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Spatial tissue profiling by imaging-free molecular tomography

Halima Hannah Schede, Christian G. Schneider, Johanna Stergiadou, Lars E. Borm, Anurag Ranjak, Tracy M. Yamawaki, Fabrice P.A. David, Peter Lönnerberg, Gilles Laurent, Maria Antonietta Tosches, Simone Codeluppi, View ORCID ProfileGioele La Manno
doi: https://doi.org/10.1101/2020.08.04.235655
Halima Hannah Schede
1Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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Christian G. Schneider
1Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
2NeuroCure Cluster of Excellence, Charité-Universitäts-medizin Berlin, corporate member of the Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
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Johanna Stergiadou
3Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177, Stockholm, Sweden
4Cartana AB, S-17165, Stockholm, Sweden
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Lars E. Borm
3Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177, Stockholm, Sweden
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Anurag Ranjak
1Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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Tracy M. Yamawaki
5Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
6Amgen, Inc, South San Francisco, CA 94080
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Fabrice P.A. David
1Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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Peter Lönnerberg
3Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177, Stockholm, Sweden
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Gilles Laurent
5Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
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Maria Antonietta Tosches
7Department of Biological Sciences, Columbia University, NY10027 New York, USA
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Simone Codeluppi
3Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, S-17177, Stockholm, Sweden
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Gioele La Manno
1Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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  • ORCID record for Gioele La Manno
  • For correspondence: gioele.lamanno@epfl.ch
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Abstract

Genomics techniques are currently being adapted to provide spatially resolved omics profiling. However, the adaptation of each new method typically requires the setup of specific detection strategies or specialized instrumentation. A generic approach to spatially resolve different types of high throughput data is missing. Here, we describe an imaging-free framework to localize high throughput readouts within a tissue by combining compressive sampling and image reconstruction. We implemented this framework to transform a low-input RNA sequencing protocol into an imaging-free spatial transcriptomics technique (STRP-seq) and validated this method with a transcriptome profiling of the murine brain. To verify the broad applicability of STRP-seq, we applied the technique on the brain of the Australian bearded dragon Pogona vitticeps. Our results reveal the molecular anatomy of the telencephalon of this lizard, providing evidence for a marked regionalization of the reptilian pallium and subpallium. Overall, the proposed framework constitutes a new approach that allows upgrading in a generic fashion conventional genomic assays to spatially resolved techniques.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/lamanno-epfl/tomographer

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted August 04, 2020.
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Spatial tissue profiling by imaging-free molecular tomography
Halima Hannah Schede, Christian G. Schneider, Johanna Stergiadou, Lars E. Borm, Anurag Ranjak, Tracy M. Yamawaki, Fabrice P.A. David, Peter Lönnerberg, Gilles Laurent, Maria Antonietta Tosches, Simone Codeluppi, Gioele La Manno
bioRxiv 2020.08.04.235655; doi: https://doi.org/10.1101/2020.08.04.235655
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Spatial tissue profiling by imaging-free molecular tomography
Halima Hannah Schede, Christian G. Schneider, Johanna Stergiadou, Lars E. Borm, Anurag Ranjak, Tracy M. Yamawaki, Fabrice P.A. David, Peter Lönnerberg, Gilles Laurent, Maria Antonietta Tosches, Simone Codeluppi, Gioele La Manno
bioRxiv 2020.08.04.235655; doi: https://doi.org/10.1101/2020.08.04.235655

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