Researchers have developed a highly sensitive new tool that analyzes a cell’s DNA and its RNA transcripts simultaneously, providing a direct link between genetic variants and gene expression within a single cell. This technology, called single-cell DNA-RNA-sequencing (SDR-seq), overcomes major limitations of previous methods, offering a powerful way to investigate the vast, non-coding regions of the genome where the majority of disease-associated variants are located. By connecting specific genetic sequences to the activity of genes in the same cell, SDR-seq promises to accelerate the discovery of the molecular roots of complex diseases.
The development provides a crucial capability that scientists have sought for years: the ability to precisely link an individual’s unique genetic makeup to the functional output of their cells at a massive scale. While it has long been understood that inherited DNA variations contribute to disease, pinpointing how these variants exert their influence has been a formidable challenge, especially when they lie outside of protein-coding genes. The new method was successfully used to show how even minor DNA changes can affect gene regulation in human stem cells and in a model of B-cell lymphoma, a type of blood cancer, demonstrating its potential to unravel the complex interplay between our genome and disease.
Unraveling an Ancient Mystery
The observation that diseases can “run in families” is ancient, with historical accounts dating back to Hippocrates. This intuitive understanding of heredity has driven centuries of scientific inquiry, culminating in the mapping of the human genome. However, this achievement revealed a new layer of complexity. Scientists found that genome-wide association studies (GWAS), which scan genomes to find variations associated with a particular disease, frequently pointed to regions of DNA that do not code for proteins. In fact, more than 95% of the genetic variants linked to common diseases reside in this “non-coding” DNA, which was once dismissed as “junk.”
These non-coding regions are now understood to contain critical regulatory elements like enhancers and silencers, which act as switches that control the activity of genes, dictating when and where they are turned on or off. A variant in one of these regions can disrupt normal gene regulation, leading to disease. The central difficulty for researchers has been the inability to draw a straight line from a specific non-coding variant to its effect on gene expression in a specific type of cell. Previous single-cell methods could typically only analyze either DNA or RNA, but not both together with high throughput, making it nearly impossible to establish this direct causal link. This technological gap left the function of most disease-associated variants largely unexplained.
A Dual-Omic Breakthrough in a Droplet
The SDR-seq method represents a significant technological leap by enabling the simultaneous analysis of both the genome (DNA) and the transcriptome (RNA) from the same cell. This dual-omic capability provides a direct readout of how genetic variants influence which genes are actively being expressed. The platform was developed by scientists at the European Molecular Biology Laboratory (EMBL) in collaboration with researchers from Stanford University School of Medicine and Heidelberg University Hospital.
How the Technology Functions
At the core of SDR-seq is a sophisticated microfluidics system that uses oil-water emulsion droplets. Each tiny droplet encapsulates a single cell, creating a miniature, isolated laboratory. Inside this contained environment, the cell is broken open, and its genetic material is processed. Special molecular barcodes are attached to both the DNA fragments and the RNA transcripts, ensuring that every piece of genetic information is tagged with the unique identifier of its cell of origin. This process allows researchers to pool the material from thousands of cells for sequencing and then computationally trace every DNA sequence and RNA molecule back to the individual cell it came from. This innovative design allows for the analysis of thousands of cells in a single experiment, a dramatic increase in scale and efficiency.
Surpassing Previous Limitations
Prior attempts to jointly profile DNA and RNA in single cells were hampered by several significant issues. They often had low throughput, meaning only a small number of cells could be analyzed at once. Furthermore, they lacked the sensitivity needed to capture the full picture, frequently failing to detect variants unless they were located in highly expressed genes. According to Dominik Lindenhofer, lead author of the paper published in Nature Methods, these methods were also technically complicated and could not reliably analyze variants regardless of their location in the genome. SDR-seq overcomes these hurdles, providing a scalable, precise, and sensitive tool that works across the entire genome, not just the coding regions.
From Genetic Code to Disease Insights
By applying SDR-seq, the research team demonstrated its power to forge direct links between genetic variation and cellular function. The tool allows scientists to observe how a subtle change in the DNA sequence of a regulatory region directly corresponds to a change in the expression level of a nearby gene within the same cell. This provides a level of granular evidence that was previously unattainable.
Initial Findings in Cell Models
The researchers applied the technique to study human stem cells and a B-cell lymphoma model. In both cases, they were able to identify how specific genetic variants altered gene regulation. For example, a single nucleotide change in a non-coding region could be directly linked to an increase or decrease in the transcription of a particular gene. These initial applications serve as a proof of principle, showing that SDR-seq can effectively uncover the functional consequences of genetic variants implicated in both normal development and in cancer. The ability to perform this analysis at the single-cell level is critical, as it can reveal cellular heterogeneity that is missed in bulk tissue analysis.
Future of Genomic Medicine
The development of SDR-seq opens up a wide array of new possibilities for understanding and eventually treating complex human diseases. By providing a tool to systematically link variants to function, it can help researchers prioritize which of the thousands of variants identified by GWAS are most likely to be causal and therefore the best targets for further study or therapeutic development.
Lars Steinmetz, a senior author on the paper and an EMBL group leader, stated that the tool provides a capability that “opens up a wide range of biology that we can now discover.” In the near term, the technology could be used to create more sophisticated diagnostic tools. For example, it could help screen for disease risk by identifying how a person’s individual genetic variants affect their cellular functions. In the long term, by clarifying the precise molecular mechanisms that underlie diseases, SDR-seq could guide the development of new precision medicines tailored to a patient’s unique genetic profile. The platform’s high-throughput nature makes it suitable for large-scale projects, including efforts to map the functional impact of genetic variation across all the different cell types in the human body.