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Non-coding RNAs in Cancer, Aging and Regeneration
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Non-coding RNAs in Cancer, Aging and Regeneration

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (20 February 2024) | Viewed by 13344

Special Issue Editors

Prof. Dr. Yao Li

E-Mail Website
Guest Editor
State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai 200433, China
Interests: functional genomics of cancer; regulation of gene expression; non-coding RNAs
Dr. Bruno Bernardes de Jesus

E-Mail Website
Guest Editor
Institute of Biomedicine - iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
Interests: aging; stem cells; cancer; lncRNAs; iPSC
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Non-coding RNAs (ncRNAs) are a diverse and prevalent group of RNAs including highly abundant and functionally important RNAs such as tRNA and rRNA, as well as different kinds of small RNAs, long ncRNAs and circRNA. Over the past two decades, transcriptomic and bioinformatic studies suggest the existence of tens of thousands of ncRNAs in eukaryotic cells, with tissue- and cell-type-specific expression patterns. Although their function as regulators of gene expression could be mediated through their role at the epigenetic, transcriptional, and post-transcriptional levels, many of the newly identified ncRNAs have not yet been validated for their function. From those that have been characterized, it is clear that ncRNAs can function through a variety of mechanisms, participating in the formation and regulation of protein complexes to perform their functions, dynamically regulating various signaling pathways in several biological processes. Noteworthy are the lncRNA family, which are ncRNAs longer than 200 bp, suggested to have a role in a variety of cellular processes spanning regeneration and cancer.

This Special Issue of International Journal of Molecular Sciences focuses on ncRNAs and, preferentially but not exclusively in the family of the lncRNAs, welcoming both original research articles and review papers that deal with the molecular mechanisms underlying the role of ncRNAs in cancer, aging and regeneration.

Prof. Dr. Yao Li
Dr. Bruno Bernardes de Jesus
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • aging
  • stem cells
  • regeneration
  • cancer
  • ncRNAs
  • iPSC

Published Papers (7 papers)

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Editorial

Jump to: Research, Review

4 pages, 193 KiB  
Editorial
Non–Coding RNA Performs Its Biological Function by Interacting with Macromolecules
by Yao Li
Int. J. Mol. Sci. 2023, 24(22), 16246; https://doi.org/10.3390/ijms242216246 - 13 Nov 2023
Viewed by 622
Abstract
One of the most significant discoveries resulting from the sequencing of the human genome is the realization that a large portion (over 85%) of the genome is transcribed into RNA, yet less than 2% of it encodes protein-coding genes [...] Full article
(This article belongs to the Special Issue Non-coding RNAs in Cancer, Aging and Regeneration)

Research

Jump to: Editorial, Review

16 pages, 8868 KiB  
Article
Identification of Long Noncoding RNAs That Exert Transcriptional Regulation by Forming RNA–DNA Triplexes in Prostate Cancer
by Yugang Liang, Yali Lu, Qin Chen, Yihang Cheng, Yunsheng Ma, Yan Huang, Minyan Qiu and Yao Li
Int. J. Mol. Sci. 2023, 24(3), 2035; https://doi.org/10.3390/ijms24032035 - 19 Jan 2023
Cited by 2 | Viewed by 1626
Abstract
Long noncoding RNAs (lncRNAs) are involved in transcriptional regulation, and their deregulation is associated with the development of various human cancers, including prostate cancer (PCa). However, their underlying mechanisms remain unclear. In this study, lncRNAs that interact with DNA and regulate mRNA transcription [...] Read more.
Long noncoding RNAs (lncRNAs) are involved in transcriptional regulation, and their deregulation is associated with the development of various human cancers, including prostate cancer (PCa). However, their underlying mechanisms remain unclear. In this study, lncRNAs that interact with DNA and regulate mRNA transcription in PCa were screened and identified to promote PCa development. First, 4195 protein-coding genes (PCGs, mRNAs) were obtained from the The Cancer Genome Atlas (TCGA) database, in which 1148 lncRNAs were differentially expressed in PCa. Then, 44,270 pairs of co-expression relationships were calculated between 612 lncRNAs and 2742 mRNAs, of which 42,596 (96%) were positively correlated. Among the 612 lncRNAs, 392 had the potential to interact with the promoter region to form DNA:DNA:RNA triplexes, from which lncRNA AD000684.2(AC002128.1) was selected for further validation. AC002128.1 was highly expressed in PCa. Furthermore, AD000684.2 positively regulated the expression of the correlated genes. In addition, AD000684.2 formed RNA–DNA triplexes with the promoter region of the regulated genes. Functional assays also demonstrated that lncRNA AD000684.2 promotes cell proliferation and motility, as well as inhibits apoptosis, in PCa cell lines. The results suggest that AD000684.2 could positively regulate the transcription of target genes via triplex structures and serve as a candidate prognostic biomarker and target for new therapies in human PCa. Full article
(This article belongs to the Special Issue Non-coding RNAs in Cancer, Aging and Regeneration)
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16 pages, 2537 KiB  
Article
Androgen-Responsive Oncogenic lncRNA RP11-1023L17.1 Enhances c-Myc Protein Stability in Prostate Cancer
by Wenhua Huang, Qin Chen, Yali Lu, Zhe Kong, Xuechao Wan, Yan Huang, Minyan Qiu and Yao Li
Int. J. Mol. Sci. 2022, 23(20), 12219; https://doi.org/10.3390/ijms232012219 - 13 Oct 2022
Cited by 4 | Viewed by 1651
Abstract
Long noncoding RNAs (lncRNAs) have been found as novel participants in the pathophysiology of prostate cancer (PCa), which is predominantly regulated by androgen and its receptor. The biological function of androgen-responsive lncRNAs remains poorly understood. Here, we identified that lncRNA RP11-1023L17.1, which is [...] Read more.
Long noncoding RNAs (lncRNAs) have been found as novel participants in the pathophysiology of prostate cancer (PCa), which is predominantly regulated by androgen and its receptor. The biological function of androgen-responsive lncRNAs remains poorly understood. Here, we identified that lncRNA RP11-1023L17.1, which is highly expressed in PCa. RP11-1023L17.1 expression, can be directly repressed by the androgen receptor in PCa cells. RP11-1023L17.1 depletion inhibited the proliferation, migration, and cell cycle progression, and promoted the apoptosis of PCa cells, indicating that RP11-1023L17.1 acts as an oncogene in PCa cells. Microarray results revealed that RP11-1023L17.1 depletion downregulated the c-Myc transcription signature in PCa cells. RP11-1023L17.1 depletion-induced cellular phenotypes can be overcome by ectopically overexpressed c-Myc. Mechanistically, RP11-1023L17.1 represses FBXO32 mRNA expression, thereby enhancing c-Myc protein stability by blocking FBXO32-mediated c-Myc degradation. Our findings reveal the previously unrecognized roles of RP11-1023L17.1 in c-Myc-dependent PCa tumorigenesis. Full article
(This article belongs to the Special Issue Non-coding RNAs in Cancer, Aging and Regeneration)
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22 pages, 10644 KiB  
Article
The Expression and Function of lincRNA-154324 and the Adjoining Protein-Coding Gene vmp1 in the Caudal Fin Regeneration of Zebrafish
by Jing Li, Wenjun Wen, Shuqiang Zhang, Chune Zhou, Yiyi Feng and Xiaoyu Li
Int. J. Mol. Sci. 2022, 23(16), 8944; https://doi.org/10.3390/ijms23168944 - 11 Aug 2022
Cited by 2 | Viewed by 1868
Abstract
Caudal fin regeneration is regulated by a variety of mechanisms, but the role of long non-coding RNA (lncRNA) has rarely been studied. The present study aimed to describe the landscape of lncRNAs during caudal fin regeneration using whole transcriptome sequencing, and then to [...] Read more.
Caudal fin regeneration is regulated by a variety of mechanisms, but the role of long non-coding RNA (lncRNA) has rarely been studied. The present study aimed to describe the landscape of lncRNAs during caudal fin regeneration using whole transcriptome sequencing, and then to conduct a functional study on the target lncRNAs using real-time fluorescent quantitative PCR (RT-qPCR), in situ hybridization, and the CRISPR/Cas9 method for lncRNA gene knockout. The results of the transcriptome sequencing showed that a total of 381 lncRNAs were differentially expressed, among which ENSDART00000154324 (lincRNA-154324) was found to be highly related to caudal fin regeneration, and thus it was chosen as the target lncRNA for the subsequent functional study. The results regarding the temporal and spatial expression of lincRNA-154324 and the gene knockout results from CRISPR/Cas9 indicated that lincRNA-154324 is involved in the caudal fin regeneration of zebrafish. Importantly, we serendipitously discovered that the cis correlation coefficient between lincRNA-154324 and its neighboring gene vacuole membrane protein 1 (vmp1) is extremely high, and they are essential for the process of caudal fin regeneration. Moreover, studies have found that vmp1 plays an important role in protein secretion, organelle formation, multicellular development, and autophagy. Collectively, our result may provide a framework for the identification and analysis of lncRNAs involved in the regeneration of the zebrafish caudal fin. Full article
(This article belongs to the Special Issue Non-coding RNAs in Cancer, Aging and Regeneration)
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Review

Jump to: Editorial, Research

19 pages, 3585 KiB  
Review
Long Non-Coding RNAs: New Insights in Neurodegenerative Diseases
by Adithya K. Anilkumar, Puneet Vij, Samantha Lopez, Sophia M. Leslie, Kyle Doxtater, Mohammad Moshahid Khan, Murali M. Yallapu, Subhash C. Chauhan, Gladys E. Maestre and Manish K. Tripathi
Int. J. Mol. Sci. 2024, 25(4), 2268; https://doi.org/10.3390/ijms25042268 - 14 Feb 2024
Viewed by 1378
Abstract
Neurodegenerative diseases (NDDs), including Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS), are gradually becoming a burden to society. The adverse effects and mortality/morbidity rates associated with these NDDs are a cause of many healthcare concerns. The pathologic alterations of [...] Read more.
Neurodegenerative diseases (NDDs), including Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS), are gradually becoming a burden to society. The adverse effects and mortality/morbidity rates associated with these NDDs are a cause of many healthcare concerns. The pathologic alterations of NDDs are related to mitochondrial dysfunction, oxidative stress, and inflammation, which further stimulate the progression of NDDs. Recently, long non-coding RNAs (lncRNAs) have attracted ample attention as critical mediators in the pathology of NDDs. However, there is a significant gap in understanding the biological function, molecular mechanisms, and potential importance of lncRNAs in NDDs. This review documents the current research on lncRNAs and their implications in NDDs. We further summarize the potential implication of lncRNAs to serve as novel therapeutic targets and biomarkers for patients with NDDs. Full article
(This article belongs to the Special Issue Non-coding RNAs in Cancer, Aging and Regeneration)
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14 pages, 2048 KiB  
Review
Roles and Mechanisms of Long Non-Coding RNAs in Breast Cancer
by Jia Su, Lihao Deng and Yan-Dong Wang
Int. J. Mol. Sci. 2023, 24(1), 89; https://doi.org/10.3390/ijms24010089 - 21 Dec 2022
Cited by 4 | Viewed by 2477
Abstract
Breast cancer is a major health threat and the second leading cause of cancer-related deaths in women worldwide. The detailed mechanisms involved in the initiation and progression of breast cancer remain unclear. In recent years, amounting evidence indicated that long non-coding RNAs (lncRNAs) [...] Read more.
Breast cancer is a major health threat and the second leading cause of cancer-related deaths in women worldwide. The detailed mechanisms involved in the initiation and progression of breast cancer remain unclear. In recent years, amounting evidence indicated that long non-coding RNAs (lncRNAs) played crucial roles in regulating various biological processes and malignancy tumors, including breast cancer. In this review, we briefly introduce the functions and underlying mechanisms by which lncRNAs are involved in breast cancer. We summarize the roles of the lncRNAs in regulating malignant behaviors of breast cancer, such as cell proliferation, migration and invasion, epithelial–mesenchymal transition (EMT), apoptosis, and drug resistance. Additionally, we also briefly summarize the roles of circular RNAs (circRNAs) in breast cancer carcinogenesis. Full article
(This article belongs to the Special Issue Non-coding RNAs in Cancer, Aging and Regeneration)
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24 pages, 2032 KiB  
Review
Extracellular Vesicle (EVs) Associated Non-Coding RNAs in Lung Cancer and Therapeutics
by Anjugam Paramanantham, Rahmat Asfiya, Siddharth Das, Grace McCully and Akhil Srivastava
Int. J. Mol. Sci. 2022, 23(21), 13637; https://doi.org/10.3390/ijms232113637 - 7 Nov 2022
Cited by 11 | Viewed by 2793
Abstract
Lung cancer is one of the most lethal forms of cancer, with a very high mortality rate. The precise pathophysiology of lung cancer is not well understood, and pertinent information regarding the initiation and progression of lung cancer is currently a crucial area [...] Read more.
Lung cancer is one of the most lethal forms of cancer, with a very high mortality rate. The precise pathophysiology of lung cancer is not well understood, and pertinent information regarding the initiation and progression of lung cancer is currently a crucial area of scientific investigation. Enhanced knowledge about the disease will lead to the development of potent therapeutic interventions. Extracellular vesicles (EVs) are membrane-bound heterogeneous populations of cellular entities that are abundantly produced by all cells in the human body, including the tumor cells. A defined class of EVs called small Extracellular Vesicles (sEVs or exosomes) carries key biomolecules such as RNA, DNA, Proteins and Lipids. Exosomes, therefore, mediate physiological activities and intracellular communication between various cells, including constituent cells of the tumor microenvironment, namely stromal cells, immunological cells, and tumor cells. In recent years, a surge in studying tumor-associated non-coding RNAs (ncRNAs) has been observed. Subsequently, studies have also reported that exosomes abundantly carry different species of ncRNAs and these exosomal ncRNAs are functionally involved in cancer initiation and progression. Here, we discuss the function of exosomal ncRNAs, such as miRNAs and long non-coding RNAs, in the pathophysiology of lung tumors. Further, the future application of exosomal-ncRNAs in clinics as biomarkers and therapeutic targets in lung cancer is also discussed due to the multifaceted influence of exosomes on cellular physiology. Full article
(This article belongs to the Special Issue Non-coding RNAs in Cancer, Aging and Regeneration)
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