SM-Omics is an automated platform for high-throughput spatial multi-omics

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.

Spatial host-microbiome sequencing

“…We developed SHM-seq by adapting Spatial Transcriptomics [23], where mRNA is captured by probes on a glass slide followed by profiling, to enable simultaneous capture of polyadenylated (host) transcripts and hypervariable regions of the 16S ribosomal RNA (rRNA) (Methods, Fig1). Specifically, we produced solid phase Spatial Transcriptomics slides covered with uniquely barcoded and spatially addressable capture probes [23][24][25], with ~1,000 distinct addressable DNA features (i.e. spatial spots) deposited and covalently linked to a glass substrate.…”

“…Finally, after imaging, we permeabilized the cells, allowing capture of host polyadenylated transcripts and bacterial 16S sequences on the array. The result was direct spatial DNA barcoding of host transcripts and bacterial species, which were sequenced by Illumina sequencing [24].…”

“…Imaging of stained H&E tissue sections on glass arrays was performed on a Metafer Vslide scanning system (MetaSystems, Germany) installed on an Axio Imager Z2 microscope (Carl Zeiss, Germany) with a LED transmitted light source and a CCD camera. Using an A-P 10x/0.25 Ph1 objective lens (Carl Zeiss, Germany) and a configuration program [24], focusing and scanning of each tissue section on the glass array was done automatically. Image stitching was done using Vslide (v.1.0.0) with 60µm overlap and linear blending between fields of views.…”

“…The copyright holder for this preprint (which this version posted July 19, 2022. ; https://doi.org/10.1101/2022.07. 18.500470 doi: bioRxiv preprint Here, we bridge this gap, by developing spatial host-microbiome sequencing (SHM-seq, Fig1), a robust all-sequencing based technology that leverages previous advancements in spatial transcriptomics [23,24], and provides histology, spatial RNA-seq and spatial 16S sequencing using readily available instrumentation to profile the host's expression responses in relation to microbial biogeography. We apply it in the model system of the mouse colon, showing a roadmap for interrogating spatial gene expression programs in correlation to bacterial presence.…”

Unraveling protein dynamics to understand the brain – the next molecular frontier

“…Detection will also be improved by methods allowing for alternative enrichment strategies outside of click chemistry, such as with biotinylation of proteins directly in live animals via TurboID [ 59 ]. Spatial omics may also be combined with these methods in the future to determine if proteins are detected in cells without the corresponding RNA, likely indicating the protein originated from another cell [ 89 ]. Data from all these tools increasingly offer ample opportunities for machine learning and multi-modal data analysis, as almost all individual molecules in all cells, fluids, and tissues are beginning to be accessible.…”