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Harnessing the Power of RNA-Seq in RNA Therapeutics: A Valuable Tool for Discovery and Testing

Harnessing the Power of RNA-Seq in RNA Therapeutics: A Valuable Tool for Discovery and Testing


RNA therapeutics are a rapidly expanding category of drugs based on RNA with great potential against systemic diseases, such as cancer or infectious diseases. They offer incredible advantages: precision, versatility, and potential for personalized medicine (Kim, 2022; Zogg et al., 2022). In our previous blog article we discussed the extraordinary potential and modes of action of diverse classes of RNA-based therapeutics, including small interfering RNAs (siRNAs), antisense oligonucleotides (ASOs), and mRNA-based therapies. This time we would like to focus on the importance and benefit of RNA-Seq in the discovery process and in assessing the activity and effectiveness of RNA-based therapeutics.

RNA-Seq is a cutting-edge technology that, in its simplest form, allows measuring gene expression levels and identifying RNA molecules within cells and tissues present at the moment of sampling. Proper and carefully executed data analysis opens a window into the magnificent world of complex RNA landscapes, so-called transcriptomes. This invaluable insight enables researchers to decipher detailed and subtle changes in response to various factors, including drug responses, diseases, post-transcriptional modifications, and alternatively spliced transcripts, among others.

As with other drugs, RNA-based therapeutics elicit changes in the transcriptome of treated cells, tissues, and organisms. By harnessing the power of RNA-Seq, researchers studying RNA therapeutics can get a truly comprehensive understanding of the plethora of effects of RNA therapeutics on the changes in gene expression across the genome. This understanding is essential during their discovery especially when gauging their activity, effectiveness, and safety. So, let’s look at how exactly RNA-Seq can be utilized in the field of RNA therapeutics.


RNA-Seq in RNA Therapeutics Discovery


Both gene expression microarray and high-throughput RNA-Seq have been used routinely to drive the discovery of biomarkers in diseases and targets of drugs. RNA-Seq holds many benefits over expression microarrays, especially when discovering new target genes, as RNA-Seq, unlike microarrays, is not limited to detecting known transcripts. In addition, RNA-Seq can also be used to study the spatial and temporal expression of specific tissue or cell genes and discovering some unknown small RNAs. These features of RNA-Seq, with its high resolution, throughput, and sensitivity, make it invaluable for disease diagnosis and drug screening. By comparing RNA-Seq-derived gene expression profiles in diseased tissues to healthy ones, researchers can identify differentially expressed genes and noncoding RNAs associated with diseases (Yang et al., 2020b).

A magnificent example is The Cancer Genome Atlas (TCGA), a massive cancer genomics program, which characterized over 20,000 primary cancer and matched healthy samples spanning 33 cancer types, using RNA sequencing for gene expression profiling. This knowledge is helping to uncover novel targets for therapies, including RNA-based therapeutics (Dewaele et al., 2022).


RNA-Seq for Optimizing and Evaluating the Safety of RNA Therapeutics


RNA-Seq can also be used to assess the safety of RNA-based drugs. By analyzing changes in gene expression in response to treatment, researchers can identify potential off-target effects or other unintended consequences of the therapy. In a publication where authors were exploring mechanisms to induce the endosomal release of siRNAs (typical RNA-based therapeutics) without disturbing the cell homeostasis, RNA-Seq was used to understand the impact of these mechanisms on the cell transcriptome and detect possible safety issues. Differential gene expression analysis was performed for various conditions – and our QuantSeq library preparation kit was used to prepare RNA-Seq libraries directly from cell lysates (Fraire et al., 2020).


Mechanisms of Action of RNA Therapeutics and Confirmation of their Activity


Due to the complexity of some diseases, such as cancer or infectious diseases, the pharmacological industry has granted omics-based approaches more attention (Yang et al., 2020a). RNA-Seq nowadays plays a pivotal role in unraveling the intricate mechanisms underlying RNA-based therapeutics (Zhu et al., 2022). Using different variations of RNA-Seq (e.g., whole transcriptome sequencing or mRNA-Seq), researchers can investigate the functional consequences of the treatment with RNA therapeutics, such as siRNAs and ASOs on gene expression, alternative splicing, and noncoding RNA regulation, and confirm if they achieved the wished effect. For example, our CORALL, library prep kit for whole transcriptome sequencing was used to confirm the anticancer activity of siRNAs against oncogenes in cervical cancer cells (Gu et al., 2021). Then again, QuantSeq was used for shallow sequencing of primary and metastatic cancer cell lines treated with ASOS silencing a long-noncoding RNA SAMMSON, an oncogene in a type of a skin melanoma (Dewaele et al., 2022), followed by a differential gene expression analysis. In a consecutive study, QuantSeq was a method of choice to elucidate the mechanism underlying the synergistic effectt of RNA therapeutic with an mTOR inhibitor (Dewaele et al., 2022).




RNA-Seq has emerged as a transformative tool in the pursuit of RNA therapeutics. Through its ability to unravel gene expression changes, identify potential therapeutic targets, and shed light on the mechanisms of RNA-based interventions, RNA-Seq is propelling biomedical research forward. As technologies advance, the future of RNA-Seq looks even brighter, promising breakthroughs in personalized medicine and the development of targeted RNA therapies. By embracing RNA-Seq, scientists can illuminate the path to more effective and precise treatments for a wide range of diseases.


Our offer


When developing therapeutics of any kind, it is of crucial importance to perform all the tests and confirmations of activity, safety and efficiency with well-established methods and products. It is important to select a trustworthy, robust, and efficient library preparation kit, and invest in high-quality, properly executed data analysis pipeline, to obtain the best possible sequencing results – hence having the best possible insight into the transcriptome perturbations following treatment. Our library prep kits CORALL and QuantSeq have been successfully used as products of choice for obtaining high-quality RNA-Seq libraries when testing the activity and safety of RNA therapeutics.

Besides products, we also offer Lexogen NGS Services, where our team of experts will treat your project as their own, taking care of every detail, from initial consultations and experimental planning, nucleic acid extractions to data analysis and secure data transfer. To provide you with the best possible results for your specific experiments, our Services, R&D and bioinformatics teams have designed state-of-the-art, streamlined, and customizable workflows for all types of samples, even the most challenging ones. If you would like to experience first-class NGS Service, contact us at


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Written by Masa Ivin, PhD

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