Hybridization Chain Reaction: In Situ Ampli?cation for Biological Imaging Life is orchestrated by programmable biomolecules ? DNA, RNA, and proteins ? interacting within complex biolog- ical circuits. RNA in situ hybridization (RNA-ISH) methods provide biologists with a crucial window into the spatial organization of this circuitry, enabling imaging of mRNA expression in an anatomical context from subcellular to organismal length scales. Due to variability between specimens, examination of detailed spatial relationships requires multiplexed experiments in which multiple target mRNAs are imaged with high resolution within a single biological sample. Using traditional RNA-ISH methods in thick auto?uorescent samples including whole-mount vertebrate embryos, multiplexing is cumbersome or impractical, spatial resolution is frequently compromised by diffusion of reporter molecules, and staining is non-quantitative. The same drawbacks apply using traditional immunohistochemistry (IHC) methods to image protein expression in these challenging samples, while with tradi- tional DNA in situ hybridization (DNA-ISH) methods, it is not currently routine to image single-copy small genomic loci in any sample, much less in vertebrate embryos. These longstanding shortcomings of traditional ISH and IHC methods are a signi?cant impediment to the study of genetic regulatory networks in systems most relevant to human development and disease. In situ ampli?cation based on the mechanism of hybridization chain reaction (HCR) draws on concepts from the emerging discipline of dynamic nucleic acid nanotechnology to achieve three mRNA imaging breakthroughs in whole-mount vertebrate embryos and thick tissue sections: straightforward 5-channel multiplexing, subcellular relative quantitation, and single-molecule resolution and sensitivity. The proposed research will build on these unique capabilities to dramatically advance the robustness, multiplexing, and quantitation capabilities of HCR for RNA-ISH and to extend the bene?ts of multiplexed, quantitative, enzyme-free HCR signal ampli?cation to IHC and DNA-ISH in thick auto?uorescent samples. Major goals are: In situ HCR v3.0: automatic background suppression using cooperative probes for next-generation robust- ness and signal-to-background imaging mRNAs and short RNA targets (miRNAs, mRNA splice junctions, and closely related RNA sequences) in diverse organisms. Next-generation multiplexing (15-plex with simultaneous HCR signal ampli?cation for all targets) and quan- titation (high-?delity mRNA absolute quantitation with subcellular resolution and whole-embryo scale). Next-generation versatility: extend the bene?ts of HCR imaging to protein targets, single-copy small ge- nomic loci, and molecular complexes, enabling compatible multiplexed imaging of all target classes. Realization of these goals would have a broad impact on research in the biological sciences, providing an un- precedented combination of multiplexing, quantitation, resolution, sensitivity, and versatility for the study of genetic regulatory networks in an anatomical context.

Public Health Relevance

Hybridization Chain Reaction: In Situ Ampli?cation for Biological Imaging We propose to engineer molecular technologies with unprecedented capabilities for simultaneously and quan- titatively imaging DNA, RNA, and protein molecules within intact vertebrate embryos and thick tissue sections, providing biologists with crucial tools for elucidating the molecular underpinnings of human development and disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of Biomedical Imaging and Bioengineering (NIBIB)
Type
Research Project (R01)
Project #
5R01EB006192-10
Application #
9784815
Study Section
Cellular and Molecular Technologies Study Section (CMT)
Program Officer
Atanasijevic, Tatjana
Project Start
2005-09-22
Project End
2023-05-31
Budget Start
2020-06-01
Budget End
2021-05-31
Support Year
10
Fiscal Year
2020
Total Cost
Indirect Cost
Name
California Institute of Technology
Department
Engineering (All Types)
Type
Biomed Engr/Col Engr/Engr Sta
DUNS #
009584210
City
Pasadena
State
CA
Country
United States
Zip Code
91125
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Trivedi, Vikas; Choi, Harry M T; Fraser, Scott E et al. (2018) Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Development 145:
Choi, Harry M T; Calvert, Colby R; Husain, Naeem et al. (2016) Mapping a multiplexed zoo of mRNA expression. Development 143:3632-3637
Schwarzkopf, Maayan; Pierce, Niles A (2016) Multiplexed miRNA northern blots via hybridization chain reaction. Nucleic Acids Res 44:e129
Shah, Sheel; Lubeck, Eric; Schwarzkopf, Maayan et al. (2016) Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing. Development 143:2862-7
Huss, David; Choi, Harry M T; Readhead, Carol et al. (2015) Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction. Cold Spring Harb Protoc 2015:259-68
Choi, Harry M T; Beck, Victor A; Pierce, Niles A (2014) Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano 8:4284-94
Rosenthal, Adam Z; Zhang, Xinning; Lucey, Kaitlyn S et al. (2013) Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy. Proc Natl Acad Sci U S A 110:16163-8
Tu, Chuqiao; Osborne, Elizabeth A; Louie, Angelique Y (2011) Activatable T? and T? magnetic resonance imaging contrast agents. Ann Biomed Eng 39:1335-48
Tu, Chuqiao; Ma, Xuchu; Pantazis, Periklis et al. (2010) Paramagnetic, silicon quantum dots for magnetic resonance and two-photon imaging of macrophages. J Am Chem Soc 132:2016-23

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