A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract

Gustavo Monasterio, Rodrigo A. Morales, David A. Bejarano, Xesús M. Abalo, Jennifer Fransson, Ludvig Larsson, Andreas Schlitzer, Joakim Lundeberg, Srustidhar Das, Eduardo J. Villablanca

Published: 2024-06-20 DOI: 10.1038/s41596-024-01001-2

Supplementary information

A comprehensive demonstration of the essential procedures involved in tissue isolation, processing, and mounting. Each critical step is depicted in detail to ensure clarity and to facilitate the replication of the methods presented in this protocol.

Genetic manipulation and immortalized culture of ex vivo primary human germinal center B cells

The cell-line-derived subcutaneous tumor model in preclinical cancer research

Subcellular patch-clamp techniques for single-bouton stimulation and simultaneous pre- and postsynaptic recording at cortical synapses

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

Genome-wide pooled CRISPR screening in neurospheres

High-throughput cultivation and identification of bacteria from the plant root microbiota

Viral crosslinking and solid-phase purification enables discovery of ribonucleoprotein complexes on incoming RNA virus genomes

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice

Multiplexed single-cell proteomics using SCoPE2

查看全部

Sections

Figures

References

Supplementary information

Moffitt, J. R., Lundberg, E. & Heyn, H. The emerging landscape of spatial profiling technologies. Nat. Rev. Genet. 23, 741–759 (2022).
Ke, R. et al. In situ sequencing for RNA analysis in preserved tissue and cells. Nat. Methods 10, 857–860 (2013).
Black, S. et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat. Protoc. 16, 3802–3835 (2021).
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, aaa6090 (2015).
Marx, V. Method of the year: spatially resolved transcriptomics. Nat. Methods 18, 9–14 (2021).
Li, H. et al. A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics. Nat. Commun. 14, 1548 (2023).
Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 185, 1777–1792 e1721 (2022).
Casteleyn, C., Rekecki, A., Van der Aa, A., Simoens, P. & Van den Broeck, W. Surface area assessment of the murine intestinal tract as a prerequisite for oral dose translation from mouse to man. Lab Anim. 44, 176–183 (2010).
Taniguchi, T. et al. Plasmodium berghei ANKA causes intestinal malaria associated with dysbiosis. Sci. Rep. 5, 15699 (2015).
Mowat, A. M. & Agace, W. W. Regional specialization within the intestinal immune system. Nat. Rev. Immunol. 14, 667–685 (2014).
Kayisoglu, O., Schlegel, N. & Bartfeld, S. Gastrointestinal epithelial innate immunity-regionalization and organoids as new model. J. Mol. Med. 99, 517–530 (2021).
Parigi, S. M. et al. The spatial transcriptomic landscape of the healing mouse intestine following damage. Nat. Commun. 13, 828 (2022).
Moolenbeek, C. & Ruitenberg, E. J. The ‘Swiss roll’: a simple technique for histological studies of the rodent intestine. Lab Anim. 15, 57–59 (1981).
Titford, M. A short history of histopathology technique. J. Histotechnol. 29, 99–110 (2006).
Kaufman, J. A., Castro, M. J., Sandoval-Skeet, N. & Al-Nakkash, L. Optical clearing of small intestine for three-dimensional visualization of cellular proliferation within crypts. J. Anat. 232, 152–157 (2018).
Johansson, M. E. & Hansson, G. C. Preservation of mucus in histological sections, immunostaining of mucins in fixed tissue, and localization of bacteria with FISH. Methods Mol. Biol. 842, 229–235 (2012).
Swidsinski, A., Loening-Baucke, V., Lochs, H. & Hale, L. P. Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice. World J. Gastroenterol. 11, 1131–1140 (2005).
Pichat, J., Iglesias, J. E., Yousry, T., Ourselin, S. & Modat, M. A survey of methods for 3D histology reconstruction. Med. Image Anal. 46, 73–105 (2018).
Vaishnava, S. et al. The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine. Science 334, 255–258 (2011).
Matsuo, K., Ota, H., Akamatsu, T., Sugiyama, A. & Katsuyama, T. Histochemistry of the surface mucous gel layer of the human colon. Gut 40, 782–789 (1997).
Sheth, R. U. et al. Spatial metagenomic characterization of microbial biogeography in the gut. Nat. Biotechnol. 37, 877–883 (2019).
Mirzazadeh, R. et al. Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nat. Commun. 14, 509 (2023).
Frede, A. et al. B cell expansion hinders the stroma–epithelium regenerative cross talk during mucosal healing. Immunity 55, 2336–2351 e2312 (2022).
Du, Z. et al. Qualifying antibodies for image–based immune profiling and multiplexed tissue imaging. Nat. Protoc. 14, 2900–2930 (2019).
Bayerl, F. et al. Guidelines for visualization and analysis of DC in tissues using multiparameter fluorescence microscopy imaging methods. Eur. J. Immunol. https://doi.org/10.1002/eji.202249923 (2023).
Goltsev, Y. et al. Deep profiling of mouse splenic architecture with CODEX multiplexed imaging. Cell 174, 968–981 e915 (2018).
van Gastel, N. et al. Induction of a timed metabolic collapse to overcome cancer chemoresistance. Cell Metab. 32, 391–403 e396 (2020).
Schurch, C. M. et al. Coordinated cellular neighborhoods orchestrate antitumoral immunity at the colorectal cancer invasive front. Cell 183, 838 (2020).
Stumm, M. M. et al. Validation of a postfixation tissue storage and transport medium to preserve histopathology and molecular pathology analyses (total and phosphoactivated proteins, and FISH). Am. J. Clin. Pathol. 137, 429–436 (2012).
Schmidt, U., Weigert, M., Broaddus, C. & Myers, G. in Medical Image Computing and Computer Assisted Intervention – MICCAI 2018 (eds. Frangi, A. et al.) 265–273 (2018).
Weigert, M. & Schmidt, U. in IEEE International Symposium on Biomedical Imaging Challenges (ISBIC) https://doi.org/10.1109/ISBIC56247.2022.9854534 (IEEE, 2022).
Kleshchevnikov, V. et al. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat. Biotechnol. 40, 661–671 (2022).
Cable, D. M. et al. Robust decomposition of cell type mixtures in spatial transcriptomics. Nat. Biotechnol. 40, 517–526 (2022).
Biancalani, T. et al. Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nat. Methods 18, 1352–1362 (2021).
Li, B. et al. Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution. Nat. Methods 19, 662–670 (2022).

A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract

Supplementary information

推荐阅读