Spatial transcriptomics (ST) shows which genes are active and where within a tissue, while spatial metabolomics (SM) maps the location of metabolites, the small molecules cells produce and use. A new open, low-cost imaging-based ST platform can now integrate SM on the same slide, addressing two problems that have limited the field: high cost and incompatibility between the two methods.
The platform, called OpenFISH, was described in a study led by Duan Lihui at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences, published in Neuron. A biological system can be thought of as a multistory building, with information flowing from genome to transcripts to proteins to metabolites and finally to phenotype, and every layer interacting with the others. Measuring only one layer can miss the full picture and the connections between them. Existing ST technologies can detect molecular features within tissue at single-cell resolution, but they remain expensive and hard for many labs to use, and pairing imaging-based ST with the untargeted SM method MALDI-MSI on the same tissue section adds a further challenge.
To bring costs down, the researchers used a modular probe design along with a simple gene-coding system that removes the need for a microfluidic system, and they streamlined the experimental procedure so wet-lab time runs no more than 13 hours. A standard 20x widefield fluorescence microscope is enough to capture clear signals in situ. Together, these changes cut OpenFISH's total cost by about 95 percent compared with leading commercial platforms.
The team tested OpenFISH in two neuroscience applications: tracking cell-type-associated transposable element (TE) elevation during inflammation, and examining neuronal cell lamination distortion after knocking out the Reln gene. Reproducible TE upregulation pointed to TEs as active drivers or modulators of neuroinflammatory pathways, and beyond the known anatomical effects of Reln knockout, the researchers also found a decrease in D1-type inhibitory striatal neurons.
Because ST and SM are usually run on separate, adjacent tissue sections, differences between those sections can complicate interpretation. To combine both methods on one section, the researchers modified conductive glass slides for MALDI-MSI, using polyacrylamide gel embedding, protein digestion, and lipid removal so that OpenFISH signals remained detectable even after the harsh laser processing MALDI-MSI requires. Ion feature signals and transcript detection were barely affected by this integration, and the combined pipeline revealed cell-type-associated metabolites in mouse brain cells, with the merged modalities improving anatomical depiction.
Applied to 5xFAD mice, a model for Alzheimer's disease, the pipeline showed that microglia had the strongest changes, with multiple cell-type-associated metabolites elevated compared with healthy controls. The researchers describe the work as introducing a cost-effective ST tool that pairs with SM platforms to help untangle complex molecular interactions in biological systems.
The platform, called OpenFISH, was described in a study led by Duan Lihui at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences, published in Neuron. A biological system can be thought of as a multistory building, with information flowing from genome to transcripts to proteins to metabolites and finally to phenotype, and every layer interacting with the others. Measuring only one layer can miss the full picture and the connections between them. Existing ST technologies can detect molecular features within tissue at single-cell resolution, but they remain expensive and hard for many labs to use, and pairing imaging-based ST with the untargeted SM method MALDI-MSI on the same tissue section adds a further challenge.
To bring costs down, the researchers used a modular probe design along with a simple gene-coding system that removes the need for a microfluidic system, and they streamlined the experimental procedure so wet-lab time runs no more than 13 hours. A standard 20x widefield fluorescence microscope is enough to capture clear signals in situ. Together, these changes cut OpenFISH's total cost by about 95 percent compared with leading commercial platforms.
The team tested OpenFISH in two neuroscience applications: tracking cell-type-associated transposable element (TE) elevation during inflammation, and examining neuronal cell lamination distortion after knocking out the Reln gene. Reproducible TE upregulation pointed to TEs as active drivers or modulators of neuroinflammatory pathways, and beyond the known anatomical effects of Reln knockout, the researchers also found a decrease in D1-type inhibitory striatal neurons.
Because ST and SM are usually run on separate, adjacent tissue sections, differences between those sections can complicate interpretation. To combine both methods on one section, the researchers modified conductive glass slides for MALDI-MSI, using polyacrylamide gel embedding, protein digestion, and lipid removal so that OpenFISH signals remained detectable even after the harsh laser processing MALDI-MSI requires. Ion feature signals and transcript detection were barely affected by this integration, and the combined pipeline revealed cell-type-associated metabolites in mouse brain cells, with the merged modalities improving anatomical depiction.
Applied to 5xFAD mice, a model for Alzheimer's disease, the pipeline showed that microglia had the strongest changes, with multiple cell-type-associated metabolites elevated compared with healthy controls. The researchers describe the work as introducing a cost-effective ST tool that pairs with SM platforms to help untangle complex molecular interactions in biological systems.