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MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 October 2025) | Viewed by 14906

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Dr. Erika Cione

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1. Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Cosenza, Italy
2. Galascreen Laboratories, University of Calabria, Cosenza, Italy
Interests: vitamin A and its provitamin; microRNAs; gene expression; ketogenic diet; lipedema; cognitive and neurodegeneration
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Dear Colleagues,

Out of the central dogma of molecular biology, messenger RNA (mRNA) is translated into protein. The transcriptome biochemical machinery relies on noncoding RNA (ncRNAs), which, unlike mRNA, is not translated into protein. Such ncRNAs comprise over 80% of the transcriptome by mass and are linked to a growing list of functional roles in human physiology, biology, biochemistry, and disease. RNA modulation has become a promising therapeutic approach for the treatment of several types of disease. The emerging field of noncoding RNA-based biomarkers and/or therapies has now come to the attention of several fields of application, in which it could provide valuable advancements compared to current clinical biochemistry and pharmacological treatment, such as small-molecule drugs or antibodies. Microarray technology and the advent of next-generation sequencing (NGS) have significantly broadened our understanding of ncRNAs in recent decades and introduced new opportunities for clinical applications.

The Special Issue is guest edited by Prof. Dr. Erika Cione, with the assistance of Dr. Diana Marisol Abrego Guandique (University of Magna Graecia-Catanzaro). We would like to gather the recent advances in this field, and we are delighted to invite you to contribute.

Prof. Dr. Erika Cione
Guest Editor

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Keywords

miRNA
ncRNA
biomarkers
therapeutics
microarray
NGS

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Published Papers (10 papers)

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Research

19 pages, 2018 KB

Open AccessArticle

Identification of a Novel Salivary Four-miRNA Signature for Non-Invasive Diagnosis of Oral Squamous Cell Carcinoma

by Alessia Ciringione, Giovanni Lilloni, Lucas Moron Dalla Tor, Giuseppe Perlangeli, Federica Rizzi and Tito Poli

Int. J. Mol. Sci. 2025, 26(23), 11373; https://doi.org/10.3390/ijms262311373 - 25 Nov 2025

Viewed by 327

Abstract

Oral squamous cell carcinoma (OSCC) is the most common type of oral cancer, often diagnosed at advanced stages due to the lack of early symptoms and limitations of current invasive diagnostic methods. Salivary microRNAs (miRNAs) have emerged as promising non-invasive biomarkers for early detection. This study evaluated the diagnostic potential of ten miRNAs, selected from literature, in saliva samples from 30 OSCC patients and 30 healthy controls. The workflow included RNA extraction, reverse transcription, qRT-PCR amplification, and data normalization using the mean expression of the two most stable miRNAs identified across and within groups. Five miRNAs showed significant differential expression: miR-21 and miR-424 were upregulated, while miR-31, miR-146a, and let-7a were downregulated in OSCC patients. Receiver operating characteristic (ROC) curve analysis indicated moderate individual diagnostic power (AUC 0.658–0.720). A multivariate logistic regression combining miR-21, miR-31, miR-146a, and miR-424 yielded an AUC of 0.959, 96.7% specificity, and 86.7% sensitivity. Although limited by sample size, this study provides the first step for larger validation studies aimed at confirming the diagnostic utility of our salivary four-miRNA signature as a cost-effective and minimally invasive diagnostic tool for OSCC. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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14 pages, 2363 KB

Open AccessArticle

MicroRNA-210 Suppresses NF-κB Signaling in Lipopolysaccharide-Stimulated Dental Pulp Cells Under Hypoxic Conditions

by Xiyuan Bai, Nobuyuki Kawashima, Shihan Wang, Peifeng Han, Mayuko Fujii, Keisuke Sunada-Nara, Ziniu Yu, Takashi Okiji and Yoshio Yahata

Int. J. Mol. Sci. 2025, 26(22), 10837; https://doi.org/10.3390/ijms262210837 - 7 Nov 2025

Viewed by 428

Abstract

Dental pulp tissue, enclosed within rigid dentin, is susceptible to bacterial invasion via dentinal tubules, often leading to severe pulpal inflammation. This condition is typically associated with a hypoxic microenvironment, yet the mechanistic link between hypoxia and inflammation remains unclear. We identified a marked upregulation of microRNA-210 (miR-210) in human dental pulp cells (hDPCs) cultured under hypoxic conditions. This study investigated the role of miR-210 in modulating inflammation in lipopolysaccharide (LPS)-stimulated hDPCs. Hypoxic conditions and enforced expression of hypoxia-inducible factor 1α (HIF1α) significantly increased miR-210 levels. While LPS stimulation elevated proinflammatory cytokines (Interleukin-6, Monocyte Chemoattractant Protein-1, and Tumor Necrosis Factor Alpha) and activated nuclear factor-kappa B (NF-κB) signaling, miR-210 overexpression suppressed LPS-mediated cytokine production and NF-κB activity. Luciferase assays revealed that miR-210 targets and negatively regulates TGF-beta activated kinase 1 binding protein 1 (TAB1), a key upstream regulator of NF-κB. Transfection with an miR-210 mimic reduced TAB1 expression, NF-κB activation, and cytokine output in both LPS-stimulated hDPCs and rat pulp tissue ex vivo. Conversely, miR-210 inhibition enhanced TAB1 levels and inflammatory cytokine expression under hypoxic conditions. These findings suggest that miR-210 mitigates inflammation via the TAB1–NF-κB pathway, functioning as a negative feedback regulator. miR-210 may represent a promising therapeutic target for pulpal inflammation. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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12 pages, 5310 KB

Open AccessArticle

Overexpression of miR-320-3p, miR-381-3p, and miR-27a-3p Suppresses Genes Related to Midline Facial Cleft in Mouse Cranial Neural Crest Cells

by Chihiro Iwaya, Akiko Suzuki and Junichi Iwata

Int. J. Mol. Sci. 2025, 26(21), 10730; https://doi.org/10.3390/ijms262110730 - 4 Nov 2025

Viewed by 411

Abstract

Midline facial clefts are severe craniofacial defects that occur due to an underdeveloped frontonasal process. While genetic studies in mice have identified several genes that are crucial for midfacial development, the interactions and regulatory mechanisms of these genes during development remain unclear. In this study, we conducted a systematic review and database search to curate genes associated with midline facial clefts in mice. We identified a total of 78 relevant genes, which included 69 single-gene mutant mice, nine spontaneous models, and 20 compound mutant mice. We then performed bioinformatic analyses with these genes to identify candidate microRNAs (miRNAs) that may regulate the expression of genes related to midline facial clefts. Furthermore, we experimentally evaluated the four highest-ranking candidates—miR-320-3p, miR-381-3p, miR-27a-3p, and miR-124-3p—in O9-1 cells. Our results indicated that overexpression of any of these miRNAs inhibited cell proliferation through the suppression of genes associated with midline facial clefts. Thus, our results suggest that miR-320-3p, miR-381-3p, miR-27a-3p, and miR-124-3p are involved in the cause of midline facial anomalies. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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19 pages, 3656 KB

Open AccessArticle

Large-Scale Profiling of Coding and Long Noncoding Transcriptomes in the Hippocampus of Mice Acutely Exposed to Vaporized CBD or THC

by Mi Ran Choi, Jihun Kim, Chaeeun Park, Seok Hwan Chang, Han-Na Kim, Yeung Bae Jin and Sang-Rae Lee

Int. J. Mol. Sci. 2025, 26(15), 7106; https://doi.org/10.3390/ijms26157106 - 23 Jul 2025

Cited by 1 | Viewed by 930

Abstract

Cannabis vaping, particularly involving cannabidiol (CBD) and delta-9-tetrahydrocannabinol (THC), rapidly delivers highly concentrated cannabinoids to the brain, potentially affecting the hippocampus. This study examined differential expression of long noncoding RNAs (lncRNAs) and mRNAs in the hippocampus after acute exposure to vaporized CBD or THC. Male ICR mice were exposed to vaporized CBD or THC (50 mg, n = 5/group), and hippocampal tissues were collected at 1, 3, and 14 days post-exposure. Total RNA sequencing was conducted on day 1 samples, and selected transcripts were validated using qRT-PCR across multiple time points. CBD led to significant up- or downregulation of L3mbtl1, Wnt7a, and Camk2b at day 1. However, Wnt7a showed gradual recovery at days 3 and 14. In the THC group, Grin2a, Gria3, and Golga2 were significantly upregulated, while Drd1, Drd2, Gnal, and Adcy5 were significantly downregulated at day 1. Time-course analysis showed that Drd2 expression returned to baseline by day 14, whereas Adcy5 remained persistently downregulated through days 3 and 14. In the CBD group, NONMMUT069014.2 was upregulated, while NONMMUT033147.2 and NONMMUT072606.2 were downregulated at day 1; notably, NONMMUT072606.2 showed a transient increase at day 3 before returning to baseline. In the THC group, NONMMUT085523.1 and NONMMUT123548.1 were upregulated, whereas NONMMUT019734.2, NONMMUT057101.2, and NONMMUT004928.2 were downregulated, with most showing gradual recovery by day 14. Correlation analysis revealed that THC-responsive lncRNAs—including NONMMUT004928.2, NONMMUT057101.2, and NONMMUT019734.2—were strongly associated with downregulated mRNAs such as Drd2 and Adcy5. These findings highlight cannabinoid-specific hippocampal transcriptomic responses and suggest potential regulatory roles for lncRNA–mRNA interactions in cannabinoid-induced neural changes. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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19 pages, 2651 KB

Open AccessArticle

Temporal Shifts in MicroRNAs Signify the Inflammatory State of Primary Murine Microglial Cells

by Keren Zohar, Elyad Lezmi, Fanny Reichert, Tsiona Eliyahu, Shlomo Rotshenker, Marta Weinstock and Michal Linial

Int. J. Mol. Sci. 2025, 26(12), 5677; https://doi.org/10.3390/ijms26125677 - 13 Jun 2025

Cited by 1 | Viewed by 1212

Abstract

The primary function of microglia is to maintain brain homeostasis. In neurodegenerative diseases like Alzheimer’s, microglia contribute to neurotoxicity and inflammation. In this study, we exposed neonatal murine primary microglial cultures to stimuli mimicking pathogens, injury, or toxins. Treatment with benzoyl ATP (bzATP) and lipopolysaccharide (LPS) triggered a coordinated increase in interleukin and chemokine expression. We analyzed statistically significant differentially expressed microRNAs (DEMs) at 3 and 8 h post-activation, identifying 33 and 57 DEMs, respectively. Notably, miR-155, miR-132, miR-3473e, miR-222, and miR-146b showed strong temporal regulation, while miR-3963 was sharply downregulated by bzATP. These DEMs regulate inflammatory pathways, including TNFα and NFκB signaling. We also examined the effect of ladostigil, a neuroprotective agent known to reduce oxidative stress and inflammation. At 8 h post-activation, ladostigil induced upregulation of anti-inflammatory miRNAs, such as miR-27a, miR-27b, and miR-23b. Our findings suggest that miRNA profiles reflect microglial responses to inflammatory cues and that ladostigil modulates these responses. This model of controlled microglial activation offers a powerful tool with which to study inflammation in the aging brain and the progression of neurodegenerative diseases. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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20 pages, 12993 KB

Open AccessArticle

MicroRNA Profiling Identifies Age-Associated MicroRNAs and Potential Biomarkers for Early Diagnosis of Autism

by Salam Salloum-Asfar, Samia M. Ltaief, Rowaida Z. Taha, Wared Nour-Eldine, Sara A. Abdulla and Abeer R. Al-Shammari

Int. J. Mol. Sci. 2025, 26(5), 2044; https://doi.org/10.3390/ijms26052044 - 26 Feb 2025

Cited by 3 | Viewed by 2127 | Correction

Abstract

Autism spectrum disorder (ASD) is a neurodevelopmental disorder in which early diagnosis is critical for effective intervention and improved outcomes. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression and have emerged as promising biomarkers for neurological disorders, including ASD. In our previous discovery study, we identified dysregulated expression of several miRNAs in the plasma samples of children with ASD aged 5–12 years. In this study, we aimed to validate these findings in a younger cohort with ASD (aged 2–4 years) and assess their potential use as biomarkers for the early diagnosis of ASD. A total of 108 young children aged 2–4 years were recruited, including 66 children with ASD and 42 age- and sex-matched controls. Using next-generation sequencing and advanced bioinformatics, we validated the differential expression of 17 miRNAs in ASD, which showed consistent dysregulation across both the current and previous cohorts. We also observed significant correlations between several miRNAs and participants’ age, suggesting that age is a key factor influencing dynamic miRNA changes, particularly in the ASD group. Pathway analysis linked these miRNAs to critical regulatory networks involved in neurodevelopment and immune responses. Finally, we found that a combination of four miRNAs (miR-4433b-5p, miR-15a-5p, miR-335-5p, and miR-1180-3p) exhibited high diagnostic accuracy, with an area under the curve (ROC-AUC) of 0.936 (95% CI = 0.892, 0.980; p < 0.001). These findings support the use of this four-miRNA panel as a robust biomarker for early ASD diagnosis and lay the groundwork for future research into miRNA-based diagnostic tools and therapeutic strategies for ASD. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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25 pages, 3766 KB

Open AccessArticle

Identification and Functional Analysis of Key microRNAs in the Early Extrauterine Environmental Adaptation of Piglets

by Mingxing Wen, Jing Li, Wanling Qiu, Jinwei Zhang, Keren Long, Lu Lu, Long Jin, Jing Sun, Liangpeng Ge, Xuewei Li, Mingzhou Li and Jideng Ma

Int. J. Mol. Sci. 2025, 26(3), 1316; https://doi.org/10.3390/ijms26031316 - 4 Feb 2025

Viewed by 1226

Abstract

Neonatal mammals must rapidly adapt to significant physiological changes during the transition from the intrauterine to extrauterine environments. This adaptation, particularly in the metabolic and respiratory systems, is essential for survival. MicroRNAs (miRNAs) are small noncoding RNAs that regulate various physiological and pathological processes by binding to the 3′ untranslated regions of mRNAs. This study aimed to identify miRNAs involved in the early extrauterine adaptation of neonatal piglets and explore their functions. We performed small RNA sequencing on six tissues (heart, liver, spleen, lung, multifidus muscle, and duodenum) from piglets 24 h before birth (day 113 of gestation) and 6 h after birth. A total of 971 miRNA precursors and 1511 mature miRNAs were identified. Tissue-specific expression analysis revealed 881 tissue-specific miRNAs and 164 differentially expressed miRNAs (DE miRNAs) across the tissues. Functional enrichment analysis showed that these DE miRNAs are significantly enriched in pathways related to early extrauterine adaptation, such as the NFκB, PI3K/AKT, and Hippo pathways. Specifically, miR-22-3p was significantly upregulated in the liver post-birth and may regulate the PI3K/AKT pathway by targeting AKT3, promoting gluconeogenesis, and maintaining glucose homeostasis. Dual-luciferase reporter assays and HepG2 cell experiments confirmed AKT3 as a target of miR-22-3p, which activates the AKT/FoxO1 pathway, enhancing gluconeogenesis and glucose production. Furthermore, changes in blood glucose and liver glycogen levels in newborn piglets further support the role of miR-22-3p in glucose homeostasis. This study highlights the importance of miRNAs, particularly miR-22-3p, in the early extrauterine adaptation of neonatal piglets, offering new insights into the physiological adaptation of neonatal mammals. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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22 pages, 5135 KB

Open AccessArticle

β-Carotene Impacts the Liver MicroRNA Profile in a Sex-Specific Manner in Mouse Offspring of Western Diet-Fed Mothers: Results from Microarray Analysis by Direct Hybridization

by Diana Marisol Abrego-Guandique, Sebastià Galmés, Adrián García-Rodríguez, Roberto Cannataro, Maria Cristina Caroleo, Joan Ribot, Maria Luisa Bonet and Erika Cione

Int. J. Mol. Sci. 2024, 25(23), 12899; https://doi.org/10.3390/ijms252312899 - 30 Nov 2024

Cited by 4 | Viewed by 1851

Abstract

Maternal unbalanced diets cause adverse metabolic programming and affect the offspring’s liver microRNA (miRNA) profile. The liver is a site of β-carotene (BC) metabolism and a target of BC action. We studied the interaction of maternal Western diet (WD) and early-life BC supplementation on the epigenetic remodeling of offspring’s liver microRNAs. Mouse offspring of WD-fed mothers were given a daily placebo (controls) or BC during suckling. Biometric parameters and liver miRNAome by microarray hybridization were analyzed in newly weaned animals. BC sex-dependently impacted the liver triacylglycerol content. The liver miRNAome was also differently affected in male and female offspring, with no overlap in differentially expressed (DE) miRNAs between sexes and more impact in females. Bioinformatic analysis of DE miRNA predicted target genes revealed enrichment in biological processes/pathways related to metabolic processes, regulation of developmental growth and circadian rhythm, liver homeostasis and metabolism, insulin resistance, and neurodegeneration, among others, with differences between sexes. Fifty-five percent of the overlapping target genes in both sexes identified were targeted by DE miRNAs changed in opposite directions in males and females. The results identify sex-dependent responses of the liver miRNA expression profile to BC supplementation during suckling and may sustain further investigations regarding the long-term impact of early postnatal life BC supplementation on top of an unbalanced maternal diet. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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14 pages, 2345 KB

Open AccessArticle

The Protective Role of miR-130b-3p Against Palmitate-Induced Lipotoxicity in Cardiomyocytes Through PPARγ Pathway

by Elena Alonso-Villa, Alipio Mangas, Fernando Bonet, Óscar Campuzano, Maribel Quezada-Feijoo, Mónica Ramos, Carlos García-Padilla, Diego Franco and Rocio Toro

Int. J. Mol. Sci. 2024, 25(22), 12161; https://doi.org/10.3390/ijms252212161 - 13 Nov 2024

Cited by 3 | Viewed by 2081

Abstract

Excess lipid accumulation in the heart is associated with lipotoxicity and cardiac dysfunction due to excessive fatty acid oxidation. Peroxisome proliferator-activated receptor gamma (PPARγ) modulates the expression of key molecules involved in the FA metabolic pathway. Cardiomyocyte-specific overexpression of PPARγ causes dilated cardiomyopathy associated with lipotoxicity in mice. miR-130b-3p has been shown to be downregulated in the plasma of idiopathic dilated cardiomyopathy patients, but its role in modulating cardiomyocyte lipotoxicity via PPARγ remains unclear. Our objective was to investigate the protective role of miR-130b-3p against palmitate-induced lipotoxicity in cardiomyocytes through the modulation of the PPARγ signaling pathway. Human cardiomyoblasts were treated with palmitate. Intracellular lipid accumulation and expression of PPARγ and its downstream targets (CD36, FABP3, CAV1, VLDLR) were analyzed. Mitochondrial oxidative stress was assessed via MitoTracker Green and Redox Sensor Red staining and expression of CPT1B and SOD2. Endoplasmic reticulum stress and apoptosis were determined by examining GRP78, ATF6, XBP1s, CHOP, and caspase-3 expression. miR-130b-3p overexpression was achieved using transfection methods, and its effect on these parameters was evaluated. Luciferase assays were used to confirm PPARγ as a direct target of miR-130b-3p. Palmitate treatment led to increased lipid accumulation and upregulation of PPARγ and its downstream targets in human cardiomyoblasts. Palmitate also increased mitochondrial oxidative stress, endoplasmic reticulum stress and apoptosis. miR-130b-3p overexpression reduced PPARγ expression and its downstream signaling, alleviated mitochondrial oxidative stress and decreased endoplasmic reticulum stress and apoptosis in palmitate-stimulated cardiomyoblasts. Luciferase assays confirmed PPARγ as a direct target of miR-130b-3p. Our findings suggest that miR-130b-3p plays a protective role against palmitate-induced lipotoxicity in cardiomyocytes by modulating the PPARγ signaling pathway. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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25 pages, 2287 KB

Open AccessArticle

Long Non-Coding RNAs and Alzheimer’s Disease: Towards Personalized Diagnosis

by Maria I. Mosquera-Heredia, Oscar M. Vidal, Luis C. Morales, Carlos Silvera-Redondo, Ernesto Barceló, Ricardo Allegri, Mauricio Arcos-Burgos, Jorge I. Vélez and Pilar Garavito-Galofre

Int. J. Mol. Sci. 2024, 25(14), 7641; https://doi.org/10.3390/ijms25147641 - 11 Jul 2024

Cited by 5 | Viewed by 3053

Abstract

Alzheimer’s disease (AD), a neurodegenerative disorder characterized by progressive cognitive decline, is the most common form of dementia. Currently, there is no single test that can diagnose AD, especially in understudied populations and developing countries. Instead, diagnosis is based on a combination of medical history, physical examination, cognitive testing, and brain imaging. Exosomes are extracellular nanovesicles, primarily composed of RNA, that participate in physiological processes related to AD pathogenesis such as cell proliferation, immune response, and neuronal and cardiovascular function. However, the identification and understanding of the potential role of long non-coding RNAs (lncRNAs) in AD diagnosis remain largely unexplored. Here, we clinically, cognitively, and genetically characterized a sample of 15 individuals diagnosed with AD (cases) and 15 controls from Barranquilla, Colombia. Advanced bioinformatics, analytics and Machine Learning (ML) techniques were used to identify lncRNAs differentially expressed between cases and controls. The expression of 28,909 lncRNAs was quantified. Of these, 18 were found to be differentially expressed and harbored in pivotal genes related to AD. Two lncRNAs, ENST00000608936 and ENST00000433747, show promise as diagnostic markers for AD, with ML models achieving > 95% sensitivity, specificity, and accuracy in both the training and testing datasets. These findings suggest that the expression profiles of lncRNAs could significantly contribute to advancing personalized AD diagnosis in this community, offering promising avenues for early detection and follow-up. Full article

(This article belongs to the Special Issue MicroRNA and Non-Coding RNA: From Basic Research to Potential Clinical Application)

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