Special Issue "Nucleic Acids in Cancer Diagnosis and Therapy"

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Causes, Screening and Diagnosis".

Deadline for manuscript submissions: 31 August 2021.

Special Issue Editor

Dr. Taewan Kim
E-Mail Website
Guest Editor
Ohio State University Comprehensive Cancer Center,1070 Biomedical Research Tower, 460W 12th Ave, Columbus, OH 43210, USA
Shenzhen University International Cancer Center, Building A1-107, Shenzhen University Xili Campus, 1066 Xili Xueyuan Ave, Nanshan District, Shenzhen, Guangdong, China
Interests: noncoding RNA; microRNA; lncRNA; p53; MYC

Special Issue Information

Dear Colleagues,

Cancer research has been focused on the coding genes occupying 1%–2% of the human genome. Moreover, the cancer research in the coding genes has been concentrated on their genetic mutations and protein activities/functions. Since the functions of noncoding RNAs in cancer have been revealed, cancer researchers are expanding their focus from the 1%–2% coding genes to the 98%–99% noncoding transcripts of the human genome. As a result, a number of noncoding RNAs and their functional mechanisms have been identified and characterized in most types of cancer. Meanwhile, the scientific view of DNA and RNA as generators or products of proteins has changed. Many scientists have started to look at and focus on the function and potential of DNA and RNA as nucleic acids. So, the increasing research interest in nucleic acids has spontaneously increased the research interest in the functions and mechanisms of nucleic acids featuring RNA-binding proteins, RNA modifications, cell-free circulating DNA/RNA, and unique types of RNA such as tRNA fragments and circular RNAs.

In this Special Issue, articles about the potential of nucleic acids in cancer diagnosis and therapeutics are welcome.

Dr. Taewan Kim
Guest Editor

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 papers will be 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. Cancers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). 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

  • noncoding RNA
  • RNA-binding protein
  • circular RNA
  • tRNA fragment
  • cell-free DNA
  • cell-free RNA
  • RNA editing and modification
  • cancer

Published Papers (8 papers)

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Editorial

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Editorial
Nucleic Acids in Cancer Diagnosis and Therapy
Cancers 2020, 12(9), 2597; https://doi.org/10.3390/cancers12092597 - 11 Sep 2020
Viewed by 468
Abstract
Cancer research has been focused on the coding genes occupying 1–2% of the human genome [...] Full article
(This article belongs to the Special Issue Nucleic Acids in Cancer Diagnosis and Therapy)

Research

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Article
miRNA Expression Signatures of Therapy Response in Squamous Cell Carcinomas
Cancers 2021, 13(1), 63; https://doi.org/10.3390/cancers13010063 - 28 Dec 2020
Cited by 1 | Viewed by 704
Abstract
Introduction: Squamous cell carcinomas (SCC) are a major subgroup of malignant tumors with a platinum-based first-line systematic chemotherapy. miRNAs play a role in various diseases and modulate therapy response as well. The aim of this study was to identify predictive miRNAs in platinum-treated [...] Read more.
Introduction: Squamous cell carcinomas (SCC) are a major subgroup of malignant tumors with a platinum-based first-line systematic chemotherapy. miRNAs play a role in various diseases and modulate therapy response as well. The aim of this study was to identify predictive miRNAs in platinum-treated SCCs. Methods: miRNA expression data of platinum-treated head and neck (HNSC), cervical (CESC) and lung (LUSC) cancer were collected from the TCGA repositories. Treatment response was defined based on presence or absence of disease progression at 18 months. Responder and nonresponder cohorts were compared using Mann–Whitney and Receiver Operating Characteristic tests. Logistic regression was developed to establish a predictive miRNA signature. Significance was set at FDR < 5%. Results: The integrated database includes 266 SCC patient samples with platinum-based therapy and available follow-up. We uncovered 16, 103, and 9 miRNAs correlated to chemotherapy response in the CESC, HNSC, and LUSC cohorts, respectively. Eight miRNAs overlapped between the CESC and HNSC subgroups, and three miRNAs overlapped between the LUSC and HNSC subgroups. We established a logistic regression model in HNSC and CESC which included six miRNAs: hsa-miR-5586 (Exp (B): 2.94, p = 0.001), hsa-miR-632 (Exp (B): 10.75, p = 0.002), hsa-miR-2355 (Exp (B): 0.48, p = 0.004), hsa-miR-642a (Exp (B): 2.22, p = 0.01), hsa-miR-101-2 (Exp (B): 0.39, p = 0.013) and hsa-miR-6728 (Exp (B): 0.21, p = 0.016). The model using these miRNAs was able to predict chemotherapy resistance with an AUC of 0.897. Conclusions: We performed an analysis of RNA-seq data of squamous cell carcinomas samples and identified significant miRNAs correlated to the response against platinum-based therapy in cervical, head and neck, and lung tumors. Full article
(This article belongs to the Special Issue Nucleic Acids in Cancer Diagnosis and Therapy)
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Article
DKC1 Overexpression Induces a More Aggressive Cellular Behavior and Increases Intrinsic Ribosomal Activity in Immortalized Mammary Gland Cells
Cancers 2020, 12(12), 3512; https://doi.org/10.3390/cancers12123512 - 25 Nov 2020
Viewed by 644
Abstract
Dyskerin is a nucleolar protein involved in the small nucleolar RNA (snoRNA)-guided pseudouridylation of specific uridines on ribosomal RNA (rRNA), and in the stabilization of the telomerase RNA component (hTR). Loss of function mutations in DKC1 causes X-linked dyskeratosis congenita, which is characterized [...] Read more.
Dyskerin is a nucleolar protein involved in the small nucleolar RNA (snoRNA)-guided pseudouridylation of specific uridines on ribosomal RNA (rRNA), and in the stabilization of the telomerase RNA component (hTR). Loss of function mutations in DKC1 causes X-linked dyskeratosis congenita, which is characterized by a failure of proliferating tissues and increased susceptibility to cancer. However, several tumors show dyskerin overexpression. We observed that patients with primary breast cancers with high dyskerin levels are more frequently characterized by shorter survival rates and positive lymph node status than those with tumors with a lower dyskerin expression. To functionally characterize the effects of high dyskerin expression, we generated stably overexpressing DKC1 models finding that increased dyskerin levels conferred a more aggressive cellular phenotype in untransformed immortalized MCF10A cells. Contextually, DKC1 overexpression led to an upregulation of some snoRNAs, including SNORA67 and a significantly increased U1445 modification on 18S rRNA, the known target of SNORA67. Lastly, we found that dyskerin overexpression strongly enhanced the synthetic activity of ribosomes increasing translational efficiency in MCF10A. Altogether, our results indicate that dyskerin may sustain the neoplastic phenotype from an early stage in breast cancer endowing ribosomes with an augmented translation efficiency. Full article
(This article belongs to the Special Issue Nucleic Acids in Cancer Diagnosis and Therapy)
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Review

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Review
Detecting and Characterizing A-To-I microRNA Editing in Cancer
Cancers 2021, 13(7), 1699; https://doi.org/10.3390/cancers13071699 - 03 Apr 2021
Cited by 1 | Viewed by 477
Abstract
Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either [...] Read more.
Adenosine to inosine (A-to-I) editing consists of an RNA modification where single adenosines along the RNA sequence are converted into inosines. Such a biochemical transformation is catalyzed by enzymes belonging to the family of adenosine deaminases acting on RNA (ADARs) and occurs either co- or post-transcriptionally. The employment of powerful, high-throughput detection methods has recently revealed that A-to-I editing widely occurs in non-coding RNAs, including microRNAs (miRNAs). MiRNAs are a class of small regulatory non-coding RNAs (ncRNAs) acting as translation inhibitors, known to exert relevant roles in controlling cell cycle, proliferation, and cancer development. Indeed, a growing number of recent researches have evidenced the importance of miRNA editing in cancer biology by exploiting various detection and validation methods. Herein, we briefly overview early and currently available A-to-I miRNA editing detection and validation methods and discuss the significance of A-to-I miRNA editing in human cancer. Full article
(This article belongs to the Special Issue Nucleic Acids in Cancer Diagnosis and Therapy)
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Review
Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer
Cancers 2021, 13(6), 1372; https://doi.org/10.3390/cancers13061372 - 18 Mar 2021
Cited by 1 | Viewed by 515
Abstract
Over the last several decades, clinical evaluation and treatment of lung cancers have largely improved with the classification of genetic drivers of the disease, such as EGFR, ALK, and ROS1. There are numerous regulatory factors that exert cellular control over key oncogenic pathways [...] Read more.
Over the last several decades, clinical evaluation and treatment of lung cancers have largely improved with the classification of genetic drivers of the disease, such as EGFR, ALK, and ROS1. There are numerous regulatory factors that exert cellular control over key oncogenic pathways involved in lung cancers. In particular, non-coding RNAs (ncRNAs) have a diversity of regulatory roles in lung cancers such that they have been shown to be involved in inducing proliferation, suppressing apoptotic pathways, increasing metastatic potential of cancer cells, and acquiring drug resistance. The dysregulation of various ncRNAs in human cancers has prompted preclinical studies examining the therapeutic potential of restoring and/or inhibiting these ncRNAs. Furthermore, ncRNAs demonstrate tissue-specific expression in addition to high stability within biological fluids. This makes them excellent candidates as cancer biomarkers. This review aims to discuss the relevance of ncRNAs in cancer pathology, diagnosis, and therapy, with a focus on lung cancer. Full article
(This article belongs to the Special Issue Nucleic Acids in Cancer Diagnosis and Therapy)
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Review
MicroRNA in Papillary Thyroid Carcinoma: A Systematic Review from 2018 to June 2020
Cancers 2020, 12(11), 3118; https://doi.org/10.3390/cancers12113118 - 25 Oct 2020
Cited by 2 | Viewed by 647
Abstract
The involvement of micro-ribonucleic acid (microRNAs) in metabolic pathways such as regulation, signal transduction, cell maintenance, and differentiation make them possible biomarkers and therapeutic targets. The purpose of this review is to summarize the information published in the last two and a half [...] Read more.
The involvement of micro-ribonucleic acid (microRNAs) in metabolic pathways such as regulation, signal transduction, cell maintenance, and differentiation make them possible biomarkers and therapeutic targets. The purpose of this review is to summarize the information published in the last two and a half years about the involvement of microRNAs in papillary thyroid carcinoma (PTC). Another goal is to understand the perspective offered by the new findings. Main microRNA features such as origin, regulation, targeted genes, and metabolic pathways will be presented in this paper. We interrogated the PubMed database using several keywords: “microRNA” + “thyroid” + “papillary” + “carcinoma”. After applying search filters and inclusion criteria, a selection of 137 articles published between January 2018–June 2020 was made. Data regarding microRNA, metabolic pathways, gene/protein, and study utility were selected and included in the table and later discussed regarding the matter at hand. We found that most microRNAs regularly expressed in the normal thyroid gland are downregulated in PTC, indicating an important tumor-suppressor action by those microRNAs. Moreover, we showed that one gene can be targeted by several microRNAs and have nominally described these interactions. We have revealed which microRNAs can target several genes at once. Full article
(This article belongs to the Special Issue Nucleic Acids in Cancer Diagnosis and Therapy)
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Review
RNA-Binding Proteins in Cancer: Functional and Therapeutic Perspectives
Cancers 2020, 12(9), 2699; https://doi.org/10.3390/cancers12092699 - 21 Sep 2020
Cited by 4 | Viewed by 1305
Abstract
RNA-binding proteins (RBPs) crucially regulate gene expression through post-transcriptional regulation, such as by modulating microRNA (miRNA) processing and the alternative splicing, alternative polyadenylation, subcellular localization, stability, and translation of RNAs. More than 1500 RBPs have been identified to date, and many of them [...] Read more.
RNA-binding proteins (RBPs) crucially regulate gene expression through post-transcriptional regulation, such as by modulating microRNA (miRNA) processing and the alternative splicing, alternative polyadenylation, subcellular localization, stability, and translation of RNAs. More than 1500 RBPs have been identified to date, and many of them are known to be deregulated in cancer. Alterations in the expression and localization of RBPs can influence the expression levels of oncogenes, tumor-suppressor genes, and genome stability-related genes. RBP-mediated gene regulation can lead to diverse cancer-related cellular phenotypes, such as proliferation, apoptosis, angiogenesis, senescence, and epithelial-mesenchymal transition (EMT)/invasion/metastasis. This regulation can also be associated with cancer prognosis. Thus, RBPs can be potential targets for the development of therapeutics for the cancer treatment. In this review, we describe the molecular functions of RBPs, their roles in cancer-related cellular phenotypes, and various approaches that may be used to target RBPs for cancer treatment. Full article
(This article belongs to the Special Issue Nucleic Acids in Cancer Diagnosis and Therapy)
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Review
Coding of Glioblastoma Progression and Therapy Resistance through Long Noncoding RNAs
Cancers 2020, 12(7), 1842; https://doi.org/10.3390/cancers12071842 - 08 Jul 2020
Cited by 8 | Viewed by 885
Abstract
Glioblastoma is the most aggressive and lethal primary brain malignancy, with an average patient survival from diagnosis of 14 months. Glioblastoma also usually progresses as a more invasive phenotype after initial treatment. A major step forward in our understanding of the nature of [...] Read more.
Glioblastoma is the most aggressive and lethal primary brain malignancy, with an average patient survival from diagnosis of 14 months. Glioblastoma also usually progresses as a more invasive phenotype after initial treatment. A major step forward in our understanding of the nature of glioblastoma was achieved with large-scale expression analysis. However, due to genomic complexity and heterogeneity, transcriptomics alone is not enough to define the glioblastoma “fingerprint”, so epigenetic mechanisms are being examined, including the noncoding genome. On the basis of their tissue specificity, long noncoding RNAs (lncRNAs) are being explored as new diagnostic and therapeutic targets. In addition, growing evidence indicates that lncRNAs have various roles in resistance to glioblastoma therapies (e.g., MALAT1, H19) and in glioblastoma progression (e.g., CRNDE, HOTAIRM1, ASLNC22381, ASLNC20819). Investigations have also focused on the prognostic value of lncRNAs, as well as the definition of the molecular signatures of glioma, to provide more precise tumor classification. This review discusses the potential that lncRNAs hold for the development of novel diagnostic and, hopefully, therapeutic targets that can contribute to prolonged survival and improved quality of life for patients with glioblastoma. Full article
(This article belongs to the Special Issue Nucleic Acids in Cancer Diagnosis and Therapy)
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