Synthetic RNA Molecules Research Articles

RNA modifications in physiology and pathology: Progressing towards application in clinical settings

The potential to modify individual nucleotides through chemical means in order to impact the electrostatic charge, hydrophobic properties, and base pairing of RNA molecules is harnessed in the medical application of stable synthetic RNAs like mRNA vaccines and synthetic small RNA molecules. These modifications are used to either increase or decrease the production of therapeutic proteins. Additionally, naturally occurring biochemical alterations of nucleotides play a role in regulating RNA metabolism and function, thereby modulating essential cellular processes. Research elucidating the mechanisms through which RNA modifications govern fundamental cellular functions in multicellular organisms has enhanced our comprehension of how irregular RNA modification profiles can lead to human diseases. Collectively, these fundamental scientific findings have unveiled the molecular and cellular functions of RNA modifications, offering new opportunities for therapeutic intervention and paving the way for a variety of innovative clinical strategies.

Phase 2 randomized study of rintatolimod following FOLFIRINOX in patients with locally advanced pancreatic adenocarcinoma.

TPS4214 Background: The immunosuppressive microenvironment of pancreatic ductal adenocarcinoma (PDAC) is a driver of its lethality and resistance to immunotherapy. Strategies which modulate the immunosuppressive milieu have the potential to improve the anti-tumor response and improve outcomes in patients with PDAC. Rintatolimod is a synthetic double-stranded RNA molecule that activates the toll-like receptor 3 (TLR3) present on dendritic cells, B-cells, natural killer cells and pancreatic epithelial cells. TLR3 stimulation may increase cytotoxic T-cell activity in PDAC through dendritic cell maturation, antigen priming and downstream proliferation of cytotoxic T-cells. Twenty-seven patients were treated with rintatolimod in a single center Named Patient Program at Erasmus University Medical Center in Rotterdam between January 2017 and February 2019. All had locally advanced or metastatic PDAC which had not progressed on FOLFIRINOX (median 8 cycles). Maintenance rintatolimod, administered intravenously twice weekly for up to 18 weeks, was generally well tolerated. The most common toxicities were grade 1-2 myalgia (30%), chills (52%) and fatigue (30%); no toxicities ≥ grade 3 were observed. Progression-free and overall survival (from cycle 1 FOLFIRINOX) were 13 and 19 months. Methods: This is a phase 2 randomized, open-label, multicenter clinical trial. The primary objective is to assess the efficacy of rintatolimod compared to observation in subjects with locally advanced PDAC which has not progressed after FOLFIRINOX. Eligible patients have completed at least 4 months of FOLFIRINOX, have no evidence of progressive disease, have measurable disease by RECIST v1.1, Karnofsky Performance Status ≥80 and have adequate organ function. Subjects with resected PDAC or metastatic disease are not eligible. Subjects are randomized 2:1 to rintatolimod vs. observation. Rintatolimod is administered intravenously twice weekly until disease progression in the experimental arm. Cross-sectional imaging is performed every 8 weeks in both arms. The primary endpoint is progression-free survival, as assessed by the investigator. Secondary endpoints include overall survival, objective response rate, duration of response and safety, as assessed by CTCAE v5.0. Exploratory endpoints include quality of life and changes in immune cell composition and T-cell response in the peripheral blood to characterize the immunomodulatory effects of rintatolimod. The planned sample size is 90 subjects. The final analysis will be performed after 64 events (disease progression or death) have been observed. The study is powered to detect a hazard ratio of 0.47 for median PFS with 80% power and significance level of 5%. Clinical trial information: NCT05494697 .

Antisense oligonucleotides: a novel Frontier in pharmacological strategy.

Antisense oligonucleotides (ASOs) are short single stranded synthetic RNA or DNA molecules, whereas double-stranded RNA nucleotide sequences are called small interfering RNA (siRNA). ASOs bind to complementary nucleic acid sequences impacting the associated functions of the targeted nucleic acids. They represent an emerging class of drugs that, through a revolutionary mechanism of action, aim to directly regulate disease-causing genes and their variants, providing an alternative tool to traditional "protein-specific" therapies. The majority of the ASOs are designed to treat orphan genetic disorders that in most of the cases are seriously disabling and still lacking an adequate therapy. In order to translate ASOs into clinical success, constant technological advances have been instrumental in overcoming several pharmacological, toxicological and formulation limitations. Accordingly, chemical structures have been recently implemented and new bio-conjugation and nanocarriers formulation strategies explored. The aim of this work is to offer an overview of the antisense technology with a comparative analysis of the oligonucleotides approved by the Food and Drug Administration (FDA) and the European Medicines Agency (EMA).

RNA modifications in physiology and disease: towards clinical applications.

The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.

Development of Shortened miR-506-3p Mimics Exhibiting Strong Differentiation-Inducing Activity in Neuroblastoma Cells.

microRNA mimics are synthetic RNA molecules that imitate the mature miRNA duplexes and their functions. These mimics have shown promise in treating cancers. Nucleotide chemical modifications of microRNA mimics have been investigated and have improved the stability of miRNA mimics. However, the potential therapeutic benefit of mimic analogs based on sequence modifications has not been explored. miR-506-3p was identified as a differentiation-inducing microRNA in neuroblastoma cells, suggesting the potential of applying the miR-506-3p mimic in neuroblastoma differentiation therapy. In this study, we explored the possibility of developing shortened miR-506-3p analogs that can maintain differentiation-inducing activities comparable to the wild-type miR-506-3p mimic. We found that deleting up to two nucleotides at either the 3' end or within the middle region of the miR-506-3p sequence fully maintained the differentiation-inducing activity when compared to the wild-type mimic. Deleting up to four nucleotides from the 3' end or deleting three nucleotides in the middle positions diminished the differentiation-inducing activity, but the analogs still maintained differentiation-inducing activities that were significantly higher than the negative control oligo. The shortened analog designs potentially benefit patients from two perspectives: (1) the reduced cost of manufacturing shortened analogs, and (2) the reduced non-specific toxicity due to their smaller molecular sizes.

RNA tertiary structure prediction using RNAComposer in CASP15.

As CASP15 participants, in the new category of 3D RNA structure prediction, we applied expert modeling with the support of our proprietary system RNAComposer. Although RNAComposer is primarily known as an automated web server, its features allow it to be used interactively, for example, for homology-based modeling or assembling models from user-provided structural elements. In the paper, we present various scenarios of applying the system to predict the 3D RNA structures that we employed. Their combination with expert input, comparative analysis of models, and routines to select representative resultant structures form a ready-for-reuse workflow. With selected examples, we demonstrate its application for the in silico modeling of natural and synthetic RNA molecules targeted in CASP15.

Differential Expression of Endogenous Retroviruses and Inflammatory Mediators in Female and Male Offspring in a Mouse Model of Maternal Immune Activation.

Maternal infections during pregnancy and the consequent maternal immune activation (MIA) are the major risk factors for autism spectrum disorder (ASD). Epidemiological evidence is corroborated by the preclinical models in which MIA leads to ASD-like behavioral abnormalities and altered neuroinflammatory profiles, with an increase in pro-inflammatory cytokines and microglial markers. In addition to neuroinflammatory response, an abnormal expression of endogenous retroviruses (ERVs) has been identified in neurodevelopmental disorders and have been found to correlate with disease severity. Our aim was to evaluate the transcriptional profile of several ERV families, ERV-related genes, and inflammatory mediators (by RT real-time PCR) in mouse offspring of both sexes, prenatally exposed to polyinosinic:polycytidylic acid (Poly I:C), a synthetic double-stranded RNA molecule targeting TLR-3 that mimics viral maternal infection during pregnancy. We found that prenatal exposure to Poly I:C deregulated the expression of some ERVs and ERV-related genes both in the prefrontal cortex (PFC) and hippocampus, while no changes were detected in the blood. Interestingly, sex-related differences in the expression levels of some ERVs, ERV-related genes, and inflammatory mediators that were higher in females than in males emerged only in PFC. Our findings support the tissue specificity of ERV and ERV-related transcriptional profiles in MIA mice.

Formation of synthetic RNA protein granules using engineered phage-coat-protein -RNA complexes

Liquid-solid transition, also known as gelation, is a specific form of phase separation in which molecules cross-link to form a highly interconnected compartment with solid – like dynamical properties. Here, we utilize RNA hairpin coat-protein binding sites to form synthetic RNA based gel-like granules via liquid-solid phase transition. We show both in-vitro and in-vivo that hairpin containing synthetic long non-coding RNA (slncRNA) molecules granulate into bright localized puncta. We further demonstrate that upon introduction of the coat-proteins, less-condensed gel-like granules form with the RNA creating an outer shell with the proteins mostly present inside the granule. Moreover, by tracking puncta fluorescence signals over time, we detected addition or shedding events of slncRNA-CP nucleoprotein complexes. Consequently, our granules constitute a genetically encoded storage compartment for protein and RNA with a programmable controlled release profile that is determined by the number of hairpins encoded into the RNA. Our findings have important implications for the potential regulatory role of naturally occurring granules and for the broader biotechnology field.

The Potential of CRISPR/Cas9 Gene Editing as a Treatment Strategy for Inherited Diseases.

Clustered regularly interspaced short palindromic repeats (CRISPR) is a promising innovative technology for genomic editing that offers scientists the chance to edit DNA structures and change gene function. It has several possible uses consisting of editing inherited deficiencies, treating, and reducing the spread of disorders. Recently, reports have demonstrated the creation of synthetic RNA molecules and supplying them alongside Cas9 into genome of eukaryotes, since distinct specific regions of the genome can be manipulated and targeted. The therapeutic potential of CRISPR/Cas9 technology is great, especially in gene therapy, in which a patient-specific mutation is genetically edited, or in the treating of human disorders that are untreatable with traditional treatments. This review focused on numerous, in vivo, in vitro, and ex vivo uses of the CRISPR/Cas9 technology in human inherited diseases, discovering the capability of this versatile in medicine and examining some of the main limitations for its upcoming use in patients. In addition to introducing a brief impression of the biology of the CRISPR/Cas9 scheme and its mechanisms, we presented the utmost recent progress in the uses of CRISPR/Cas9 technology in editing and treating of human genetic diseases.

Development of Point-of-Care Lateral Flow Assay Devices for Salivary Endotoxin Detection

Endotoxins, also known as lipopolysaccharides (LPS), are important macromolecules in outer membrane of Gram-negative bacteria, which are generated when the bacteria are in growing and stationary phases, and disintegrate after death. While endotoxins induce a strong immune response in hosts, it also can serve as an important biomarker to diagnose various bacterial diseases. Among various pathogenic bacteria, Porphyromonas gingivalis is attracting much attention in recent years. P. gingivalis is a major Gram-negative bacterium that is responsible for chronic periodontitis, among > 500 bacteria species found in subgingival plaque. Periodontal disease presents a chronic inflammation caused by bacterial infection, leading to gum disease and even loss of teeth. LPS from P. gingivalis (PG LPS) induces significant host responses in gingival tissue by increasing the production of inflammatory biomarkers, such as interleukin (IL)-1, IL-6, IL-8, and tumor necrosis factor alpha (TNF- a) in gingival fibroblasts.[1] Furthermore, because of the close relationship between P. gingivalis and other important systemic diseases such as cardiovascular diseases (e.g. atherosclerosis[2]) and neurodegenerative Alzheimer’s disease[3] that has emerged in recent years, quantitative evaluation of PG LPS has become a key measure in oral health as well as in the whole body health system.Considering the increasing significance of P. gingivalis LPS, high demand for a novel point-of-care device has emerged for both early diagnosis and frequent monitoring PG LPS levels. Traditional qualitative detection of bacterial biomarkers is carried out mostly utilizing the well-known PCR method, which requires trained personnel and relatively longer time span in a laboratory setting. Lateral flow assay is one of the most promising POC platforms with many benefits, such as low cost, simple fabrication process, user-friendly colorimetric interface, rapid turnaround time, and no need for external instruments.[4] We have developed two different approaches for LFA-based POC devices to detect and quantify PG LPS concentrations. First, traditional immunoassay based LFA was developed to detect the PG LPS. Because PG LPS is a large macromolecule, multiple binding sites can be present on PG LPS. The sandwich assay mechanism was adopted using two different antibodies against PG LPS (Fig. 1a). Monoclonal antibodies are conjugated on the surface of gold nanoparticles (AuNP) to capture PG LPS molecules in the sample solution, and polyclonal antibodies are printed on the nitrocellulose membrane to form a test line by capturing PG LPS bound AuNP conjugate from the sample solution. After dispensing the sample solution on LFA, the test line is formed based on the PG LPS presence in the sample solution (Fig. 1b). Higher LPS concentration leads to a stronger test line. The second approach is to replace antibodies with aptamers as a bio-recognition molecule for target analytes. Aptamer-based assay uses a short synthetic DNA or RNA molecules that replace the traditional antibody/antigen immunoassay. Aptamer can be designed and synthesized in vitro with excellent sensitivity and selectivity to various target molecules. In addition, excellent long-term and thermal stability can also be provided because aptamers are chemically synthetized molecules. As shown in Fig. 2a, duplex aptamer was covalently conjugated to AuNPs. When LPS is introduced, the aptamer binds to the target LPS and is released from the duplex aptamer. In the competitive binding approach (Fig. 2b), a stronger test line is formed when less LPS is present. As shown in Fig. 2c, an increasing difference in test line intensity is observed as the LPS concentration is varied between 0 and 1 ng/mL. Interestingly, although usually the competitive assay is less sensitive than sandwich assay, in this case so far the competitive aptamer-based LFA presented higher sensitivity than that of sandwich immunoassay-based LFA test results. To further increase the assay sensitivity, future work will focus on enhancing the sandwich aptamer based LFA device using two different aptamers binding to the different sites on PG LPS. Wang, P.-L. and K. Ohura, Porphyromonas gingivalis Lipopolysaccharide Signaling in Gingival Fibroblasts–CD14 and Toll-like Receptors. Critical Reviews Oral Bio & Med, 2002. 13(2): 132-142.Mougeot, J.L.C., et al., Porphyromonas gingivalis is the most abundant species detected in coronary and femoral arteries. J. Oral Microbiology, 2017. 9(1): p. 1281562.Dominy, S.S., et al., Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors. Science Advances, 2019. 5(1): p. eaau3333.Dalirirad, S., D. Han, and A.J. Steckl, Aptamer-Based Lateral Flow Biosensor for Rapid Detection of Salivary Cortisol. ACS Omega, 2020.doi: 10.1021/acsomega.0c03223 Figure 1

Developing miR‐506‐3p Mimics with Enhanced Differentiation‐Inducing Activity

Neuroblastoma is one of the most prominent childhood cancers that results from the failure of neural crest cell differentiation. Inducing cell differentiation is a vital therapeutic strategy for neuroblastoma. MicroRNAs (miRNAs) are a class of endogenously expressed RNAs that regulate expression of target genes by complementary binding to the 3’ untranslated region (3’UTR) of mRNA. Previous studies have shown the miRNA-506-3p seed family to be a strong inducer of neuroblastoma cell differentiation. Differentiation-inducing miRNA mimics, synthetic RNA molecules that imitate the mature miRNA duplexes and their functions, are potential therapeutic agents for neuroblastoma differentiation therapy. In the effort to develop miR-506-3p-based differentiation agents, we identified mutant miRNA-506-3p mimics that potentially have enhanced differentiation-inducing activity based on the predicted interaction of the mutant miR-506-3p with its key differentiation-regulating targets, STAT3 and CDK4, suggesting these mutant mimics may have enhanced therapeutic potential compared to wild type (WT) miR-506-3p mimic. The objectives of my project are: 1) to compare the effect of these mutant mimics on neuroblastoma cell differentiation to that of WT mimic by measuring neurite outgrowth, a morphological differentiation marker, in neuroblastoma cells, and 2) to compare the effect of these mutants on cell growth arrest to that of WT mimic using MTT cell viability assay. This study will help to determine whether the mutant miR-506-3p mimics have higher therapeutic potential to treat neuroblastoma and widen efforts to develop more targeted therapies for high-risk patients.

Recent advances in optical aptasensor technology for amplification strategies in cancer diagnostics

Aptamers are chemically synthetic single-stranded DNA or RNA molecules selected by molecular evolution. They have been widely used as attractive tools in biosensing and bioimaging because they can bind to a large variety of targets with high sensitivity and high affinity and specificity. As recognition elements, aptamers contribute in particular to cancer diagnostics by recognizing different cancer biomarkers, while they can also facilitate ultrasensitive detection by further employing signal amplification elements. Optical techniques have been widely used for direct and real-time monitoring of cancer-related biomolecules and bioprocesses due to the high sensitivity, quick response, and simple operation, which has greatly benefited cancer diagnostics. In this review, we highlight recent advances in optical platform-based sensing strategies for cancer diagnostics aided by aptamers. Limitations and current challenges are also discussed.

CRISPR/Cas9 gene editing: A new therapeutic approach in the treatment of infection and autoimmunity.

CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein9) may be viewed as an adaptive bacterial immune system. When a virus infects a bacterium, a fragment of the virus genome is inserted into the CRISPR sequence of the bacterial genome as a memory. When the bacterium becomes infected again with the same virus, an RNA molecule that is a transcript of the memory sequence, directs Cas9, an endonuclease, to the complementary region of the virus genome, and Cas9 disables the virus by a double-strand break. In recent years, studies have shown that by designing synthetic RNA molecules and delivering them along with Cas9 into eukaryotic cells, different regions of the cell's genome can be targeted and manipulated. These findings have drawn much attention to this new technology and it has been shown that CRISPR/Cas9 gene editing can be used to treat some human diseases. These include infectious diseases and autoimmune diseases. In this review article, in addition to a brief overview of the biology of the CRISPR/Cas9 system, we collected the most recent findings on the applications of CRISPR/Cas9 technology for better investigation of the pathogenesis and treatment of viral infections (human immunodeficiency virus infection, hepatitis virus infections, and onco-virus infections), non-viral infections (parasitic, fungal, and bacterial infections), and autoimmune diseases.

Maternal Immune Activation with the Viral Mimetic Poly:IC in Pregnant Rats.

Maternal immune activation (MIA) is increasingly well appreciated as an environmental risk factor for some psychiatric disorders. Administration of proinflammatory compounds such as the synthetic double-stranded RNA molecule polyinosinic-polycytidylic acid (polyI:C) to pregnant rodents results in the release of proinflammatory cytokines in the maternal circulation. Various behavioural and brain changes are produced in the offspring that are associated with psychiatric disorders such as autism and schizophrenia. This protocol describes the steps necessary for inducing MIA in pregnant rat dams, which will allow for investigations into the mechanisms in the dam and offspring that mediate the long-term effects of exposure to inflammation while in utero. Increasing our understanding of these mechanisms may provide new insights for the diagnosis, treatment, and prevention of psychiatric disorders. This protocol has been developed and improved over the years by various researchers in Dr. Howland's laboratory at the University of Saskatchewan.

Shape Therapeutics raises funds to edit RNA

Seattle-based Shape Therapeutics has raised $35.5 million in series A financing to develop RNA-editing therapies. Unlike DNA, RNA is made continually in the cell, so some scientists view RNA editing as potentially safer than gene editing. Shape was cofounded by University of California San Diego scientist Prashant Mali. His lab has designed synthetic RNA molecules that direct enzymes called ADAR to make precise, single-letter changes to RNA in human cells. Mali’s lab has already tested the technique in a mouse model of muscular dystrophy.

Developing a DNA aptamer-based approach for biosensing cystatin-c in serum: An alternative to antibody-based methods

Oligonucleotide aptamers are short, synthetic and single-stranded DNA or RNA molecules capable of binding to a wide range of molecules, from small molecules to large cells. Nowadays, aptamers are valuable tools in research, clinical diagnosis and treatment. Their small size and high specificity in addition to their lack of immunogenicity make them great alternatives to other diagnosing candidates such as antibodies. In this study, we have introduced a new method based on competitive Enzyme-Linked Aptamer Sorbent Assay (ELASA) using single-stranded DNA (ssDNA) aptamers to measure cystatin-c levels in serum samples. To this aim, through a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process a number of aptamers were selected from which an aptamer with a Kd (dissociation constant) value of 65.5 ± 0.007 nM was chosen for further analyses. The limit of detection (LoD) was found to be 216.077 pg/ml. The results of the analytical application of this method in serum samples were comparable to those of commonly used commercial kits.

RNA Modifications Modulate Activation of Innate Toll-Like Receptors.

Self/foreign discrimination by the innate immune system depends on receptors that identify molecular patterns as associated to pathogens. Among others, this group includes endosomal Toll-like receptors, among which Toll-like receptors (TLR) 3, 7, 8, and 13 recognize and discriminate mammalian from microbial, potentially pathogen-associated, RNA. One of the discriminatory principles is the recognition of endogenous RNA modifications. Previous work has identified a couple of RNA modifications that impede activation of TLR signaling when incorporated in synthetic RNA molecules. Of note, work that is more recent has now shown that RNA modifications in their naturally occurring context can have immune-modulatory functions: Gm, a naturally occurring ribose-methylation within tRNA resulted in a lack of TLR7 stimulation and within a defined sequence context acted as antagonist. Additional RNA modifications with immune-modulatory functions have now been identified and recent work also indicates that RNA modifications within the context of whole prokaryotic or eukaryotic cells are indeed used for immune-modulation. This review will discuss new findings and developments in the field of immune-modulatory RNA modifications.

X-Ray Crystallographic Studies of G-Quadruplex Structures.

The application of X-ray crystallographic methods toward a structural understanding of G-quadruplex (G4) motifs at atomic level resolution can provide researchers with exciting opportunities to explore new structural arrangements of putative G4 forming sequences and investigate their recognition by small molecule compounds. The crowded and ordered crystalline environment requires the self-assembly of stable G4 motifs, allowing for an understanding of their inter- and intramolecular interactions in a packed environment, revealing thermodynamically stable topologies. Additionally, crystallographic data derived from these experiments in the form of electron density provides valuable opportunities to visualize various solvent molecules associated with G4s along with the geometries of the metal ions associated within the central channel-elements critical to the understanding G4 stability and topology. Now, with the advent of affordable, commercially sourced and purified synthetic DNA and RNA molecules suitable for immediate crystallization trials, and combined with the availability of specialized and validated crystallization screens, researchers can now undertake in-house crystallization trials without the need for local expertise. When this is combined with access to modern synchrotron platforms that offer complete automation of the data collection process-from the receipt of crystals to delivery of merged and scaled data for the visualization of electron density-the application of X-ray crystallographic techniques is made open to nonspecialist researchers. In this chapter we aim to provide a simple how-to guide to enable the reader to undertake crystallographic experiments involving G4s, encompassing the design of oligonucleotide sequences, fundamentals of the crystallization process and modern strategies used in setting up successful crystallization trials. We will also describe data collection strategies, phasing, electron density visualization, and model building. We will draw on our own experiences in the laboratory and hopefully build an appreciation of the utility of the X-ray crystallographic approaches to investigating G4s.

An Insight into DNA-free Reprogramming Approaches to Generate Integration-free Induced Pluripotent Stem Cells for Prospective Biomedical Applications.

More than a decade ago, a pioneering study reported generation of induced Pluripotent Stem Cells (iPSCs) by ectopic expression of a cocktail of reprogramming factors in fibroblasts. This study has revolutionized stem cell research and has garnered immense interest from the scientific community globally. iPSCs hold tremendous potential for understanding human developmental biology, disease modeling, drug screening and discovery, and personalized cell-based therapeutic applications. The seminal study identified Oct4, Sox2, Klf4 and c-Myc as a potent combination of genes to induce reprogramming. Subsequently, various reprogramming factors were identified by numerous groups. Most of these studies have used integrating viral vectors to overexpress reprogramming factors in somatic cells to derive iPSCs. However, these techniques restrict the clinical applicability of these cells as they may alter the genome due to random viral integration resulting in insertional mutagenesis and tumorigenicity. To circumvent this issue, alternative integration-free reprogramming approaches are continuously developed that eliminate the risk of genomic modifications and improve the prospects of iPSCs from lab to clinic. These methods establish that integration of transgenes into the genome is not essential to induce pluripotency in somatic cells. This review provides a comprehensive overview of the most promising DNA-free reprogramming techniques that have the potential to derive integration-free iPSCs without genomic manipulation, such as sendai virus, recombinant proteins, microRNAs, synthetic messenger RNA and small molecules. The understanding of these approaches shall pave a way for the generation of clinical-grade iPSCs. Subsequently, these iPSCs can be differentiated into desired cell type(s) for various biomedical applications.

Dimerization of an aptamer generated from Ligand-guided selection (LIGS) yields a high affinity scaffold against B-cells

Nucleic Acid Aptamers (NAAs) are a class of synthetic DNA or RNA molecules that bind specifically to their target. We recently introduced an aptamer termed R1.2 against membrane Immunoglobulin M (mIgM) expressing B-cell neoplasms using Ligand Guided Selection (LIGS). While LIGS-generated aptamers are highly specific, their lower affinity prevents aptamers from being used for translational applications. Highly specific aptamers with higher affinity can increase targetability, boosting the application of aptamers as diagnostic and therapeutic molecules. Herein, we report that dimerization of R1.2, an aptamer generated from LIGS, leads to high affinity variants without compromising the specificity. Three dimeric aptamer analogues with variable linker lengths were designed to evaluate the effect of linker length in affinity. The optimized dimeric R1.2 against cultured B-cell neoplasms, four donor B-cell samples and mIgM-positive Waldenström's Macroglobulinemia (WM) showed specificity. Furthermore, confocal imaging of dimeric aptamer and anti-IgM antibody in purified B-cells suggests co-localization. Binding assays against IgM knockout Burkitt's Lymphoma cells utilizing CRISPR/Cas9 further validated specificity of dimeric R1.2. Collectively, our findings show that LIGS-generated aptamers can be re-engineered into dimeric aptamers with high specificity and affinity, demonstrating wide-range of applicability of LIGS in developing clinically practical diagnostic and therapeutic aptamers.