SpinSeq

Project Summary RNA sequencing technologies are crucial for understanding gene expression, regulation, and the role of RNA modifications in health and disease. These technologies allow researchers to explore how genes are turned on and off as well as how RNA modifications influence cellular processes, contributing to a wide range of biological functions and disease mechanisms. Traditional RNA sequencing technologies often require the conversion of RNA into complementary DNA (cDNA) before sequencing, which results in the loss of critical RNA modifications. Without accurate detection of RNA modifications, our understanding of the regulatory mechanisms that control RNA and protein production—vital for cellular function and adaptation to environmental changes—suffers significantly. Alternatively, direct RNA sequencing platforms, such as those relying on motor-driven nanopore technologies, offer the potential to sequence RNA molecules without converting them to cDNA, thus preserving the modifications. However, these methods suffer from high error rates, making it difficult to accurately detect and quantify RNA modifications, while the complex secondary structures of RNA molecules further complicate the sequencing process, often resulting in incomplete or inaccurate data. New and advanced RNA sequencing technologies are urgently needed to overcome these challenges, enabling precise modification detection and full transcriptome analysis. This Phase I SBIR project aims to develop SpinSeq, an innovative platform designed to deliver highly precise and accurate RNA sequencing, setting a new standard for transcriptomic analysis. During this Phase I project, we will develop and refine a unique, tailored RNA sequencing technology, focusing on maintaining RNA integrity and ensuring precise sequencing. The project will focus on developing and optimizing the SpinSeq platform’s functionality, demonstrating its capability to be multiplexed for eventual high- throughput sequencing applications, and testing its performance on various RNA samples with and without our target modifications, e.g., N6-methyladenosine (m6A), 5-methylcytosine (m5C), and pseudouridine (Ψ), which are crucial for understanding gene expression regulation and disease mechanisms. The PI's career development and mentoring plans are integral to the success of this project. The PI will receive guidance from seasoned researchers, participate in the NIH I-Corps program to enhance entrepreneurial skills, and receive training in cutting-edge sequencing technologies. Additionally, the PI will actively engage in scientific conferences and workshops to build a professional network and gain insights from experts in the field. These efforts will not only enhance the PI’s technical and entrepreneurial expertise but will also ensure the successful commercialization of the SpinSeq platform. Ultimately, this project aims to establish SpinSeq as a groundbreaking tool for RNA research by addressing the limitations of existing technologies and delivering a more accurate, reliable, and scalable solution for both transcriptomic and epitranscriptomic studies.