Stamp Technique Revolutionizes Single-Cell RNA Sequencing Cost-Effectively

In a groundbreaking advancement in genomic research, scientists from St. Jude Children’s Research Hospital, the National Center for Genomic Analysis, and the University of Adelaide have developed a new method for single-cell RNA sequencing that dramatically reduces costs by 47 times. This innovative technique, known as Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging (STAMP), significantly enhances the scalability and accessibility of single-cell profiling, which is crucial for understanding gene expression in both health and disease. The findings were published in the prestigious journal Cell on June 12, 2025.

Single-cell RNA sequencing (scRNA-seq) is a powerful technique that allows researchers to examine gene expression at the individual cell level. However, traditional methods are often prohibitively expensive and require sophisticated, specialized equipment, limiting their use to well-funded laboratories. According to Dr. Jasmine Plummer, PhD, director of the St. Jude Center for Spatial Omics and co-corresponding author of the study, “We’ve created a technique that gives us an advantage in the numbers game of single-cell analysis.” The STAMP methodology can analyze millions of cells simultaneously at a fraction of the cost of existing techniques, which typically only allow for the profiling of tens of thousands of cells.

The STAMP technique involves separating cells from tissues until they are individual and unconnected, then fixing these cells onto microscopy slides. This process preserves the cells' morphology and gene expression profiles, effectively 'locking' them in time. Researchers then introduce specific molecules that emit signals under a microscope when bound to targeted RNA sequences, enabling the identification and characterization of various cell types.

Dr. Plummer highlighted the practical implications of STAMP, noting that analyzing immune cells from 1,000 individuals would normally cost approximately $3.56 million, while using STAMP would reduce this cost to around $75,000. “Current techniques for single-cell RNA sequencing require inference to determine things such as cell type, but STAMP allows us to directly examine the cells,” she explained. This direct observation capability helps mitigate biases that can arise from the movement of cells through tubes in traditional methods, which typically favors more spherical cells and may overlook irregularly shaped ones, such as neurons.

To test the sensitivity of this new method, the researchers diluted cancer cells into a suspension of over 850,000 other cells on a single slide. Remarkably, STAMP was able to detect two cancer cells, demonstrating its potential in identifying rare cell types within a large population.

Dr. Plummer emphasized the clinical relevance of this work, stating, “Being able to profile a million cells is crucial because it only takes one cell to escape cancer treatment.” The researchers envision that STAMP could pave the way for new clinical applications, providing a cost-effective solution for laboratories that may lack the funding or infrastructure required for traditional scRNA-seq methods.

In addition to the significant cost reduction, the accessibility of standard microscopes in most research institutions enhances the potential for widespread adoption of STAMP. Dr. Plummer stated, “We as scientists believe what we can see. STAMP gives us the best of both worlds in single-cell analysis: quantitative gene expression data and the ability to visually examine the cells under a microscope.” The hope is that this novel approach will empower researchers to uncover new biological insights and clinical applications, accelerating the pace of discovery in genomic research.

As the field of transcriptomics continues to evolve, the implications of STAMP extend beyond cost savings. The method’s ability to provide detailed insights into cellular diversity and function could have far-reaching effects on cancer research, immunology, and regenerative medicine. The researchers plan to further refine the technique and explore its applications across various biological contexts, reinforcing the critical role of innovative methodologies in advancing scientific knowledge and improving healthcare outcomes.