Current Gene Therapy - Volume 22, Issue 2, 2022

The increasing resistance of the disease-causing pathogens to antimicrobial drugs is a public health concern and a socio-economic burden. The emergence of multi-drug resistant strains has made it harder to treat and combat infectious diseases with available conventional antibiotics. There are currently few effective therapeutic regimens for the successful prevention of infections caused by drug-resistant microbes. Various alternative strategies used in the recent past to decrease and limit antibiotic resistance in pathogens include bacteriophages, vaccines, anti-biofilm peptides, and antimicrobial peptides. However, in this review, we focus on the novel and robust molecular approach of antisense RNA (asRNA) technology and the clustered regulatory interspaced short palindromic repeat (CRISPR)-based antibiotic therapy, which can be exploited to selectively eradicate the drug-resistant bacterial strain in a sequence-specific fashion establishing opportunities in the treatment of multi-drug resistant related infections.

Gene therapy has made significant development since the commencement of the first clinical trials a few decades ago and has remained a dynamic area of research regardless of obstacles such as immune response and insertional mutagenesis. Progression in various technologies like next-generation sequencing (NGS) and nanotechnology has established the importance of non-- coding segments of a genome, thereby taking gene therapy to the next level. In this review, we have summarized the importance of non-coding elements, highlighting the advantages of using full- length genomic DNA loci (gDNA) compared to complementary DNA (cDNA) or minigene, currently used in gene therapy. The focus of this review is to provide an overview of the advances and the future of potential use of gDNA loci in gene therapy, expanding the therapeutic repertoire in molecular medicine.

This review provides comprehensive information about the advances in gene therapy in the anterior segment of the eye, including cornea, conjunctiva, lacrimal gland, and trabecular meshwork. We discuss gene delivery systems, including viral and non-viral vectors as well as gene editing techniques, mainly CRISPR-Cas9, and epigenetic treatments, including antisense and siRNA therapeutics. We also provide a detailed analysis of various anterior segment diseases where gene therapy has been tested with corresponding outcomes. Disease conditions include corneal and conjunctival fibrosis and scarring, corneal epithelial wound healing, corneal graft survival, corneal neovascularization, genetic corneal dystrophies, herpetic keratitis, glaucoma, dry eye disease, and other ocular surface diseases. Although most of the analyzed results on the use and validity of gene therapy at the ocular surface have been obtained in vitro or using animal models, we also discuss the available human studies. Gene therapy approaches are currently considered very promising as emerging future treatments of various diseases, and this field is rapidly expanding.

With new developments in biomedical technology, it is now a viable therapeutic treatment to alter genes with techniques like CRISPR. At the same time, it is increasingly cheaper to perform whole genome sequencing, resulting in rapid advancement in gene therapy and editing in precision medicine. Understanding the current industry and academic applications of gene therapy provides an important backdrop to future scientific developments. Additionally, machine learning and artificial intelligence techniques allow for the reduction of time and money spent in the development of new gene therapy products and techniques. In this paper, we survey the current progress of gene therapy treatments for several diseases and explore machine learning applications in gene therapy. We also discuss the ethical implications of gene therapy and the use of machine learning in precision medicine. Machine learning and gene therapy are both topics gaining popularity in various publications, and we conclude that there is still room for continued research and application of machine learning techniques in the gene therapy field.

Background: Increasing research reveals that long non-coding RNAs (lncRNAs) play an important role in various biological processes of human diseases. Nonetheless, only a handful of lncRNA-disease associations have been experimentally verified. The study of lncRNA-disease association prediction based on the computational model has provided a preliminary basis for biological experiments to a great degree so as to cut down the huge cost of wet lab experiments. Objective: This study aims to learn the real distribution of lncRNA-disease association from a limited number of known lncRNA-disease association data. This paper proposes a new lncRNA-disease association prediction model called LDA-GAN based on a Generative Adversarial Network (GAN). Methods: Aiming at the problems of slow convergence rate, training instabilities, and unavailability of discrete data in traditional GAN, LDA-GAN utilizes the Gumbel-softmax technology to construct a differentiable process for simulating discrete sampling. Meanwhile, the generator and the discriminator of LDA-GAN are integrated to establish the overall optimization goal based on the pairwise loss function. Results: Experiments on standard datasets demonstrate that LDA-GAN achieves not only high stability and high efficiency in the process of confrontation learning but also gives full play to the semisupervised learning advantage of generative adversarial learning framework for unlabeled data, which further improves the prediction accuracy of lncRNA-disease association. Besides, case studies show that LDA-GAN can accurately generate potential diseases for several lncRNAs. Conclusion: We introduce a generative adversarial model to identify lncRNA-disease associations.

Background: Bone marrow mononuclear cells (BM-MNCs), as a collection of hematopoietic and mesenchymal stem cells (MSCs), are capable of producing all blood cell lineages. The use of cytokines, growth factors or cells capable of secreting these factors will help in stimulating the proliferation and differentiation of these cells into mature cell lines. On the other hand, MSCs are multipotent stromal cells that can be differentiated into various cell lineages. Moreover, these cells can control the process of hematopoiesis by secreting cytokines and growth factors. The present study aimed to investigate the effect of BM-derived MSCs on the differentiation of MNCs based on the assessment of cell surface markers by flow cytometry analysis. Methods: For this purpose, the MNCs were purified from rat BM using density gradient centrifugation. Thereafter, they were cultured, expanded, and characterized. Next, BM-derived-MSCs were cocultured with MNCs, and then were either cultured MNCs alone (control group) or co-cultured MNCs with BM-derived-MSCs (experimental group). Finally, they were collected on day 7 and subjected to flow cytometry analysis for granulocyte markers and ERK protein investigation. Results: It was found that the expression levels of CD34, CD16, CD11b, and CD18 granulocyte markers as well as protein expression of ERK have significantly increased in the experimental group compared to the control group. Conclusion: Therefore, it can be concluded that MSCs could affect the granulocyte differentiation of MNCs via ERK protein expression, which is a key component of the ERK signaling pathway.

Background: Scaffold-based gene therapy provides a promising approach for tissue engineering, which was important and popular as it combined medical applications and engineering materials’ knowledge. Objective: The decellularization techniques were employed to remove the cellular components from porcine elastic cartilages, leaving a native decellularized Extracellular Matrix (dECM) composition and architecture integrity of largely insoluble collagen, elastin, and tightly bound glycosaminoglycans. For newly designed collagen scaffold samples, elastic cartilages were hydrolyzed by protease with different concentrations to gain state completely and clearly. Methods: An extraction process of Supercritical Carbon Dioxide (ScCO2) was used to remove cellular components from porcine elastic cartilage. The dECM scaffolds with collagen must be characterized by Fourier transform infrared spectroscopy(FTIR), Thermo-Gravimetric Analysis (TGA), and Scanning Electron Microscope (SEM). Results: The study provided a new treatment combined with supercritical carbon dioxide and alkaline/ protease to prepare dECM scaffolds with hole-scaffold microstructures and introduce into a potential application on osteochondral tissue engineering using scaffold-based gene therapy. The new process is simple and efficient. The pore-scaffold microstructures were observed in dECM scaffolds derived from porcine elastic cartilages. The Tdmax values of the resulting dECM scaffolds were observed at over 330°C. Conclusion: A series of new scaffolds were successfully obtained from porcine tissue by using ScCO2 and alkaline/enzyme treatments such as a mixing aqueous solution of NH4OH and papain. The dECM scaffolds with high thermal stability were obtained. The resulting scaffold with clean pore-scaffold microstructure could be a potential application for scaffold-based gene therapy.

Background: Non-viral transposon-mediated gene delivery can overcome viral vectors’ limitations. Transposon gene delivery offers the safe and life-long expression of genes such as Pigment Epithelium-Derived Factor (PEDF) and granulocyte-macrophage colony-stimulating factor (GM-CSF) to counteract retinal degeneration by reducing oxidative stress damage. Objective: The study aimed at using Sleeping Beauty transposon to transfect human Retinal Pigment Epithelial (RPE) cells with the neuroprotective factors PEDF and GM-CSF to investigate the effect of these factors on oxidative stress damage. Methods: Human RPE cells were transfected with PEDF and GM-CSF by electroporation, using the hyperactive Sleeping Beauty transposon gene delivery system (SB100X). Gene expression was determined by RT-qPCR, and protein level by Western Blot as well as ELISA. The cellular stress level and the neuroprotective effect of the proteins were determined by measuring the concentrations of the antioxidant glutathione in human RPE cells, and conducting immunohistochemical examination of retinal integrity, inflammation, and apoptosis of rat Retina-Organotypic Cultures (ROC) exposed to H2O2. Results: Human RPE cells were efficiently transfected showing a significantly augmented gene expression and protein secretion. Human RPE cells overexpressing PEDF and/or GM-CSF or pretreated with recombinant proteins presented significantly increased glutathione levels post- H2O2 incubation than non-transfected/untreated controls. rPEDF and/or rGM-CSF-treated ROC exhibited decreased inflammatory reactions and cell degeneration. Conclusion: GM-CSF and/or PEDF could be delivered successfully to RPE cells with combined use of SB100X and electroporation. PEDF and/or GM-CSF reduced H2O2-mediated oxidative stress damage in RPE cells and ROC offering an encouraging technique to re-establish a cell protective environment to halt age-related retinal degeneration.