkers or therapeutic targets for SLE.

Inhibition of lncEPS by TLR4/NF-κB pathway induces ventilator-induced lung injury by decreasing its binding to and upregulating Hspa5

Whether LincRNA erythroid prosurvival (LncEPS) reduces VILI remains unclear. A GSE200932 microarray was used to screen differentially expressed genes (DEGs). A VILI mouse model was constructed by mechanical ventilation (MV), with or without TAK242 or SN50 pretreatment. Airway transfection with adeno-associated virus (AAV) was used to overexpress lncEPS in alveolar macrophages (AMs). Lung tissues were collected to assess pathological injury and macrophage polarization. NLRP3 inflammasome, TLR4/NF-κB pathway activation and heat shock protein family A member 5 (Hspa5) in lung tissue and AMs wre evaluated. LncEPS localization and regulatory changes were assessed using in situ hybridization and RT-PCR. Lung tissues after lncEPS overexpression were subjected to transcriptomics. Chromatin isolation and mass spectrometry (MS) were performed to identify proteins interacting with lncEPS. GSE200932 microarray showed that the DEGs were related to NF-κB pathway, Toll-like receptor pathway and NOD-like receptor pathway. TAK242 or SN50 treatment increased polarization of M2 macrophages and decreased NLRP3 inflammasome activation by inhibiting TLR4/NF-κB pathway in VILI. Inhibition of TLR4/NF-κB pathway upregulated lncEPS expression in AMs. Overexpression of lncEPS increased polarization of M2 macrophages and decreased NLRP3 inflammasome activation, eventually alleviating VILI in mice. Mechanistically, lncEPS bound to Hspa5 and downregulated its expression to inhibit inflammatory response.

Integrating bioinformatics and machine learning to uncover lncRNA LINC00269 as a key regulator in Parkinson's disease via pyroptosis pathways

BACKGROUND

Pyroptosis, a specific type of programmed cell death, which has become a significant factor to Parkinson's disease (PD). Concurrently, long non-coding RNAs (lncRNAs) have garnered attention for their regulatory roles in neurodegenerative disorders. This study was designed to ascertain the key lncRNAs in pyroptosis pathways of PD and elucidate their regulatory mechanisms.

METHODS

Employing a combination of bioinformatics and machine learning, we analyzed PD data sets GSE133347 and GSE110716. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) recognized different lncRNAs. Through various algorithms such as Least Absolute Shrinkage and Selection Operator (LASSO), Random Forest (RF), and Weighted Gene Co-expression Network Analysis (WGCNA), we recognized LINC01606 and LINC00269, which are key factors during the emergence and development of PD. Furthermore, experimental validation was conducted in PD mouse models to confirm these bioinformatics findings.

RESULTS

The analysis showed that there were a large number of apoptosis-related gene expression changes in Parkinson's syndrome, for example, CASP1 and GSDME were up-regulated, and CASP9 and AIM2 were down-regulated. Among the lncRNAs, LINC01606 and LINC00269 were identified as potential modulators of pyroptosis. Notably, LINC00269 was observed to be significantly downregulated in the brain tissues of a PD mouse model, supporting its involvement in PD. The study also highlighted potential interactions of these lncRNAs with genes like ONECUT2, PRLR, CTNNA3, and LRP2.

CONCLUSIONS

This study identifies LINC00269 as a potential contributor to pyroptosis pathways in PD. While further investigation is required to fully elucidate its role, these findings provide new insights into PD pathogenesis and suggest potential avenues for future research on diagnostic and therapeutic targets. The study underscores the importance of integrating bioinformatics with experimental validation in neurodegenerative disease research.

Genome-wide profiling of long non-coding RNA following ozone exposure: A randomized, controlled exposure trial

BACKGROUND

Exposure to ambient ozone has been associated with extrapulmonary health, but the underlying mechanisms remain to be understood. LncRNAs are involved in the regulation of gene expression, but their regulatory mechanisms in ozone-related health effects are scarcely explored.

OBJECTIVE

To investigate genome-wide lncRNA changes after short-term ozone exposure and their regulatory roles in ozone exposure and gene expression.

METHOD

We conducted a randomized, crossover, controlled exposure trial in 32 healthy college students in Shanghai, China. Each participant received both 200-ppb ozone exposure and filtered air exposure for 2 h in a random order with a 14-day washout period. Blood samples were collected after each exposure and used for lncRNA sequencing. Differentially expressed lncRNAs between the two exposures were identified using orthogonal partial least squares discriminant analysis and linear regression analysis. LncRNAs-targeted mRNAs were mapped and subjected to enrichment analyses. We also constructed lncRNA-miRNA-mRNA networks.

RESULTS

A total of 90 lncRNAs were differentially expressed after exposure to ozone, with 49 up-regulated and 41 down-regulated. Enrichment analyses suggested that these dysregulated lncRNAs were involved in a variety of biological processes, including those related to oxidative stress, inflammation response, and cell proliferation, development, and differentiation. Multiple pathways such as IL-17 signaling, NF-kB signaling, and Rho GTPases signaling were also enriched. Furthermore, the lncRNA-miRNA-mRNA network revealed that specific lncRNAs may regulate the expression of inflammation- and angiogenesis-related genes by interacting with miRNAs, such as NEAT1/hsa-miR-500a-3p/SIGLEC8, NEAT1/hsa-miR-6835-3p/SLC16A14, OIP5-AS1/miR-183-5p/EGR1, and SNHG25/hsa-miR-663a/FOSB axes.

CONCLUSION

This study characterized a thorough profile of human lncRNAs following short-term ozone exposure and suggested the regulatory roles of these lncRNAs in ozone-induced inflammatory responses and angiogenesis, providing novel epigenetic insights into the mechanisms of the health effects of ozone exposure.

Molecular mechanism of Wilms tumour 1-associated protein in diabetes-related dry eye disease by mediating m6A methylation modification of lncRNA NEAT1

Background: Dry eye disease (DED) is often secondary to diabetes mellitus (DM).Purpose: This study is to explore the action of Wilms tumor 1-associated protein (WTAP) in DM-DED via lncRNA NEAT1 m6A methylation.Methods: DM-DED mouse models were treated with sh-WTAP/sh-NEAT1, followed by assessment of corneal epithelial damage/histopathological changes. HCE-2 cells were exposed to hyperosmotic conditions to establish in vitro DED models and treated with oe-NEAT1/sh-NEAT1/sh-WTAP/nigericin (an NLRP3 inflammasome inducer). Cell viability/apoptosis were evaluated by CCK-8/TUNEL. Levels of WTAP/NEAT1/inflammatory factors/NLRP3 inflammasome- and apoptosis-related markers were determined. m6A modification was examined by MeRIP-qPCR and NEAT1 stability was also detected.Results: DM-DED mice exhibited up-regulated WTAP/NEAT1 expression and severe corneal damage, whereas WTAP/NEAT1 knockdown alleviated inflammation/corneal damage. In hyperosmolarity-induced HCE-2 cells, NEAT1 aggravated inflammation and apoptosis, while NEAT1 knockdown suppressed NLRP3 inflammasome activation and ameliorated cell injury. Hyperosmolarity-induced WTAP expression increased m6A modification and NEAT1 mRNA stability. WTAP mediated m6A methylation of NEAT1 and NLRP3 inflammasome activation in DM-DED mice.

LncRNA (BCO1-AS) regulate inflammatory responses in bacterial infection through caspase-1 in turbot (Scophthalmus maximus)

LncRNA plays key role in several biological processes, including transcriptional regulation, post transcriptional control and epigenetic regulation. However, research on the functional roles of lncRNAs in teleost species remains limited. Here, we discovered a lncRNA (BCO1-AS) with a critical role in antibacterial responses. Briefly, the full length of BCO1-AS was 2005 bp. Subsequently, BCO1-AS was distributed throughout the nucleus, where it may either trans- or cis-regulate the nearby genes. In addition, BCO1-AS was widely expressed in all the examined tissues with the highest expression level in intestine, while the lowest expression level was detected in muscle. Moreover, following Vibrio anguillarum challenge, BCO1-AS was significantly down-regulated in intestine, and up-regulated in gill and skin. In CHIRP experiment, BCO1-AS could effectively enrich RNA and might interact with several immune-related genes. Furthermore, we found that LPS could induce the expression of BCO1-AS. Finally, BCO1-AS could positively regulate caspase-1 at the mRNA and protein level. The BCO1-AS was speculated to inhibit the synthesis of inflammatory components. In summary, these results showed the roles of BCO1-AS in the regulation of inflammatory in turbot, which provided valuable information for further understanding the immune regulation network of lncRNA in teleost fish.

P2X7 receptors from the perspective of NLRP3 inflammasome pathway in depression: Potential role of cannabidiol

Many patients with depressive disorder do not respond to conventional antidepressant treatment. There is an ongoing interest in investigating potential mechanisms of treatment resistance in depression to provide alternative treatment options involving inflammatory mechanisms. Increasing evidence implicates the NOD-like receptor pyrin domain containing 3 (NLRP3) inflammasome as a critical factor in neuroinflammation. ATP-induced P2X7 receptor (P2X7R) activation is a major trigger for inflammation, activating the canonical NLRP3 inflammatory cascade. Psychosocial stress, the primary environmental risk factor for depression, is associated with changes in ATP-mediated P2X7R signaling. Depression and stress response can be alleviated by Cannabidiol (CBD). CBD has an anti-inflammatory activity related to the regulation of NLRP3 inflammasome activation. However, CBD's effects on the inflammasome pathway are poorly understood in central nervous system (CNS) cells, including microglia, astrocytes, and neurons. This review will emphasize some findings for neuroinflammation and NLRP3 inflammasome pathway involvement in depression, particularly addressing the ATP-induced P2X7R activation. Moreover, we will underline evidence for the effect of CBD on depression and address its potential impacts on neuroinflammation through the NLRP3 inflammasome cascade.

Mechanistic role of long non-coding RNAs in the pathogenesis of metabolic dysfunction-associated steatotic liver disease and fibrosis

Metabolic dysfunction-associated steatotic liver disease (MASLD), previously referred to as non-alcoholic fatty liver disease, encompasses a broad range of hepatic metabolic disorders primarily characterised by the disruption of hepatic lipid metabolism, hepatic lipid accumulation and steatosis. Severe cases of MASLD might progress to metabolic dysfunction-associated steatohepatitis, characterised by hepatic inflammation, hepatocyte ballooning degeneration, activation of hepatic stellate cells (HSCs) and fibrogenesis. It may further progress to hepatocellular carcinoma. In the liver, long non-coding RNAs (lncRNAs) target multiple metabolic pathways in hepatocytes, HSCs, and Kupffer cells at different stages of MASLD and liver fibrosis. In this study, we overview recent findings on the potential role of lncRNAs in the pathogenesis of MASLD and liver fibrosis via modulation of de novo lipid synthesis, fatty acid β-oxidation, lipotoxicity, oxidative stress, metabolic inflammation, mammalian target of rapamycin signalling, apoptosis, ubiquitination and fibrogenesis. We critically assess the literature reports that investigate the complex interplay between lncRNA, microRNA and key mediators in liver injury, in both human participants and animal models of MASLD and liver fibrosis. We also highlight the therapeutic potential of lncRNAs in chronic liver diseases.

LncRNAs in tumor metabolic reprogramming and tumor microenvironment remodeling

The tumor microenvironment (TME) is a complex and dynamic ecosystem composed of tumor cells, immune cells, supporting cells, and the extracellular matrix. Typically, the TME is characterized by an immunosuppressive state. To meet the demands of rapid proliferation, cancer cells undergo metabolic reprogramming, which enhances their biosynthesis and bioenergy supply. Immune cells require similar nutrients for activation and proliferation, leading to competition and immunosuppression within the TME. Additionally, tumor metabolites inhibit immune cell activation and function. Consequently, an immunosuppressed and immune-tolerant TME promotes cancer cell proliferation and metastasis. Long non-coding RNAs (lncRNAs), a category of non-coding RNA longer than 200 nucleotides, regulate tumor metabolic reprogramming by interacting with key enzymes, transporters, and related signaling pathways involved in tumor metabolism. Furthermore, lncRNAs can interact with both cellular and non-cellular components in the TME, thereby facilitating tumor growth, metastasis, drug resistance, and inducing immunosuppression. Recent studies have demonstrated that lncRNAs play a crucial role in reshaping the TME by regulating tumor metabolic reprogramming. In this discussion, we explore the potential mechanisms through which lncRNAs regulate tumor metabolic reprogramming to remodel the TME. Additionally, we examine the prospects of lncRNAs as targets for anti-tumor therapy and as biomarkers for tumor prognosis.

Immunological characteristics of bronchoalveolar lavage fluid and blood across connective tissue disease-associated interstitial lung diseases

Interstitial lung disease (ILD) is a serious complication of connective tissue diseases (CTDs). The heterogeneity of ILDs reflects differences in pathogenesis among diseases. This study aimed to clarify the characteristics of CTD-ILDs via a detailed analysis of the bronchoalveolar lavage fluid (BALF) and blood immune cells. BALF and blood samples were collected from 39 Japanese patients with newly diagnosed ILD: five patients with Sjögren's syndrome (SS), eight patients with dermatomyositis (DM), six patients with rheumatoid arthritis (RA), six patients with systemic sclerosis, four patients with anti-neutrophil cytoplasmic antibody-associated vasculitis, and 10 patients with idiopathic interstitial pneumonia. We performed single-cell RNA sequencing to analyze the gene expression profiles in these patients' immune cells. In patients with SS, B cells in the BALF were increased and genes associated with the innate and acquired immunity were enriched in both the BALF and blood. In contrast, patients with DM showed an upregulation of genes associated with viral infection in both the BALF and blood. In patients with RA, neutrophils in the BALF tended to increase, and their gene expression patterns changed towards inflammation. These disease-specific characteristics may help us understand the pathogenesis for each disease and discover potential biomarkers.

Integrative genomics approach identifies glial transcriptomic dysregulation and risk in the cortex of individuals with Alcohol Use Disorder

Alcohol use disorder (AUD) is a prevalent neuropsychiatric disorder that is a major global health concern, affecting millions of people worldwide. Past molecular studies of AUD used underpowered single cell analysis or bulk homogenates of postmortem brain tissue, which obscures gene expression changes in specific cell types. Here we performed single nuclei RNA-sequencing analysis of 73 post-mortem samples from individuals with AUD (N=36, N nuclei = 248,873) and neurotypical controls (N=37, N nuclei = 210,573) in both sexes across two institutional sites. We identified 32 clusters and found widespread cell type-specific transcriptomic changes across the cortex in AUD, particularly affecting glia. We found the greatest dysregulation in novel microglial and astrocytic subtypes that accounted for the majority of differential gene expression and co-expression modules linked to AUD. Analysis for cell type-specific enrichment of aggregate genetic risk for AUD identified subtypes of microglia and astrocytes as potential key players not only affected by but causally linked to the progression of AUD. These results highlight the importance of cell-type specific molecular changes in AUD and offer opportunities to identify novel targets for treatment.

LncRNA MAAMT facilitates macrophage recruitment and proinflammatory activation and exacerbates autoimmune myocarditis through the SRSF1/NF-κB axis

Long non-coding RNAs (lncRNAs) have been implicated in dilated cardiomyopathy (DCM). However, the biological functions and regulatory mechanisms of lncRNAs in DCM remain elusive. Using a mouse model of experimental autoimmune myocarditis (EAM) to mimic DCM, we successfully constructed a dynamic lncRNA expression library for EAM by lncRNA microarray and found that the expression of a macrophage-enriched lncRNA, MAAMT, was significantly increased in the myocardial tissue of mice at the acute stage of EAM. Functionally, MAAMT knockdown alleviated the recruitment and proinflammatory activation of macrophages in the heart, spleen, and peripheral blood of mice at the acute stage of EAM, reduced myocardial inflammation and injury, and eventually reversed ventricular remodelling and improved cardiac function in mice at the chronic stage of EAM. Mechanistically, we identified serine/arginine-rich splicing factor 1 (SRSF1) as an MAAMT-interacting protein in macrophages using RNA pull-down assays coupled with mass spectrometry. MAAMT knockdown attenuated the ubiquitination-mediated degradation of SRSF1, increased the protein expression of SRSF1, and restrained the activation of the NF-κB pathway in macrophages, thereby inhibiting the proinflammatory activation of macrophages. Collectively, our results demonstrate that MAAMT is a key proinflammatory regulator of myocarditis that promotes macrophage activation through the SRSF1-NF-κB axis, providing a new insight into early effective treatment strategies for DCM.

Analysis of the heterogeneity and complexity of murine extraorbital lacrimal gland via single-cell RNA sequencing

PURPOSE

The lacrimal gland is essential for maintaining ocular surface health and avoiding external damage by secreting an aqueous layer of the tear film. However, a healthy lacrimal gland's inventory of cell types and heterogeneity remains understudied.

METHODS

Here, 10X Genome-based single-cell RNA sequencing was used to generate an unbiased classification of cellular diversity in the extraorbital lacrimal gland (ELG) of C57BL/6J mice. From 43,850 high-quality cells, we produced an atlas of cell heterogeneity and defined cell types using classic marker genes. The possible functions of these cells were analyzed through bioinformatics analysis. Additionally, the CellChat was employed for a preliminary analysis of the cell-cell communication network in the ELG.

RESULTS

Over 37 subclasses of cells were identified, including seven types of glandular epithelial cells, three types of fibroblasts, ten types of myeloid-derived immune cells, at least eleven types of lymphoid-derived immune cells, and five types of vascular-associated cell subsets. The cell-cell communication network analysis revealed that fibroblasts and immune cells play a pivotal role in the dense intercellular communication network within the mouse ELG.

CONCLUSIONS

This study provides a comprehensive transcriptome atlas and related database of the mouse ELG.

Unveiling the intricacies of paraspeckle formation and function

Paraspeckle nuclear bodies form when the NEAT1 long noncoding RNA is transcribed and bound by multiple RNA-binding proteins. First described 20 years ago, in recent years a growing appreciation of paraspeckle dynamics has led to new understandings, in both structure and function. Structurally, paraspeckles form via distinct physico-chemical domains arising from the composition of key proteins, recruited to different parts of NEAT1. These domains interact, creating a core-shell structured paraspeckle via microphase separation. Functionally, many environmental, chemical, and mechanical triggers can alter paraspeckle abundance, with important consequences depending on the cell type, developmental stage, and trigger identity. Underpinning these insights are new tools for paraspeckle research, including screening assays, proximity-based identification tools, and RNA processing modulators. A picture is emerging of paraspeckles as gene regulatory condensates in many healthy and disease settings. Critically, however, paraspeckle functional importance is generally most apparent when cells and organisms face external stressors.

Host long noncoding RNAs in bacterial infections

Bacterial infections remain a significant global health concern, necessitating a comprehensive understanding of the intricate host-pathogen interactions that play a critical role in the outcome of infectious diseases. Recent investigations have revealed that noncoding RNAs (ncRNAs) are key regulators of these complex interactions. Among them, long noncoding RNAs (lncRNAs) have gained significant attention because of their diverse regulatory roles in gene expression, cellular processes and the production of cytokines and chemokines in response to bacterial infections. The host utilizes lncRNAs as a defense mechanism to limit microbial pathogen invasion and replication. On the other hand, some host lncRNAs contribute to the establishment and maintenance of bacterial pathogen reservoirs within the host by promoting bacterial pathogen survival, replication, and dissemination. However, our understanding of host lncRNAs in the context of bacterial infections remains limited. This review focuses on the impact of host lncRNAs in shaping host-pathogen interactions, shedding light on their multifaceted functions in both host defense and bacterial survival, and paving the way for future research aimed at harnessing their regulatory potential for clinical applications.

Long non-coding RNA NEAT1 exacerbates NLRP3-mediated pyroptosis in allergic rhinitis through regulating the PTBP1/FOXP1 cascade

BACKGROUND

Allergic Rhinitis (AR) is a prevalent chronic non-infectious inflammation affecting the nasal mucosa. NLRP3-mediated pyroptosis of epithelial cells plays a pivotal role in AR pathogenesis. Herein, we evaluated the impact of the long non-coding RNA nuclear paraspeckle assembly transcript 1 (lncRNA NEAT1) on NLR family pyrin domain containing 3 (NLRP3)-mediated pyroptosis in AR.

METHODS

Nasal inflammation levels in ovalbumin (OVA)-induced AR mice were assessed using HE staining, and NLRP3 expression was evaluated through immunohistochemistry. ELISA was utilized to detect OVA-specific IgE, IL-6, IL-5, and inflammatory cytokines (IL-1β, IL-18). Human nasal epithelial cells (HNEpCs) stimulated with IL4/IL13 were used to analyze the mRNA and protein levels of associated genes utilizing RT-qPCR and western blot, respectively. Cell viability and pyroptosis were assessed by CCK-8 and flow cytometry. The targeting relationship between NEAT1, PTBP1 and FOXP1 were analyzed by RIP and RNA pull down assays. FISH and IF analysis were performed to assess the co-localization of NEAT1 and PTBP1.

RESULTS

In both the AR mouse and cellular models, increased levels of NEAT1, PTBP1 and FOXP1 were observed. AR mice exhibited elevated inflammatory infiltration and pyroptosis, evidenced by enhanced expressions of OVA-specific IgE, IL-6, and IL-5, NLRP3, Cleaved-caspase 1, GSDMD-N, IL-1β and IL-18. Functional assays revealed that knockdown of PTBP1 or NEAT1 inhibited pyroptosis while promoting the proliferation of IL4/IL13-treated HNEpCs. Mechanistically, NEAT1 directly interacted with PTBP1, thereby maintaining FOXP1 mRNA stability. Rescue assays demonstrated that FOXP1 upregulation reversed the inhibitory effects of silencing NEAT1 or PTBP1 on IL4/IL13-stimulated pyroptosis activation in HNEpCs.

CONCLUSION

NEAT1 acts as a RNA scaffold for PTBP1, activating the PTBP1/FOXP1 signaling cascade, subsequently triggering NLRP3-mediated pyroptosis in HNEpCs, and ultimately promoting AR progression. These findings highlight some new insights into the pathogenesis of AR.

Single-cell and spatial transcriptomics of vulvar lichen sclerosus reveal multi-compartmental alterations in gene expression and signaling cross-talk

Vulvar diseases are a critical yet often neglected area of women's health, profoundly affecting patients' quality of life and frequently resulting in long-term physical and psychological challenges. Lichen sclerosus (LS) is a chronic inflammatory skin disorder that predominantly affects the vulva, leading to severe itching, pain, scarring, and an increased risk of malignancy. Despite its profound impact on affected individuals, the molecular pathogenesis of vulvar LS (VLS) is not well understood, hindering the development of FDA-approved therapies. Here, we utilize single-cell and spatial transcriptomics to analyze lesional and non-lesional skin from VLS patients, as well as healthy control vulvar skin. Our findings demonstrate histologic, cellular, and molecular heterogeneities within VLS, yet highlight unifying molecular changes across keratinocytes, fibroblasts, immune cells, and melanocytes in lesional skin. They reveal cellular stress and damage in fibroblasts and keratinocytes, enhanced T cell activation and cytotoxicity, aberrant cell-cell signaling, and increased activation of the IFN, JAK/STAT, and p53 pathways in specific cell types. Using both monolayer and organotypic culture models, we also demonstrate that knockdown of select genes, which are downregulated in VLS lesional keratinocytes, partially recapitulates VLS-like stress-associated changes. Collectively, these data provide novel insights into the pathogenesis of VLS, identifying potential biomarkers and therapeutic targets for future research.

Breaking the vicious cycle: Targeting the NLRP3 inflammasome for treating sepsis-associated encephalopathy

Sepsis-associated encephalopathy (SAE) is a collection of clinical syndromes resulting from sepsis and characterized by widespread brain dysfunction. The high prevalence of SAE has adverse outcomes on the clinical management and prognosis of sepsis patients. However, currently, there are no effective treatments to ameliorate SAE. The pathogenesis of SAE is complex, including neuroinflammation and microglia activation, destruction of the blood-brain barrier (BBB), neurotransmitter dysfunction, cerebral metabolism and mitochondrial impairment, accumulation of amyloid beta and tauopathy, complement activation, among others. Furthermore, these mechanisms intertwine with each other, further complicating the comprehension of SAE. Among them, neuroinflammation mediated by hyperactivated microglia is considered the primary etiology of SAE. This instigates a detrimental cycle wherein BBB permeability escalates, facilitating direct damage to the central nervous system (CNS) by various neurotoxic substances. Activation of the NLRP3 inflammasome, situated within microglia, can be triggered by diverse danger signals, leading to cell pyroptosis, apoptosis, and tauopathy. These complex processes intricately regulate the onset and progression of neuroinflammation. In this review, we focus on elucidating the inhibitory regulatory mechanism of the NLRP3 inflammasome in microglia, which ultimately manifests as suppression of the inflammatory response. Our ultimate objective is to augment comprehension regarding the role of microglial NLRP3 inflammasome as we explore potential targets for therapeutic interventions against SAE.

Long Non-coding RNA NEAT1 , NOD-Like Receptor Family Protein 3 Inflammasome, and Acute Kidney Injury

Key Points

Background

AKI is common in hospitalized patients and is associated with high mortality. Inflammation plays a key role in the pathophysiology of AKI. Long non-coding RNAs (lncRNAs) are increasingly recognized as regulators of the inflammatory and immune response, but its role in AKI remains unclear.

Methods

We explored the role of lncRNA nuclear-enriched abundant transcript 1 (NEAT1) in (1) a cross-sectional and longitudinal cohort of AKI in humans, (2) three murine models of septic and aseptic AKI, and (3) cultured C1.1 mouse kidney tubular cells.

Results

In humans, hospitalized patients with AKI (N=66) demonstrated significantly higher lncRNA NEAT1 levels in urinary sediment cells and buffy coat versus control participants (N=152) from a primary care clinic; among six kidney transplant recipients, NEAT1 levels were the highest immediately after transplant surgery, followed by a prompt decline to normal levels in parallel with recovery of kidney function. In mice with AKI induced by sepsis (by LPS injection or cecal ligation and puncture) and renal ischemia-reperfusion, kidney tubular Neat1 was increased versus sham-operated mice. Knockdown of Neat1 in the kidney using short hairpin RNA preserved kidney function and suppressed overexpression of the AKI biomarker neutrophil gelatinase-associated lipocalin, leukocyte infiltration, and both intrarenal and systemic inflammatory cytokines IL-6, CCL-2, and IL-1β. In LPS-treated C1.1 cells, Neat1 was overexpressed by TLR4/NF-κB signaling and translocated from the cell nucleus into the cytoplasm where it promoted activation of nucleotide oligomerization domain-like receptor family protein 3 inflammasomes by binding with the scaffold protein receptor of activated protein C kinase 1. Silencing Neat1 ameliorated LPS-induced cell inflammation, whereas its overexpression upregulated IL-6 and CCL-2 expression even without LPS stimulation.

Conclusions

Our findings demonstrate a pathogenic role of NEAT1 induction in human and mice during AKI with alleviation of kidney injury in three experimental models of septic and aseptic AKI after knockdown of Neat1. LPS/TLR4-induced Neat1 overexpression in tubular epithelial cells increased the inflammatory response by binding with the scaffold protein, receptor of activated protein C kinase 1, to activate nucleotide oligomerization domain-like receptor family protein 3 inflammasomes.

Illuminating the pathogenic role of SARS-CoV-2: Insights into competing endogenous RNAs (ceRNAs) regulatory networks

The appearance of SARS-CoV-2 in 2019 triggered a significant economic and health crisis worldwide, with heterogeneous molecular mechanisms that contribute to its development are not yet fully understood. Although substantial progress has been made in elucidating the mechanisms behind SARS-CoV-2 infection and therapy, it continues to rank among the top three global causes of mortality due to infectious illnesses. Non-coding RNAs (ncRNAs), being integral components across nearly all biological processes, demonstrate effective importance in viral pathogenesis. Regarding viral infections, ncRNAs have demonstrated their ability to modulate host reactions, viral replication, and host-pathogen interactions. However, the complex interactions of different types of ncRNAs in the progression of COVID-19 remains understudied. In recent years, a novel mechanism of post-transcriptional gene regulation known as "competing endogenous RNA (ceRNA)" has been proposed. Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and viral ncRNAs function as ceRNAs, influencing the expression of associated genes by sequestering shared microRNAs. Recent research on SARS-CoV-2 has revealed that disruptions in specific ceRNA regulatory networks (ceRNETs) contribute to the abnormal expression of key infection-related genes and the establishment of distinctive infection characteristics. These findings present new opportunities to delve deeper into the underlying mechanisms of SARS-CoV-2 pathogenesis, offering potential biomarkers and therapeutic targets. This progress paves the way for a more comprehensive understanding of ceRNETs, shedding light on the intricate mechanisms involved. Further exploration of these mechanisms holds promise for enhancing our ability to prevent viral infections and develop effective antiviral treatments.

Combination MEG3 lncRNA and Ciprofloxacin dramatically decreases cell migration and viability as well as induces apoptosis in GC cells in vitro

Gastric cancer (GC) is a prominent cause of cancer-related mortality worldwide. Long noncoding RNA (lncRNA) maternal expression gene3 (MEG3) participates in numerous signaling pathways by targeting the miRNA-mRNA axis. Studies on human tumors have demonstrated that the antibiotic Ciprofloxacin induces cell cycle changes, programmed cell death, and growth suppression. In this study, we transfected MEG3 lncRNA and Ciprofloxacin into the MKN-45 GC cell line. qRT-PCR was employed to evaluate the effects on the specific microRNA and mRNA. The wound healing test, MTT assay, and flow cytometry were used to assess the impact of their administration on cell migration, viability, and apoptosis, respectively. Research showed that miR-147 expression fell even more after MEG3 lncRNA transfection, leading to an increase in B-cell lymphoma 2 (BCL-2) levels. Ciprofloxacin transfection did not significantly affect the axis, except for MEG3, which led to its slight upregulation. MEG3 lncRNA inhibited the migration of MKN-45 cells compared to the control group. When MEG3 lncRNA was coupled with Ciprofloxacin, there was a significant reduction in cell migration compared to untreated groups and controls. MTT assay and flow cytometry demonstrated that MEG3 lncRNA decreased cell viability and triggered apoptosis. Simultaneous administration of MEG3 lncRNA and Ciprofloxacin revealed a significant reduction in cell viability caused by increased apoptosis obtained from MTT or flow cytometry assays. Modulating the miR-147-BCL-2 axis decreases cell migration and survival while promoting cell death. In conclusion, combining MEG3 lncRNA with Ciprofloxacin may be an effective therapeutic approach for GC treatment by influencing the miR-14-BCl-2 axis, resulting in reduced cell viability, migration, and increased apoptosis.