LncRNAs and the Angiogenic Switch in Cancer: Clinical Significance and Therapeutic Opportunities

Angiogenesis is one of the hallmarks of cancer, and the establishment of new blood vessels is vital to allow for a tumour to grow beyond 1–2 mm in size. The angiogenic switch is the term given to the point where the number or activity of the pro-angiogenic factors exceeds that of the anti-angiogenic factors, resulting in the angiogenic process proceeding, giving rise to new blood vessels accompanied by increased tumour growth, metastasis, and potential drug resistance. Long noncoding ribonucleic acids (lncRNAs) have been found to play a role in the angiogenic switch by regulating gene expression, transcription, translation, and post translation modification. In this regard they play both anti-angiogenic and pro-angiogenic roles. The expression levels of the pro-angiogenic lncRNAs have been found to correlate with patient survival. These lncRNAs are also potential drug targets for the development of therapies that will inhibit or modify tumour angiogenesis. Here we review the roles of lncRNAs in regulating the angiogenic switch. We cover specific examples of both pro and anti-angiogenic lncRNAs and discuss their potential use as both prognostic biomarkers and targets for the development of future therapies.

The Role of Exosomes in Viral Hepatitis and Its Associated Liver Diseases

Exosomes, the important carriers between cells, can carry proteins, micro ribonucleic acids (miRNAs), long non-coding RNAs (lncRNAs) and other molecules to mediate cellular information transduction. They also play an important role in the pathogenesis, prognosis and treatment of viral hepatitis and its associated liver diseases. Several studies have reported that viral hepatitis and its associated liver diseases, including hepatitis A, B, C and E; hepatic fibrosis and hepatocellular carcinoma, were closely associated with exosomes. Exploring the role of exosomes in viral hepatitis and associated liver diseases will enhance our understanding of these diseases. Therefore, this review mainly summarised the role of exosomes in viral hepatitis and its associated liver diseases to identify new strategies for liver diseases in clinical practise.

The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines

The current COVID-19 pandemic is a massive source of global disruption, having led so far to two hundred and fifty million COVID-19 cases and almost five million deaths worldwide. It was recognized in the beginning that only an effective vaccine could lead to a way out of the pandemic, and therefore the race for the COVID-19 vaccine started immediately, boosted by the availability of the viral sequence data. Two novel vaccine platforms, based on mRNA technology, were developed in 2020 by Pfizer-BioNTech and Moderna Therapeutics (comirnaty® and spikevax®, respectively), and were the first ones presenting efficacies higher than 90%. Both consisted of N1-methyl-pseudouridine-modified mRNA encoding the SARS-COVID-19 Spike protein and were delivered with a lipid nanoparticle (LNP) formulation. Because the delivery problem of ribonucleic acids had been known for decades, the success of LNPs was quickly hailed by many as the unsung hero of COVID-19 mRNA vaccines. However, the clinical trial efficacy results of the Curevac mRNA vaccine (CVnCoV) suggested that the delivery system was not the only key to the success. CVnCoV consisted of an unmodified mRNA (encoding the same spike protein as Moderna and Pfizer-BioNTech’s mRNA vaccines) and was formulated with the same LNP as Pfizer-BioNTech’s vaccine (Acuitas ALC-0315). However, its efficacy was only 48%. This striking difference in efficacy could be attributed to the presence of a critical RNA modification (N1-methyl-pseudouridine) in the Pfizer-BioNTech and Moderna’s mRNA vaccines (but not in CVnCoV). Here we highlight the features of N1-methyl-pseudouridine and its contributions to mRNA vaccines.

Identification of Micro Ribonucleic Acids and Their Targets in Response to Plasmodiophora brassicae Infection in Brassica napus

Clubroot disease, which is caused by the soil-borne pathogen Plasmodiophora brassicae War (P. brassicae), is one of the oldest and most destructive diseases of Brassica and cruciferous crops in the world. Plant microRNAs [micro ribonucleic acids (miRNAs)] play important regulatory roles in several developmental processes. Although the role of plant miRNAs in plant-microbe interaction has been extensively studied, there are only few reports on the specific functions of miRNAs in response to P. brassicae. This study investigated the roles of miRNAs and their targets during P. brassicae infection in a pair of Brassica napus near-isogenic lines (NILs), namely clubroot-resistant line 409R and clubroot-susceptible line 409S. Small RNA sequencing (sRNA-seq) and degradome-seq were performed on root samples of 409R and 409S with or without P. brassicae inoculation. sRNA-seq identified a total of 48 conserved and 72 novel miRNAs, among which 18 had a significant differential expression in the root of 409R, while only one miRNA was differentially expressed in the root of 409S after P. brassicae inoculation. The degradome-seq analysis identified 938 miRNA target transcripts, which are transcription factors, enzymes, and proteins involved in multiple biological processes and most significantly enriched in the plant hormone signal transduction pathway. Between 409R and 409S, we found eight different degradation pathways in response to P. brassicae infection, such as those related to fatty acids. By combining published transcriptome data, we identified a total of six antagonistic miRNA-target pairs in 409R that are responsive to P. brassicae infection and involved in pathways associated with root development, hypersensitive cell death, and chloroplast metabolic synthesis. Our results reveal that P. brassicae infection leads to great changes in miRNA pool and target transcripts. More interestingly, these changes are different between 409R and 409S. Clarification of the crosstalk between miRNAs and their targets may shed new light on the possible mechanisms underlying the pathogen resistance against P. brassicae.

Facile Synthesis of N-Doped Graphene Quantum Dots as Novel Transfection Agents for mRNA and pDNA

In the wake of the coronavirus disease 2019 (COVID-19) pandemic, global pharmaceutical companies have developed vaccines for the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Some have adopted lipid nanoparticles (LNPs) or viral vectors to deliver the genes associated with the spike protein of SARS-CoV-2 for vaccination. This strategy of vaccination by delivering genes to express viral proteins has been successfully applied to the mRNA vaccines for COVID-19, and is also applicable to gene therapy. However, conventional transfection agents such as LNPs and viral vectors are not yet sufficient to satisfy the levels of safety, stability, and efficiency required for the clinical applications of gene therapy. In this study, we synthesized N-doped graphene quantum dots (NGQDs) for the transfection of various genes, including messenger ribonucleic acids (mRNAs) and plasmid deoxyribonucleic acids (pDNAs). The positively charged NGQDs successfully formed electrostatic complexes with negatively charged mRNAs and pDNAs, and resulted in the efficient delivery and transfection of the genes into target cells. The transfection efficiency of NGQDs is found to be comparable to that of commercially available LNPs. Considering their outstanding stability even at room temperature as well as their low toxicity, NGQDs are expected to be novel universal gene delivery platforms that can outperform LNPs and viral vectors.

Chitosan Oleate Coated PLGA Nanoparticles as siRNA Drug Delivery System

Oligonucleotide therapeutics such as miRNAs and siRNAs represent a class of molecules developed to modulate gene expression by interfering with ribonucleic acids (RNAs) and protein synthesis. These molecules are characterized by strong instability and easy degradation due to nuclease enzymes. To avoid these drawbacks and ensure efficient delivery to target cells, viral and non-viral vectors are the two main approaches currently employed. Viral vectors are one of the major vehicles in gene therapy; however, the potent immunogenicity and the insertional mutagenesis is a potential issue for the patient. Non-viral vectors, such as polymeric nanocarriers, provide a safer and more efficient delivery of RNA-interfering molecules. The aim of this work is to employ PLGA core nanoparticles shell-coated with chitosan oleate as siRNA carriers. An siRNA targeted on HIV-1, directed against the viral Tat/Rev transcripts was employed as a model. The ionic interaction between the oligonucleotide’s moieties, negatively charged, and the positive surface charges of the chitosan shell was exploited to associate siRNA and nanoparticles. Non-covalent bonds can protect siRNA from nuclease degradation and guarantee a good cell internalization and a fast release of the siRNA into the cytosolic portion, allowing its easy activation.

The Emerging Roles of Long Noncoding RNAs as Hallmarks of Lung Cancer

Noncoding ribonucleic acids (ncRNAs) are closely associated with tumor initiation, growth, and progress in lung cancer. Long ncRNAs (lncRNAs), as one of the three subclasses of ncRNAs, play important roles in chromatin modification, transcription, and post-transcriptional processing. Various lncRNAs have recently been reported to be dysfunctional or dysregulated in cancers and have pro- or anti-tumor potential. Importantly, as a new class of cancer biomarkers, studies have demonstrated the plausibility of using certain subsets of lncRNAs as promising diagnostic, therapeutic, or prognostic strategies to manage cancers. This review focuses on lncRNAs associated with hallmarks of lung cancer, especially those discovered in the last five years. The expression levels of these lncRNAs in tumor samples are discussed, alongside their mechanisms of action, drug resistance, and potential as diagnostic and prognostic markers for lung cancer.

Using Immune-Related Long Non-coding Ribonucleic Acids to Develop a Novel Prognosis Signature and Predict the Immune Landscape of Colon Cancer

Purpose: This study aimed to construct a novel signature to predict the survival of patients with colon cancer and the associated immune landscape, based on immune-related long noncoding ribonucleic acids (irlncRNAs).Methods: Expression profiles of irlncRNAs in 457 patients with colon cancer were retrieved from the TCGA database (https://portal.gdc.cancer.gov). Differentially expressed (DE) irlncRNAs were identified and irlncRNA pairs were recognized using Lasso regression and Cox regression analyses. Akaike information criterion (AIC) values of receiver operating characteristic (ROC) curve were calculated to identify the ideal cut-off point for dividing patients into two groups and constructing the prognosis signature. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to validate the expression of LINC02195 and SCARNA9 in colon cancer.Results: We identified 22 irlncRNA pairs and patients were divided into high-risk and low-risk groups based on the calculated risk score using these 22 irlncRNA pairs. The irlncRNA pairs were significantly related to patient survival. Low-risk patients had a significantly longer survival time than high-risk patients (p < 0.001). The area under the curve of the signature to predict 5-year survival was 0.951. The risk score correlated with tumor stage, infiltration depth, lymph node metastasis, and distant metastasis. The risk score remained significant after univariate and multivariate Cox regression analyses. A nomogram model to predict patient survival was developed based on the results of Cox regression analysis. Immune cell infiltration status, expression of some immune checkpoint genes, and sensitivity to chemotherapeutics were also related to the risk score. The results of qRT-PCR revealed that LINC02195 and SCARNA9 were significantly upregulated in colon cancer tissues.Conclusion: The constructed prognosis signature showed remarkable efficiency in predicting patient survival, immune cell infiltration status, expression of immune checkpoint genes, and sensitivity to chemotherapeutics.

Circular Ribonucleic Acid Expression Alteration in the Spinal Cord Tissue after Spinal Cord Injury in Rats

<b><i>Background and Purpose:</i></b> Increased researches focus into pathophysiological mechanisms of spinal cord injury (SCI), particularly toward the relationship between relevant biomarkers and the degree of SCI and prognosis. Circular ribonucleic acids (circRNAs) possess microRNA (miRNA) binding sites that can play the role of miRNA sponges and thus participate in the expression of parental gene modification. This study focused on rat SCI models and explore the relationship between circRNAs and SCI at a genomic level. <b><i>Methods:</i></b> We first established a rat SCI model and extracted the target spinal cord tissue according to 4 time points. Then investigated the alterations in the circRNA expression by high-throughput whole transcriptome sequencing, analyzed data by gene ontology and the Kyoto Encyclopedia of Genes and Genomes, and constructed the circRNA-miRNA network. <b><i>Results:</i></b> A total of 178 circRNAs were dysregulated (89 upregulated/89 downregulated). Differential circRNAs were found to be mainly involved in the composition of specific organelles in the cytoplasm and are mainly involved in the energy transfer process associated with electron transfer (and similar activities). In all the signaling pathways identified in this study, the MAPK, Wnt, and mTOR signaling pathways are intimately associated with the pathophysiological process of rats post-SCI. In this study, 10 circRNAs with obvious dysregulation were selected for prediction, 26 miRNAs with additional interactions were obtained, and a network diagram of circRNAs-miRNAs was constructed. In this manner, one can understand in further detail the pathogenesis of SCI and to provide new strategies for the prevention, diagnosis, and treatment of SCI-related injuries at the genetic level.