Multiplexed Error-Robust Fluorescence in situ Hybridization, or MERFISH, is a technology that maps gene activity within biological tissues. This method allows scientists to visualize and count individual RNA molecules, indicators of gene expression, directly within their native cellular environment. MERFISH provides a detailed picture of active genes and their exact location within cells and tissues. This offers a new way to understand complex biological processes at high resolution.
The Concept of Spatial Transcriptomics
Understanding where genes are active within a tissue is important, as it goes beyond simply knowing if they are active. Traditional bulk RNA sequencing methods average gene expression across many cells in a sample, losing information about specific gene activity locations. This averaging can obscure the unique contributions of different cell types and their interactions within a complex tissue.
Single-cell RNA sequencing (scRNA-seq) identifies different cell types based on their gene expression profiles. However, this technique requires dissociating tissues into individual cells, destroying their original spatial arrangement. The loss of this spatial information hinders our understanding of how cells interact with their neighbors and how their location influences their function. Knowing the precise spatial distribution of gene expression helps researchers understand cellular organization, identify cell subtypes, and analyze molecular mechanisms driving disease.
Decoding Gene Expression with MERFISH
MERFISH technology provides spatially resolved gene expression profiling of single cells within intact biological samples. This method uses a unique barcoding system to assign a distinct identifier to each RNA species targeted for detection. Specific probes are designed to bind to RNA molecules of interest, carrying error-robust barcodes.
The process involves sequential imaging rounds, where fluorescently tagged readout probes bind to barcoded RNA molecules. In each imaging round, specific “bits” of the barcode are read by detecting the presence or absence of a fluorescent signal at the location of an RNA molecule. If a signal is detected, it represents a “one” in the binary barcode, while no signal indicates a “zero”. This sequential readout allows for the reconstruction of each RNA molecule’s unique barcode.
MERFISH’s error robustness means barcode sequences tolerate misread bits without incorrect identification. This design helps ensure high accuracy and reproducibility of the data. After multiple imaging rounds, the decoded barcodes are matched to specific genes, allowing researchers to precisely quantify and map the spatial distribution of hundreds to tens of thousands of different RNA species within individual cells. The result is a high-resolution map that shows not only which genes are expressed but also their exact location within the tissue, sometimes even at subcellular detail.
Revolutionizing Biological Discovery
MERFISH technology is transforming biological research by providing insights into complex tissue organization and disease mechanisms. By mapping gene expression in its native spatial context, researchers can identify distinct cell populations and understand how their locations relate to their functions. This allows for the precise characterization of cell types and even the detection of rare cell populations that might be overlooked by other methods.
The ability to visualize cellular interactions and gene expression patterns within their original environment is impactful in fields like neuroscience, developmental biology, and cancer research. For example, MERFISH helps to delineate the spatial organization of cells in the brain, revealing how specific neuronal subtypes are distributed and how their gene activity contributes to brain function. In cancer, it can uncover the spatial heterogeneity within tumors, showing how different cancer cell populations and their surrounding microenvironment influence disease progression and treatment response. This spatially resolved information provides a deeper understanding of biological processes, guiding discoveries in fundamental biology and supporting the development of new therapeutic strategies.