RNA Editing Research Articles

A Novel Prognostic Risk Score Model Based on RNA Editing Level in Lower-Grade Glioma

BackgroundLower-grade glioma (LGG) refers to WHO grade 2 and 3 gliomas. Surgery combined with radiotherapy and chemotherapy can significantly improve the prognosis of LGG patients, but tumor progression is still unavoidable. As a form of posttranscriptional regulation, RNA editing (RE) has been reported to be involved in tumorigenesis and progression and has been intensively studied recently. MethodsSurvival data and RE data were subjected to univariate and multivariate Cox regression analysis and lasso regression analysis to establish an RE risk score model. A nomogram combining the risk score and clinicopathological features was built to predict the 1-, 3-, and 5-year survival probability of patients. The relationship among ADAR1, SOD2 and SOAT1 was verified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) ResultsA risk model associated with RE was constructed and patients were divided into different risk groups based on risk scores. The model demonstrated strong prognostic capability, with the area under the ROC curve (AUC) values of 0.882, 0.938, and 0.947 for 1-, 3-, and 5-year survival predictions, respectively. Through receiver operating characteristic curve (ROC) curves and calibration curves, it was verified that the constructed nomogram had better performance than age, grade, and risk score in predicting patient survival probability. Apart from this functional analysis, the results of correlation analyses between risk differentially expressed genes (RDEGs) and RE help us to understand the underlying mechanism of RE in LGG. ADAR may regulate the expression of SOD2 and SOAT1 through gene editing. ConclusionIn conclusion, this study establishes a novel and accurate 17-RE model and a nomogram for predicting the survival probability of LGG patients. ADAR may affect the prognosis of glioma patients by influencing gene expression.

REMR: Identification of RNA Editing-mediated MiRNA Regulation in Cancers

Dysregulation of adenosine-to-inosine (A-to-I) RNA editing has been implicated in cancer progression. However, a comprehensive understanding of how A-to-I RNA editing is incorporated into miRNA regulation to modulate gene expression in cancer remains unclear, given the lack of effective identification methods. To this end, we introduced an information theory-based algorithm named REMR to systematically identify 12,006 A-to-I RNA editing-mediated miRNA regulatory triplets (RNA editing sites, miRNAs, and genes) across ten major cancer types based on multi-omics profiling data from The Cancer Genome Atlas (TCGA). Through analyses of functional enrichment, transcriptional regulatory networks, and protein-protein interaction (PPI) networks, we showed that RNA editing-mediated miRNA regulation potentially affects critical cancer-related functions, such as apoptosis, cell cycle, drug resistance, and immunity. Furthermore, triplets can serve as biomarkers for classifying cancer subtypes with distinct prognoses or drug responses, highlighting the clinical relevance of such regulation. In addition, an online resource (http://www.jianglab.cn/REMR/) was constructed to support the convenient retrieval of our findings. In summary, our study systematically dissected the RNA editing-mediated miRNA regulations, thereby providing a valuable resource for understanding the mechanism of RNA editing as an epitranscriptomic regulator in cancer.

Transcriptome and molecular evidence of HvMORF8 conferring drought-tolerance in barley

Drought is one of the most devastating abiotic stresses worldwide, which severely limits crop yield. Tibetan wild barley is a treasure trove of useful genes for crop improvement including drought tolerance. Here, we detected large-scale changes of gene expression in response to drought stress with a substantial difference among contrasting Tibetan barley genotypes XZ5 (drought-tolerant), XZ54 (drought-sensitive) and cv. Tadmor (drought-tolerant). Drought stress led to upregulations of 142 genes involved in transcription, metabolism, protein synthesis, stress defense, transport and signal transduction in XZ5, but those genes were down-regulated or unchanged in XZ54 and Tadmor. We identified and functionally characterized a novel multiple organellar RNA editing factors 8 (HvMORF8), which was up-regulated by drought stress in XZ5, but unchanged in XZ54 and Tadmor under drought stress. Phylogenetic analysis showed that orthologues of HvMORF8 can be traced back to the closest gymnosperm species such as Cycas micholitzii, implicating a potential evolutionary origin for MORF8 from a common ancestor in early seed plants. Virus-induced HvMORF8 silencing in XZ5 led to hypersensitivity to drought stress, demonstrating it is a positive regulator of drought tolerance in barley. RNA sequencing of BSMV:HvMORF8 and control plants reveals that silencing of HvMORF8 suppresses genes involved in osmolytes transport, cell wall modification and antioxidants, resulting in water metabolism disorder and overaccumulation of reactive oxygen species (ROS) under drought stress. Therefore, we propose HvMORF8-mediated regulatory drought tolerance mechanisms at transcriptomic level in XZ5, providing new insight into the genetic basis of plastid RNA editing function of HvMORF8 for barley drought tolerance.

Role of apoptosis repressor with caspase recruitment domain in human health and chronic diseases.

Apoptosis repressor with caspase recruitment domain (ARC) is a highly potent and multifunctional suppressor of various types of programmed cell death (PCD) (e.g. apoptosis, necroptosis, and pyroptosis) and plays a key role in determining cell fate. Under physiological conditions, ARC is predominantly expressed in terminally differentiated cells, such as cardiomyocytes and skeletal muscle cells. Its expression and activity are tightly controlled by a complicated system consisting of transcription factor (TF), non-coding RNA (ncRNA), and post-translational modification (PTM). ARC dysregulation has been shown to be closely associated with many chronic diseases, including cardiovascular disease, cancer, diabetes, and neurodegenerative disease. However, the detailed mechanisms of ARC involved in the progression of these diseases remain unclear to a large extent. In this review, we mainly focus on the regulatory mechanisms of ARC expression and activity and its role in PCD. We also discuss the underlying mechanisms of ARC in health and disease and highlight the potential implications of ARC in the clinical treatment of patients with chronic diseases. This information may assist in developing ARC-based therapeutic strategies for patients with chronic diseases and expand researchers' understanding of ARC.

Long-term therapeutic efficacy and safety profiles of hpCas13d RNA editing in treating early-onset hypertrophic cardiomyopathy

AimsThrough evolving a precise RNA nuclease, hpCas13d, we have successfully inhibited hypertrophic cardiomyopathy in a compound heterozygous model. However, further investigation is needed to assess the long-term therapeutic effects and safety profiles of hpCas13d treatment. Materials and methodsAAV-hpCas13d[RQ] was subcutaneously injected into neonatal Myh6RH/RQ mice. Sequential echocardiography analyses were conducted at 4 months and 12 months to evaluate the sustained therapeutic effects of hpCas13d. Electrocardiography was employed to assess cardiac arrhythmias, and mice were euthanized at 12 months. Quantification of Myh6RQ degradation induced by hpCas13d[RQ] was performed using digital droplet PCR and cDNA sequencing. Histological analysis, RNA sequencing, and proteomic analyses were utilized to examine the inhibitory effects on pathological phenotypes and downstream signaling pathways. Biodistribution, tissue damage, and host immune response to AAV-hpCas13d[RQ] were assessed to evaluate long-term safety profiles. Key findingsThe allele-specific RNA degradation persisted for 12 months in AAV-hpCas13d[RQ]-treated Myh6RH/RQ mice. Partial degradation of pathogenic Myh6RQ transcripts proved adequate for the long-term inhibition of cardiac hypertrophy, arrhythmias, fibrosis, and cellular apoptosis in Myh6RH/RQ mice. RNA sequencing and proteomic analyses revealed that hpCas13d[RQ] treatment impeded hypertrophy and fibrosis, mitochondrial dysfunction, and abnormalities in ion channels downstream of mutant Myh6. Prolonged treatment with AAV-hpCas13d from the neonatal stage did not induce significant tissue damage, liver toxicity, humoral responses, or cellular immune reactions against the AAV9 capsid and bacterial hpCas13d. SignificanceThese results underscore the promising translational potential of AAV-hpCas13d in treating cardiovascular diseases and advancing in vivo gene therapy.

Enhancing Radiofrequency Ablation for Hepatocellular Carcinoma: Nano-Epidrug Effects on Immune Modulation and Antigenicity Restoration.

Radiofrequency ablation (RFA), a critical therapy for hepatocellular carcinoma (HCC), carries a significant risk of recurrence and metastasis, particularly owing to mechanisms involving immune evasion and antigen downregulation via epigenetic modifications. This study introduces a "nano-epidrug" named MFMP. MFMP, which is composed of hollow mesoporous manganese dioxide (MnO2) nanoparticles, FIDAS-5 as an MAT2A inhibitor, macrophage membrane, and anti-PD-L1 (aPD-L1), targets HCC cells. By selectively binding to these cells, MFMP initially reverses immune suppression via PD-L1 inhibition. After endocytosis, MFMP disassembles in the tumor microenvironment, releasing FIDAS-5 and Mn2+. FIDAS-5 prevents cGAS methylation, whereas Mn2+ aids STING pathway restoration. In addition, FIDAS-5 reduces m6A RNA modification, suppressing EGFR expression. These changes enhance HCC antigenicity to promote cytotoxic T cell recognition and cytotoxic killing. Furthermore, MFMP mediates immunogenic cell death in HCC by synergizing with RFA through cGAS DNA demethylation, EGFR mRNA demethylation, and TBK1 protein phosphorylation, thereby inhibiting recurrence and metastasis and enhancing immune memory. Thus, MFMP is a potential adjunctive therapy requiring clinical validation.

High-throughput detection of RNA modifications at single base resolution.

RNA is modified by > 170 chemical modifications that affect its structure and function. Accordingly, RNA modifications have been implicated in regulation of gene expression and cellular outcomes in a variety of species spanning the phylogenetic tree. The study of RNA modifications is accelerated by generation of high-throughput methods for detecting RNA modifications at single base resolution. Here, we review recent advancement in next generation sequencing based approaches for detection of 14 distinct RNA modifications present in rRNA, tRNA and mRNA. We further outline the molecular and computational principles underlying currently available methods.

Abstract PR013: Identification, therapeutic potential, and regulatory networks of tumor suppressing miRNAs in angiosarcoma

Abstract Angiosarcoma (AS) is an aggressive cancer of endothelial cells arising in the blood and lymphatic vasculature. Among all the rare soft tissue sarcomas, AS patients have some of the worst outcomes, with an estimated 5-year survival rate of only 30%. In mouse models, we discovered that endothelial loss of miRNAs through the conditional deletion of Dicer1 leads to AS development. Since most cells, and even most cancer cells require some level of miRNA expression for survival, this demonstrates that endothelial cells are uniquely sensitive to miRNA loss mediated transformation. Consistent with this finding we have found that Dgcr8 deletion with aP2-Cre phenocopies Dicer1 loss resulting in AS with 100% penetrance. This implicates miRNAs as critical tumor suppressors in AS. Thus, we tested the repurposing of the antibiotic, enoxacin as an anticancer therapeutic based on its known potential to enhance miRNA processing. Indeed, enoxacin significantly reduces AS cell proliferation and migration. Small RNA-sequencing revealed that several known tumor suppressing miRNAs were increased in abundance following enoxacin treatment. To discover other miRNAs critical in AS, we conducted an unbiased CRISPR-Cas9 screen with a miRNA specific gRNA library and identified several potential candidates. Among these, our preliminary data indicates miR-410 as a potent tumor suppressor. To determine the miRNA and mRNA target interactome of these miRNAs in AS, we are utilizing AgoTRIBE. This method fuses the Ago2 miRNA effector protein to the RNA editing domain of ADAR2 to generate RNA edits on transcripts that are associated with Ago2-miRNAs as determined by RNA-seq. This work will further utilize in vitro and in vivo tools to dissect the underlying biology and role of these tumor suppressing miRNAs in AS. We aim to leverage these findings to develop novel strategies for therapeutic interventions, including miRNA-based approaches that may improve patient outcomes. Citation Format: Bozhi Liu, Ant Murphy, Annaleighh Benton, Lauren E. Gartenhaus, Jason A Hanna. Identification, therapeutic potential, and regulatory networks of tumor suppressing miRNAs in angiosarcoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr PR013.

Abstract I006: Programmable RNA sensors for internal states and external cues in living cells

Abstract Cell and gene therapies against cancer could be empowered by sensors that produce proteins in response to specific intracellular markers (e.g., expressing a cytotoxic payload in response to oncogenes) or extracellular cues (e.g., expressing a chimeric antigen receptor only when T cells are in the tumor microenvironment). An emerging delivery modality is in vitro transcribed mRNA, which holds the promise of superior safety and affordability than more conventional DNA vectors. While synthetic biology tools have predominantly relied on DNA-level regulations, here I will share two sensor designs uniquely compatible with mRNA delivery. First, for intracellular markers, a promising strategy is sensing mRNA transcripts. It is now straightforward to obtain single-cell transcriptomics, which are highly informative of cell type/state. If we can build RNA sensors to output arbitrary proteins in direct response to specific RNAs, we will access virtually any cell type/state for research and therapy. Furthermore, RNA base pairing would facilitate programmable designs. Previous RNA sensors relied on base pairing-induced conformational changes of RNA, and have met with limited success in mammalian cells. As an alternative strategy, we took advantage of endogenous ADAR (adenosine deaminases acting on RNA) enzymes that specifically edit adenosines to inosines (treated as guanosines during translation) in dsRNA, and created RADAR (RNA sensing using ADAR, Kaseniit et al., 2023). RADAR relies on the formation of dsRNA between the sensor RNA we introduce and the endogenous input RNA we’d like to detect; ADAR then edits a strategically positioned stop codon (UAG) into a tryptophan codon (UIG), enabling the translation of the downstream output coding sequence. We validated and optimized RADAR, and reported its compatibility with human/mouse transcriptomes. We showed that RADAR is programmable and modular. It also uniquely enables compact implementation of AND logic, important for integrating the inputs from multiple markers and unambiguously identifying cells of interest. We have since demonstrated RADAR in a variety of contexts including cancer lines with an elevated oncogene. Second, while transcripts mark cell types/states, extracellular ligands reflect the other key aspect that payload production could be conditioned on – the microenvironment. Although our field has plenty of synthetic receptors to offer when it comes to sensing ligands, all previously engineered modular ones require DNA-level operation. Inspired by the power of ADAR editing, we created LIDAR (Ligand-Induced Dimerization Activating RNA editing, Zhang & Mille et al., 2024). LIDAR brings an attenuated ADAR to the proximity of a stop codon in a ligand-dependent fashion, and is compatible with diverse inputs, outputs, and cellular contexts. We are in the process of demonstrating RADAR and LIDAR to improve cell therapies and enable non-invasive diagnostics. Citation Format: Xiaojing Gao. Programmable RNA sensors for internal states and external cues in living cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr I006.

Abstract PR001: Targeting mRNA methyltransferase in RNA-dependent DNA repair in cancer therapy

Abstract The treatment of many solid tumors presents significant challenges with chemotherapy, radiation therapy, and the limited effectiveness of immunotherapy. Targeted therapy offers a promising approach, yet the lack of validated targets limits its applicability across the spectrum of solid tumors. Our past studies have revealed that an R-loop and mRNA-dependent DNA repair (RDDR) pathway, induced by damage at the transcribed regions of the genome, contributes to cell survival and drug resistance in cancer cells. This is particularly due to the high levels of transcription and DNA damage in these cells. We identified the RNA methyltransferase TRDMT1 as the primary modifier of mRNA methyl-5-cytosine in the RDDR pathway. Overcoming technical difficulties in monitoring RNA modifications, we developed the first TRDMT1 inhibitor (TRDMT1i) using in-house built cell-based and in vitro assays. We have identified highly potent and specific lead compounds that significantly reduce TRDMT1 activity at nanomolar concentrations. Our current lead TRDMT1 inhibitors meets most of the criteria that are required for optimal lead. Initial assessments involving the screening of normal and cancer cell lines, xenograft models, and patient specimens indicate that TRDMT1i sensitizes tumors with genomic instability when used as monotherapy. We aim to develop TRDMT1i as an investigational new drug (IND) for future clinical trials, initially targeting ovarian cancer as a monotherapy or in combination therapy for first-line maintenance and systematic therapy. Our goal is to pioneer the discovery of the RDDR pathway, leading to the development of innovative platforms and next-generation medications to revolutionize the targeting of mRNA modifications in cancer treatment. Citation Format: Li Lan. Targeting mRNA methyltransferase in RNA-dependent DNA repair in cancer therapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr PR001.

Abstract A039: A sensitive tool for the detection of RNA modifications in blood samples

Abstract The epitranscriptome is the set of chemical modifications applied naturally to RNA to regulate seemingly all aspects of its function, including splicing, translation initiation and fidelity, trafficking, RNA folding and stability, and transcript lifetime. Detecting RNA in blood reliably continues to be a challenge due to its labile nature, and detecting RNA modifications is an even greater challenge. For this reason, current liquid biopsy approaches concentrate on determining the mutational burden in cell-free DNA and do not harness the potential of cfRNA. In contrast to cfDNA, cfRNA is a biomarker for dynamic events that are known to occur at early stages of carcinogenesis, such as alterations to transcriptional profiles and other aspects of the regulatory state of cells. In many RNA species, the modification state is linked to the RNA lifecycle, thus providing important insights into cell state. For example, pre-miRNA is modified before miRNA maturation, tRNA cleavage is initiated by changes to the modification pattern and mRNA is decapped for storage in stress granules. AlidaBio is introducing the EpiPlex platform, an assay platform with an integrated bioinformatics solution that is designed for ultra-low RNA input and has been tested with blood samples. In addition to its sensitivity, the EpiPlex platform has the advantage of detecting multiple RNA modifications in the same reaction, enabling users to elucidate how RNA modifications act in concert to fine-tune RNA function. The approach uses targeted, multiplexed barcoding to reveal co-localization of modifications on the same molecule and to provide semi-quantitative data on mod abundance. This sensitive, multiplexed target detection has the potential to advance the field of RNA liquid biopsy with new biomarker discovery. Citation Format: Andrew Price, Zachary Miles, Byron Purse, Gudrun Stengel. A sensitive tool for the detection of RNA modifications in blood samples [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A039.

Charting and probing the activity of ADARs in human development and cell-fate specification.

Adenosine deaminases acting on RNA (ADARs) impact diverse cellular processes and pathological conditions, but their functions in early cell-fate specification remain less understood. To gain insights here, we began by charting time-course RNA editing profiles in human organs from fetal to adult stages. Next, we utilized hPSC differentiation to experimentally probe ADARs, harnessing brain organoids as neural specific, and teratomas as pan-tissue developmental models. We show that time-series teratomas faithfully recapitulate fetal developmental trends, and motivated by this, conducted pan-tissue, single-cell CRISPR-KO screens of ADARs in teratomas. Knocking out ADAR leads to a global decrease in RNA editing across all germ-layers. Intriguingly, knocking out ADAR leads to an enrichment of adipogenic cells, revealing a role for ADAR in human adipogenesis. Collectively, we present a multi-pronged framework charting time-resolved RNA editing profiles and coupled ADAR perturbations in developmental models, thereby shedding light on the role of ADARs in cell-fate specification.

Alterations Expression of Key RNA Methylation (m6A) Enzymes in Testicular Tissue of Rats with Induced Varicocele.

Epigenetics impacts male fertility and reproductive disorders. RNA modifications, like m6A, influence RNA metabolism. Varicocele contributes to male infertility, and oxidative stress affects sperm function. This study investigates the expression of key RNA modification enzymes in a rat varicocele model, aiming to elucidate the relationship between varicocele, oxidative stress, and fertility. Fifteen male Wistar rats were divided into Control, Sham, and Varicocele induction groups. Varicocele was induced in the rats surgically. After 8 weeks, testicular tissues and sperm were collected for analysis, including histopathological assessment and evaluation of sperm parameters, functional tests, and gene expression of key RNA modification enzymes: METTL3 as a writer, ALKBH5 and FTO as erasers, and YTHDF2 as a reader involved in recognizing m6A-modified RNA using qRT-PCR. One-way ANOVAwithpost-hoc Tukey HSDwas used forcomparing tests within groups. Varicocele induction resulted in histological changes in testicular tissues, including irregularly variable-sized seminiferous tubules. Sperm parameters were significantly affected, with lower concentration, motility, and higher percentage of abnormal sperm in the varicocele group. Increased levels of oxidative stress markers (Sperm lipid peroxidation, and intracytoplasmic ROS) and sperm DNA damage were observed, indicating the presence of oxidative stress in varicocele. Moreover, the expression of key enzymes involved in RNA metabolism was downregulated in the varicocele group. These findings highlight the detrimental impact of varicocele on testicular health, sperm quality, and gene expression, providing insights into the underlying mechanisms of male infertility associated with varicocele.

Comprehensive analysis of the relationship between RNA modification writers and immune microenvironment in head and neck squamous cell carcinoma.

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. Four types of RNA modification writers (m6A, m1A, A-I editing, and APA) are widely involved in tumorigenesis and the TME. We aimed to comprehensively explore the role of the four RNA modification writers in the progression and immune microenvironment of HNSCC. We first obtained transcription profile data and transcriptional variation of the four types of RNA modification writers from The Cancer Genome Atlas (TCGA) database. HNSCC patients in TCGA dataset were divided into different clusters based on the four types of RNA modification writers. Univariate Cox and Least absolute shrinkage and selection operator (LASSO) analyses were performed to conduct a Writer-score scoring system, which was successfully verified in the GSE65858 dataset and our clinical sample dataset. Finally, we evaluated the relationship between different RNA modification clusters (Writer-score) and immunological characteristics of HNSCC. Two different RNA modification clusters (A and B) were obtained. These RNA modification clusters (Writer-score) were strongly associated with immunological characteristics (immunomodulators, cancer immunity cycles, infiltrating immune cells (TIICs), inhibitory immune checkpoints, and T cell inflamed score (TIS)) of HNSCC. This study identified two different RNA modification clusters and explored the potential relationship between RNA modification clusters (Writer-score) and immunological characteristics, offering a new theoretical basis for precision immunotherapy in patients with HNSCC.

Abstract 4137846: Smooth muscle expression of RNA editing enzyme ADAR1 controls vascular integrity and progression of atherosclerosis

Mapping the genomic architecture of complex disease has been predicated on the understanding that genetic variants influence disease risk through modifying gene expression. However, recent discoveries have revealed that a significant burden of disease heritability in common autoinflammatory disorders and coronary artery disease is mediated through genetic variation modifying post-transcriptional modification of RNA through adenosine-to-inosine (A-to-I) RNA editing. This common RNA modification is catalyzed by ADAR enzymes, where ADAR1 edits specific immunogenic double stranded RNA (dsRNA) to prevent activation of the double strand RNA (dsRNA) sensor MDA5 ( IFIH1 ) and stimulation of an interferon stimulated gene (ISG) response. Multiple lines of human genetic data indicate impaired RNA editing and increased dsRNA sensing to be an important mechanism of coronary artery disease (CAD) risk. Here, we provide a crucial link between observations in human genetics and mechanistic cell biology leading to progression of CAD. Through analysis of human atherosclerotic plaque, we implicate the vascular smooth muscle cell (SMC) to have a unique requirement for RNA editing, and that ISG induction occurs in SMC phenotypic modulation, implicating MDA5 activation. Through culture of human coronary artery SMCs, generation of a conditional SMC specific Adar1 deletion mouse model on a pro-atherosclerosis background, and with incorporation of single cell RNA sequencing cellular profiling, we further show that Adar1 controls SMC phenotypic state, is required to maintain vascular integrity, and controls progression of atherosclerosis and vascular calcification. Our data implicates MDA5 activation to occur in SMC phenotypic modulation and accelerates formation of chondromyocytes in a distinct cellular lineage trajectory — indicating a cell type and context specific requirement of RNA editing. Through this work, we describe a fundamental new mechanism of CAD, where RNA editing and sensing of dsRNA in a cell type and context specific mechanism mediates disease progression, bridging our understanding of human genetics and disease causality.

Current insights on m6A RNA modification in acute leukemia: therapeutic targets and future prospects

RNA modification is the critical mechanism for regulating post-transcriptional processes. There are more than 150 RNA modifications reported so far, among which N6-Methyladenosine is the most prevalent one. M6A RNA modification complex consists of ‘writers’, ‘readers’ and ‘erasers’ which together in a group catalyze, recognize and regulate the methylation process of RNA and thereby regulate the stability and translation of mRNA. The discovery of erasers also known as demethylases, revolutionized the research on RNA modifications as it revealed that this modification is reversible. Since then, various studies have focused on discovering the role of m6A modification in various diseases especially cancers. Aberrant expression of these ‘readers’, ‘writers’, and ‘erasers’ is found to be altered in various cancers resulting in disturbance of cellular homeostasis. Acute leukemias are the most common cancer found in pediatric patients and account for 20% of adult cases. Dysregulation of the RNA modifying complex have been reported in development and progression of hematopoietic malignancies. Further, targeting m6A modification is the new approach for cancer immunotherapy and is being explored extensively. This review provides detailed information about current information on the role of m6A RNA modification in acute leukemia and their therapeutic potential.

Processing of N-glycans in the ER and Golgi influences the production of surface sialylated glycoRNA.

Glycoconjugates, including glycans on proteins and lipids, have obtained significant attention due to their critical roles in both intracellular and intercellular biological functions and processes. Notably, recent discoveries have revealed the presence of glycosylated RNAs (glycoRNAs) on cell surfaces. Despite the well-characterized roles of RNA modifications, RNA glycosylation remains relatively unexplored. In this study, we investigate the relationship between N-glycosylation and RNA glycosylation. Using a recombinant Siglec11-Fc as a probe, we detected surface sialylated glycoRNAs in human cell lines and identified their dependency on the catalytic isoforms of the oligosaccharyltransferase (OST) complex, implicating STT3A-dependent protein glycosylation as a predominant contributor for affecting indirect generation of glycoRNAs. Additionally, perturbations in N-glycan biosynthesis pathways or changes in N-glycan structure impact surface sialylated glycoRNA levels, indicating a regulatory role of glycan metabolic pathways in RNA glycosylation. Together, our results underscore the intricate relationship between protein N-glycosylation and processing and RNA biology.

METTL3 alters capping enzyme expression and its activity on ribosomal proteins.

The 5' cap, catalyzed by RNA guanylyltransferase and 5'-phosphatase (RNGTT), is a vital mRNA modification for the functionality of mRNAs. mRNA capping occurs in the nucleus for the maturation of the functional mRNA and in the cytoplasm for fine-tuning gene expression. Given the fundamental importance of RNGTT in mRNA maturation and expression there is a need to further investigate the regulation of RNGTT. N6-methyladenosine (m6A) is one of the most abundant RNA modifications involved in the regulation of protein translation, mRNA stability, splicing, and export. We sought to investigate whether m6A could regulate the expression and activity of RNGTT. In this short report, we demonstrated that the 3'UTR of RNGTT mRNA is methylated with m6a by the m6A writer methyltransferase 3 (METTL3). Knockdown of METTL3 resulted in reduced protein expression of RNGTT. Sequencing of capped mRNAs identified an underrepresentation of ribosomal protein mRNA overlapping with 5' terminal oligopyrimidine (TOP) mRNAs, and genes are dysregulated when cytoplasmic capping is inhibited. Pathway analysis identified disruptions in the mTOR and p70S6K pathways. A reduction in RPS6 mRNA capping, protein expression, and phosphorylation was detected with METTL3 knockdown.

The interplay between epitranscriptomic RNA modifications and neurodegenerative disorders: Mechanistic insights and potential therapeutic strategies

AbstractNeurodegenerative disorders encompass a group of age‐related conditions characterized by the gradual decline in both the structure and functionality of the central nervous system (CNS). RNA modifications, arising from the epitranscriptome or RNA‐modifying protein mutations, have recently been observed to contribute significantly to neurodegenerative disorders. Specific modifications like N6‐methyladenine (m6A), N1‐methyladenine (m1A), 5‐methylcytosine (m5C), pseudouridine and adenosine‐to‐inosine (A‐to‐I) play key roles, with their regulators serving as crucial therapeutic targets. These epitranscriptomic changes intricately control gene expression, influencing cellular functions and contributing to disease pathology. Dysregulation of RNA metabolism, affecting mRNA processing and noncoding RNA biogenesis, is a central factor in these diseases. This review underscores the complex relationship between RNA modifications and neurodegenerative disorders, emphasizing the influence of RNA modification and the epitranscriptome, exploring the function of RNA modification enzymes in neurodegenerative processes, investigating the functional consequences of RNA modifications within neurodegenerative pathways, and evaluating the potential therapeutic advancements derived from assessing the epitranscriptome.

Quantitative detection of pseudouridine in RNA by mass spectrometry.

Pseudouridine (Ψ) is one of the most prevalent and dynamic modification in RNA, and was shown to evade the host immune response in mRNA vaccines. Despite its significance, the biological role of Ψ remains poorly understood as certain key limitations and challenges in the detection of Ψ are yet to be overcome. In account of this, we report the usage of a chemical labelling strategy for the first quantitative detection of Ψ by mass spectrometry. We demonstrate a labelling efficiency exceeding 99% in isolated yeast tRNAs hosting multiple Ψs. LC-MS/MS analysis enables precise mapping of Ψ at single-base resolution, while simultaneously capturing a wide array of additional post-transcriptional modifications, which is not achieved with current sequencing technologies. This advancement may help unravel the dynamics and biological implications of Ψ, shedding light on its interplay with other modifications and deepening our understanding of its functional role.