Non-coding RNAs in Health and Disease 2.0

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Cell Biology and Pathology".

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 7529

Special Issue Editor

Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
Interests: cancer cell biology; microRNAs; pediatric brain tumors; metabolic diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The idea that genetic information travelling towards proteins has long represented the “central dogma” of molecular biology. However, proteins are encoded only from the 2% of the human genome, while the widest part is represented by non-coding transcriptome. Non-coding RNAs (nc-RNAs) indeed comprise the largest part of the transcriptional production of the human genome, playing pivotal roles in both health and disease processes. Some of them, such as microRNAs and circular RNAs (circRNAs), are highly conserved across species; others, such as long non-coding RNAs (lnc-RNAs), lack conservation. Nc-RNAs are especially involved in regulatory functions; moreover, they can interact with each other to regulate stability or abundance. These interactions are of the utmost importance in the regulation of many different cellular programs. As a result, their dysregulation, as well as the perturbation of their interactions, may have striking consequences. In addition, nc-RNAs have also recently been described in the extracellular compartment, therefore inferring that they mediate cell-to-cell communication and act as disease-specific diagnostic, prognostic and treatment response biomarkers.

This Special Issue aims to focus on the role of the different species of nc-RNAs in controlling pivotal biological mechanisms, such as gene expression and developmental pathways, and on analyzing their dysregulation in the context of many different human diseases, spanning from metabolic, neurological and cardiovascular diseases to cancer. Moreover, it will concentrate on the possibility of using these molecules as biomarkers, with the potential to use liquid biopsies in modern precision medicine. Original research articles and comprehensive reviews are both welcomed here.

Dr. Giuseppina Catanzaro
Guest Editor

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Keywords

  • non-coding RNAs
  • cellular pathways
  • developmental pathways
  • gene expression
  • metabolic diseases
  • neurological diseases
  • cardiovascular diseases
  • cancer
  • liquid biopsy
  • biomarkers

Published Papers (5 papers)

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13 pages, 1435 KiB  
Article
Development of a Novel Endometrial Signature Based on Endometrial microRNA for Determining the Optimal Timing for Embryo Transfer
by Ching-Hung Chen, Farn Lu, Wen-Jui Yang, Wei-Ming Chen, Pok Eric Yang, Shih-Ting Kang, Tiffany Wang, Po-Chang Chang, Chi-Ting Feng, Jung-Hsuan Yang, Chen-Yu Liu, Chi-An Hsieh, Lily Hui-Ching Wang and Jack Yu-Jen Huang
Biomedicines 2024, 12(3), 700; https://doi.org/10.3390/biomedicines12030700 - 21 Mar 2024
Viewed by 343
Abstract
Though tremendous advances have been made in the field of in vitro fertilization (IVF), a portion of patients are still affected by embryo implantation failure issues. One of the most significant factors contributing to implantation failure is a uterine condition called displaced window [...] Read more.
Though tremendous advances have been made in the field of in vitro fertilization (IVF), a portion of patients are still affected by embryo implantation failure issues. One of the most significant factors contributing to implantation failure is a uterine condition called displaced window of implantation (WOI), which refers to an unsynchronized endometrium and embryo transfer time for IVF patients. Previous studies have shown that microRNAs (miRNAs) can be important biomarkers in the reproductive process. In this study, we aim to develop a miRNA-based classifier to identify the WOI for optimal time for embryo transfer. A reproductive-related PanelChip® was used to obtain the miRNA expression profiles from the 200 patients who underwent IVF treatment. In total, 143 out of the 167 miRNAs with amplification signals across 90% of the expression profiles were utilized to build a miRNA-based classifier. The microRNA-based classifier identified the optimal timing for embryo transfer with an accuracy of 93.9%, a sensitivity of 85.3%, and a specificity of 92.4% in the training set, and an accuracy of 88.5% in the testing set, showing high promise in accurately identifying the WOI for the optimal timing for embryo transfer. Full article
(This article belongs to the Special Issue Non-coding RNAs in Health and Disease 2.0)
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13 pages, 3278 KiB  
Article
CircAFF1 Is a Circular RNA with a Role in Alveolar Rhabdomyosarcoma Cell Migration
by Alvaro Centrón-Broco, Francesca Rossi, Chiara Grelloni, Raffaele Garraffo, Dario Dattilo, Andrea Giuliani, Gaia Di Timoteo, Alessio Colantoni, Irene Bozzoni and Manuel Beltran Nebot
Biomedicines 2023, 11(7), 1893; https://doi.org/10.3390/biomedicines11071893 - 04 Jul 2023
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Abstract
Circular RNAs (circRNAs), covalently closed RNAs that originate from back-splicing events, participate in the control of several processes, including those that occur in the development of pathological conditions such as cancer. Hereby, we describe circAFF1, a circular RNA overexpressed in alveolar rhabdomyosarcoma. Using [...] Read more.
Circular RNAs (circRNAs), covalently closed RNAs that originate from back-splicing events, participate in the control of several processes, including those that occur in the development of pathological conditions such as cancer. Hereby, we describe circAFF1, a circular RNA overexpressed in alveolar rhabdomyosarcoma. Using RH4 and RH30 cell lines, a classical cell line models for alveolar rhabdomyosarcoma, we demonstrated that circAFF1 is a cytoplasmatic circRNA and its depletion impacts cell homeostasis favouring cell migration through the downregulation of genes involved in cell adhesion pathways. The presented data underline the importance of this circular RNA as a new partial suppressor of the alveolar rhabdomyosarcoma tumour progression and as a putative future therapeutic target. Full article
(This article belongs to the Special Issue Non-coding RNAs in Health and Disease 2.0)
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27 pages, 4077 KiB  
Article
MicroRNA Signatures in Cartilage Ageing and Osteoarthritis
by Panagiotis Balaskas, Katarzyna Goljanek-Whysall, Peter D. Clegg, Yongxiang Fang, Andy Cremers, Aibek Smagul, Tim J. M. Welting and Mandy J. Peffers
Biomedicines 2023, 11(4), 1189; https://doi.org/10.3390/biomedicines11041189 - 17 Apr 2023
Cited by 5 | Viewed by 1569
Abstract
Osteoarthritis is the most common degenerative joint disorder. MicroRNAs are gene expression regulators that act post-transcriptionally to control tissue homeostasis. Microarray analysis was undertaken in osteoarthritic intact, lesioned and young intact cartilage. Principal component analysis showed that young intact cartilage samples were clustered [...] Read more.
Osteoarthritis is the most common degenerative joint disorder. MicroRNAs are gene expression regulators that act post-transcriptionally to control tissue homeostasis. Microarray analysis was undertaken in osteoarthritic intact, lesioned and young intact cartilage. Principal component analysis showed that young intact cartilage samples were clustered together; osteoarthritic samples had a wider distribution; and osteoarthritic intact samples were separated into two subgroups, osteoarthritic-Intact-1 and osteoarthritic-Intact-2. We identified 318 differentially expressed microRNAs between young intact and osteoarthritic lesioned cartilage, 477 between young intact and osteoarthritic-Intact-1 cartilage and 332 between young intact and osteoarthritic-Intact-2 cartilage samples. For a selected list of differentially expressed microRNAs, results were verified in additional cartilage samples using qPCR. Of the validated DE microRNAs, four—miR-107, miR-143-3p, miR-361-5p and miR-379-5p—were selected for further experiments in human primary chondrocytes treated with IL-1β. Expression of these microRNAs decreased in human primary chondrocytes treated with IL-1β. For miR-107 and miR-143-3p, gain- and loss-of-function approaches were undertaken and associated target genes and molecular pathways were investigated using qPCR and mass spectrometry proteomics. Analyses showed that WNT4 and IHH, predicted targets of miR-107, had increased expression in osteoarthritic cartilage compared to young intact cartilage and in primary chondrocytes treated with miR-107 inhibitor, and decreased expression in primary chondrocytes treated with miR-107 mimic, suggesting a role of miR-107 in chondrocyte survival and proliferation. In addition, we identified an association between miR-143-3p and EIF2 signalling and cell survival. Our work supports the role of miR-107 and miR-143-3p in important chondrocyte mechanisms regulating proliferation, hypertrophy and protein translation. Full article
(This article belongs to the Special Issue Non-coding RNAs in Health and Disease 2.0)
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16 pages, 4651 KiB  
Article
A Panel of Circulating Non-Coding RNAs in the Diagnosis and Monitoring of Therapy in Egyptian Patients with Breast Cancer
by Nadine Wehida, Wafaa Abdel-Rehim, Hazem El Mansy, Ahmed Karmouty and Maher A. Kamel
Biomedicines 2023, 11(2), 563; https://doi.org/10.3390/biomedicines11020563 - 15 Feb 2023
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Abstract
Background: Non-coding RNAs (ncRNAs) have recently been identified to have a pivotal role in many diseases, including breast cancer (BC). This study aims to investigate the relative quantification of long non-coding RNA (lncRNA) H19, microRNA (miR) 675-5p, 675-3p, and miR-let 7 in breast [...] Read more.
Background: Non-coding RNAs (ncRNAs) have recently been identified to have a pivotal role in many diseases, including breast cancer (BC). This study aims to investigate the relative quantification of long non-coding RNA (lncRNA) H19, microRNA (miR) 675-5p, 675-3p, and miR-let 7 in breast cancer patients. Methods: The study was performed on three groups: Group 1: 30 non-intervened BC female patients about to undergo breast surgery; group 2: 30 postoperative female BC patients about to receive adjuvant anthracycline chemotherapy; and group 3: 30 apparently healthy female volunteers as the control group. Plasma samples were drawn before and after the intervention in groups 1 and 2, with a single sample drawn from group 3. The relative quantification levels were compared with healthy control subjects and were related with the clinicopathological statuses of these patients. Results: There was a statistically significant increase in H19, miR-675-5p, miR-675-3p, and miR-let 7 in the non-intervened BC patients when compared to the control group. Surgery resulted in a significant reduction in all four ncRNAs under investigation. Chemotherapy brought about a significant increase in the level of miR-let 7, with no significant effect on the remaining parameters measured. The assay discriminated normal from BC where a receiver operating characteristic for the area under the curve (ROCAUC) of miR-675-3p showed the maximal AUC of 1.000. The diagnostic sensitivity and specificity were also 100% when CA 15-3 and H19 were combined. Conclusion: The results strongly indicate that the panel of ncRNAs in this study can all potentially act as novel biomarkers whether alone or combined in the diagnosis of BC. Full article
(This article belongs to the Special Issue Non-coding RNAs in Health and Disease 2.0)
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20 pages, 2522 KiB  
Systematic Review
MiRNAs Action and Impact on Mitochondria Function, Metabolic Reprogramming and Chemoresistance of Cancer Cells: A Systematic Review
by Daiane Rosolen, Emanuelle Nunes-Souza, Rafael Marchi, Maria Vitoria Tofolo, Valquíria C. Antunes, Fernanda C. B. Berti, Aline S. Fonseca and Luciane R. Cavalli
Biomedicines 2023, 11(3), 693; https://doi.org/10.3390/biomedicines11030693 - 24 Feb 2023
Cited by 8 | Viewed by 1982
Abstract
MicroRNAs (miRNAs) are involved in the regulation of mitochondrial function and homeostasis, and in the modulation of cell metabolism, by targeting known oncogenes and tumor suppressor genes of metabolic-related signaling pathways involved in the hallmarks of cancer. This systematic review focuses on articles [...] Read more.
MicroRNAs (miRNAs) are involved in the regulation of mitochondrial function and homeostasis, and in the modulation of cell metabolism, by targeting known oncogenes and tumor suppressor genes of metabolic-related signaling pathways involved in the hallmarks of cancer. This systematic review focuses on articles describing the role, association, and/or involvement of miRNAs in regulating the mitochondrial function and metabolic reprogramming of cancer cells. Following the PRISMA guidelines, the articles reviewed were published from January 2010 to September 2022, with the search terms “mitochondrial microRNA” and its synonyms (mitochondrial microRNA, mitochondrial miRNA, mito microRNA, or mitomiR), “reprogramming metabolism,” and “cancer” in the title or abstract). Thirty-six original research articles were selected, revealing 51 miRNAs with altered expression in 12 cancers: bladder, breast, cervical, colon, colorectal, liver, lung, melanoma, osteosarcoma, pancreatic, prostate, and tongue. The actions of miRNAs and their corresponding target genes have been reported mainly in cell metabolic processes, mitochondrial dynamics, mitophagy, apoptosis, redox signaling, and resistance to chemotherapeutic agents. Altogether, these studies support the role of miRNAs in the metabolic reprogramming hallmark of cancer cells and highlight their potential as predictive molecular markers of treatment response and/or targets that can be used for therapeutic intervention. Full article
(This article belongs to the Special Issue Non-coding RNAs in Health and Disease 2.0)
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