Integrated spatial protein and RNA analysis on the same section using MICS technology

Neil, E.; Park, D.; Hennessey, R. C.; DiBiasio, E. C.; DiBuono, M.; Lafayette, H.; Lloyd, E.; Lo, H.; Femel, J.; Makrigiorgos, A.; Soliman, S.; Mangiardi, D.; Praveen, P.; Rüberg, S.; Staubach, F.; Hindman, R.; Rothmann, T.; Meyer, H.; Wantenaar, T.; Wang, J.; Müller, W.; Pinard, R.; Bosio, A.

doi:10.1101/2023.10.27.564191

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bioRxiv · 10.1101/2023.10.27.564191

Integrated spatial protein and RNA analysis on the same section using MICS technology

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Abstract

Spatial Biology has evolved from the molecular characterization of microdissected cells to high throughput spatial RNA and protein expression analysis at scale. The main limitation of spatial technologies so far is the inability to resolve protein and RNA information in the same histological section. Here, we report for the first time the integration of highly multiplexed RNA and protein detection on the same tissue section. We developed a new, automated, spatial RNA detection method (RNAsky), which is based on targeted rolling circle amplification and iterative staining. We combine RNAsky with MACSima Imaging Cyclic Staining (MICS) based protein analysis and show compatibility with subsequent standard hematoxylin and eosin (H&E) staining. Using both, open-source tools and our recently developed software suite MACS(R) iQ View, we demonstrate our multiomics MICS workflow by characterizing key immune-oncology markers at subcellular resolution across normal and diseased tissues.

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Neil, E., Park, D., Hennessey, R. C., DiBiasio, E. C., DiBuono, M., Lafayette, H., Lloyd, E., Lo, H., Femel, J., Makrigiorgos, A., Soliman, S., Mangiardi, D., Praveen, P., Rüberg, S., Staubach, F., Hindman, R., Rothmann, T., Meyer, H., Wantenaar, T., Wang, J., Müller, W., Pinard, R., Bosio, A.. 2023-10-27. Integrated spatial protein and RNA analysis on the same section using MICS technology. https://doi.org/10.1101/2023.10.27.564191

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