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RNA in Human Diseases: Challenges and Opportunities

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

Deadline for manuscript submissions: 20 January 2025 | Viewed by 7098

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Prof. Nicoletta Potenza

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Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania “L. Vanvitelli”, Via Vivaldi, 43-81100 Caserta, Italy
Interests: microRNAs; lncRNA; non-coding RNA; cancer
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Special Issue Information

Dear Colleagues,

Our understanding of RNA biology has expanded tremendously over the last two decades. On the one hand, the deep knowledge of post-transcriptional processes sustained by RNA molecules, including splicing, editing, chemical modification, translation and degradation, has revealed the impact of their mis-regulation on human diseases, recently referred to as “RNA disease”. On the other hand, the discovery of a plethora of non-coding RNA biotypes, representing the majority of mammalian transcriptomes, including microRNAs, long non-coding RNAs and circular RNAs, unveiled the previously unappreciated regulatory role of RNA, beyond serving as a carrier of genetic information between DNA and proteins. Many studies revealed functional interactions among coding and non-coding RNAs, often in a competitive way when they bind to shared microRNAs, giving rise to complex RNA regulatory networks, wherein the unbalancing of any network component can act as a driving force for human diseases, as demonstrated for various cancer types.

The double face of RNA biology studies, representing a challenge for human diseases but also an opportunity for therapeutics, has become particularly clear during the COVID-19 pandemic: people outside the research world are also now aware that RNA molecules, even carried by viruses, impact our health but can indeed save the day by exploiting them as innovative and effective vaccines.

This Special Issue welcomes original research manuscripts unraveling new facets of RNA biology and novel RNA regulatory networks, potentially useful as RNA-targeted and RNA-based therapies for drug hunters, or reporting innovative methodological approaches, including new diagnostic and bioinformatic tools, shaping the future of personalized medicine. Critical review manuscripts with an RNA-centric perspective vision setting the stage for future research are also especially welcome.

Prof. Nicoletta Potenza
Guest Editor

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Keywords

microRNA
piRNA
lncRNA
circRNA
RNA therapeutics
ceRNET
RNA disease
RNA processing
RNA modification

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19 pages, 1095 KiB

Open AccessArticle

Exploring the Chemopreventive Effect of Medication on Gene Expression Linked to Colorectal Cancer: An Observational and Mendelian Randomization Analysis in Healthy Colon Mucosa

by Ferran Moratalla-Navarro, Robert Carreras-Torres, Virginia Díez-Obrero, Matthew Devall, Mireia Obón-Santacana, Anna Díez-Villanueva, Elisabet Guinó, Graham Casey, Li Li and Victor Moreno

Int. J. Mol. Sci. 2024, 25(21), 11395; https://doi.org/10.3390/ijms252111395 - 23 Oct 2024

Viewed by 786

Abstract

Gene expression appears altered in apparently normal tissue surrounding tumor tissue. The observed biological alterations in the tumor microenvironment play a crucial role in cancer development and are named the cancer field effect (FE). A robust set of overexpressed FE genes in tissue surrounding colorectal cancer (CRC) tumor were identified in previous studies. Our study aimed to investigate the influence of common medication intake and modifiable risk factors on FE gene expression using a colonic mucosa sample dataset of healthy individuals (BarcUVa-Seq). We applied expression enrichment analysis of the FE genes for each studied medication and factor. Both observational and instrumental (Mendelian randomization) analysis were conducted, and the results were validated using independent datasets. The findings from the observational and instrumental analyses consistently showed that medication intake, especially metformin, considerably downregulated the FE genes. Chemopreventive effects were also noted for antihypertensive drugs targeting the renin–angiotensin system. Conversely, benzodiazepines usage might upregulate FE genes, thus fostering a tumor-promoting microenvironment. In contrast, the findings from the observational and instrumental analyses on modifiable risk factors showed some discrepancies. The instrumental results indicated that obesity and smoking might promote a tumor-favorable microenvironment. These findings offer insights into the biological mechanisms through which risk factors might influence CRC development and highlight the potential chemopreventive roles of metformin and antihypertensive drugs in CRC risk. Full article

(This article belongs to the Special Issue RNA in Human Diseases: Challenges and Opportunities)

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34 pages, 31389 KiB

Open AccessArticle

Identification of Stage-Specific microRNAs that Govern the Early Stages of Sequential Oral Oncogenesis by Strategically Bridging Human Genetics with Epigenetics and Utilizing an Animal Model

by Iphigenia Gintoni, Stavros Vassiliou, George P. Chrousos and Christos Yapijakis

Int. J. Mol. Sci. 2024, 25(14), 7642; https://doi.org/10.3390/ijms25147642 - 12 Jul 2024

Viewed by 927

Abstract

Oral squamous cell carcinoma (OSCC) is a highly prevalent and aggressive malignancy, with mortality rates reaching 60%, mainly due to its excessive diagnostic delay. MiRNAs, a class of crucial epigenetic gene-expression regulators, have emerged as potential diagnostic biomarkers, with >200 molecules exhibiting expressional dysregulation in OSCC. We had previously established an in silico methodology for the identification of the most disease-specific molecules by bridging genetics and epigenetics. Here, we identified the stage-specific miRNAs that govern the asymptomatic early stages of oral tumorigenesis by exploiting seed-matching and the reverse interplay between miRNA levels and their target genes’ expression. Incorporating gene-expression data from our group’s experimental hamster model of sequential oral oncogenesis, we bioinformatically detected the miRNAs that simultaneously target/regulate >75% of the genes that are characteristically upregulated or downregulated in the consecutive stages of hyperplasia, dysplasia, and early invasion, while exhibiting the opposite expressional dysregulation in OSCC-derived tissue and/or saliva specimens. We found that all stages share the downregulation of miR-34a-5p, miR124-3p, and miR-125b-5p, while miR-1-3p is under-expressed in dysplasia and early invasion. The malignant early-invasion stage is distinguished by the downregulation of miR-147a and the overexpression of miR-155-5p, miR-423-3p, and miR-34a-5p. The identification of stage-specific miRNAs may facilitate their utilization as biomarkers for presymptomatic OSCC diagnosis. Full article

(This article belongs to the Special Issue RNA in Human Diseases: Challenges and Opportunities)

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15 pages, 1661 KiB

Open AccessArticle

Serum Expression of miR-23a-3p and miR-424-5p Indicate Specific Polycystic Ovary Syndrome Phenotypes: A Pilot Study

by Olivia Trummer, Jonas Hoeller, Sharmaine Reintar, Veronika Tandl, Ines Foessl, Valentin Borzan, Verena Theiler-Schwetz, Christian Trummer, Elisabeth Lerchbaum and Barbara Obermayer-Pietsch

Int. J. Mol. Sci. 2024, 25(6), 3205; https://doi.org/10.3390/ijms25063205 - 11 Mar 2024

Viewed by 1463

Abstract

MicroRNAs (miRNAs) are single-stranded, non-coding RNAs that regulate mRNA expression on a post-transcriptional level. Observational studies suggest an association of serum miRNAs and polycystic ovary syndrome (PCOS), a common heterogeneous endocrinopathy characterized by hyperandrogenism (HA), oligo- or amenorrhea (OM) and polycystic ovaries. It is not known whether these miRNA profiles also differ between PCOS phenotypes. In this pilot study, we compared serum expression profiles between the four PCOS phenotypes (A–D) and analyzed them both in PCOS (all phenotypes) and in phenotypes with HA by quantitative-real-time PCR (qRT-PCR). The serum expression of miR-23a-3p was upregulated in phenotype B (n = 10) and discriminated it from phenotypes A (n = 11), C (n = 11) and D (n = 11, AUC = 0.837; 95%CI, 0.706–0.968; p = 0.006). The expression of miR-424-5p was downregulated in phenotype C (n = 11) and discriminated it from phenotypes A, B and D (AUC = 0.801; 95%CI, 0.591–1.000; p = 0.007). MiR-93-5p expression was downregulated in women with PCOS (all phenotypes, n = 42) compared to controls (n = 8; p = 0.042). Phenotypes with HA (A, B, C; n = 32) did not show differences in the analyzed expression pattern. Our data provide new insights into phenotype-specific miRNA alterations in the serum of women with PCOS. Understanding the differential hormonal and miRNA profiles across PCOS phenotypes is important to improve the pathophysiological understanding of PCOS heterogeneity. Full article

(This article belongs to the Special Issue RNA in Human Diseases: Challenges and Opportunities)

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12 pages, 4177 KiB

Open AccessArticle

Comparative RNA-Seq Analysis Revealed Tissue-Specific Splicing Variations during the Generation of the PDX Model

by Eun Ji Lee, Seung-Jae Noh, Huiseon Choi, Min Woo Kim, Su Jin Kim, Yeon Ah Seo, Ji Eun Jeong, Inkyung Shin, Jong-Seok Kim, Jong-Kwon Choi, Dae-Yeon Cho and Suhwan Chang

Int. J. Mol. Sci. 2023, 24(23), 17001; https://doi.org/10.3390/ijms242317001 - 30 Nov 2023

Cited by 1 | Viewed by 1349

Abstract

Tissue-specific gene expression generates fundamental differences in the function of each tissue and affects the characteristics of the tumors that are created as a result. However, it is unclear how much the tissue specificity is conserved during grafting of the primary tumor into an immune-compromised mouse model. Here, we performed a comparative RNA-seq analysis of four different primary-patient derived xenograft (PDX) tumors. The analysis revealed a conserved RNA biotype distribution of primary−PDX pairs, as revealed by previous works. Interestingly, we detected significant changes in the splicing pattern of PDX, which was mainly comprised of skipped exons. This was confirmed by splicing variant-specific RT-PCR analysis. On the other hand, the correlation analysis for the tissue-specific genes indicated overall strong positive correlations between the primary and PDX tumor pairs, with the exception of gastric cancer cases, which showed an inverse correlation. These data propose a tissue-specific change in splicing events during PDX formation as a variable factor that affects primary−PDX integrity. Full article

(This article belongs to the Special Issue RNA in Human Diseases: Challenges and Opportunities)

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10 pages, 3647 KiB

Open AccessHypothesis

RNA Activators of Stress Kinase PKR within Human Genes That Control Splicing or Translation Create Novel Targets for Hereditary Diseases

by Raymond Kaempfer

Int. J. Mol. Sci. 2024, 25(2), 1323; https://doi.org/10.3390/ijms25021323 - 22 Jan 2024

Viewed by 1417

Abstract

Specific sequences within RNA encoded by human genes essential for survival possess the ability to activate the RNA-dependent stress kinase PKR, resulting in phosphorylation of its substrate, eukaryotic translation initiation factor-2α (eIF2α), either to curb their mRNA translation or to enhance mRNA splicing. Thus, interferon-γ (IFNG) mRNA activates PKR through a 5′-terminal 203-nucleotide pseudoknot structure, thereby strongly downregulating its own translation and preventing a harmful hyper-inflammatory response. Tumor necrosis factor-α (TNF) pre-mRNA encodes within the 3′-untranslated region (3′-UTR) a 104-nucleotide RNA pseudoknot that activates PKR to enhance its splicing by an order of magnitude while leaving mRNA translation intact, thereby promoting effective TNF protein expression. Adult and fetal globin genes encode pre-mRNA structures that strongly activate PKR, leading to eIF2α phosphorylation that greatly enhances spliceosome assembly and splicing, yet also structures that silence PKR activation upon splicing to allow for unabated globin mRNA translation essential for life. Regulatory circuits resulting in each case from PKR activation were reviewed previously. Here, we analyze mutations within these genes created to delineate the RNA structures that activate PKR and to deconvolute their folding. Given the critical role of intragenic RNA activators of PKR in gene regulation, such mutations reveal novel potential RNA targets for human disease. Full article

(This article belongs to the Special Issue RNA in Human Diseases: Challenges and Opportunities)

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