Non-Coding RNA

23 pages, 2452 KiB

Open AccessArticle

Analysis of RNA Transcribed by RNA Polymerase III from B2 SINEs in Mouse Cells

by Olga R. Borodulina, Sergey A. Kosushkin, Ilia G. Ustyantsev, Nikita S. Vassetzky and Dmitri A. Kramerov

Non-Coding RNA 2025, 11(3), 39; https://doi.org/10.3390/ncrna11030039 - 14 May 2025

Abstract

Background/Objectives: SINEs (short interspersed elements) are eukaryotic non-autonomous retrotransposons. They are transcribed by RNA polymerase III (pol III) and generate non-coding RNAs. The 3′ end of many mammalian SINEs contains a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail. [...] Read more.

Background/Objectives: SINEs (short interspersed elements) are eukaryotic non-autonomous retrotransposons. They are transcribed by RNA polymerase III (pol III) and generate non-coding RNAs. The 3′ end of many mammalian SINEs contains a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail. Studies have shown that, in human HeLa cells that have been transiently transfected with such SINEs, short pol III-generated SINE transcripts undergo polyadenylation, resulting in the addition of a long poly(A)-tail. Notably, this AAUAAA-dependent polyadenylation is not characteristic of any other transcripts synthesized by pol III. B2 SINEs, found in the genomes of mouse-like rodents, exemplify all these features. Methods: In this study, we implemented a novel approach to sequencing pol III-generated B2 transcripts from mouse cell cultures (L929 and 4T1) and organs (brain and testis). Results: Transcription occurred in 16,000–20,000 B2 copies in each cell type, 51–62% of which were transcribed in all four cell types. Effective transcription terminators (e.g., TCT_>3 and T_≥4) were found in approximately 40% of the transcribed B2 copies. The transcripts of these B2 copies contained a truncated terminator sequence, as pol III transcriptional arrest is known to occur within the terminator, with a poly(A)-tail immediately downstream. Such a tail could only have formed through RNA polyadenylation. Conclusions: These results demonstrate that B2 transcripts synthesized by pol III are capable of polyadenylation in mouse cells. We discuss the transcription of B2 copies with and without moderately efficient pol III terminators (TCTTT) and provide examples of the polyadenylation of such transcripts. Full article

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15 pages, 4295 KiB

Open AccessFeature PaperArticle

Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer

by Mafalda Antunes-Ferreira, Ilias Glogovitis, Diogo Fortunato, Silvia D’Ambrosi, Mariona Colom Saborit, Galina Yahubyan, Vesselin Baev, Michael Hackenberg, Natasa Zarovni, Thomas Wurdinger and Danijela Koppers-Lalic

Non-Coding RNA 2025, 11(3), 38; https://doi.org/10.3390/ncrna11030038 - 7 May 2025

Abstract

Background: Platelet-derived Extracellular Vesicles, or “Platelet Dust” (PD), are reported as the most-abundant extracellular vesicles in plasma. However, the PD molecular content, especially the small RNA profile, is still poorly characterized. This study aims to characterize PD and other extracellular vesicles (EVs) in [...] Read more.

Background: Platelet-derived Extracellular Vesicles, or “Platelet Dust” (PD), are reported as the most-abundant extracellular vesicles in plasma. However, the PD molecular content, especially the small RNA profile, is still poorly characterized. This study aims to characterize PD and other extracellular vesicles (EVs) in patients with non-small-cell lung cancer (NSCLC), focusing on their small RNA signatures and diagnostic potential. Methods: The EVs were isolated directly from the plasma of healthy donors and patients with NSCLC using the surface markers CD9, CD63, CD81 (overall EVs), and CD61 (PD). Small RNA sequencing was then performed to comprehensively profile the miRNAs. Results: Our analysis revealed distinct small RNA profiles in the EVs and the PD from the patients with NSCLC. The EVs (CD9-, CD63-, and CD81-positive) showed the enrichment of four miRNAs and the depletion of ten miRNAs, while the PD (CD61-positive) exhibited a more complex profile, with nineteen miRNAs enriched and nine miRNAs depleted in the patients with NSCLC compared to those of the healthy controls. Conclusions: This exploratory study enhances our understanding of miRNA composition within different plasma vesicle populations, shedding light on the biology of plasma vesicles and their contents. Furthermore, utilizing an extracellular vesicle isolation method with potential clinical applicability offers the prospect of improved cancer characterization and detection by selecting the most informative subpopulation of plasma vesicles. Full article

(This article belongs to the Special Issue Extracellular Vesicles and ncRNA)

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14 pages, 364 KiB

Open AccessSystematic Review

Expression of miRNAs in the Relationship Between Periodontitis and Cardiovascular Diseases: A Systematic Review

by Montiel Guerrero-Sabater, María Cosín-Villanueva, Pedro Almiñana-Pastor and Andrés López-Roldán

Non-Coding RNA 2025, 11(3), 37; https://doi.org/10.3390/ncrna11030037 - 6 May 2025

Abstract

Objectives: Periodontitis is a chronic inflammatory disease that could influence the pathophysiology of cardiovascular diseases through immunoinflammatory and epigenetic mechanisms. MicroRNAs (miRNAs) could be key mediators in this interaction, regulating gene expression and the synthesis of inflammatory molecules. The objective of this systematic [...] Read more.

Objectives: Periodontitis is a chronic inflammatory disease that could influence the pathophysiology of cardiovascular diseases through immunoinflammatory and epigenetic mechanisms. MicroRNAs (miRNAs) could be key mediators in this interaction, regulating gene expression and the synthesis of inflammatory molecules. The objective of this systematic review was to evaluate the relationship between periodontitis and cardiovascular diseases by analyzing the expression of miRNAs involved in both pathologies. Methods: A systematic search was performed in the PubMed, Scopus, Embase, and Web of Science databases following the PRISMA guidelines. A total of 320 studies were identified, of which seven were included after applying eligibility criteria. Data on study design, sample characteristics, periodontal and cardiovascular diagnostic methodology, and the analyzed miRNAs were extracted. Results: The included studies were observational case-control studies in humans (n = 5) and experimental studies in animal models (n = 3). The miRNAs selected by the studies to link both pathologies were miR-155, miR-155-5p, miR-146a, miR-143, miR-145, and miR-23b. Most studies observed the overexpression of these miRNAs in patients with periodontitis and cardiovascular disease, with miR-146a being the most frequently associated. Conclusions: The findings suggest that certain miRNAs, particularly miR-146a, may play a key role in the connection between periodontitis and cardiovascular disease. Its overexpression in patients with both pathologies reinforces the hypothesis of its involvement in the inflammatory processes associated with both conditions. It would be interesting to conduct studies to validate their clinical applicability as biomarkers of susceptibility to cardiovascular disease. Full article

(This article belongs to the Topic MicroRNA: Mechanisms of Action, Physio-Pathological Implications, and Disease Biomarkers, 3rd Edition)

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45 pages, 2779 KiB

Open AccessReview

Tiny but Mighty: Small RNAs—The Micromanagers of Bacterial Survival, Virulence, and Host–Pathogen Interactions

by Rajdeep Banerjee

Non-Coding RNA 2025, 11(3), 36; https://doi.org/10.3390/ncrna11030036 - 5 May 2025

Abstract

Bacterial pathogens have evolved diverse strategies to infect hosts, evade immune responses, and establish successful infections. While the role of transcription factors in bacterial virulence is well documented, emerging evidence highlights the significant contribution of small regulatory RNAs (sRNAs) in bacterial pathogenesis. These [...] Read more.

Bacterial pathogens have evolved diverse strategies to infect hosts, evade immune responses, and establish successful infections. While the role of transcription factors in bacterial virulence is well documented, emerging evidence highlights the significant contribution of small regulatory RNAs (sRNAs) in bacterial pathogenesis. These sRNAs function as posttranscriptional regulators that fine-tune gene expression, enabling bacteria to adapt rapidly to challenging environments. This review explores the multifaceted roles of bacterial sRNAs in host–pathogen interactions. Firstly, it examines how sRNAs regulate pathogenicity by modulating the expression of key virulence factors, including fimbriae, toxins, and secretion systems, followed by discussing the role of sRNAs in bacterial stress response mechanisms that counteract host immune defenses, such as oxidative and envelope stress. Additionally, this review investigates the involvement of sRNAs in antibiotic resistance by regulating efflux pumps, biofilm formation, and membrane modifications, which contribute to multi-drug resistance phenotypes. Lastly, this review highlights how sRNAs contribute to intra- and interspecies communication through quorum sensing, thereby coordinating bacterial behavior in response to environmental cues. Understanding these regulatory networks governed by sRNAs is essential for the development of innovative antimicrobial strategies. This review highlights the growing significance of sRNAs in bacterial pathogenicity and explores their potential as therapeutic targets for the treatment of bacterial infections. Full article

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15 pages, 7171 KiB

Open AccessReview

Human XIST: Origin and Divergence of a cis-Acting Silencing RNA

by Maria Jose Navarro-Cobos and Carolyn J. Brown

Non-Coding RNA 2025, 11(3), 35; https://doi.org/10.3390/ncrna11030035 - 1 May 2025

Abstract

Dimorphism of sex chromosomes often leads to a need for dosage compensation. In eutherian mammals, XIST, a long non-coding RNA, is expressed from the X chromosome that will be silenced, triggering X-chromosome inactivation (XCI). XIST originated from the ancestral protein-coding Lnx3 gene with [...] Read more.

Dimorphism of sex chromosomes often leads to a need for dosage compensation. In eutherian mammals, XIST, a long non-coding RNA, is expressed from the X chromosome that will be silenced, triggering X-chromosome inactivation (XCI). XIST originated from the ancestral protein-coding Lnx3 gene with contributions from various mobile elements that contributed to the striking domains of tandem repeats within the first and sixth exons. Modular domains of XIST are now involved in recruiting heterochromatic marks and proteins essential for XCI initiation and maintenance. This review presents a comparative analysis of human XIST with five other eutherian mammals—chimpanzees, cats, pigs, sheep, and mice—examining conservation across exons as well as the tandem repeats. Notably, repeats exhibited higher conservation than exons, underscoring their functional importance. Additionally, a species-specific G repeat, previously described in pigs, was also identified in sheep and cats. These findings provide insights into the domains of XIST, a cis-acting silencer that has been used to proposed to alleviate the impact of a supernumerary chromosome in Down syndrome. Full article

(This article belongs to the Special Issue Evolution of Regulatory ncRNAs and ncRNA Genes)

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30 pages, 2375 KiB

Open AccessSystematic Review

Building a Hand-Curated ceRNET for Endometrial Cancer, Striving for Clinical as Well as Medicolegal Soundness: A Systematic Review

by Roberto Piergentili, Stefano Sechi, Lina De Paola, Simona Zaami and Enrico Marinelli

Non-Coding RNA 2025, 11(3), 34; https://doi.org/10.3390/ncrna11030034 - 30 Apr 2025

Abstract

Background/Objectives: Competing endogenous RNAs (ceRNA) are molecules that compete for the binding to a microRNA (miR). Usually, there are two ceRNA, one of which is a protein-coding RNA (mRNA), with the other being a long non-coding RNA (lncRNA). The miR role is to [...] Read more.

Background/Objectives: Competing endogenous RNAs (ceRNA) are molecules that compete for the binding to a microRNA (miR). Usually, there are two ceRNA, one of which is a protein-coding RNA (mRNA), with the other being a long non-coding RNA (lncRNA). The miR role is to inhibit mRNA expression, either promoting its degradation or impairing its translation. The lncRNA can “sponge” the miR, thus impeding its inhibitory action on the mRNA. In their easier configuration, these three molecules constitute a regulatory axis for protein expression. However, each RNA can interact with multiple targets, creating branched and intersected axes that, all together, constitute what is known as a competing endogenous RNA network (ceRNET). Methods: In this systematic review, we collected all available data from PubMed about experimentally verified (by luciferase assay) regulatory axes in endometrial cancer (EC), excluding works not using this test; Results: This search allowed the selection of 172 bibliographic sources, and manually building a series of ceRNETs of variable complexity showed the known axes and the deduced intersections. The main limitation of this search is the highly stringent selection criteria, possibly leading to an underestimation of the complexity of the networks identified. However, this work allows us not only to hypothesize possible gap fillings but also to set the basis to instruct artificial intelligence, using adequate prompts, to expand the EC ceRNET by comparing it with ceRNETs of other cancers. Moreover, these networks can be used to inform and guide research toward specific, though still unidentified, axes in EC, to complete parts of the network that are only partially described, or even to integrate low complexity subnetworks into larger more complex ones. Filling the gaps among the existing EC ceRNET will allow physicians to hypothesize new therapeutic strategies that may either potentiate or substitute existing ones. Conclusions: These ceRNETs allow us to easily visualize long-distance interactions, thus helping to select the best treatment, depending on the molecular profile of each patient, for personalized medicine. This would yield higher efficiency rates and lower toxicity levels, both of which are extremely relevant factors not only for patients’ wellbeing, but also for the legal, regulatory, and ethical aspects of miR-based innovative treatments and personalized medicine as a whole. This systematic review has been registered in PROSPERO (ID: PROSPERO 2025 CRD420251035222). Full article

(This article belongs to the Special Issue Non-coding RNA as Biomarker in Cancer)

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24 pages, 4722 KiB

Open AccessArticle

Bromodomain and Extra-Terminal Family Proteins BRD2, BRD3, and BRD4 Contribute to H19-Dependent Transcriptional Regulation of Cell Adhesion Molecules, Modulating Metastatic Dissemination Program in Prostate Cancer

by Valeria Pecci, Melissa Borsa, Aurora Aiello, Sara De Martino, Luca Cis, Cristian Ripoli, Dante Rotili, Francesco Pierconti, Francesco Pinto, Claudio Grassi, Carlo Gaetano, Antonella Farsetti and Simona Nanni

Non-Coding RNA 2025, 11(3), 33; https://doi.org/10.3390/ncrna11030033 - 29 Apr 2025

Abstract

Background/Objectives: Metastatic prostate cancer (PCa) remains a major clinical challenge with limited therapeutic options. The long non-coding RNA H19 has been implicated in regulating cell adhesion molecules and collective migration, key features of metastatic dissemination. This study investigates the role of the Bromodomain [...] Read more.

Background/Objectives: Metastatic prostate cancer (PCa) remains a major clinical challenge with limited therapeutic options. The long non-coding RNA H19 has been implicated in regulating cell adhesion molecules and collective migration, key features of metastatic dissemination. This study investigates the role of the Bromodomain and Extra-Terminal (BET) proteins BRD2, BRD3, and BRD4 in the H19-dependent transcriptional regulation of cell adhesion molecules. Currently, the major effects of BET inhibitors require androgen receptor (AR) expression. Methods: H19 was stably silenced in PC-3 (AR-null) and 22Rv1 (AR-positive) castration-resistant PCa cells. The cells were treated with the pan-BET inhibitors JQ1 and OTX015 or the BET degrader dBET6. In vivo, the effects of JQ1 were evaluated in xenograft mouse models. Chromatin immunoprecipitation (ChIP) and RNA-ChIP were used to assess BET protein recruitment and interaction with cell adhesion gene loci and H19. Organotypic slice cultures (OSCs) from fresh PCa surgical specimens were used as ex vivo models to validate transcriptional changes and BRD4 recruitment. Results: BET inhibition significantly reduced the expression of β4 integrin and E-cadherin and cell proliferation in both basal conditions, and following H19 knockdown in PC-3 and 22Rv1 cells. These effects were mirrored in JQ1-treated tumor xenografts, which showed marker downregulation and tumor regression. ChIP assays revealed that BRD4, more than BRD2/3, was enriched on β4 integrin and E-cadherin promoters, especially in regions marked by H3K27ac. H19 silencing markedly enhanced BRD4 promoter occupancy. RNA-ChIP confirmed a specific interaction between BRD4 and H19. These findings were validated in OSCs, reinforcing their clinical relevance. Conclusions: Our study demonstrates that BRD4 epigenetically regulates the H19-mediated transcriptional control of adhesion molecules involved in collective migration and metastatic dissemination. Importantly, these effects are independent of AR status, suggesting that targeting the H19/BRD4 axis may represent a promising therapeutic avenue for advanced PCa. Full article

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20 pages, 15276 KiB

Open AccessArticle

In Silico Prioritization of STAT1 3′ UTR SNPs Identifies rs190542524 as a miRNA-Linked Variant with Potential Oncogenic Impact

by Ebtihal Kamal

Non-Coding RNA 2025, 11(3), 32; https://doi.org/10.3390/ncrna11030032 - 29 Apr 2025

Abstract

Background: Single-nucleotide polymorphisms (SNPs) are associated with multiple disorders and various cancer types. In the context of cancer, alterations within non-coding regions, specifically 3′ untranslated regions (3′ UTR), have proven substantially important. Methods: In this study, we utilized various bioinformatics tools to examine [...] Read more.

Background: Single-nucleotide polymorphisms (SNPs) are associated with multiple disorders and various cancer types. In the context of cancer, alterations within non-coding regions, specifically 3′ untranslated regions (3′ UTR), have proven substantially important. Methods: In this study, we utilized various bioinformatics tools to examine the effect of SNPs in the 3′ UTR. We retrieved the 3′ UTR SNPs of the Signal Transducer and Activator of Transcription 1 (STAT1) gene from the National Centre for Biotechnology Information (NCBI) website. Next, we employed the Polymorphism in miRNAs and their corresponding target sites (PolymiRTS) database to predict the 3′ UTR SNPs that create new microRNA (miRNA) binding sites and their respective miRNAs. The effect of the 3′ UTR SNPs on the messenger RNA structure was studied using RNAfold server. We used Cscape tool to predict the oncogenic 3′ UTR SNPs. Then, we submitted the miRNAs to the miRNet database to visualize the miRNA-miRNAs’ target genes interaction, for which gene enrichment analysis was performed using ShinyGO. Protein–protein interactions were conducted using the STRING database. We conducted miRNA enrichment analysis utilizing miRPathDB, subsequently performing miRNA differential expression analysis through oncoMIR, and the StarBase database. The survival analysis of the upregulated miRNAs in cancer was investigated using the Kaplan–Meier Plotter. Result: Twelve SNPs were predicted to create new miRNA binding sites. Two of them, rs188557905 and rs190542524, were predicted to destabilize the mRNA structures. We predicted rs190542524, rs11305, rs186033487, and rs188557905 to be oncogenic 3′ UTR SNPs, with high-confidence predictions and scores > 0.5. Using miRNAs’ target genes enrichment analysis, this study indicated that the miRNA target genes were more likely to be involved in cancer-related pathways. Our comprehensive analysis of miRNAs, their functional enrichment, their expression in various types of cancer, and the correlation between miRNA expression and survival outcome yielded these results. Our research shows that the oncogenic 3′ UTR SNP rs190542524 creates a new binding site for the oncogenic miRNA hsa-miR-136-5p. This miRNA is significantly upregulated in BLCA, LUSC, and STAD and is linked to poor survival. Additionally, rs114360225 creates a new binding site for hsa-miR-362-3p, influencing LIHC. Conclusions: These analyses suggest that these 3′ UTR SNPs may have a functional impact on the STAT1 gene’s regulation through their predicted effect on miRNA binding sites. Future experimental validation could establish their potential role in the diagnosis and treatment of various diseases, including cancer. Full article

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28 pages, 7091 KiB

Open AccessArticle

Role of Long Non-Coding RNA X-Inactive-Specific Transcript (XIST) in Neuroinflammation and Myelination: Insights from Cerebral Organoids and Implications for Multiple Sclerosis

by Nihan Aktas Pepe, Busra Acar, Gozde Erturk Zararsiz, Serife Ayaz Guner and Alaattin Sen

Non-Coding RNA 2025, 11(3), 31; https://doi.org/10.3390/ncrna11030031 - 29 Apr 2025

Abstract

Background/Objectives: X-inactive-specific transcript (XIST) is a factor that plays a role in neuroinflammation. This study investigated the role of XIST in neuronal development, neuroinflammation, myelination, and therapeutic responses within cerebral organoids in the context of Multiple Sclerosis (MS) pathogenesis. Methods [...] Read more.

Background/Objectives: X-inactive-specific transcript (XIST) is a factor that plays a role in neuroinflammation. This study investigated the role of XIST in neuronal development, neuroinflammation, myelination, and therapeutic responses within cerebral organoids in the context of Multiple Sclerosis (MS) pathogenesis. Methods: Human cerebral organoids with oligodendrocytes were produced from XIST-silenced H9 cells, and the mature organoids were subsequently treated with either FTY720 or DMF. Gene expression related to inflammation and myelination was subsequently analyzed via qRT-PCR. Immunofluorescence staining was used to assess the expression of proteins related to inflammation, myelination, and neuronal differentiation. Alpha-synuclein protein levels were also checked via ELISA. Finally, transcriptome analysis was conducted on the organoid samples. Results: XIST-silenced organoids presented a 2-fold increase in the expression of neuronal stem cells, excitatory neurons, microglia, and mature oligodendrocyte markers. In addition, XIST silencing increased IL-10 mRNA expression by 2-fold and MBP and PLP1 expression by 2.3- and 0.6-fold, respectively. Although XIST silencing tripled IBA1 protein expression, it did not affect organoid MBP expression. FTY720, but not DMF, distinguished MBP and IBA1 expression in XIST-silenced organoids. Furthermore, XIST silencing reduced the concentration of alpha-synuclein from 300 to 100 pg/mL, confirming its anti-inflammatory role. Transcriptomic and gene enrichment analyses revealed that the differentially expressed genes are involved in neural development and immune processes, suggesting the role of XIST in neuroinflammation. The silencing of XIST modified the expression of genes associated with inflammation, myelination, and neuronal growth in cerebral organoids, indicating a potential involvement in the pathogenesis of MS. Conclusions: XIST may contribute to the MS pathogenesis as well as neuroinflammatory diseases such as and Alzheimer’s and Parkinson’s diseases and may be a promising therapeutic target. Full article

(This article belongs to the Section Long Non-Coding RNA)

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26 pages, 1665 KiB

Open AccessReview

Role of Non-Coding RNAs in White and Brown Adipose Tissue Differentiation and Development

by Lea Sleiman and Sorina Dinescu

Non-Coding RNA 2025, 11(3), 30; https://doi.org/10.3390/ncrna11030030 - 29 Apr 2025

Abstract

Adipocyte differentiation is a complex process in which pluripotent mesenchymal stem cells (MSCs) differentiate and develop into mature fat cells, also known as adipocytes. This process is controlled by various transcription factors, hormones, and signaling molecules that regulate the development of these cells. [...] Read more.

Adipocyte differentiation is a complex process in which pluripotent mesenchymal stem cells (MSCs) differentiate and develop into mature fat cells, also known as adipocytes. This process is controlled by various transcription factors, hormones, and signaling molecules that regulate the development of these cells. Recently, an increasing number of non-coding RNAs (ncRNAs), especially microRNAs (miRNAs), have been established to be involved in the regulation of many biological processes, including adipocyte differentiation, development, metabolism, and energy homeostasis of white and brown adipose tissue. Several in vitro and in vivo studies reported the significant role of ncRNAs in either promoting or inhibiting adipocyte differentiation into white or brown fat cells by targeting specific transcription factors and regulating the expression of key adipogenic genes. Identifying the function of ncRNAs and their subsequent targets contributes to our understanding of how these molecules can be used as potential biomarkers and tools for therapies against obesity, diabetes, and other diseases related to obesity. This could also contribute to advancements in tissue-engineering based treatments. In this review, we intended to present an up-to-date comprehensive literature overview of the role of ncRNAs, including miRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), focusing particularly on miRNAs, in regulating the differentiation and development of cells into white and brown adipose tissue. In addition, we further discuss the potential use of these molecules as biomarkers for the development of novel therapeutic strategies for future personalized treatment options for patients. Full article

(This article belongs to the Special Issue Non-coding RNAs in Stem Cell Differentiation and Disease)

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15 pages, 656 KiB

Open AccessReview

The Role of Long Non-Coding RNAs in Human Endoderm Differentiation

by Annanda Lyra Ribeiro and Bruno Dallagiovanna

Non-Coding RNA 2025, 11(2), 29; https://doi.org/10.3390/ncrna11020029 - 13 Apr 2025

Abstract

The human genome sequencing revealed a vast complexity of transcripts, with over 80% of the genome being transcribed into non-coding RNAs. In particular, long non-coding RNAs (lncRNAs) have emerged as critical regulators of various cellular processes, including embryonic development and stem cell differentiation. [...] Read more.

The human genome sequencing revealed a vast complexity of transcripts, with over 80% of the genome being transcribed into non-coding RNAs. In particular, long non-coding RNAs (lncRNAs) have emerged as critical regulators of various cellular processes, including embryonic development and stem cell differentiation. Despite extensive efforts to identify and characterize lncRNAs, defining their mechanisms of action in state-specific cellular contexts remains a significant challenge. Only recently has the involvement of lncRNAs in human endoderm differentiation of pluripotent stem cells begun to be addressed, creating an opportunity to explore the mechanisms by which lncRNAs exert their functions in germ layer formation, lineage specification, and commitment. This review summarizes current findings on the roles of lncRNAs in endoderm differentiation, highlighting the functional mechanisms and regulatory aspects underlying their involvement in cell fate decisions leading to endoderm development. The key lncRNAs implicated in endoderm differentiation are discussed, along with their interaction with transcription factors and RNA-binding proteins and modulation of signaling pathways essential for endoderm development. Gaining insight into the regulatory roles of lncRNAs in endoderm differentiation enhances the understanding of developmental biology and provides a foundation for discovering novel lncRNAs involved in cell fate determination. Full article

(This article belongs to the Section Long Non-Coding RNA)

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20 pages, 1899 KiB

Open AccessReview

Decoding Salivary ncRNAomes as Novel Biomarkers for Oral Cancer Detection and Prognosis

by Subhadeep Das, Sampad Basak and Soumyadev Sarkar

Non-Coding RNA 2025, 11(2), 28; https://doi.org/10.3390/ncrna11020028 - 20 Mar 2025

Abstract

Oral cancer (OC) ranks among the most prevalent head and neck cancers, becoming the eleventh most common cancer worldwide with ~350,000 new cases and 177,000 fatalities annually. The rising trend in the occurrence of OC among young individuals and women who do not [...] Read more.

Oral cancer (OC) ranks among the most prevalent head and neck cancers, becoming the eleventh most common cancer worldwide with ~350,000 new cases and 177,000 fatalities annually. The rising trend in the occurrence of OC among young individuals and women who do not have tobacco habits is escalating rapidly. Surgical procedures, radiation therapy, and chemotherapy are among the most prevalent treatment options for oral cancer. To achieve better therapy and an early detection of the cancer, it is essential to understand the disease’s etiology at the molecular level. Saliva, the most prevalent body fluid obtained non-invasively, holds a collection of distinct non-coding RNA pools (ncRNAomes) that can be assessed as biomarkers for identifying oral cancer. Non-coding signatures, which are transcripts lacking a protein-coding function, have been identified as significant in the progression of various cancers, including oral cancer. This review aims to examine the role of various salivary ncRNAs (microRNA, circular RNA, and lncRNA) associated with disease progression and to explore their functions as potential biomarkers for early disease identification to ensure better survival outcomes for oral cancer patients. Full article

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17 pages, 1363 KiB

Open AccessReview

The Role of Non-Coding RNAs in MYC-Mediated Metabolic Regulation: Feedback Loops and Interactions

by Aliaa Amr Alamoudi

Non-Coding RNA 2025, 11(2), 27; https://doi.org/10.3390/ncrna11020027 - 18 Mar 2025

Abstract

Metabolic reprogramming is a hallmark of cancer, crucial for supporting the rapid energy demands of tumor cells. MYC, often deregulated and overexpressed, is a key driver of this shift, promoting the Warburg effect by enhancing glycolysis. However, there remains a gap in understanding [...] Read more.

Metabolic reprogramming is a hallmark of cancer, crucial for supporting the rapid energy demands of tumor cells. MYC, often deregulated and overexpressed, is a key driver of this shift, promoting the Warburg effect by enhancing glycolysis. However, there remains a gap in understanding the mechanisms and factors influencing MYC’s metabolic roles. Recently, non-coding RNAs (ncRNAs) have emerged as important modulators of MYC functions. This review focuses on ncRNAs that regulate MYC-driven metabolism, particularly the Warburg effect. The review categorizes these ncRNAs into three main groups based on their interaction with MYC and examines the mechanisms behind these interactions. Additionally, we explore how different types of ncRNAs may collaborate or influence each other’s roles in MYC regulation and metabolic function, aiming to identify biomarkers and synthetic lethality targets to disrupt MYC-driven metabolic reprogramming in cancer. Finaly, the review highlights the clinical implications of these ncRNAs, providing an up-to-date summary of their potential roles in cancer prognosis and therapy. With the recent advances in MYC-targeted therapy reaching clinical trials, the exciting potential of combining these therapies with ncRNA-based strategies holds great promise for enhancing treatment efficacy. Full article

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20 pages, 2390 KiB

Open AccessArticle

A miRNA Signature for Non-Invasive Colorectal Cancer Diagnosis in Morocco: miR-21, miR-29a and miR-92a

by Sofia Fathi, Oussama Aazzane, Salma Guendaoui, Nezha Tawfiq, Souha Sahraoui, Fadila Guessous and Mehdi Karkouri

Non-Coding RNA 2025, 11(2), 26; https://doi.org/10.3390/ncrna11020026 - 17 Mar 2025

Abstract

Colorectal cancer (CRC) is the third most diagnosed cancer and a leading cause of cancer-related mortality in Morocco, often detected at late stages. Circulating microRNAs (miRNAs) have emerged as promising non-invasive biomarkers for CRC detection, with miR-21, miR-29a, and miR-92a showing significant diagnostic [...] Read more.

Colorectal cancer (CRC) is the third most diagnosed cancer and a leading cause of cancer-related mortality in Morocco, often detected at late stages. Circulating microRNAs (miRNAs) have emerged as promising non-invasive biomarkers for CRC detection, with miR-21, miR-29a, and miR-92a showing significant diagnostic potential. This study aimed to evaluate the expression levels of these miRNAs in a Moroccan population and their efficacy as diagnostic biomarkers. Methods: A prospective study was conducted using blood samples from 50 CRC patients and 50 healthy controls. Circulating miRNA expression levels were quantified through reverse transcription quantitative PCR (RT-qPCR), with normalization to miR-1228-3p. Statistical analyses, including the Mann–Whitney U test, Receiver Operating Characteristic (ROC) curve analysis, sensitivity (Sen), and specificity (Spe) evaluations, were performed to assess the diagnostic accuracy of individual miRNAs and their combined performance as panels. Results: The expression levels of miR-21, miR-29a, and miR-92a were significantly elevated in CRC patients compared to healthy controls (all p < 0.001). ROC analysis demonstrated that miR-92a exhibited the highest individual diagnostic performance (AUC: 0.938), followed by miR-21 (AUC: 0.907) and miR-29a (AUC: 0.898). Sensitivity and specificity were 88% and 90%, 92% and 56%, and 76% and 94%, respectively. Combinatorial analysis revealed that the miR-29a and miR-92a panel achieved the highest diagnostic accuracy (AUC: 0.976), surpassing individual miRNAs and other combinations, highlighting its potential as a robust, non-invasive biomarker panel for CRC. Conclusions: This study highlights the potential of the miR-29a and miR-92a combination, which achieved excellent diagnostic efficiency (AUC: 0.976). These findings underscore miRNA utility in enhancing early detection and reducing CRC-related mortality in Morocco. Full article

(This article belongs to the Special Issue Non-coding RNA as Biomarker in Cancer)

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9 pages, 1035 KiB

Open AccessCommunication

Chromatin Structure Around Long Non-Coding RNA (lncRNA) Genes in Schistosoma mansoni Gonads

by Ronaldo C. Augusto, Thomas Quack, Christoph G. Grevelding and Christoph Grunau

Non-Coding RNA 2025, 11(2), 25; https://doi.org/10.3390/ncrna11020025 - 12 Mar 2025

Abstract

In this study, we employed a total of eight distinct modifications of histone proteins (H3K23ac, H3K27me3, H3K36me3, H3K4me3, H3K9ac, H3K9me3, H4K12ac, and H4K20me1) to discern the various chromatin colors encompassing lncRNA genes in both mature and immature gonads of the human parasite Schistosoma [...] Read more.

In this study, we employed a total of eight distinct modifications of histone proteins (H3K23ac, H3K27me3, H3K36me3, H3K4me3, H3K9ac, H3K9me3, H4K12ac, and H4K20me1) to discern the various chromatin colors encompassing lncRNA genes in both mature and immature gonads of the human parasite Schistosoma mansoni. Our investigation revealed that these chromatin colors exhibit a tendency to aggregate based on the similarities in their metagene shapes, leading to the formation of less than six distinct clusters. Moreover, these clusters can be further grouped according to their resemblances by shape, which are co-linear with specific regions of the genes, and potentially associated with transcriptional stages. Full article

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21 pages, 1415 KiB

Open AccessReview

Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer

by Mahnoor Naseer Gondal and Hafiz Muhammad Umer Farooqi

Non-Coding RNA 2025, 11(2), 24; https://doi.org/10.3390/ncrna11020024 - 10 Mar 2025

Abstract

Non-coding RNAs (ncRNAs) play crucial roles in colorectal cancer (CRC) development and progression. Recent developments in single-cell transcriptome profiling methods have revealed surprising levels of expression variability among seemingly homogeneous cells, suggesting the existence of many more cell types than previously estimated. This [...] Read more.

Non-coding RNAs (ncRNAs) play crucial roles in colorectal cancer (CRC) development and progression. Recent developments in single-cell transcriptome profiling methods have revealed surprising levels of expression variability among seemingly homogeneous cells, suggesting the existence of many more cell types than previously estimated. This review synthesizes recent advances in ncRNA research in CRC, emphasizing single-cell bioinformatics approaches for their analysis. We explore computational methods and tools used for ncRNA identification, characterization, and functional prediction in CRC, with a focus on single-cell RNA sequencing (scRNA-seq) data. The review highlights key bioinformatics strategies, including sequence-based and structure-based approaches, machine learning applications, and multi-omics data integration. We discuss how these computational techniques can be applied to analyze differential expression, perform functional enrichment, and construct regulatory networks involving ncRNAs in CRC. Additionally, we examine the role of bioinformatics in leveraging ncRNAs as diagnostic and prognostic biomarkers for CRC. We also discuss recent scRNA-seq studies revealing ncRNA heterogeneity in CRC. This review aims to provide a comprehensive overview of the current state of single-cell bioinformatics in ncRNA CRC research and outline future directions in this rapidly evolving field, emphasizing the integration of computational approaches with experimental validation to advance our understanding of ncRNA biology in CRC. Full article

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26 pages, 2988 KiB

Open AccessArticle

A Multi-Input Neural Network Model for Accurate MicroRNA Target Site Detection

by Mohammad Mohebbi, Amirhossein Manzourolajdad, Ethan Bennett and Phillip Williams

Non-Coding RNA 2025, 11(2), 23; https://doi.org/10.3390/ncrna11020023 - 7 Mar 2025

Abstract

(1) Background: MicroRNAs are non-coding RNA sequences that regulate cellular functions by targeting messenger RNAs and inhibiting protein synthesis. Identifying their target sites is vital to understanding their roles. However, it is challenging due to the high cost and time demands of experimental [...] Read more.

(1) Background: MicroRNAs are non-coding RNA sequences that regulate cellular functions by targeting messenger RNAs and inhibiting protein synthesis. Identifying their target sites is vital to understanding their roles. However, it is challenging due to the high cost and time demands of experimental methods and the high false-positive rates of computational approaches. (2) Methods: We introduce a Multi-Input Neural Network (MINN) algorithm that integrates diverse biologically relevant features, including the microRNA duplex structure, substructures, minimum free energy, and base-pairing probabilities. For each feature derived from a microRNA target-site duplex, we create a corresponding image. These images are processed in parallel by the MINN algorithm, allowing it to learn a comprehensive and precise representation of the underlying biological mechanisms. (3) Results: Our method, on an experimentally validated test set, detects target sites with an AUPRC of 0.9373, Precision of 0.8725, and Recall of 0.8703 and outperforms several commonly used computational methods of microRNA target-site predictions. (4) Conclusions: Incorporating diverse biologically explainable features, such as duplex structure, substructures, their MFEs, and binding probabilities, enables our model to perform well on experimentally validated test data. These features, rather than nucleotide sequences, enhance our model to generalize beyond specific sequence contexts and perform well on sequentially distant samples. Full article

(This article belongs to the Topic MicroRNA: Mechanisms of Action, Physio-Pathological Implications, and Disease Biomarkers, 3rd Edition)

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24 pages, 3439 KiB

Open AccessReview

Mechanism of Action of circRNA/miRNA Network in DLBCL

by Elena Golovina, Cory Eaton, Virginia Cox, Jozef Andel and Karina Savvulidi Vargova

Non-Coding RNA 2025, 11(2), 22; https://doi.org/10.3390/ncrna11020022 - 4 Mar 2025

Abstract

Circular RNAs (circRNAs) make up approximately 10% of the human transcriptome. CircRNAs belong to the broad group of non-coding RNAs and characteristically are formed by backsplicing into a stable circular loop. Their main role is to regulate transcription through the inhibition of miRNAs’ [...] Read more.

Circular RNAs (circRNAs) make up approximately 10% of the human transcriptome. CircRNAs belong to the broad group of non-coding RNAs and characteristically are formed by backsplicing into a stable circular loop. Their main role is to regulate transcription through the inhibition of miRNAs’ expression, termed miRNA sponging. CircRNAs promote tumorigenesis/lymphomagenesis by competitively binding to miRNAs at miRNA binding sites. In diffuse large B-cell lymphoma (DLBCL), several circRNAs have been identified and their expression is related to both progression and response to therapy. DLBCL is the most prevalent and aggressive subtype of B-cell lymphomas and accounts for about 25% to 30% of all non-Hodgkin lymphomas. DLBCL displays great heterogeneity concerning histopathology, biology, and genetics. Patients who have relapsed or have refractory disease after first-line therapy have a very poor prognosis, demonstrating an important unmet need for new treatment options. As more circRNAs are identified in the future, we will better understand their biological roles and potential use in treating cancer, including DLBCL. For example, circAmotl1 promotes nuclear translocation of MYC and upregulation of translational targets of MYC, thus enhancing lymphomagenesis. Another example is circAPC, which is significantly downregulated in DLBCL and correlates with disease aggressiveness and poor prognosis. CircAPC increases expression of the host gene adenomatous polyposis coli (APC), and in doing so inactivates the canonical Wnt/β-catenin signaling and restrains DLBCL growth. MiRNAs belong to the non-coding regulatory molecules that significantly contribute to lymphomagenesis through their target mRNAs. In DLBCL, among the highly expressed miRNAs, are miR-155-5p and miR-21-5p, which regulate NF-ĸB and PI3K/AKT signaling pathways. The aim of this review is to describe the function and mechanism of regulation of circRNAs on miRNAs’ expression in DLBCL. This will help us to better understand the regulatory network of circRNA/miRNA/mRNA, and to propose novel therapeutic targets to treat DLBCL. Full article

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14 pages, 978 KiB

Open AccessReview

MicroRNAs: A Novel Approach for Monitoring Treatment Response in Major Depressive Disorder?

by Cristina-Sorina Cătană, Monica Mihaela Marta, Daniel Ungureanu and Cătălina-Angela Crișan

Non-Coding RNA 2025, 11(2), 21; https://doi.org/10.3390/ncrna11020021 - 3 Mar 2025

Abstract

Major depressive disorder (MDD) is one of the most prevalent psychiatric disorders, with an increasing incidence each year and an important socioeconomic burden. Although new treatments are continuously being developed, there is no effective monitoring method to determine the suitability of treatment and [...] Read more.

Major depressive disorder (MDD) is one of the most prevalent psychiatric disorders, with an increasing incidence each year and an important socioeconomic burden. Although new treatments are continuously being developed, there is no effective monitoring method to determine the suitability of treatment and ensure positive outcomes. Therefore, patients often struggle with ineffective antidepressants and their potential adverse effects, which halts any future progress in managing the disorder. Considering the potential of microRNAs (miRNAs) as biomarkers for various pathologies and the increasing evidence of the modulation of several genes involved in MDD, this minireview aimed to evaluate the literature data on the impact of miRNAs in MDD and their usefulness in monitoring treatment response. The correlations between antidepressants and the expression of several miRNAs support the existence of a common epigenetic mechanism of antidepressants and explain the epigenetic differences influencing treatment efficacy in MDD. Full article

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