Exosomal RNA Sequencing: A New Frontier in Biomarker Discovery

What is Exosomal RNA?

Exosomal RNA refers to the RNA molecules contained within exosomes, which are small extracellular vesicles released by cells. These vesicles play a crucial role in cell-to-cell communication, carrying a cargo of RNA, proteins, and lipids that reflect the state of their parent cells. The RNA within exosomes includes various species such as messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), and other non-coding RNAs. This RNA cargo can be transferred to recipient cells, influencing their biology and contributing to various physiological and pathological processes.

The Importance of Exosomal RNA Sequencing

Exosomal RNA sequencing has emerged as a powerful tool for the discovery of novel biomarkers and therapeutic targets. The RNA within exosomes can provide a snapshot of the genetic material within the cells that released them, without the need for direct access to those cells. This is particularly valuable for tissues that are difficult to biopsy or in situations where a non-invasive diagnostic is desired.

Exosomal RNA sequencing can reveal the specific types and amounts of RNA molecules present within the exosomes. This information can be used to identify patterns or signatures that are associated with particular diseases or conditions. For example, exosomal RNA sequencing has shown promise for the early detection of cancer, including pancreatic, lung, and breast cancer. In one study, researchers were able to identify a set of exosomal miRNAs that could distinguish pancreatic cancer patients from healthy controls with high accuracy. Similarly, another study found that exosomal lncRNAs in the blood could be used to detect lung cancer in its early stages. This approach may also aid in the monitoring of disease progression and response to therapy.

The Steps of Exosomal RNA Sequencing

The process of exosomal RNA sequencing involves several key steps:

• Isolation of Exosomes: This is typically accomplished through a combination of differential centrifugation and filtration steps. More recently, commercial kits and instruments have been developed to simplify this process. For example, ultracentrifugation-based methods can be used to isolate exosomes with high purity. Alternatively, technologies such as nanoparticle-tracking analysis and microfluidics-based devices offer faster and more streamlined approaches.
• RNA Extraction: The RNA is then extracted from the isolated exosomes. This often involves the use of specialized reagents and protocols to maximize yield and quality. For example, the use of carrier RNA and optimized lysis buffers can help to improve RNA recovery from these challenging samples.
• Library Preparation: The extracted RNA is then converted into a sequencing library through several steps. This typically includes polyadenylation of the RNA, ligation of adapters, and PCR amplification. The specific protocols used can vary depending on the sequencing platform and the goals of the study. For example, some methods may employ size selection steps to enrich for particular RNA species.
• Sequencing: The prepared library is then sequenced using a next-generation sequencing platform. This generates millions of reads that correspond to the RNA molecules present within the exosomes. The depth and breadth of sequencing data obtained can provide a comprehensive view of the exosomal RNA landscape.
• Bioinformatics Analysis: The sequencing data is then analyzed through a bioinformatics pipeline. This involves quality control, mapping to a reference genome, quantification of RNA abundance, and identification of differentially expressed RNAs. A variety of tools and algorithms are available for the analysis of exosomal RNA-seq data, each with their own strengths and limitations.

Challenges and Future Directions

While exosomal RNA sequencing holds great promise, there are several challenges that must be addressed. The isolation and analysis of exosomal RNA can be technically challenging due to the low yields and degraded nature of the RNA. Standardization of protocols and analytical pipelines is also needed to ensure reproducibility across studies. Furthermore, the field requires larger, well-designed studies to validate the clinical utility of exosomal RNA sequencing.

Despite these challenges, the potential of exosomal RNA sequencing is vast. As technologies continue to evolve and our understanding of exosomal biology deepens, this approach is likely to play an increasingly important role in both research and clinical applications. For example, the use of machine learning and other computational approaches may help to improve the analysis and interpretation of exosomal RNA-seq data. Additionally, the integration of exosomal RNA sequencing with other omics technologies may provide a more comprehensive view of disease biology.

Creative Biostructure provides support for your biomarker profiling and screening from various aspects. Exosomes carry markers of cells of origin and can be used as biomarkers of systemic response to infection and/or disease progression. We offer efficient solutions and a full range of services for exosome analysis. Creative Biostructure established cutting-edge exospmal RNA sequencing platform, allowing to get more details for exosome characterization and aid in disease diagnosis.

The Importance of Exosomal RNA Sequencing

Exosomes mainly contain short RNA, such as mRNA and miRNA, and little or no ribosomal RNA, which differs from that of cellular RNA. Exosomes can transfer these RNAs to achieve cell-to-cell communication, regardless of the distance between the cells. Exosome-mediated RNA transfer plays an important role in cell signal transduction. The study of RNAs in exosomes not only offers new insights into the functions of exosomes, but also provides a promise for exosomes as biomarkers for diseases or to be used as vectors in gene therapy. The next-generation sequencing is a powerful tool for characterization of exosomal RNAs.

Exosomal RNA Sequencing Service

Creative Biostructure is equipped with the cutting-edge devices and the first-class experts. We are devoted to solving any tough questions in your project and providing accurate and reliable results. The experimental workflow of exosomal RNA sequencing analysis involves 4 steps:

• Exosome isolation and enrichment. We provide various methods for exosome isolation including ultracentrifugation and extraction kit. We can deal with a full range of samples, such as serum, cell culture supernatant, urine, saliva or any other fluid.
• RNA isolation. Our experts offer optimal solutions for high quality RNA isolation.
• RNA library preparation and next-generation sequencing. With years of experience in RNA sequencing, Creative Biostructure offers specialized methods for little contaminations and higher percentage of usable exosomal RNA sequence reads.
• RNA-Seq data processing, alignment and analysis. We provide abundance difference analysis, family analysis, comparative analysis, and conservative analysis of mRNAs and miRNAs.

References

[1] Théry C, Zitvogel L, Amigorena S. Exosomes: composition, biogenesis and function. Nat Rev Immunol. 2002;2(8):569–579.

[2] Valadi H, Ekström K, Bossios A, Sjöstrand M, Lee JJ, Lötvall JO. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol. 2007;9(6):654–659.

[3] Li P, Kaslan M, Lee SH, Yao J, Gao Z. Progress in Exosome Isolation Techniques. Theranostics. 2017;7(3):789–804.

[4] Reiner AT, Witwer KW. Extracellular Vesicle RNA: From Basics to Biological and Therapeutic Potential. Wiley Interdiscip Rev RNA. 2019;10(2):e1514.

[5] Yang Y, Li Q, Zhao H. Exosomal RNA in the Diagnosis and Treatment of Cancer and Other Diseases. BioMed Res Int. 2019;2019:8572309.

[6] Zhang H, Deng T, Liu R, et al. Exosome-delivered EGFR regulates liver microenvironment to promote gastric liver metastasis. Nat Commun. 2017;8:15016.

[7] Li W, Li C, Zhong T, et al. Exosome-delivered EGFR regulates liver microenvironment to promote gastric liver metastasis. Oncotarget. 2018;9(25):16961–16972.

[8] Figliolini F, Cantaluppi V, De Lena M, et al. Isolation, characterization and potential therapeutic use of mesenchymal stromal cells. Arterioscler Thromb Vasc Biol. 2010;30(9):654–669.

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We have developed all-in-one, gene-to-structure pipelines for the structure determination of macromolecules of your interest. With a team of experienced professionals, Creative Biostructure is able to solve the structure of many challenging proteins including GPCRs, ion channels, transporters, enzymes and viral targets. We also provide a comprehensive list of products and other related services to facilitate your research in structural biology.

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