Effect of biological matrix and sample preparation on qPCR quantitation of siRNA drugs in animal tissues

Advancements in small interfering RNAs therapy for acute lymphoblastic leukemia: promising results and future perspectives

Acute lymphoblastic leukemia (ALL) is the most common type of cancer among children, presenting significant healthcare challenges for some patients, including drug resistance and the need for targeted therapies. SiRNA-based therapy is one potential solution, but problems can arise in administration and the need for a delivery system to protect siRNA during intravenous injection. Additionally, siRNA encounters instability and degradation in the reticuloendothelial system, off-target effects, and potential immune system stimulation. Despite these limitations, some promising results about siRNA therapy in ALL patients have been published in recent years, showing the potential for more effective and precise treatment, reduced side effects, and personalized approaches. While siRNA-based therapies demonstrate safety and efficacy, addressing the mentioned limitations is crucial for further optimization. Advancements in siRNA-delivery technologies and combination therapies hold promise to improve treatment effectiveness and overcome drug resistance. Ultimately, despite its challenges, siRNA therapy has the potential to revolutionize ALL treatments and improve patient outcomes.

Evidence Supporting the Safety of Pegylated Diethylaminoethyl-Chitosan Polymer as a Nanovector for Gene Therapy Applications

PURPOSE

Diethylaminoethyl-chitosan (DEAE-CH) is a derivative with excellent potential as a delivery vector for gene therapy applications. The aim of this study is to evaluate its toxicological profile for potential future clinical applications.

METHODS

An endotoxin-free chitosan (CH) modified with DEAE, folic acid (FA) and polyethylene glycol (PEG) was used to complex small interfering RNA (siRNA) and form nanoparticles (DEAE12-CH-PEG-FA2/siRNA). Based on the guidelines from the International Organization for Standardization (ISO), the American Society for Testing and Materials (ASTM), and the Nanotechnology Characterization Laboratory (NCL), we evaluated the effects of the interaction between these nanoparticles and blood components. In vitro screening assays such as hemolysis, hemagglutination, complement activation, platelet aggregation, coagulation times, cytokine production, and reactive species, such as nitric oxide (NO) and reactive oxygen species (ROS), were performed on erythrocytes, plasma, platelets, peripheral blood mononuclear cells (PBMC) and Raw 264.7 macrophages. Moreover, MTS and LDH assays on Raw 264.7 macrophages, PBMC and MG-63 cells were performed.

RESULTS

Our results show that a targeted theoretical plasma concentration (TPC) of DEAE12-CH-PEG-FA2/siRNA nanoparticles falls within the guidelines' thresholds: <1% hemolysis, 2.9% platelet aggregation, no complement activation, and no effect on coagulation times. ROS and NO production levels were comparable to controls. Cytokine secretion (TNF-α, IL-6, IL-4, and IL-10) was not affected by nanoparticles except for IL-1β and IL-8. Nanoparticles showed a slight agglutination. Cell viability was >70% for TPC in all cell types, although LDH levels were statistically significant in Raw 264.7 macrophages and PBMC after 24 and 48 h of incubation.

CONCLUSION

These DEAE12-CH-PEG-FA2/siRNA nanoparticles fulfill the existing ISO, ASTM and NCL guidelines' threshold criteria, and their low toxicity and blood biocompatibility warrant further investigation for potential clinical applications.

RT-qPCR Methods to Support Pharmacokinetics and Drug Mechanism of Action to Advance Development of RNAi Therapeutics

The goal of this study was to develop a reverse transcription quantitative polymerase chain reaction (RT-qPCR) method for the accurate quantification of chemically modified small interfering RNA (siRNA) including but not restricted to thermally destabilizing modifications such as glycol nucleic acid (GNA). RT-qPCR was found to be superior to mass spectrometry-based siRNA detection in terms of sensitivity and throughput. However, mass spectrometry is still the preferred method when specific metabolite detection is required and is also insensitive to siRNA chemical modifications such as GNA. The RT-qPCR approach can be optimized to take chemical modifications into account and works robustly in different matrices without optimization, unlike mass spectrometry. RT-qPCR and mass spectrometry both have their strengths and weaknesses for the detection of siRNA and must be used appropriately depending on the questions at hand. Considerations such as desired throughput, assay sensitivity, and metabolite identification must be weighed when choosing which methodology to apply.

Overcoming analytical challenges to generate data critical to understanding lipid nanoparticle-delivered modified mRNA biodistribution

Aim: Chemically modified mRNA offers a novel approach to treat disease. Due to susceptibility to extracellular nucleases in vivo, dosed modified mRNA therapeutics can benefit from encapsulation within novel delivery systems, such as lipid nanoparticles (LNPs). To understand the holistic effect of dosing LNP-encapsulated modified mRNA therapeutics can require bioanalysis of several components including the mRNA, protein and LNP. Methodology: These components can require bespoke preanalytical strategies to preserve analyte integrity to achieve successful analysis. Here we describe the sample collection, processing steps and bioanalytical technologies that can be used to overcome these challenges. Discussion: Understanding the biodistribution and holistic effects of the different components allow the pharmaceutical industry to evaluate safety and efficacy of modified mRNA therapeutics.

Measurement of mRNA therapeutics: method development and validation challenges

The progression of chemically modified mRNA therapeutics through development pipelines is accelerating for many disease indications and the need to assess these analytes is becoming more routine for the pharmaceutical industry and contract research organizations. This article describes some of the challenges and strategies for performing regulated bioanalysis of modified mRNA therapeutics by comparing the two main analytical approaches – quantitative reverse transcription PCR and branched DNA.

Intratracheal Administration of siRNA Triggers mRNA Silencing in the Lung to Modulate T Cell Immune Response and Lung Inflammation

Clinical application of siRNA-based therapeutics outside of the liver has been hindered by the inefficient delivery of siRNA effector molecules into extra-hepatic organs and cells of interest. To understand the parameters that enable RNAi activity in vivo, it is necessary to develop a systematic approach to identify which cells within a tissue are permissive to oligonucleotide internalization and activity. In the present study, we evaluate the distribution and activity within the lung of chemically stabilized siRNA to characterize cell-type tropism and structure-activity relationship. We demonstrate intratracheal delivery of fully modified siRNA for RNAi-mediated target knockdown in lung CD11c⁺ cells (dendritic cells, alveolar macrophages) and alveolar epithelial cells. Finally, we use an allergen-induced model of lung inflammation to demonstrate the capacity of inhaled siRNA to induce target knockdown in dendritic cells and ameliorate lung pathology.

Advances in quantitative bioanalysis of oligonucleotide biomarkers and therapeutics

Technical advances and demands for high-throughput accurate quantification of oligonucleotide therapeutics and biomarkers in pharmaceutical research and clinical diagnosis have aided evolution in quantitative bioanalysis of oligonucleotides. Many bioanalytical methods are available for absolute quantification of oligonucleotides in biological matrices. They can be broadly classified into two categories: hybridization-based assays commonly used by molecular biologists and chromatographic assays routinely used by chemists. Each category has its own advantages and disadvantages for specific applications. This review summarizes the mechanisms and applications of some of the current most commonly used techniques in each category.

Technologies for investigating the physiological barriers to efficient lipid nanoparticle-siRNA delivery

Small interfering RNA (siRNA) therapeutics have advanced from bench to clinical trials in recent years, along with new tools developed to enable detection of siRNA delivered at the organ, cell, and subcellular levels. Preclinical models of siRNA delivery have benefitted from methodologies such as stem-loop quantitative polymerase chain reaction, histological in situ immunofluorescent staining, endosomal escape assay, and RNA-induced silencing complex loading assay. These technologies have accelerated the detection and optimization of siRNA platforms to overcome the challenges associated with delivering therapeutic oligonucleotides to the cytosol of specific target cells. This review focuses on the methodologies and their application in the biodistribution of siRNA delivered by lipid nanoparticles.

Enzyme-linked bridging assay method for the quantification of oligonucleotide-based drugs in biological matrices

With ongoing efforts to develop oligonucleotide-based (ODN-based) therapeutics, there is a need for a sensitive, high-throughput method of quantification of ODN-based drugs in biological matrices. To overcome the insufficient sensitivity and time-consuming sample extraction procedures involved in conventional capillary gel electrophoresis (CGE) and high-performance liquid chromatography (HPLC), we developed a nucleic acid hybridization-based enzyme-linked bridging assay (ELBA), which shows significant advantages over CGE methods in evaluating ODN-based drugs in plasma and tissue: (1) It has higher sensitivity; (2) it involves easier sample extraction procedures; (3) it is suitable for many ODN-based drugs, even those with different secondary structures and modifications, including phosphorothioate oligonucleotide (PSODN), mixed backbones with 2'-O-Me (MBO), locked nucleic acid (LNA) modifications, and B- and C-type CpG sequences; and (4) it is highly selective, even during simultaneous quantification, with regard to intact ODNs and their 3'-metabolites. This universal design produces a rapid, sensitive, specific assay with minimal method development time. It is well suited to high-throughput analysis of various ODN-based drugs.

RNA interference and cancer therapy

Since its discovery in 1998, RNA interference (RNAi) has revolutionized basic and clinical research. Small RNAs, including small interfering RNA (siRNA), short hairpin RNA (shRNA) and microRNA (miRNA), mediate RNAi effects through either cleavage-dependent or cleavage-independent RNA inducible silencing complex (RISC) effector processes. As a result of its efficacy and potential, RNAi has been elevated to the status of "blockbuster therapeutic" alongside recombinant protein and monoclonal antibody. RNAi has already contributed to our understanding of neoplasia and has great promise for anti-cancer therapeutics, particularly so for personalized cancer therapy. Despite this potential, several hurdles have to be overcome for successful development of RNAi-based pharmaceuticals. This review will discuss the potential for, challenges to, and the current status of RNAi-based cancer therapeutics.

Biodistribution of small interfering RNA at the organ and cellular levels after lipid nanoparticle-mediated delivery

Chemically stabilized small interfering RNA (siRNA) can be delivered systemically by intravenous injection of lipid nanoparticles (LNPs) in rodents and primates. The biodistribution and kinetics of LNP-siRNA delivery in mice at organ and cellular resolution have been studied using immunofluorescence (IF) staining and quantitative polymerase chain reaction (qPCR). At 0.5 and 2 hr post tail vein injection of Cy5-labeled siRNA encapsulated in LNP, the organ rank-order of siRNA levels is liver > spleen > kidney, with only negligible accumulation in duodenum, lung, heart, and brain. Similar conclusions were drawn by using qPCR to measure tissue siRNA levels as a secondary end point. siRNA levels in these tissues decreased by more than 10-fold after 24 hr. Within the liver, LNPs delivered siRNA to hepatocytes, Kupffer cells, and sinusoids in a time-dependent manner, as revealed by IF staining and signal quantitation methods established using OPERA/Columbus software. siRNA first accumulated in liver sinusoids and trafficked to hepatocytes by 2 hr post dose, corresponding to the onset of target mRNA silencing. Fluorescence in situ hybridization methods were used to detect both strands of siRNA in fixed tissues. Collectively, the authors have implemented a platform to evaluate biodistribution of siRNA across cell types and across tissues in vivo, with the objective of elucidating the pharmacokinetic and pharmacodynamic relationship to guide optimization of delivery vehicles.