Insight into the complexity of male infertility: a multi-omics review

Male infertility is a reproductive disorder, accounting for 40-50% of infertility. Currently, in about 70% of infertile men, the cause remains unknown. With the introduction of novel omics and advancement in high-throughput technology, potential biomarkers are emerging. The main purpose of our work was to overview different aspects of omics approaches in association with idiopathic male infertility and highlight potential genes, transcripts, non-coding RNA, proteins, and metabolites worth further exploring. Using the Gene Ontology (GO) analysis, we aimed to compare enriched GO terms from each omics approach and determine their overlapping. A PubMed database screening for the literature published between February 2014 and June 2022 was performed using the keywords: male infertility in association with different omics approaches: genomics, epigenomics, transcriptomics, ncRNAomics, proteomics, and metabolomics. A GO enrichment analysis was performed using the Enrichr tool. We retrieved 281 global studies: 171 genomics (DNA level), 21 epigenomics (19 of methylation and two histone residue modifications), 15 transcriptomics, 31 non-coding RNA, 29 proteomics, two protein posttranslational modification, and 19 metabolomics studies. Gene ontology comparison showed that different omics approaches lead to the identification of different molecular factors and that the corresponding GO terms, obtained from different omics approaches, do not overlap to a larger extent. With the integration of novel omics levels into the research of idiopathic causes of male infertility, using multi-omic systems biology approaches, we will be closer to finding the potential biomarkers and consequently becoming aware of the entire spectrum of male infertility, their cause, prognosis, and potential treatment.

Crosstalk between m6A modification and non-coding RNAs in HCC

Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide, with high morbidity and occurrence. Although various therapeutic approaches have been rapidly developed in recent years, the underlying molecular mechanisms in the pathogenesis of HCC remain enigmatic. The N6-methyladenosine (m6A) RNA modification is believed to regulate RNA metabolism and further gene expression. This process is intricately regulated by multiple regulators, such as methylases and demethylases. Non-coding RNAs (ncRNAs) are involved in the regulation of the epigenetic modification, mRNA transcription and other biological processes, exhibiting crucial roles in tumor occurrence and development. The m6A-ncRNA interaction has been implicated in the malignant phenotypes of HCC and plays an important role in drug resistance. This review summarizes the effect of m6A-ncRNA crosstalk on HCC progression and their clinical implications as prognostic markers and therapeutic targets in this disease.

The relationship between the network of non-coding RNAs-molecular targets and N6-methyladenosine modification in tumors of urinary system

N6-methyladenosine (m6A) methylation, a prevalent eukaryotic post-transcriptional modification, is involved in multiple biological functions, including mediating variable splicing, RNA maturation, transcription, and nuclear export, and also is vital for regulating RNA translation, stability, and cytoplasmic degradation. For example, m6A methylation can regulate pre-miRNA expression by affecting both splicing and maturation. Non-coding RNA (ncRNA), which includes microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), does not encode proteins but has powerful impacts on transcription and translation. Conversely, ncRNAs may impact m6A methylation by affecting the expression of m6A regulators, including miRNAs targeting mRNA of m6A regulators, or lncRNAs, and circRNAs, acting as scaffolds to regulate transcription of m6A regulatory factors. Dysregulation of m6A methylation is common in urinary tumors, and the regulatory role of ncRNAs is also important for these malignancies. This article provides a systematic review of the role and mechanisms of action of m6A methylation and ncRNAs in urinary tumors.

Biological functions and clinical significance of tRNA-derived small fragment (tsRNA) in tumors: Current state and future perspectives

A new class of noncoding RNAs, tsRNAs are not only abundant in humans but also have high tissue specificity. Recently, an increasing number of studies have explored the correlations between tsRNAs and tumors, showing that tsRNAs can affect biological behaviors of tumor cells, such as proliferation, apoptosis and metastasis, by modulating protein translation, RNA transcription or posttranscriptional regulation. In addition, tsRNAs are widely distributed and stably expressed, which endows them with broad application prospects in diagnosing and predicting the prognosis of tumors, and they are expected to become new biomarkers. However, notably, the current research on tsRNAs still faces problems that need to be solved. In this review, we describe the characteristics of tsRNAs as well as their unique features and functions in tumors. Moreover, we also discuss the potential opportunities and challenges in clinical applications and research of tsRNAs.

Decoding the role of long non-coding RNAs in gallbladder cancer pathogenesis: A review focus on signaling pathways interplay

Gallbladder cancer (GBC) is one of the most aggressive types of biliary tree cancers and the commonest despite its rarity. It is infrequently diagnosed at an early stage, further contributing to its poor prognosis and low survival rate. The lethal nature of the disease has underlined a crucial need to discern the underlying mechanisms of GBC carcinogenesis which are still largely unknown. However, with the continual evolution in the research of cancer biology and molecular genetics, studies have found that non-coding RNAs (ncRNAs) play an active role in the molecular pathophysiology of GBC development. Dysregulated long non-coding RNAs (lncRNAs) and their interaction with intracellular signaling pathways contribute to malignancy and disease development. LncRNAs, a subclass of ncRNAs with over 200 nucleotides, regulate gene expression at transcriptional, translational, and post-translational levels and especially as epigenetic modulators. Thus, their expression abnormalities have been linked to malignancy and therapeutic resistance. lnsRNAs have also been found in GBC patients' serum and tumor tissue biopsies, highlighting their potential as novel biomarkers and for targeted therapy. This review will examine the growing involvement of lncRNAs in GBC pathophysiology, including related signaling pathways and their wider clinical use.

ciRS-7 and miR-7 regulate ischemia-induced neuronal death via glutamatergic signaling

Brain functionality relies on finely tuned regulation of gene expression by networks of non-coding RNAs (ncRNAs) such as the one composed by the circular RNA ciRS-7 (also known as CDR1as), the microRNA miR-7, and the long ncRNA Cyrano. We describe ischemia-induced alterations in the ncRNA network both in vitro and in vivo and in transgenic mice lacking ciRS-7 or miR-7. Our data show that cortical neurons downregulate ciRS-7 and Cyrano and upregulate miR-7 expression during ischemia. Mice lacking ciRS-7 exhibit reduced lesion size and motor impairment, while the absence of miR-7 alone results in increased ischemia-induced neuronal death. Moreover, miR-7 levels in pyramidal excitatory neurons regulate neurite morphology and glutamatergic signaling, suggesting a potential molecular link to the in vivo phenotype. Our data reveal the role of ciRS-7 and miR-7 in modulating ischemic stroke outcome, shedding light on the pathophysiological function of intracellular ncRNA networks in the brain.

Common changes in rat cortical gene expression after antidepressant drug treatment: Impacts on metabolism of polyamines, mRNA splicing, regulation of RAS by GAPs, neddylation and GPCR ligand binding

OBJECTIVES

This study sought to identify pathways affected by rat cortical RNA that were changed after treatment with fluoxetine or imipramine.

METHODS

We measured levels of cortical RNA in male rats using GeneChip® Rat Exon 1.0 ST Array after treatment with vehicle (0.9% NaCl), fluoxetine (10 mg/kg/day) or imipramine (20 mg/kg/day) for 28 days. Levels of coding and non-coding RNA in vehicle treated rats were compared to those in treated rats using ANOVA in JMP Genomics 13 and the Panther Gene Ontology Classification System was used to identify pathways involving the changed RNAs.

RESULTS

18,876 transcripts were detected; there were highly correlated changes in 1010 levels of RNA after both drug treatments that would principally affect the metabolism of polyamines, mRNA splicing, regulation of RAS by GAPs, neddylation and GPCR ligand binding. Using our previously published data, we compared changes in transcripts after treatment with antipsychotic and mood stabilising drugs.

CONCLUSIONS

Our study shows there are common, correlated, changes in coding and non-coding RNA in the rat cortex after treatment with fluoxetine or imipramine; we propose the pathways affected by these changes are involved in the therapeutic mechanisms of action of antidepressant drugs.

Research progress and potential application of microRNA and other non-coding RNAs in forensic medicine

At present, epigenetic markers have been extensively studied in various fields and have a high value in forensic medicine due to their unique mode of inheritance, which does not involve DNA sequence alterations. As an epigenetic phenomenon that plays an important role in gene expression, non-coding RNAs (ncRNAs) act as key factors mediating gene silencing, participating in cell division, and regulating immune response and other important biological processes. With the development of molecular biology, genetics, bioinformatics, and next-generation sequencing (NGS) technology, ncRNAs such as microRNA (miRNA), circular RNA (circRNA), long non-coding RNA (lncRNA), and P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) are increasingly been shown to have potential in the practice of forensic medicine. NcRNAs, mainly miRNA, may provide new strategies and methods for the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. In this review, we describe the research progress and application status of ncRNAs, mainly miRNA, and other ncRNAs such as circRNA, lncRNA, and piRNA, in forensic practice, including the identification of tissues and body fluids, cause-of-death analysis, time-related estimation, age estimation, and the identification of monozygotic twins. The close links between ncRNAs and forensic medicine are presented, and their research values and application prospects in forensic medicine are also discussed.

CD73 mitigates ZEB1 expression in papillary thyroid carcinoma

BACKGROUND

ZEB1, a core transcription factor involved in epithelial-mesenchymal transition (EMT), is associated with aggressive cancer cell behavior, treatment resistance, and poor prognosis across various tumor types. Similarly, the expression and activity of CD73, an ectonucleotidase implicated in adenosine generation, is an important marker of tumor malignancy. Growing evidence suggests that EMT and the adenosinergic pathway are intricately linked and play a pivotal role in cancer development. Therefore, this study focuses on exploring the correlations between CD73 and ZEB1, considering their impact on tumor progression.

METHODS

We employed CRISPR/Cas9 technology to silence CD73 expression in cell lines derived from papillary thyroid carcinoma. These same cells underwent lentiviral transduction of a reporter of ZEB1 non-coding RNA regulation. We conducted studies on cell migration using scratch assays and analyses of cellular speed and polarity. Additionally, we examined ZEB1 reporter expression through flow cytometry and immunocytochemistry, complemented by Western blot analysis for protein quantification. For further insights, we applied gene signatures representing different EMT states in an RNA-seq expression analysis of papillary thyroid carcinoma samples from The Cancer Genome Atlas.

RESULTS

Silencing CD73 expression led to a reduction in ZEB1 non-coding RNA regulation reporter expression in a papillary thyroid carcinoma-derived cell line. Additionally, it also mitigated ZEB1 protein expression. Moreover, the expression of CD73 and ZEB1 was correlated with alterations in cell morphology characteristics crucial for cell migration, promoting an increase in cell polarity index and cell migration speed. RNA-seq analysis revealed higher expression of NT5E (CD73) in samples with BRAF mutations, accompanied by a prevalence of partial-EMT/hybrid state signature expression.

CONCLUSIONS

Collectively, our findings suggest an association between CD73 expression and/or activity and the post-transcriptional regulation of ZEB1 by non-coding RNA, indicating a reduction in its absence. Further investigations are warranted to elucidate the relationship between CD73 and ZEB1, with the potential for targeting them as therapeutic alternatives for cancer treatment in the near future.

Comprehensive landscape and future perspectives of non-coding RNAs in esophageal squamous cell carcinoma, a bibliometric analysis from 2008 to 2023

Objectives: Summarize the progress and hot topic evolution of non-coding RNAs (ncRNAs) research in esophageal squamous cell carcinoma (ESCC) in recent years and predict future research directions. Methods: Relevant articles from the Web of Science until 31 October 2023 were obtained. Bibliometric analysis of included articles was performed using software (VOSviewer, CiteSpace, and Bibliometrix). The volume and citation of publications, as well as the country, institution, author, journal, keywords of the articles were used as variables to analyze the research trends and hot spot evolution. Results: 1,118 literature from 2008 to 2023 were retrieved from database, with 25 countries/regions, 793 institutions, 5,426 authors, 261 journals involved. Global cooperation was centered on China, Japan, and the United States. Zhengzhou University, an institution from China, had the highest publication. The most prolific author was Guo Wei, and the most prolific journal was Oncology Letters. Analysis of keywords revealed that the research in this field revolved around the role of ncRNAs in the occurrence, development, diagnosis, treatment, and prognosis of ESCC, mainly including micro RNAs, long non-coding RNAs, and then circular RNAs. Conclusion: Overall, research on ncRNAs in ESCC remains strong. Previous research has mainly focused on the basic research, with a focus on the mechanism of ncRNAs in the occurrence, development, diagnosis, treatment, and prognosis of ESCC. Combining current research with emerging disciplines to further explore its mechanisms of action or shifting the focus of research from preclinical research to clinical research based on diagnosis, treatment, and prognosis, will be the main breakthrough in this field in the future.

Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA

XIST noncoding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC-associated repressor protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of a human XIST-SPEN complex in vitro and identified novel sequence and structure determinants that may contribute to X chromosome silencing initiation. Binding of SPEN to XIST RNA requires RRM 4 of the protein, in contrast to the requirement of RRM 3 and RRM 4 for specific binding to SRA RNA. Measurements of SPEN binding to full-length, dimeric, trimeric, or other truncated versions of the A-repeat region revealed that high-affinity binding of XIST to SPEN in vitro requires a minimum of four A-repeat segments. SPEN binding to XIST A-repeat RNA changes the accessibility of the RNA at specific nucleotide sequences, as indicated by changes in RNA reactivity through chemical structure probing. Based on computational modeling, we found that inter-repeat duplexes formed by multiple A-repeats can present an unpaired adenosine in the context of a double-stranded region of RNA. The presence of this specific combination of sequence and structural motifs correlates with high-affinity SPEN binding in vitro. These data provide new information on the molecular basis of the XIST and SPEN interaction.

The pivotal role of long non-coding RNAs as potential biomarkers and modulators of chemoresistance in ovarian cancer (OC)

Ovarian cancer (OC) is a fatal gynecological disease that is often diagnosed at later stages due to its asymptomatic nature and the absence of efficient early-stage biomarkers. Previous studies have identified genes with abnormal expression in OC that couldn't be explained by methylation or mutation, indicating alternative mechanisms of gene regulation. Recent advances in human transcriptome studies have led to research on non-coding RNAs (ncRNAs) as regulators of cancer gene expression. Long non-coding RNAs (lncRNAs), a class of ncRNAs with a length greater than 200 nucleotides, have been identified as crucial regulators of physiological processes and human diseases, including cancer. Dysregulated lncRNA expression has also been found to play a crucial role in ovarian carcinogenesis, indicating their potential as novel and non-invasive biomarkers for improving OC management. However, despite the discovery of several thousand lncRNAs, only one has been approved for clinical use as a biomarker in cancer, highlighting the importance of further research in this field. In addition to their potential as biomarkers, lncRNAs have been implicated in modulating chemoresistance, a major problem in OC. Several studies have identified altered lncRNA expression upon drug treatment, further emphasizing their potential to modulate chemoresistance. In this review, we highlight the characteristics of lncRNAs, their function, and their potential to serve as tumor markers in OC. We also discuss a few databases providing detailed information on lncRNAs in various cancer types. Despite the promising potential of lncRNAs, further research is necessary to fully understand their role in cancer and develop effective strategies to combat this devastating disease.

LINC01094 promotes human nasal epithelial cell epithelial-to-mesenchymal transition and pyroptosis via upregulating HMGB1

BACKGROUND

Excessive epithelial-to-mesenchymal transition (EMT) of nasal epithelial cells (NECs) play a prominent role in chronic rhinosinusitis with nasal polyps (CRSwNP) pathogenesis. Long intergenic non-coding RNA 01094 (LINC01094) was previously reported to be overexpressed in CRSwNP, while the regulatory mechanism by which LINC01094 regulates CRSwNP progression remains unclear. Our study aimed to investigate the role of LINC01094 in CRSwNP development.

METHODS

hNEC were isolated from tissues of controls and CRSwNP patients and stimulated with interleukin (IL)-13. 3-(4, 5-Dimethylthiazolyl2)-2, 5-diphenyltetrazolium bromide (MTT) assay was employed to analyze hNEC viability. Flow cytometry was employed to analyze pyroptosis. Immunofluorescence was employed to analyze Snail nuclear translocation. The interactions between LINC01094, fused in sarcoma (FUS) and high mobility group box-1 (HMGB1) were analyzed by RNA immunoprecipitation (RIP) and RNA pull-down assays.

RESULTS

LINC01094 and EMT-related proteins were markedly upregulated in nasal polyp tissues of CRSwNP. LINC01094 knockdown inhibited IL-13-induced hNEC EMT and pyroptosis. LINC01094 promoted HMGB1 expression in CRSwNP by binding with FUS. HMGB1 promoted Snail nuclear import in GSK-B phosphorylation-dependent manner.

CONCLUSION

LINC01094 facilitated hNEC EMT and pyroptosis in CRSwNP by activating the HMGB1/GSK-B Snail axis, which suggested that LINC01094 might serve as a biomarker and therapeutic target in CRSwNP.

GATLGEMF: A graph attention model with line graph embedding multi-complex features for ncRNA-protein interactions prediction

Non-coding RNA (ncRNA) plays an important role in many fundamental biological processes, and it may be closely associated with many complex human diseases. NcRNAs exert their functions by interacting with proteins. Therefore, identifying novel ncRNA-protein interactions (NPIs) is important for understanding the mechanism of ncRNAs role. The computational approach has the advantage of low cost and high efficiency. Machine learning and deep learning have achieved great success by making full use of sequence information and structure information. Graph neural network (GNN) is a deep learning algorithm for complex network link prediction, which can extract and discover features in graph topology data. In this study, we propose a new computational model called GATLGEMF. We used a line graph transformation strategy to obtain the most valuable feature information and input this feature information into the attention network to predict NPIs. The results on four benchmark datasets show that our method achieves superior performance. We further compare GATLGEMF with the state-of-the-art existing methods to evaluate the model performance. GATLGEMF shows the best performance with the area under curve (AUC) of 92.41% and 98.93% on RPI2241 and NPInter v2.0 datasets, respectively. In addition, a case study shows that GATLGEMF has the ability to predict new interactions based on known interactions. The source code is available at https://github.com/JianjunTan-Beijing/GATLGEMF.

tRNA-derived fragments: mechanism of gene regulation and clinical application in lung cancer

Lung cancer, being the most widespread and lethal form of cancer globally, has a high incidence and mortality rate primarily attributed to challenges associated with early detection, extensive metastasis, and frequent recurrence. In the context of lung cancer development, noncoding RNA molecules have a crucial role in governing gene expression and protein synthesis. Specifically, tRNA-derived fragments (tRFs), a subset of noncoding RNAs, exert significant biological influences on cancer progression, encompassing transcription and translation processes as well as epigenetic regulation. This article primarily examines the mechanisms by which tRFs modulate gene expression and contribute to tumorigenesis in lung cancer. Furthermore, we provide a comprehensive overview of the current bioinformatics analysis of tRFs in lung cancer, with the objective of offering a systematic and efficient approach for studying the expression profiling, functional enrichment, and molecular mechanisms of tRFs in this disease. Finally, we discuss the clinical significance and potential avenues for future research on tRFs in lung cancer. This paper presents a comprehensive systematic review of the existing research findings on tRFs in lung cancer, aiming to offer improved biomarkers and drug targets for clinical management of lung cancer.

ncRNAs-mediated TIMELESS overexpression in lung adenocarcinoma correlates with reduced tumor immune cell infiltration and poor prognosis

Lung adenocarcinoma (LUAD) has a poor prognosis. Circadian genes such as TIMELESS have been associated with several pathologies, including cancer. The expression of TIMELESS and the relationship between TIMELESS, infiltration of tumors and prognosis in LUAD requires further investigation. In this study, we investigated the expression of TIMELESS and its association with survival across several types of human cancer using data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Program. Noncoding RNAs (ncRNAs) regulating overexpression of TIMELESS in lung adenocarcinoma (LUAD) were explored with expression, correlation, and survival analyses. Immune cell infiltration and biomarkers were analyzed between different TIMELESS expression levels. The relationship between TIMELESS expression and immunophenoscores, which were used to predict response to immunotherapy, was evaluated. TIMELESS was identified as a potential oncogene in LUAD. NcRNA analysis showed MIR4435-2HG/hsa-miR-1-3p may interact with TIMELESS in a competitive endogenous RNA network in LUAD tumor tissues. Most immune cells were significantly decreased in TCGA LUAD tumor tissues with high TIMELESS expression except for CD4+T cells and Th2 cells. TIMELESS expression in LUAD tumor tissues was significantly negatively correlated with neutrophil biomarkers, dendritic cell biomarkers (HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-DPA1, CD1C) and an immunophenoscore that predicted outcomes associated with the use of immune checkpoint inhibitors. These findings imply that ncRNAs-mediated TIMELESS overexpression in LUAD tumor tissues correlated with poor prognosis, reduced immune cell infiltration in the tumor microenvironment, and poor response to immune checkpoint inhibitors.

Exploring the Therapeutic Significance of microRNAs and lncRNAs in Kidney Diseases

MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are two crucial classes of transcripts that belong to the major group of non-coding RNAs (ncRNAs). These RNA molecules have significant influence over diverse molecular processes due to their crucial role as regulators of gene expression. However, the dysregulated expression of these ncRNAs constitutes a fundamental factor in the etiology and progression of a wide variety of multifaceted human diseases, including kidney diseases. In this context, over the past years, compelling evidence has shown that miRNAs and lncRNAs could be prospective targets for the development of next-generation drugs against kidney diseases as they participate in a number of disease-associated processes, such as podocyte and nephron death, renal fibrosis, inflammation, transition from acute kidney injury to chronic kidney disease, renal vascular changes, sepsis, pyroptosis, and apoptosis. Hence, in this current review, we critically analyze the recent findings concerning the therapeutic inferences of miRNAs and lncRNAs in the pathophysiological context of kidney diseases. Additionally, with the aim of driving advances in the formulation of ncRNA-based drugs tailored for the management of kidney diseases, we discuss some of the key challenges and future prospects that should be addressed in forthcoming investigations.

Combinatorial Gene Expression Profiling of Serum HULC, HOTAIR, and UCA1 lncRNAs to Differentiate Hepatocellular Carcinoma from Liver Diseases: A Systematic Review and Meta-Analysis

Hepatocellular carcinoma (HCC) presents a significant global health challenge due to limited early detection methods, primarily relying on conventional approaches like imaging and alpha-fetoprotein (AFP). Although non-coding RNAs (ncRNAs) show promise as potential biomarkers in HCC, their true utility remains uncertain. We conducted a comprehensive review of 76 articles, analyzing 88 circulating lncRNAs in 6426 HCC patients. However, the lack of a standardized workflow protocol has hampered holistic comparisons across the literature. Consequently, we herein confined our meta-analysis to only a subset of these lncRNAs. The combined analysis of serum highly upregulated in liver cancer (HULC) gene expression with homeobox transcript antisense intergenic RNA (HOTAIR) and urothelial carcinoma-associated 1 (UCA1) demonstrated markedly enhanced sensitivity and specificity in diagnostic capability compared to traditional biomarkers or other ncRNAs. These findings could have substantial implications for the early diagnosis and tailored treatment of HCC.

Regulation of bacterial gene expression by non-coding RNA: It is all about time!

Commensal and pathogenic bacteria continuously evolve to survive in diverse ecological niches by efficiently coordinating gene expression levels in their ever-changing environments. Regulation through the RNA transcript itself offers a faster and more cost-effective way to adapt than protein-based mechanisms and can be leveraged for diagnostic or antimicrobial purposes. However, RNA can fold into numerous intricate, not always functional structures that both expand and obscure the plethora of roles that regulatory RNAs serve within the cell. Here, we review the current knowledge of bacterial non-coding RNAs in relation to their folding pathways and interactions. We posit that co-transcriptional folding of these transcripts ultimately dictates their downstream functions. Elucidating the spatiotemporal folding of non-coding RNAs during transcription therefore provides invaluable insights into bacterial pathogeneses and predictive disease diagnostics. Finally, we discuss the implications of co-transcriptional folding andapplications of RNAs for therapeutics and drug targets.

Current situation and trend of non-coding RNA in rheumatoid arthritis: a review and bibliometric analysis

Background

Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease that affects multiple joints and has adverse effects on various organs throughout the body, often leading to a poor prognosis. Recent studies have shown significant progress in the research of non-coding RNAs (ncRNAs) in RA. Therefore, this study aims to comprehensively assess the current status and research trends of ncRNAs in RA through a bibliometric analysis.

Methods

This study retrieved articles relevant to ncRNAs and RA from the Science Citation Index Expanded Database of the Web of Science Core Collection between January 1st, 2003, and July 31st, 2023. The relevant articles were screened based on the inclusion criteria. VOSviewer and CiteSpace are utilized for bibliometric and visual analysis.

Results

A total of 1697 publications were included in this study, and there was a noticeable increase in annual publications from January 1st, 2003, to July 31st, 2023. China, the United States, and the United Kingdom were the most productive countries in this field, contributing to 43.81%, 13.09%, and 3.87% of the publications. Anhui Medical University and Lu Qianjin were identified as the most influential institution and author. Frontiers In Immunology stood out as the most prolific journal, while Arthritis & Rheumatology was the most co-cited journal. Additionally, the research related to "circular RNA", "oxidative stress", "proliferation", and "migration" have emerged as new hotspots in the field.

Conclusion

In this study, we have summarized the publication characteristics related to ncRNA and RA and identified the most productive countries, institutions, authors, journals, hot topics, and trends.

Liver cancer-specific mutations in functional domains of ADAR2 lead to the elevation of coding and non-coding RNA editing in multiple tumor-related genes

Mutation is the major cause of phenotypic innovations. Apart from DNA mutations, the alteration on RNA such as the ADAR-mediated A-to-I RNA editing could also shape the phenotype. These two layers of variations have not been systematically combined to study their collective roles in cancers. We collected the high-quality transcriptomes of ten hepatocellular carcinoma (HCC) and the matched control samples. We systematically identified HCC-specific mutations in the exonic regions and profiled the A-to-I RNA editome in each sample. All ten HCC samples had mutations in the CDS of ADAR2 gene (dsRNA-binding domain or catalytic domain). The consequence of these mutations converged to the elevation of ADAR2 efficiency as reflected by the global increase of RNA editing levels in HCC. The up-regulated editing sites (UES) were enriched in the CDS and UTR of oncogenes and tumor suppressor genes (TSG), indicating the possible roles of these target genes in HCC oncogenesis. We present the mutation-ADAR2-UES-oncogene/TSG-HCC axis that explains how mutations at different layers would finally lead to abnormal phenotype. In the light of central dogma, our work provides novel insights into how to fully take advantage of the transcriptome data to decipher the consequence of mutations.

Fluorescent In Situ Detection of Small RNAs in Plants Using sRNA-FISH

Plant small RNAs are 21-24 nucleotide, noncoding RNAs that function as regulators in plant growth and development. Colorimetric detection of plant small RNAs was made possible with the introduction of locked nucleic acid probes. However, fluorescent detection of plant small RNAs has been challenging due to the high autofluorescence from plant tissue. Here we report a fluorescent in situ detection method for plant small RNAs. This method can be applied to most plant samples and tissue types and also can be adapted for single-molecule detection of small RNAs with super-resolution microscopy.

Imaging and Assay of the Dynamics of Cytotoxic Huntingtin (HTT) Protein Aggregates Regulated by lncRNAs

Huntington's disease (HD) pathogenesis involves deregulation of coding and noncoding RNA transcripts of which the involvement of long noncoding RNAs (lncRNA) has been realized recently. Of these, Meg3, Neat1, and Xist showed a consistent and significant increase in HD cell and animal models. In the present study, we formulate a methodology to visualize and quantify intracellular aggregates formed by mutant HTT protein. This method employs the use of both confocal laser scanning and super resolution (N-SIM) microscopy to accurately estimate aggregate numbers. Further, to determine the role of two lncRNAs Meg3 and Neat1 in the formation of aggregates of mutant HTT, we used commercially available siRNAs against Meg3 and Neat1 for transiently knocking them down in mouse Neuro2a and human SHSY5Y cells. Co-transfection of 83Q-DsRed and siRNA specific for Neat1 or Meg3 resulted in decreased intracellular aggregates of 83Q-DsRed in both the cell lines. We have established a quantitative method to estimate and directly or indirectly modulate the formation of mutant HTT aggregates.

Interconnections between m6A RNA modification, RNA structure, and protein-RNA complex assembly

Protein-RNA complexes exist in many forms within the cell, from stable machines such as the ribosome to transient assemblies like the spliceosome. All protein-RNA assemblies rely on spatially and temporally coordinated interactions between specific proteins and RNAs to achieve a functional form. RNA folding and structure are often critical for successful protein binding and protein-RNA complex formation. RNA modifications change the chemical nature of a given RNA and often alter its folding kinetics. Both these alterations can affect how and if proteins or other RNAs can interact with the modified RNA and assemble into complexes. N6-methyladenosine (m6A) is the most common base modification on mRNAs and regulatory noncoding RNAs and has been shown to impact RNA structure and directly modulate protein-RNA interactions. In this review, focusing on the mechanisms and available quantitative information, we discuss first how the METTL3/14 m6A writer complex is specifically targeted to RNA assisted by protein-RNA and other interactions to enable site-specific and co-transcriptional RNA modification and, once introduced, how the m6A modification affects RNA folding and protein-RNA interactions.

The Functional Circular RNA Screening via RfxCas13d/BSJ-gRNA System

Although discovered decades ago, functions of circular RNAs (circRNAs) produced from exon(s) back-splicing of pre-mRNAs have only been unveiled recently. As circRNAs share overlapping sequences with their cognate linear RNAs, except for the back-splicing junction sites, it is difficult to distinguish circRNAs from cognate mRNAs in functional studies. In this chapter, we describe a programmable method for the large-scale functional circRNA screening based on the RNA-guided, RNA-targeting CRISPR-Cas13 (RfxCas13d) system. This method can be applied both in vivo and in cell to explore highly expressed circRNAs that may influence cell growth, either under natural conditions or in response to environmental stimulation, without disturbing cognate linear mRNAs.

Competing endogenous RNA network analysis of Turner syndrome patient-specific iPSC-derived cardiomyocytes reveals dysregulation of autosomal heart development genes by altered dosages of X-inactivation escaping non-coding RNAs

BACKGROUND

A 45,X monosomy (Turner syndrome, TS) is the only chromosome haploinsufficiency compatible with life. Nevertheless, the surviving TS patients still suffer from increased morbidity and mortality, with around one-third of them subjecting to heart abnormalities. How loss of one X chromosome drive these conditions remains largely unknown.

METHODS

Here, we have generated cardiomyocytes (CMs) from wild-type and TS patient-specific induced pluripotent stem cells and profiled the mRNA, lncRNA and circRNA expression in these cells.

RESULTS

We observed lower beating frequencies and higher mitochondrial DNA copies per nucleus in TS-CMs. Moreover, we have identified a global transcriptome dysregulation of both coding and non-coding RNAs in TS-CMs. The differentially expressed mRNAs were enriched of heart development genes. Further competing endogenous RNA network analysis revealed putative regulatory circuit of autosomal genes relevant with mitochondrial respiratory chain and heart development, such as COQ10A, RARB and WNT2, mediated by X-inactivation escaping lnc/circRNAs, such as lnc-KDM5C-4:1, hsa_circ_0090421 and hsa_circ_0090392. The aberrant expressions of these genes in TS-CMs were verified by qPCR. Further knockdown of lnc-KDM5C-4:1 in wild-type CMs exhibited significantly reduced beating frequencies.

CONCLUSIONS

Our study has revealed a genomewide ripple effect of X chromosome halpoinsufficiency at post-transcriptional level and provided insights into the molecular mechanisms underlying heart abnormalities in TS patients.

Progress of circRNA/lncRNA-miRNA-mRNA axis in atrial fibrillation

Atrial fibrillation (AF) is a prevalent arrhythmia that requires effective biomarkers and therapeutic targets for clinical management. In recent years, non-coding RNAs (ncRNAs) have emerged as key players in the pathogenesis of AF, particularly through the ceRNA (competitive endogenous RNA) mechanism. By acting as ceRNAs, ncRNAs can competitively bind to miRNAs and modulate the expression of target mRNAs, thereby influencing the biological behavior of AF. The ceRNA axis has shown promise as a diagnostic and prognostic biomarker for AF. This review provides a comprehensive overview of the roles of ncRNAs in the development and progression of AF, highlighting the intricate crosstalk between different ncRNAs in AF pathophysiology. Furthermore, we discuss the potential implications of targeting the circRNA/lncRNA-miRNA-mRNA axis for the diagnosis, prognosis, and therapeutic intervention of AF.

Norad Competently Binds with Pum2 to Regulate Neuronal Apoptosis and Play a Neuroprotective Role After SAH in Mice

Subarachnoid Hemorrhage (SAH) is a cerebrovascular disorder that has been found to have severe consequences, including a high mortality and disability rate. Research has indicated that neuronal death, particularly apoptosis, plays a major role in the neurological impairment that follows SAH. RNA-binding protein Pum2 can interfere with translation or other biological functions by connecting to the UGUAHAUA sequence on RNA. Noncoding RNA activated by DNA damage (Norad) contains some Pum2 recognition sequences, which may bind to Pum2 protein and affect its capacity to attach to target mRNA. The time course expression of Norad and Pum2 after SAH is analyzed by establishing a mouse SAH model. Subsequently, the purpose of this study is to investigate the potential role and mechanism of the Norad-Pum2 axis after SAH using lentivirus overexpression of Pum2 and knockdown of Norad. Analysis of Pum2 and Norad levels reveal that the former is significantly reduce and the latter is significantly increased in the SAH group compared to the sham group. Subsequent overexpression of Pum2 and Norad knockdown is found to reduce SAH-induced oxidative stress, neuronal apoptosis, and ultimately improve behavioral and cognitive changes in SAH mice. Our study indicates that Norad-Pum2 acts as a neuromodulator in SAH, and that by increasing Pum2 and decreasing Norad levels, SAH-induced neuronal apoptosis can be reduced and neurological deficits alleviated. Consequently, Norad-Pum2 may be a promising therapeutic target for SAH.

Subcellular localization and relevant mechanisms of human cancer-related micropeptides

Rapid advances in high-quality sequencing and bioinformatics have invalidated the argument that noncoding RNAs (ncRNAs) are junk transcripts that do not encode proteins. Increasing evidence suggests that small open reading frames (sORFs) in ncRNAs can encode micropeptides and polypeptides within 100 amino acids in length. Several micropeptides have been characterized and proven to have various functions in human physiology and pathology, particularly in cancer. The present review mainly highlights the latest studies on ncRNA-encoded micropeptides in different cancers and categorizes them based on their subcellular localization, thereby providing a theoretical basis for micropeptide applications in the early diagnosis and prognosis of cancer and as therapeutic targets. However, considering the inherent characteristics of micropeptides and the limitations of the assay technology methods, more detailed information is warranted.

Two for one: regulatory RNAs that encode small proteins

RNAs are commonly categorized as being either protein-coding mRNAs or noncoding RNAs. However, an increasing number of transcripts, in organisms ranging from bacteria to humans, are being found to have both coding and noncoding functions. In some cases, the sequences encoding the protein and the regulatory RNA functions are separated, while in other cases the sequences overlap. The protein and RNA can regulate similar or distinct pathways. Here we describe examples illustrating how these dual-function (also denoted bifunctional or dual-component) RNAs are identified and their mechanisms of action and cellular roles. We also discuss the synergy or competition between coding and RNA activity and how these regulators evolved, as well as how more dual-function RNAs might be discovered and exploited.

The Pivotal Role of Noncoding RNAs in Flowering Time Regulation

Noncoding RNAs constitute a substantial portion of the transcriptome and play pivotal roles in plant growth and development. Among these processes, flowering stands out as a crucial trait, ensuring reproductive success and seed set, and is meticulously controlled by genetic and environmental factors. With remarkable advancements in the identification and characterization of noncoding RNAs in plants, it has become evident that noncoding RNAs are intricately linked to the regulation of flowering time. In this article, we present an overview of the classification of plant noncoding RNAs and delve into their functions in the regulation of flowering time. Furthermore, we review their molecular mechanisms and their involvement in flowering pathways. Our comprehensive review enhances the understanding of how noncoding RNAs contribute to the regulation of flowering time and sheds light on their potential implications in crop breeding.

Differential Expression of miRNAs, lncRNAs, and circRNAs between Ovaries and Testes in Common Carp (Cyprinus carpio)

Female common carp grow faster than male individuals, implying that rearing females could be more profitable in aquaculture. Non-coding RNAs (ncRNAs) serve as versatile regulators with multiple functions in diverse biological processes. However, the roles of ncRNAs in the sex differentiation of common carp are less studied. In this study, we investigated the expression profiles of ncRNAs, including miRNAs, lncRNAs, and circRNAs, in the gonads to comprehend the roles of ncRNAs in sex differentiation in common carp. A substantial number of differentially expressed (DE) ncRNAs in ovaries and testes were identified. Some miRNAs, notably miR-205, miR-214, and miR-460-5p, might modulate hormone synthesis and thus maintain sex. A novel miRNA, novel_158, was predicted to suppress the expression of foxl3. DE lncRNAs were associated with oocyte meiosis, GnRH signaling pathways, and steroid biosynthesis, while DE circRNA target genes were enriched in the WNT signaling pathway and MAPK signaling pathway. We also analyzed ncRNA-mRNA interactions to shed light on the crosstalk between competing endogenous RNAs (ceRNAs), which is the critical mechanism by which lncRNAs and circRNAs function. Some lncRNAs and circRNAs may be able to competitively bind novel_313, a new miRNA, and thus regulate hsd17β3. Our research will provide a valuable resource for understanding the genetic basis of gonadal differentiation and development in common carp.

Coding and noncoding RNA profile of human heterotopic ossifications - Risk factors and biomarkers

Heterotopic ossification (HO) means the formation of bone in muscles and soft tissues, such as ligaments or tendons. HO could have a genetic history or develop after a traumatic event, as a result of muscle injury, fractures, burns, surgery, or neurological disorders. Many lines of evidence suggest that the formation of HO is related to the pathological differentiation of stem or progenitor cells present within soft tissues or mobilized from the bone marrow. The cells responsible for the initiation and progression of HO are generally called HO precursor cells. The exact mechanisms behind the development of HO are not fully understood. However, several factors have been identified as potential contributors. For example, local tissue injury and inflammation disturb soft tissue homeostasis. Inflammatory cells release growth factors and cytokines that promote osteogenic or chondrogenic differentiation of HO precursor cells. The bone morphogenetic protein (BMP) is one of the main factors involved in the development of HO. In this study, next-generation sequencing (NGS) and RT-qPCR were performed to analyze the differences in mRNA, miRNA, and lncRNA expression profiles between muscles, control bone samples, and HO samples coming from patients who underwent total hip replacement (THR). As a result, crucial changes in the level of gene expression between HO and healthy tissues were identified. The bioinformatic analysis allowed to describe the processes most severely impacted, as well as genes which level differed the most significantly between HO and control samples. Our analysis showed that the level of transcripts involved in leukocyte migration, differentiation, and activation, as well as markers of chronic inflammatory diseases, that is, miR-148, increased in HO, as compared to muscle. Furthermore, the levels of miR-195 and miR-143, which are involved in angiogenesis, were up-regulated in HO, as compared to bone. Thus, we suggested that inflammation and angiogenesis play an important role in HO formation. Importantly, we noticed that HO is characterized by a higher level of TLR3 expression, compared to muscle and bone. Thus, we suggest that infection may also be a risk factor in HO development. Furthermore, an increased level of transcripts coding proteins involved in osteogenesis and signaling pathways, such as ALPL, SP7, BGLAP, BMP8A, BMP8B, SMPD3 was noticed in HO, as compared to muscles. Interestingly, miR-99b, miR-146, miR-204, and LINC00320 were up-regulated in HO, comparing to muscles and bone. Therefore, we suggested that these molecules could be important biomarkers of HO formation and a potential target for therapies.

Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification

Recent studies on marine organisms have made use of third-generation sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). While these specialized bioinformatics tools have different algorithmic designs and performance capabilities, they offer scalability and can be applied to various datasets. We investigated the effectiveness of PacBio and ONT RNA sequencing methods in identifying the venom of the jellyfish species Nemopilema nomurai. We conducted a detailed analysis of the sequencing data from both methods, focusing on key characteristics such as CD, alternative splicing, long-chain noncoding RNA, simple sequence repeat, transcription factor, and functional transcript annotation. Our findings indicate that ONT generally produced higher raw data quality in the transcriptome analysis, while PacBio generated longer read lengths. PacBio was found to be superior in identifying CDs and long-chain noncoding RNA, whereas ONT was more cost-effective for predicting alternative splicing events, simple sequence repeats, and transcription factors. Based on these results, we conclude that PacBio is the most specific and sensitive method for identifying venom components, while ONT is the most cost-effective method for studying venogenesis, cnidocyst (venom gland) development, and transcription of virulence genes in jellyfish. Our study has implications for future sequencing technologies in marine jellyfish, and highlights the power of full-length transcriptome analysis in discovering potential therapeutic targets for jellyfish dermatitis.

Non-coding RNAs versus protein biomarkers to diagnose and differentiate acute stroke: Systematic review and meta-analysis

BACKGROUND

Stroke diagnosis is dependent on lengthy clinical and neuroimaging assessments, while rapid treatment initiation improves clinical outcome. Currently, more sensitive biomarker assays of both non-coding RNA- and protein biomarkers have improved their detectability, which could accelerate stroke diagnosis. This systematic review and meta-analysis compares non-coding RNA- with protein biomarkers for their potential to diagnose and differentiate acute stroke (subtypes) in (pre-)hospital settings.

METHODS

We performed a systematic review and meta-analysis of studies evaluating diagnostic performance of non-coding RNA- and protein biomarkers to differentiate acute ischemic and hemorrhagic stroke, stroke mimics, and (healthy) controls. Quality appraisal of individual studies was assessed using the QUADAS-2 tool while the meta-analysis was performed with the sROC approach and by assessing pooled sensitivity and specificity, diagnostic odds ratios, positive- and negative likelihood ratios, and the Youden Index.

SUMMARY OF REVIEW

112 studies were included in the systematic review and 42 studies in the meta-analysis containing 11627 patients with ischemic strokes, 2110 patients with hemorrhagic strokes, 1393 patients with a stroke mimic, and 5548 healthy controls. Proteins (IL-6 and S100 calcium-binding protein B (S100B)) and microRNAs (miR-30a) have similar performance in ischemic stroke diagnosis. To differentiate between ischemic- or hemorrhagic strokes, glial fibrillary acidic protein (GFAP) levels and autoantibodies to the NR2 peptide (NR2aAb, a cleavage product of NMDA neuroreceptors) were best performing whereas no investigated protein or non-coding RNA biomarkers differentiated stroke from stroke mimics with high diagnostic potential.

CONCLUSIONS

Despite sampling time differences, circulating microRNAs (< 24 h) and proteins (< 4,5 h) perform equally well in ischemic stroke diagnosis. GFAP differentiates stroke subtypes, while a biomarker panel of GFAP and UCH-L1 improved the sensitivity and specificity of UCH-L1 alone to differentiate stroke.

Bioinformatics analysis of competing endogenous RNA network in decidual natural killer cell from unexplained recurrent spontaneous abortion

BACKGROUND

Decidual natural killer (dNK) cell plays a pivotal role in maintaining pregnancy, especially in the first trimester. Noncoding-RNAs (ncRNAs) are critical regulators of transcription and protein expression. Dysregulation of ncRNAs may be involved in the pathogenesis of unexplained recurrent spontaneous abortion (URSA). However, the role of competing endogenous RNA (ceRNA) based on mRNA-miRNA-lncRNA network in regulating the incidence and progression of URSA remains elusive. The aim of the study is to identify the regulatory network of mRNA-miRNA-LncRNA ceRNA based on bioinformatics analysis in dNK from patients with URSA.

METHODS

Eligible studies were retrieved from PubMed, Embase, and the Gene Expression Omnibus (GEO) databases to identify differentially expressed genes (DEGs), miRNAs and LncRNAs in dNK cells of patients with URSA. Protein-protein interaction (PPI) network was constructed by STRING database and Cytoscape software. Potential regulatory miRNAs and lncRNAs of mRNAs were predicted by miRTarBase and RNA22 and subject to bioinformatics analysis.

RESULTS

A total of 634 DEGs were screened, including 290 upregulated and 344 downregulated DEGs. Among 207 differentially expressed lncRNAs, 110 lncRNAs were upregulated and 97 were downregulated. According to node degree, 30 hub genes were identified for subsequent research. After drawing the Venn diagram and matching to Cytoscape, an mRNA-miRNA-lncRNA network linked to the pathogenesis of URSA in dNK cells was constructed.

CONCLUSIONS

A novel regulatory network of mRNA-miRNA-lncRNA ceRNA is established in dNK cells from patients with URSA. All RNAs might be used as the biomarkers of the pathogenesis of URSA.

The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study

In recent years, a huge amount of data on ncRNA interactions has been described in scientific papers and databases. Although considerable effort has been made to annotate the available knowledge in public repositories, there are still significant discrepancies in how different resources capture and interpret data on ncRNA functional and physical associations. In the present paper, we present a collection of microRNA-mRNA interactions annotated from the scientific literature following recognized standard criteria and focused on microRNAs, which regulate genes associated with rare diseases as a case study. The list of protein-coding genes with a known role in specific rare diseases was retrieved from the Genome England PanelApp, and associated microRNA-mRNA interactions were annotated in the IntAct database and compared with other datasets. RNAcentral identifiers were used for unambiguous, stable identification of ncRNAs. The information about the interaction was enhanced by a detailed description of the cell types and experimental conditions, providing a computer-interpretable summary of the published data, integrated with the huge amount of protein interactions already gathered in the database. Furthermore, for each interaction, the binding sites of the microRNA are precisely mapped on a well-defined mRNA transcript of the target gene. This information is crucial to conceive and design optimal microRNA mimics or inhibitors to interfere in vivo with a deregulated process. As these approaches become more feasible, high-quality, reliable networks of microRNA interactions are needed to help, for instance, in the selection of the best target to be inhibited and to predict potential secondary off-target effects. Database URL https://www.ebi.ac.uk/intact.

In Cerebellar Atrophy of 12-Month-Old ATM-Null Mice, Transcriptome Upregulations Concern Most Neurotransmission and Neuropeptide Pathways, While Downregulations Affect Prominently Itpr1, Usp2 and Non-Coding RNA

The autosomal recessive disorder Ataxia-Telangiectasia is caused by a dysfunction of the stress response protein, ATM. In the nucleus of proliferating cells, ATM senses DNA double-strand breaks and coordinates their repair. This role explains T-cell dysfunction and tumour risk. However, it remains unclear whether this function is relevant for postmitotic neurons and underlies cerebellar atrophy, since ATM is cytoplasmic in postmitotic neurons. Here, we used ATM-null mice that survived early immune deficits via bone-marrow transplantation, and that reached initial neurodegeneration stages at 12 months of age. Global cerebellar transcriptomics demonstrated that ATM depletion triggered upregulations in most neurotransmission and neuropeptide systems. Downregulated transcripts were found for the ATM interactome component Usp2, many non-coding RNAs, ataxia genes Itpr1, Grid2, immediate early genes and immunity factors. Allelic splice changes affected prominently the neuropeptide machinery, e.g., Oprm1. Validation experiments with stressors were performed in human neuroblastoma cells, where ATM was localised only to cytoplasm, similar to the brain. Effect confirmation in SH-SY5Y cells occurred after ATM depletion and osmotic stress better than nutrient/oxidative stress, but not after ATM kinase inhibition or DNA stressor bleomycin. Overall, we provide pioneer observations from a faithful A-T mouse model, which suggest general changes in synaptic and dense-core vesicle stress adaptation.

Exosomal noncoding RNA-mediated spatiotemporal regulation of lipid metabolism: Implications in immune evasion and chronic inflammation

The hallmark of chronic inflammatory diseases is immune evasion. Successful immune evasion involves numerous mechanisms to suppress both adaptive and innate immune responses. Either direct contact between cells or paracrine signaling triggers these responses. Exosomes are critical drivers of these interactions and exhibit both immunogenic and immune evasion properties during the development and progression of various chronic inflammatory diseases. Exosomes carry diverse molecular cargo, including lipids, proteins, and RNAs that are crucial for immunomodulation. Moreover, recent studies have revealed that exosomes and their cargo-loaded molecules are extensively involved in lipid remodeling and metabolism during immune surveillance and disease. Many studies have also shown the involvement of lipids in controlling immune cell activities and their crucial upstream functions in regulating inflammasome activation, suggesting that any perturbation in lipid metabolism results in abnormal immune responses. Strikingly, the expanded immunometabolic reprogramming capacities of exosomes and their contents provided insights into the novel mechanisms behind the prophylaxis of inflammatory diseases. By summarizing the tremendous therapeutic potential of exosomes, this review emphasizes the role of exosome-derived noncoding RNAs in regulating immune responses through the modulation of lipid metabolism and their promising therapeutic applications.

[Advances in the Regulation of Follicular Development by Extracellular Vesicles and Non-Coding RNAs]

Extracellular vesicles (EV),nanoscale vesicles encapsulated by phospholipid bilayers,are rich in biological molecules such as nucleic acids,metabolites,proteins,and lipids derived from parental cells.They are mainly involved in intercellular communication,signal transmission,and material transport and affect the functions of target cells.Ovulation disorders account for a higher proportion in the factors causing infertility which demonstrates increasing incidence year by year.Non-coding RNAs participate in a series of physiological and pathological processes of follicular development,playing a key role in female infertility.This review systematically introduces the types and biological roles of EV and elaborates on the regulation of follicular development from the effects of EV and non-coding RNAs on granulosa cell function,oocyte maturation,ovulation,luteal formation,and steroid hormone synthesis,providing a new idea and a breakthrough point for the diagnosis and treatment of infertility.

CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides

NcRNA-encoded small peptides (ncPEPs) have recently emerged as promising targets and biomarkers for cancer immunotherapy. Therefore, identifying cancer-associated ncPEPs is crucial for cancer research. In this work, we propose CoraL, a novel supervised contrastive meta-learning framework for predicting cancer-associated ncPEPs. Specifically, the proposed meta-learning strategy enables our model to learn meta-knowledge from different types of peptides and train a promising predictive model even with few labeled samples. The results show that our model is capable of making high-confidence predictions on unseen cancer biomarkers with only five samples, potentially accelerating the discovery of novel cancer biomarkers for immunotherapy. Moreover, our approach remarkably outperforms existing deep learning models on 15 cancer-associated ncPEPs datasets, demonstrating its effectiveness and robustness. Interestingly, our model exhibits outstanding performance when extended for the identification of short open reading frames derived from ncPEPs, demonstrating the strong prediction ability of CoraL at the transcriptome level. Importantly, our feature interpretation analysis discovers unique sequential patterns as the fingerprint for each cancer-associated ncPEPs, revealing the relationship among certain cancer biomarkers that are validated by relevant literature and motif comparison. Overall, we expect CoraL to be a useful tool to decipher the pathogenesis of cancer and provide valuable information for cancer research. The dataset and source code of our proposed method can be found at https://github.com/Johnsunnn/CoraL.

Graph Convolutional Network and Contrastive Learning Small Nucleolar RNA (snoRNA) Disease Associations (GCLSDA): Predicting snoRNA-Disease Associations via Graph Convolutional Network and Contrastive Learning

Small nucleolar RNAs (snoRNAs) constitute a prevalent class of noncoding RNAs localized within the nucleoli of eukaryotic cells. Their involvement in diverse diseases underscores the significance of forecasting associations between snoRNAs and diseases. However, conventional experimental techniques for such predictions suffer limitations in scalability, protracted timelines, and suboptimal success rates. Consequently, efficient computational methodologies are imperative to realize the accurate predictions of snoRNA-disease associations. Herein, we introduce GCLSDA-graph Convolutional Network and contrastive learning predict snoRNA disease associations. GCLSDA is an innovative framework that combines graph convolution networks and self-supervised learning for snoRNA-disease association prediction. Leveraging the repository of MNDR v4.0 and ncRPheno databases, we construct a robust snoRNA-disease association dataset, which serves as the foundation to create bipartite graphs. The computational prowess of the light graph convolutional network (LightGCN) is harnessed to acquire nuanced embedded representations of both snoRNAs and diseases. With careful consideration, GCLSDA intelligently incorporates contrast learning to address the challenging issues of sparsity and over-smoothing inside correlation matrices. This combination not only ensures the precision of predictions but also amplifies the model's robustness. Moreover, we introduce the augmentation technique of random noise to refine the embedded snoRNA representations, consequently enhancing the precision of predictions. Within the domain of contrast learning, we unite the tasks of contrast and recommendation. This harmonization streamlines the cross-layer contrast process, simplifying the information propagation and concurrently curtailing computational complexity. In the area of snoRNA-disease associations, GCLSDA constantly shows its promising capacity for prediction through extensive research. This success not only contributes valuable insights into the functional roles of snoRNAs in disease etiology, but also plays an instrumental role in identifying potential drug targets and catalyzing innovative treatment modalities.

Integrated bioinformatics analysis of noncoding RNAs with tumor immune microenvironment in gastric cancer

In recent years, molecular and genetic research hotspots of gastric cancer have been investigated, including microRNAs, long noncoding RNAs (lncRNAs) and messenger RNA (mRNAs). The study on the role of lncRNAs may help to develop personalized treatment and identify potential prognostic biomarkers in gastric cancer. The RNA-seq and miRNA-seq data of gastric cancer were downloaded from the TCGA database. Differential analysis of RNA expression between gastric cancer samples and normal samples was performed using the edgeR package. The ceRNA regulatory network was visualized using Cytoscape. KEGG pathway analysis of mRNAs in the ceRNA network was performed using the clusterProfiler package. CIBERSORT was used to distinguish 22 immune cell types and the prognosis-related genes and immune cells were determined using Kaplan-Meier and Cox proportional hazard analyses. To estimate these nomograms, we used receiver operating characteristic and calibration curve studies. The ceRNA regulation network of gastric cancer was built in this study, and the genes in the network were analyzed for prognosis. A total of 980 lncRNAs were differentially expressed, of which 774 were upregulated and 206 were downregulated. A survival study identified 15 genes associated with gastric cancer prognosis, including VCAN-AS1, SERPINE1, AL139002.1, LINC00326, AC018781.1, C15orf54, hsa-miR-145. Monocytes and Neutrophils were associated with the survival rate of gastric cancer. Our research uncovers new ceRNA network for the detection, treatment, and monitoring of gastric cancer.

RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints

SUMMARY

Structure determination is a key step in the functional characterization of many non-coding RNA molecules. High-resolution RNA 3D structure determination efforts, however, are not keeping up with the pace of discovery of new non-coding RNA sequences. This increases the importance of computational approaches and low-resolution experimental data, such as from the small-angle X-ray scattering experiments. We present RNA Masonry, a computer program and a web service for a fully automated modeling of RNA 3D structures. It assemblies RNA fragments into geometrically plausible models that meet user-provided secondary structure constraints, restraints on tertiary contacts, and small-angle X-ray scattering data. We illustrate the method description with detailed benchmarks and its application to structural studies of viral RNAs with SAXS restraints.

AVAILABILITY AND IMPLEMENTATION

The program web server is available at http://iimcb.genesilico.pl/rnamasonry. The source code is available at https://gitlab.com/gchojnowski/rnamasonry.

A comprehensive insight into the role of small nucleolar RNAs (snoRNAs) and SNHGs in human cancers

Long non-coding RNAs (lncRNAs), which comprise most non-coding RNAs (ncRNAs), have recently become a focus of cancer research. How many functional ncRNAs exist is still a matter of debate. Although insufficient evidence supports that most lncRNAs function as transcriptional by-products, it is widely known that an increasing number of lncRNAs play essential roles in cells. Small nucleolar RNAs (snoRNAs), 60-300 nucleotides in length, have been better studied than long non-coding RNAs (lncRNAs) and are predominantly present in the nucleolus. Most snoRNAs are encoded in introns of protein- and non-protein-coding genes called small nucleolar RNA host genes (SNHGs). In this article, we explore the biology and characteristics of SNHGs and their role in developing human malignancies. In addition, we provide an update on the ability of these snoRNAs to serve as prognostic and diagnostic variables in various forms of cancer.

Diagnostic applications and therapeutic option of Cascade CRISPR/Cas in the modulation of miRNA in diverse cancers: promises and obstacles

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas technology is a molecular tool specific to sequences for engineering genomes. Among diverse clusters of Cas proteins, the class 2/type II CRISPR/Cas9 system, despite several challenges, such as off-target effects, editing efficiency, and efficient delivery, has shown great promise for driver gene mutation discovery, high-throughput gene screening, epigenetic modulation, nucleic acid detection, disease modeling, and more importantly for therapeutic purposes. CRISPR-based clinical and experimental methods have applications across a wide range of areas, especially for cancer research and, possibly, anticancer therapy. On the other hand, given the influential role of microRNAs (miRNAs) in the regulations of cellular division, carcinogenicity, tumorigenesis, migration/invasion, and angiogenesis in diverse normal and pathogenic cellular processes, in different stages of cancer, miRNAs are either oncogenes or tumor suppressors, according to what type of cancer they are involved in. Hence, these noncoding RNA molecules are conceivable biomarkers for diagnosis and therapeutic targets. Moreover, they are suggested to be adequate predictors for cancer prediction. Conclusive evidence proves that CRISPR/Cas system can be applied to target small non-coding RNAs. However, the majority of studies have highlighted the application of the CRISPR/Cas system for targeting protein-coding regions. In this review, we specifically discuss diverse applications of CRISPR-based tools for probing miRNA gene function and miRNA-based therapeutic involvement in different types of cancers.

Non-Coding RNA in Salivary Extracellular Vesicles: A New Frontier in Sjögren's Syndrome Diagnostics?

Sjögren's syndrome is an autoimmune rheumatic disease characterized by inflammation of the salivary and lacrimal glands, often manifesting as dry mouth and dry eyes. To simplify diagnostics of primary Sjögren's syndrome (pSS), a non-invasive marker is needed. The aim of the study was to compare the RNA content of salivary extracellular vesicles (EVs) between patients with pSS and healthy controls using microarray technology. Stimulated whole saliva was collected from 11 pSS patients and 11 age-matched controls. EV-RNA was isolated from the saliva samples using a Qiagen exoRNeasy Midi Kit and analyzed using Affymetrix Clariom D™ microarrays. A one-way ANOVA test was used to compare the mean signal values of each transcript between the two groups. A total of 9307 transcripts, coding and non-coding RNA, were detected in all samples. Of these transcripts, 1475 showed statistically significant differential abundance between the pSS and the control groups, generating two distinct EV-RNA patterns. In particular, tRNAs were downregulated in pSS patients, with the transcript tRNA-Ile-AAT-2-1 showing a 2-fold difference, and a promise as a potential biomarker candidate. This study therein demonstrates the potential for using salivary EV-RNA in pSS diagnostics.

The landscape of non-coding RNAs in the immunopathogenesis of Endometriosis

Endometriosis is a complex disorder that is characterized by the abnormal growth of endometrial-like tissue outside the uterus. It is associated with chronic inflammation, severe pelvic pain, infertility, and significantly reduced quality of life. Although the exact mechanism of endometriosis remains unknown, inflammation and altered immunity are considered key factors in the immunopathogenesis of the disorder. Disturbances of immune responses result in reduced clearance of regurgitated endometrial cells, which elicits oxidative stress and progression of inflammation. Proinflammatory mediators could affect immune cells' recruitment, fate, and function. Reciprocally, the activation of immune cells can promote inflammation. Aberrant expression of non-coding RNA (ncRNA) in patient and animal lesions could be suggestive of their role in endometriosis establishment. The engagement of these RNAs in regulating diverse biological processes, including inflammatory responses and activation of inflammasomes, altered immunity, cell proliferation, migration, invasion, and angiogenesis are widespread and far-reaching. Therefore, ncRNAs can be identified as a determining candidate regulating the inflammatory responses and immune system. This review aims in addition to predict the role of ncRNAs in the immunopathogenesis of endometriosis through regulating inflammation and altered immunity based on previous studies, it presents a comprehensive view of inflammation role in the pathogenesis of endometriosis.

Non-coding RNA in tumor-infiltrating regulatory T cells formation and associated immunotherapy

Cancer immunotherapy has exhibited promising antitumor effects in various tumors. Infiltrated regulatory T cells (Tregs) in the tumor microenvironment (TME) restrict protective immune surveillance, impede effective antitumor immune responses, and contribute to the formation of an immunosuppressive microenvironment. Selective depletion or functional attenuation of tumor-infiltrating Tregs, while eliciting effective T-cell responses, represents a potential approach for anti-tumor immunity. Furthermore, it does not disrupt the Treg-dependent immune homeostasis in healthy organs and does not induce autoimmunity. Yet, the shared cell surface molecules and signaling pathways between Tregs and multiple immune cell types pose challenges in this process. Noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), regulate both cancer and immune cells and thus can potentially improve antitumor responses. Here, we review recent advances in research of tumor-infiltrating Tregs, with a focus on the functional roles of immune checkpoint and inhibitory Tregs receptors and the regulatory mechanisms of ncRNAs in Treg plasticity and functionality.

Local RNA folding revisited

Most of the functional RNA elements located within large transcripts are local. Local folding therefore serves a practically useful approximation to global structure prediction. Due to the sensitivity of RNA secondary structure prediction to the exact definition of sequence ends, accuracy can be increased by averaging local structure predictions over multiple, overlapping sequence windows. These averages can be computed efficiently by dynamic programming. Here we revisit the local folding problem, present a concise mathematical formalization that generalizes previous approaches and show that correct Boltzmann samples can be obtained by local stochastic backtracing in McCaskill's algorithms but not from local folding recursions. Corresponding new features are implemented in the ViennaRNA package to improve the support of local folding. Applications include the computation of maximum expected accuracy structures from RNAplfold data and a mutual information measure to quantify the sensitivity of individual sequence positions.