A molecular system works like a multi-story building. Information flows from the genome, to transcripts, to proteins, to metabolites, and finally to the phenotype—and every layer talks to the others. Measure just one layer, and you miss the full picture and the connections between them. Today, scientists can detect these molecular features in place, at the resolution of single cells. But linking imaging-based spatial transcriptomics (ST) with MALDI-MSI-based spatial metabolomics (SM) has remained a formidable challenge.
Now, a team led by Prof. DUAN Lihui at the Institute of Genetics and Developmental Biology (IGDB), Chinese Academy of Sciences (CAS), has developed an open, low-cost imaging-based ST platform that can also integrate SM on the very same slide. The study was published online in Neuron on September 29.
The new technique, called OpenFISH, tackles two major problems head-on: the high cost of ST, and its incompatibility with SM.
Measuring mRNA in its native environment gives researchers a more accurate picture of a biological system. But existing ST technologies are expensive and hard for most labs to adopt, which limits the statistical power of studies below what science requires. To change that, the researchers used a modular probe design to cut probe synthesis costs, and a simple coding system for genes that eliminates the need for a microfluidic system. They also carefully optimized the entire experimental procedure, bringing the wet-lab time down to no more than 13 hours. A standard 20X widefield fluorescent microscope is all that's needed to capture clear signals in situ. Together, these efforts slash the total cost of OpenFISH by about 95% compared with leading commercial platforms.
The researchers then applied OpenFISH to two different areas of neuroscience: examining cell-type-associated transposable element (TE) elevation during inflammation, and neuronal cell lamination distortion after Reln gene knockout. They observed reproducible TE elevation, pointing to a role for TEs in regulating cells. Beyond the known anatomical changes caused by Reln knockout, they also spotted a novel decrease in D1-type inhibitory striatal neurons.
For biologists, performing ST and SM on serial sections is routine. But inherent differences between two adjacent slides can compromise how the data is interpreted. To solve this, the researchers modified conductive slides for a state-of-the-art untargeted SM method—MALDI-MSI. Through polyacrylamide gel embedding, protein digestion, and lipid removal, OpenFISH signals could still be readily detected even after the harsh laser processing used in MALDI-MSI.
Ion feature signals and transcript quality were barely affected by the integration. With this combined pipeline, the researchers revealed cell-type-associated metabolites in mouse brain cells, and found that merging the two modalities improves anatomical depiction. They also applied the pipeline to 5xFAD mice, a model for Alzheimer's disease (AD). Microglia showed the strongest changes after AD, and multiple metabolites for different specific cell types were elevated in AD mice compared with healthy controls.
In short, this work delivers an ST tool at a dramatically lower cost—one that can be paired with an SM platform to better untangle the complex interactions between the molecular layers of biology.
Contact:
Prof. DUAN Lihui
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Email: lihui.duan@genetics.ac.cn
CAS
中文
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