Abstract
The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate SM-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.
Highlights
The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease
In SMOmics, after tissue staining for traditional hematoxylin and eosin histology (H&E), IF or using DNA-barcoded antibodies, glass slides are loaded into the SM-Omics platform, where, using a liquid handler robot, cells are permeabilized, mRNAs and/or antibody barcodes are spatially tagged and converted into a sequencing-ready library (Fig. 1)
The input to these is in situ spatial tissue cDNA or DNA-barcoded antibody tags captured from glass slides in the first step, which are processed to amplify cDNA using a T7 in vitro transcription approach or standard PCR amplification, followed by a final conversion of the amplified RNAs into sequencing-ready libraries (Fig. 1II, III)
Summary
The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Companion technologies similar to our approach (e.g. Visium, 10X Genomics) rely on: (i) an antibody-based immunofluorescence (IF) read-out of 1–2 target antigens; (ii) do not employ DNA-barcoding strategies which allow us to parallelize antibody-based measurements, (iii) and process spatial RNA-Seq libraries manually, making these approaches low-throughput, laborious and not scalable due to intrinsic limitations of multiplex imaging To bridge this gap and make molecular tissue profiling a widely available and robust tool, we develop Spatial Multi-Omics (SMOmics), an end-to-end framework that uses a liquid handling platform for high-throughput combined transcriptome and antibodybased spatial tissue profiling with minimum user input and available laboratory instrumentation[45,46]. This user-friendly all-sequencing based technology allows processing of up to 64 in situ spatial reactions and up to 96 sequencing-ready libraries, of high complexity, in ~2 days, in a highthroughput platform for spatial multi-omics
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