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Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

Shahar Alon, Daniel R Goodwin, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C Payne, Chun-Chen Yao, Ho-Jun Suk, Ru Wang, Chih-Chieh (Jay) Yu, Paul Tillberg, Paul Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar P. R. Iyer, Richie E Kohman, Jeremy A Miller, Ed S Lein, Ana Lako, Nicole Cullen, Scott Rodig, Karla Helvie, Daniel L Abravanel, Nikhil Wagle, Bruce E Johnson, Johanna Klughammer, Michal Slyper, Julia Waldman, Judit Jané-Valbuena, Orit Rozenblatt-Rosen, Aviv Regev, IMAXT Consortium, George M Church, Adam H Marblestone, View ORCID ProfileEdward S Boyden
doi: https://doi.org/10.1101/2020.05.13.094268
Shahar Alon
1Media Lab, MIT
2McGovern Institute, MIT
3Faculty of Engineering, Bar-Ilan University
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Daniel R Goodwin
1Media Lab, MIT
2McGovern Institute, MIT
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Anubhav Sinha
1Media Lab, MIT
2McGovern Institute, MIT
4Harvard-MIT Program in Health Sciences and Technology, MIT
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Asmamaw T Wassie
1Media Lab, MIT
2McGovern Institute, MIT
5Department of Biological Engineering, MIT
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Fei Chen
1Media Lab, MIT
6Broad Institute of MIT and Harvard
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Evan R Daugharthy
7Department of Genetics, Harvard Medical School
8Wyss Institute for Biologically Inspired Engineering
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Yosuke Bando
1Media Lab, MIT
9Kioxia Corporation
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Atsushi Kajita
10Fixstars Solutions Inc
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Andrew G Xue
1Media Lab, MIT
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Karl Marrett
10Fixstars Solutions Inc
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Robert Prior
10Fixstars Solutions Inc
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Yi Cui
1Media Lab, MIT
2McGovern Institute, MIT
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Andrew C Payne
1Media Lab, MIT
6Broad Institute of MIT and Harvard
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Chun-Chen Yao
1Media Lab, MIT
6Broad Institute of MIT and Harvard
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Ho-Jun Suk
1Media Lab, MIT
2McGovern Institute, MIT
4Harvard-MIT Program in Health Sciences and Technology, MIT
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Ru Wang
1Media Lab, MIT
2McGovern Institute, MIT
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Chih-Chieh (Jay) Yu
1Media Lab, MIT
2McGovern Institute, MIT
5Department of Biological Engineering, MIT
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Paul Tillberg
1Media Lab, MIT
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Paul Reginato
1Media Lab, MIT
5Department of Biological Engineering, MIT
6Broad Institute of MIT and Harvard
7Department of Genetics, Harvard Medical School
8Wyss Institute for Biologically Inspired Engineering
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Nikita Pak
1Media Lab, MIT
2McGovern Institute, MIT
11Department of Mechanical Engineering, MIT
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Songlei Liu
7Department of Genetics, Harvard Medical School
8Wyss Institute for Biologically Inspired Engineering
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Sukanya Punthambaker
7Department of Genetics, Harvard Medical School
8Wyss Institute for Biologically Inspired Engineering
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Eswar P. R. Iyer
8Wyss Institute for Biologically Inspired Engineering
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Richie E Kohman
7Department of Genetics, Harvard Medical School
8Wyss Institute for Biologically Inspired Engineering
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Jeremy A Miller
12Allen Institute for Brain Science, Seattle, WA 98109
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Ed S Lein
12Allen Institute for Brain Science, Seattle, WA 98109
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Ana Lako
13Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute
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Nicole Cullen
13Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute
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Scott Rodig
13Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute
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Karla Helvie
14Center for Cancer Genomics, Dana-Farber Cancer Institute
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Daniel L Abravanel
14Center for Cancer Genomics, Dana-Farber Cancer Institute
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Nikhil Wagle
14Center for Cancer Genomics, Dana-Farber Cancer Institute
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Bruce E Johnson
14Center for Cancer Genomics, Dana-Farber Cancer Institute
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Johanna Klughammer
6Broad Institute of MIT and Harvard
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Michal Slyper
6Broad Institute of MIT and Harvard
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Julia Waldman
6Broad Institute of MIT and Harvard
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Judit Jané-Valbuena
6Broad Institute of MIT and Harvard
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Orit Rozenblatt-Rosen
6Broad Institute of MIT and Harvard
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Aviv Regev
6Broad Institute of MIT and Harvard
15Koch Institute for Integrative Cancer Research, Department of Biology, MIT
16Howard Hughes Medical Institute, Chevy Chase, MD, 20815
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17CRUK IMAXT Grand Challenge Consortium
George M Church
7Department of Genetics, Harvard Medical School
8Wyss Institute for Biologically Inspired Engineering
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Adam H Marblestone
1Media Lab, MIT
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Edward S Boyden
1Media Lab, MIT
2McGovern Institute, MIT
5Department of Biological Engineering, MIT
15Koch Institute for Integrative Cancer Research, Department of Biology, MIT
18Department of Brain and Cognitive Sciences, MIT
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  • ORCID record for Edward S Boyden
  • For correspondence: gchurch@genetics.med.harvard.edu edboyden@mit.edu
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Abstract:

Methods for highly multiplexed RNA imaging are limited in spatial resolution, and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targeted in situ RNA sequencing. We applied untargeted expansion sequencing (ExSeq) to mouse brain, yielding readout of thousands of genes, including splice variants and novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in neurons of the mouse hippocampus, revealing patterns across multiple cell types; layer-specific cell types across mouse visual cortex; and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus ExSeq enables highly multiplexed mapping of RNAs, from nanoscale to system scale.

One Sentence Summary In situ sequencing of physically expanded specimens enables multiplexed mapping of RNAs at nanoscale, subcellular resolution.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 15, 2020.
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Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems
Shahar Alon, Daniel R Goodwin, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C Payne, Chun-Chen Yao, Ho-Jun Suk, Ru Wang, Chih-Chieh (Jay) Yu, Paul Tillberg, Paul Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar P. R. Iyer, Richie E Kohman, Jeremy A Miller, Ed S Lein, Ana Lako, Nicole Cullen, Scott Rodig, Karla Helvie, Daniel L Abravanel, Nikhil Wagle, Bruce E Johnson, Johanna Klughammer, Michal Slyper, Julia Waldman, Judit Jané-Valbuena, Orit Rozenblatt-Rosen, Aviv Regev, IMAXT Consortium, George M Church, Adam H Marblestone, Edward S Boyden
bioRxiv 2020.05.13.094268; doi: https://doi.org/10.1101/2020.05.13.094268
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Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems
Shahar Alon, Daniel R Goodwin, Anubhav Sinha, Asmamaw T Wassie, Fei Chen, Evan R Daugharthy, Yosuke Bando, Atsushi Kajita, Andrew G Xue, Karl Marrett, Robert Prior, Yi Cui, Andrew C Payne, Chun-Chen Yao, Ho-Jun Suk, Ru Wang, Chih-Chieh (Jay) Yu, Paul Tillberg, Paul Reginato, Nikita Pak, Songlei Liu, Sukanya Punthambaker, Eswar P. R. Iyer, Richie E Kohman, Jeremy A Miller, Ed S Lein, Ana Lako, Nicole Cullen, Scott Rodig, Karla Helvie, Daniel L Abravanel, Nikhil Wagle, Bruce E Johnson, Johanna Klughammer, Michal Slyper, Julia Waldman, Judit Jané-Valbuena, Orit Rozenblatt-Rosen, Aviv Regev, IMAXT Consortium, George M Church, Adam H Marblestone, Edward S Boyden
bioRxiv 2020.05.13.094268; doi: https://doi.org/10.1101/2020.05.13.094268

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