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Spatial Transcriptomics in Kidney Tissue

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Kidney Research

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2664))

Abstract

Unlike bulk and single-cell/single-nuclei RNA sequencing methods, spatial transcriptome sequencing (ST-seq) resolves transcriptome expression within the spatial context of intact tissue. This is achieved by integrating histology with RNA sequencing. These methodologies are completed sequentially on the same tissue section placed on a glass slide with printed oligo-dT spots, termed ST-spots. Transcriptomes within the tissue section are captured by the underlying ST-spots and receive a spatial barcode in the process. The sequenced ST-spot transcriptomes are subsequently aligned with the hematoxylin and eosin (H&E) image, giving morphological context to the gene expression signatures within intact tissue. We have successfully employed ST-seq to characterize mouse and human kidney tissue. Here, we describe in detail the application of Visium Spatial Tissue Optimization (TO) and Visium Spatial Gene Expression (GEx) protocols for ST-seq in fresh frozen kidney tissue.

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Acknowledgments

This work was supported by Pathology Queensland-Study, Education and Research Committee, Royal Brisbane and Women’s Hospital Foundation Project Grant 2019, Robert and Janelle Bird Postdoctoral Research Fellowship 2020, and the University of Queensland (UQ)-Genome Innovation Hub. AR is supported by an Australian Government Research Training Program (RTP) Scholarship. AJM was supported by a Metro North Hospital and Health Service Clinical Research Fellowship and is supported by a Queensland Health Advancing Clinical Research Fellowship. The authors would like to thank the tissue donors; Queensland Health clinicians, pathologists, and scientists; Conjoint Internal Medicine Laboratory; the University of Queensland School of Biomedical Sciences Imaging Facility; and Institute for Molecular Bioscience Sequencing Facility. In particular, we thank Quan Nguyen, Leo Francis, Anne Stewart, Jane Ilsley, and Quinn Jones for their support and assistance with this work. Visium, 10×, and 10× Genomics are trademarks of 10× Genomics, Inc. All Rights Reserved. NextSeq and Illumina are trademarks of Illumina, Inc. All Rights Reserved. All trademarks used herein are the property of their respective owners and are used under license from the respective owners.

Author information

Authors and Affiliations

  1. Kidney Health Service, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia

    Arti M. Raghubar, Monica S. Y. Ng, Helen Healy & Andrew J. Kassianos

  2. Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia

    Arti M. Raghubar, Monica S. Y. Ng, Helen Healy & Andrew J. Kassianos

  3. Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia

    Arti M. Raghubar, Helen Healy, Andrew J. Kassianos & Andrew J. Mallett

  4. Anatomical Pathology, Pathology Queensland, Health Support Queensland, Herston, QLD, Australia

    Arti M. Raghubar

  5. Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia

    Arti M. Raghubar, Joanna Crawford, Kahli Jones, Pui Y. Lam, Monica S. Y. Ng & Andrew J. Mallett

  6. School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia

    Kahli Jones

  7. Genome Innovation Hub, University of Queensland, Brisbane, QLD, Australia

    Stacey B. Andersen

  8. UQ Sequencing Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia

    Stacey B. Andersen

  9. QCIF Facility for Advanced Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia

    Nicholas A. Matigian

  10. Nephrology Department, Princess Alexandra Hospital, Woolloongabba, QLD, Australia

    Monica S. Y. Ng

  11. College of Medicine & Dentistry, James Cook University, Townsville, QLD, Australia

    Andrew J. Mallett

  12. Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia

    Andrew J. Mallett

Authors
  1. Arti M. Raghubar
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  2. Joanna Crawford
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  3. Kahli Jones
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  4. Pui Y. Lam
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  5. Stacey B. Andersen
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  6. Nicholas A. Matigian
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  7. Monica S. Y. Ng
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  8. Helen Healy
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  9. Andrew J. Kassianos
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  10. Andrew J. Mallett
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Corresponding author

Correspondence to Andrew J. Mallett .

Editor information

Editors and Affiliations

  1. Department of Nephrology, The Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia

    Tim D. Hewitson

  2. Department of Nephrology, The Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia

    Nigel D. Toussaint

  3. Department of Nephrology, The Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia

    Edward R. Smith

1 Electronic Supplementary Material

Freezing of kidney tissue. An overview of kidney tissue dissection, freezing, and storage, including required equipment, is provided in this video. This technical video links with Subheading 3.3 Visium TO and Subheading 3.6 Visium GEx (MP4 323050 kb)

Cryosectioning of kidney tissue. An overview of the cryosectioning process, including required equipment, cryostat setup, sectioning, placement of tissue sections within the capture array, and storage of slides, is provided in this video. This technical video links with Subheading 3.3 VisiumTO and Subheading 3.6 Visium GEx (MP4 225485 kb)

Placing a slide in the slide cassette. Slide cassette assembly, slide placement, and slide removal are demonstrated in this video. This technical video links with Subheading 3.3 Visium TO and Subheading 3.6 Visium GEx (MP4 181803 kb)

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Raghubar, A.M. et al. (2023). Spatial Transcriptomics in Kidney Tissue. In: Hewitson, T.D., Toussaint, N.D., Smith, E.R. (eds) Kidney Research. Methods in Molecular Biology, vol 2664. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3179-9_17

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  • DOI: https://doi.org/10.1007/978-1-0716-3179-9_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3178-2

  • Online ISBN: 978-1-0716-3179-9

  • eBook Packages: Springer Protocols

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