Mapping a multiplexed zoo of mRNA expression

Harry M T Choi; Colby R. Calvert; Naeem Husain; David Huss; Julius C. Barsi; Benjamin E. Deverman; Ryan C. Hunter; Mihoko Kato; S. Melanie Lee; Anna C T Abelin; Adam Z. Rosenthal; Omar S. Akbari; Yuwei Li; Bruce A. Hay; Paul W. Sternberg; Paul H. Patterson; Eric H. Davidson; Sarkis K. Mazmanian; David A. Prober; Matt Van De Rijn; Jared R. Leadbetter; Dianne K. Newman; Carol Readhead; Marianne E. Bronner; Barbara Wold; Rusty Lansford; Tatjana Sauka-Spengler; Scott E. Fraser; Niles A. Pierce

doi:10.1242/dev.140137

Mapping a multiplexed zoo of mRNA expression

Harry M T Choi, Colby R. Calvert, Naeem Husain, David Huss, Julius C. Barsi, Benjamin E. Deverman, Ryan C. Hunter, Mihoko Kato, S. Melanie Lee, Anna C T Abelin, Adam Z. Rosenthal, Omar S. Akbari, Yuwei Li, Bruce A. Hay, Paul W. Sternberg, Paul H. Patterson, Eric H. Davidson, Sarkis K. Mazmanian, David A. Prober, Matt Van De RijnJared R. Leadbetter, Dianne K. Newman, Carol Readhead, Marianne E. Bronner, Barbara Wold, Rusty Lansford, Tatjana Sauka-Spengler, Scott E. Fraser, Niles A. Pierce

Microbiology

Research output: Contribution to journal › Article › peer-review

108 Scopus citations

Abstract

In situ hybridization methods are used across the biological sciences to map mRNA expression within intact specimens. Multiplexed experiments, in which multiple target mRNAs are mapped in a single sample, are essential for studying regulatory interactions, but remain cumbersome in most model organisms. Programmable in situ amplifiers based on the mechanism of hybridization chain reaction (HCR) overcome this longstanding challenge by operating independently within a sample, enabling multiplexed experiments to be performed with an experimental timeline independent of the number of target mRNAs. To assist biologists working across a broad spectrum of organisms, we demonstrate multiplexed in situ HCR in diverse imaging settings: bacteria, whole-mount nematode larvae, whole-mount fruit fly embryos, whole-mount sea urchin embryos, whole-mount zebrafish larvae, whole-mount chicken embryos, whole-mount mouse embryos and formalin-fixed paraffin-embedded human tissue sections. In addition to straightforward multiplexing, in situ HCR enables deep sample penetration, high contrast and subcellular resolution, providing an incisive tool for the study of interlaced and overlapping expression patterns, with implications for research communities across the biological sciences.

Original language	English (US)
Pages (from-to)	3632-3637
Number of pages	6
Journal	Development (Cambridge)
Volume	143
Issue number	19
DOIs	https://doi.org/10.1242/dev.140137
State	Published - Oct 1 2016

Bibliographical note

Funding Information:
This work was funded by the National Institutes of Health (NIH) [5R01EB006192]; the National Science Foundation Molecular Programming Project [NSF-CCF-1317694]; the Gordon and Betty Moore Foundation [GBMF2809]; the Beckman Institute at Caltech (PMTC); the Translational Biomedical Imaging Laboratory at CHLA; the Translational Imaging Center at USC; a Christensen Fellowship at St Catherine’s College, University of Oxford; and by the John Simon Guggenheim Memorial Foundation. Deposited in PMC for release after 12 months.

Publisher Copyright:
© 2016. Published by The Company of Biologists Ltd.

Keywords

Bacteria
Deep sample penetration
High contrast
Hybridization chain reaction (HCR)
In situ amplification
In situ hybridization
Multiplexing
Subcellular resolution
Tissue sections
Whole-mount embryos and larvae

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10.1242/dev.140137

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Choi, H. M. T., Calvert, C. R., Husain, N., Huss, D., Barsi, J. C., Deverman, B. E., Hunter, R. C., Kato, M., Lee, S. M., Abelin, A. C. T., Rosenthal, A. Z., Akbari, O. S., Li, Y., Hay, B. A., Sternberg, P. W., Patterson, P. H., Davidson, E. H., Mazmanian, S. K., Prober, D. A., ... Pierce, N. A. (2016). Mapping a multiplexed zoo of mRNA expression. Development (Cambridge), 143(19), 3632-3637. https://doi.org/10.1242/dev.140137

Choi, HMT, Calvert, CR, Husain, N, Huss, D, Barsi, JC, Deverman, BE, Hunter, RC, Kato, M, Lee, SM, Abelin, ACT, Rosenthal, AZ, Akbari, OS, Li, Y, Hay, BA, Sternberg, PW, Patterson, PH, Davidson, EH, Mazmanian, SK, Prober, DA, Van De Rijn, M, Leadbetter, JR, Newman, DK, Readhead, C, Bronner, ME, Wold, B, Lansford, R, Sauka-Spengler, T, Fraser, SE & Pierce, NA 2016, 'Mapping a multiplexed zoo of mRNA expression', Development (Cambridge), vol. 143, no. 19, pp. 3632-3637. https://doi.org/10.1242/dev.140137

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title = "Mapping a multiplexed zoo of mRNA expression",

abstract = "In situ hybridization methods are used across the biological sciences to map mRNA expression within intact specimens. Multiplexed experiments, in which multiple target mRNAs are mapped in a single sample, are essential for studying regulatory interactions, but remain cumbersome in most model organisms. Programmable in situ amplifiers based on the mechanism of hybridization chain reaction (HCR) overcome this longstanding challenge by operating independently within a sample, enabling multiplexed experiments to be performed with an experimental timeline independent of the number of target mRNAs. To assist biologists working across a broad spectrum of organisms, we demonstrate multiplexed in situ HCR in diverse imaging settings: bacteria, whole-mount nematode larvae, whole-mount fruit fly embryos, whole-mount sea urchin embryos, whole-mount zebrafish larvae, whole-mount chicken embryos, whole-mount mouse embryos and formalin-fixed paraffin-embedded human tissue sections. In addition to straightforward multiplexing, in situ HCR enables deep sample penetration, high contrast and subcellular resolution, providing an incisive tool for the study of interlaced and overlapping expression patterns, with implications for research communities across the biological sciences.",

keywords = "Bacteria, Deep sample penetration, High contrast, Hybridization chain reaction (HCR), In situ amplification, In situ hybridization, Multiplexing, Subcellular resolution, Tissue sections, Whole-mount embryos and larvae",

author = "Choi, {Harry M T} and Calvert, {Colby R.} and Naeem Husain and David Huss and Barsi, {Julius C.} and Deverman, {Benjamin E.} and Hunter, {Ryan C.} and Mihoko Kato and Lee, {S. Melanie} and Abelin, {Anna C T} and Rosenthal, {Adam Z.} and Akbari, {Omar S.} and Yuwei Li and Hay, {Bruce A.} and Sternberg, {Paul W.} and Patterson, {Paul H.} and Davidson, {Eric H.} and Mazmanian, {Sarkis K.} and Prober, {David A.} and {Van De Rijn}, Matt and Leadbetter, {Jared R.} and Newman, {Dianne K.} and Carol Readhead and Bronner, {Marianne E.} and Barbara Wold and Rusty Lansford and Tatjana Sauka-Spengler and Fraser, {Scott E.} and Pierce, {Niles A.}",

note = "Funding Information: This work was funded by the National Institutes of Health (NIH) [5R01EB006192]; the National Science Foundation Molecular Programming Project [NSF-CCF-1317694]; the Gordon and Betty Moore Foundation [GBMF2809]; the Beckman Institute at Caltech (PMTC); the Translational Biomedical Imaging Laboratory at CHLA; the Translational Imaging Center at USC; a Christensen Fellowship at St Catherine{\textquoteright}s College, University of Oxford; and by the John Simon Guggenheim Memorial Foundation. Deposited in PMC for release after 12 months. Publisher Copyright: {\textcopyright} 2016. Published by The Company of Biologists Ltd.",

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AU - Choi, Harry M T

AU - Calvert, Colby R.

AU - Husain, Naeem

AU - Huss, David

AU - Barsi, Julius C.

AU - Deverman, Benjamin E.

AU - Hunter, Ryan C.

AU - Kato, Mihoko

AU - Lee, S. Melanie

AU - Abelin, Anna C T

AU - Rosenthal, Adam Z.

AU - Akbari, Omar S.

AU - Li, Yuwei

AU - Hay, Bruce A.

AU - Sternberg, Paul W.

AU - Patterson, Paul H.

AU - Davidson, Eric H.

AU - Mazmanian, Sarkis K.

AU - Prober, David A.

AU - Van De Rijn, Matt

AU - Leadbetter, Jared R.

AU - Newman, Dianne K.

AU - Readhead, Carol

AU - Bronner, Marianne E.

AU - Wold, Barbara

AU - Lansford, Rusty

AU - Sauka-Spengler, Tatjana

AU - Fraser, Scott E.

AU - Pierce, Niles A.

N1 - Funding Information: This work was funded by the National Institutes of Health (NIH) [5R01EB006192]; the National Science Foundation Molecular Programming Project [NSF-CCF-1317694]; the Gordon and Betty Moore Foundation [GBMF2809]; the Beckman Institute at Caltech (PMTC); the Translational Biomedical Imaging Laboratory at CHLA; the Translational Imaging Center at USC; a Christensen Fellowship at St Catherine’s College, University of Oxford; and by the John Simon Guggenheim Memorial Foundation. Deposited in PMC for release after 12 months. Publisher Copyright: © 2016. Published by The Company of Biologists Ltd.

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ER -

Mapping a multiplexed zoo of mRNA expression

Abstract

Bibliographical note

Keywords

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