Innovative Single-Cell Sequencing Method Revolutionizes Drug Research

Researchers at the Herbert Irving Comprehensive Cancer Center (HICCC) have developed a groundbreaking single-cell sequencing technique that promises to transform the field of drug screening. This new method, known as DEFND-seq (DNA and Expression Following Nucleosome Depletion sequencing), allows for simultaneous analysis of RNA and DNA from individual cells, enhancing our understanding of cancer biology.

The study, published in Nature Methods, outlines how DEFND-seq utilizes a microfluidics platform capable of processing thousands of cells in parallel. This advancement is significant as it addresses the limitations of current sequencing methods, which can typically only handle a few thousand cells at a time and require extensive manual manipulation.

According to researchers, traditional methods relying on multi-well plates are not only resource-intensive but also restrict the number of cells analyzed from a single sample. The new droplet microfluidic system simplifies the process, allowing for the efficient handling of tens of thousands of cells simultaneously, thereby reducing the need for costly reagents.

The inception of DEFND-seq was somewhat serendipitous. The research team encountered consistent failures in experiments utilizing an established technique called ATAC-seq. Upon investigating these failures, the researchers realized that altering the chromatin structure could facilitate more comprehensive sequencing of the entire DNA strand. This insight led to the development of DEFND-seq, which effectively profiles genomic data more uniformly.

One of the primary applications of this new sequencing method is in the study of glioblastoma, a particularly aggressive form of brain cancer. Researcher Tim Olsen conducted benchmarking experiments using DEFND-seq on various glioblastoma samples, including archived surgical specimens. The ability to perform drug screenings directly on intact tumor tissues using this method is a significant advancement. This approach enables researchers to assess how different drug combinations affect specific cell types, including both tumor and non-tumor cells.

By integrating high-resolution DNA data from DEFND-seq, the research team can accurately map drug responses among distinct genetic subclones within heterogeneous tumors. This capability is crucial for identifying specific subclones that contribute to drug resistance, a major challenge in cancer treatment.

The implications of this research extend beyond glioblastoma. The team at HICCC is also exploring innovative strategies for local drug delivery across the blood-brain barrier, with the goal of improving treatment outcomes. The advanced drug screening platform being developed aims to optimize the combination of drugs to effectively target and eliminate tumors at a cellular level.

In conclusion, the DEFND-seq technique represents a significant step forward in cancer research, offering a scalable, cost-effective solution for single-cell sequencing that could lead to more personalized and effective treatments for patients.