WO2015127183A2 - Expansion microscopy - Google Patents

Expansion microscopy Download PDF

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Publication number
WO2015127183A2
WO2015127183A2 PCT/US2015/016788 US2015016788W WO2015127183A2 WO 2015127183 A2 WO2015127183 A2 WO 2015127183A2 US 2015016788 W US2015016788 W US 2015016788W WO 2015127183 A2 WO2015127183 A2 WO 2015127183A2
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WIPO (PCT)
Prior art keywords
sample
swellable material
swellable
interest
labeled
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PCT/US2015/016788
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English (en)
French (fr)
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WO2015127183A3 (en
Inventor
Fei Chen
Paul Warren TILLBERG
Edward Stuart Boyden
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Massachusetts Institute Of Technology
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Priority to JP2016553349A priority Critical patent/JP6456969B2/ja
Priority to EP15751396.1A priority patent/EP3108218A4/en
Publication of WO2015127183A2 publication Critical patent/WO2015127183A2/en
Publication of WO2015127183A3 publication Critical patent/WO2015127183A3/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00—Sampling; Preparing specimens for investigation
    • G01N1/28—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/36—Embedding or analogous mounting of samples
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6841—In situ hybridisation
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00—Sampling; Preparing specimens for investigation
    • G01N1/28—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/30—Staining; Impregnating ; Fixation; Dehydration; Multistep processes for preparing samples of tissue, cell or nucleic acid material and the like for analysis
    • G—PHYSICS
    • G02—OPTICS
    • G02B—OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00—Microscopes
    • G02B21/0004—Microscopes specially adapted for specific applications
    • G02B21/002—Scanning microscopes
    • G02B21/0024—Confocal scanning microscopes (CSOMs) or confocal "macroscopes"; Accessories which are not restricted to use with CSOMs, e.g. sample holders
    • G02B21/0052—Optical details of the image generation
    • G02B21/0072—Optical details of the image generation details concerning resolution or correction, including general design of CSOM objectives
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00—Sampling; Preparing specimens for investigation
    • G01N1/28—Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/36—Embedding or analogous mounting of samples
    • G01N2001/364—Embedding or analogous mounting of samples using resins, epoxy

Definitions

  • the present invention relates to microscopy and, in particular, to optical imaging of biological specimens.
  • Microscopy has provided valuable biological information by optically magnifying images of small sultures in fixed cells and tissues.
  • the resolution of such imaging techniques are restricted to approximately half the wavelength of the illuminating source. In the visible region of the spectrum this is on the order of a quarter to a third of a micron (250-330nm).
  • the present invention is a method for optical imaging of biological specimens with resolution better than the classical microscopy diffraction limit, based on physically expanding the specimen itself.
  • cultured cells, fixed tissue, or in principle other types of samples of interest, including biological materials are infused with a composition, or chemical cocktail, that results in it becoming embedded in the sample material, and then the composition can be expanded isotropically, preferably with nanoscale precision, in three dimensions.
  • the composition comprises a
  • polyelectrolyte hydrogel (or the components thereof), which can swell macroscopically, for example, in low-salt water.
  • the composition can comprise a tag or other feature of interest (for example, fluorescent dye molecules that have been delivered to the biological sample via antibody staining) which can be anchored (e.g., chemically) into the hydrogel before expansion.
  • a tag or other feature of interest for example, fluorescent dye molecules that have been delivered to the biological sample via antibody staining
  • the specimen is subjected to an enzymatic digestion (or other digestion) to disrupt the underlying network of biological molecules, leaving the tags of interest (e.g., the fluorescent dye molecules) intact and anchored to the gel.
  • the mechanical properties of the gel-biomolecule hybrid material are rendered more spatially uniform, allowing isotropic expansion with minimal artifacts.
  • the swollen material with embedded biological specimen can be imaged any optical microscope, allowing effective imaging of features below the classical diffraction limit. Since the resultant specimen can be transparent, custom microscopes capable of large volume, wide field of view, fast 3-D scanning may also be used in conjunction with the expanded sample.
  • Fig. 1 is a flowchart depicting steps in an exemplary embodiment of the method of the invention.
  • Figs. 2A and 2B are examples using standard (Fig. 2A) and expansion microscopy according to the method of the invention (Fig. 2B).
  • Figs. 3A and 3B are further examples using standard (Fig. 3A) and expansion microscopy according to the method of the invention (Fig. 3B).
  • Figs. 4A through 4F depicts Expansion microscopy (ExM) of the present invention.
  • Fig. 4A is a schematic of collapsed polyelectrolyte network (i), showing crosslinker (dot) and polymer chain (line), and expanded network (ii) after H20 dialysis.
  • Fig. 4B is a photograph of fixed mouse brain slice.
  • Fig. 4C is a photograph, post-ExM, of the sample (Fig. 4B) under side illumination.
  • Fig. 4D is a schematic of a label that can be anchored to the gel at site of a biomolecule.
  • Fig. 4E is a schematic of microtubules
  • Fig 4F shows the label of Fig. 4D hybridized to the oligo-bearing secondary antibody (gray) bound via the primary (gray) to microtubules (purple) and incorporated into the gel (orange lines) via the methacryloyl group (orange dot) and remains after proteolysis (dotted lines).
  • Scale bars in Figs. 4B and 4C are 5 mm. Schematics are not to scale.
  • Figs. 5A through 50 show that expansion microscopy physically magnifies, with nanoscale isotropy. Images acquired via conventional microscopy (blue scale bars) vs. images acquired post-expansion (orange scale bars) were compared.
  • Fig. 5A shows a confocal image of microtubules in HEK293 cells.
  • Fig. 5B shows post-expansion confocal image of sample Fig. 5A.
  • Fig. 5C depicts the root-mean-square (RMS) length
  • Fig. 5D is a super-resolution structured-illumination microscopy (SR-SIM) image of microtubules.
  • Fig. 5E shows post- expansion confocal image of the sample of Fig. 5D.
  • Figs. 5F and 5G depict magnified views of boxed regions of Fig. 5D and Fig. 5E respectively.
  • Fig. 5H depict profiles of microtubule intensity taken along the blue and orange dotted lines in Fig. 5F and Fig. 5G.
  • Fig. 51 shows RMS length measurement error of ExM vs.
  • Fig. 5J depicts a transverse profile of a representative microtubule (blue line), with Gaussian fit (black dotted line).
  • Fig. 5K is a SR-SIM image of clathrin coated pits (CCPs) in HEK293 cells.
  • Fig. 5L is a post- expansion confocal image of the sample of Fig. 5K.
  • Fig. 5M and 5N are magnified views of a single CCP in the boxed regions of Fig. 5K and Fig. 5L respectively.
  • Fig. 50 is a scatterplot of radii of CCPs measured via ExM vs.
  • FIG. 6A through 6J depict ExM imaging of mammalian brain tissue.
  • FIG. 6A is a wide field image of Thyl-YFP mouse brain slice showing fluorescence (white).
  • Fig. 6B is a Post-expansion widefield image of sample Fig. 6A.
  • Figs. 6D and 6E depict confocal fluorescence images of boxed regions in Figs. 6A and 6B respectively, stained with pre-synaptic (anti-Bassoon, blue) and post-synaptic (anti-Homer 1, red) markers, in addition to anti-GFP (green), pre- Fig.
  • FIG. 6D vs. post- Fig. 6E expansion.
  • Fig. 6F and Fig. 6G provide details of boxed regions in Figs. 6D and 6E.
  • Fig. 6H show a single representative synapse highlighted in Figs. 6G and 61 shows the staining intensity for Bassoon (blue) and Homerl (red) of the sample of Fig. 6H along white box long axis. Dotted black lines, Gaussian fits, a.u., arbitrary units.
  • Figs. 7A through 7D depicts scalable 3D super-resolution microscopy of mouse brain tissue.
  • Fig. 7 A is a volume rendering of a portion of hippocampus showing neurons (expressing Thyl-YFP, shown in green) and synapses (marked with anti-Bassoon (blue) and anti-Homerl (red)).
  • Fig. 7B is a volume rendering of dendrites in CA1 stratum lacunosum moleculare (slm).
  • Fig. 7C is a volume rendering of dendritic branch in CA1 slm.
  • Fig. 7D shows the mossy fiber bouton in hilus of the dentate gyrus.
  • the present invention relates to an enlarged sample of interest for microscopy and methods for enlarging a sample of interest and the optical imaging of a sample of interest with resolution better than the classical microscopy diffraction limit, by synthesizing a swellable polymer network within a specimen, it can be physically expanded, resulting in physical magnification.
  • the invention also includes the use of compositions described herein for enlarging a sample of interest.
  • the invention provides an expandable sample of interest for microscopy.
  • the expandable sample of interest comprises a sample of interest embedded in a swellable material.
  • the sample of interest is labeled.
  • the invention provides a method for enlarging a sample of interest for microscopy.
  • the method comprises first embedding a sample of interest in a swellable material and then swelling the material.
  • the sample of interest is labeled.
  • the invention provides a method for preparing an enlargeable sample of interest for microscopy.
  • the method comprises embedding a sample of interest in a swellable material.
  • the sample of interest is labeled.
  • the invention provides a microscopy method for producing a high-resolution image of a sample, the method comprising enlarging a sample of interest and viewing the enlarged sample under a microscope.
  • enlarging the sample of interest comprises embedding a sample of interest in a swellable material and then swelling the material.
  • the sample of interest is labeled.
  • the invention provides a method for the optical imaging of a sample of interest with resolution better than the classical microscopy diffraction limit, based on physically expanding the sample itself.
  • the method comprises embedding a sample of interest in a swellable material and then swelling the material.
  • the sample of interest is labeled.
  • sample of interest generally refers to, but not limited to, a biological, chemical or biochemical sample, such as a cell, array of cells, tumor, tissue, ceil isolate, biochemical assembly, or a distribution of molecules suitable for microscopic analysis.
  • the sample of interest can be labeled or tagged.
  • the label or tag will bind chemically (e.g., covalently, hydrogen bonding or ionic bonding) to the sample, or a component thereof.
  • the tag can be selective for a specific target (e.g., a biomarker or class of molecule), as can be accomplished with an antibody or other target specific binder.
  • the tag preferably comprises a visible component, as is typical of a dye or fluorescent molecule. Contacting the sample of interest with a label or tag results in a "labeled sample of interest.”
  • a fluorescently labeled sample of interest for example, is a sample of interest labeled through techniques such as, but not limited to, immunofluorescence, iiTsmuiiohistochemical or
  • the label or tag is preferably chemically attached to the sample of interest, or a targeted component thereof.
  • the label or tag e.g. the antibody and/or fluorescent dye, further comprises a physical, biological, or chemical anchor or moiety that attaches or crosslinks the sample to the composition, hydrogel or other swellable material.
  • the labeled sample may furthermore include more than one label.
  • each label can have a particular or distinguishable fluorescent property, e.g., distinguishable excitation and emission wavelengths.
  • each label can have a. different target specific binder that is selective for a specific and distinguishable target in, or component of the sample.
  • the term "swellable material” generally refers to a material that expands when contacted with a liquid, such as water or other solvent. Preferably, the swellable material uniformly expands in 3 dimensions. Additionally or alternatively, the material is transparent such that, upon expansion, light can pass through the sample.
  • the swellable material is a swellable polymer or hydrogel.
  • the swellable material is formed in situ from precursors thereof.
  • one or more polymerizable materials, monomers or oligomers can be used, such as monomers selected from the group consisting of water soluble groups containing a polymerizable ethylenically unsaturated group. Monomers or oligomers can comprise one or more substituted or unsubstituted methacrylates, acrylates, acrylamides,
  • Precursors can also comprise polymerization initiators and crosslinkers.
  • the swellable polymer is polyacrylate and copolymers or crosslinked copolymers thereof.
  • the swellable material can be formed in situ by chemically crosslinking water soluble oligomers or polymers.
  • the invention envisions adding precursors (such as water soluble precursors) of the swellable material to the sample and rendering the precursors swellable in situ.
  • embedding the sample in a swellable material comprises permeating (such as, perfusing, infusing, soaking, adding or other intermixing) the sample with the swellable material, preferably by adding precursors thereof.
  • embedding the sample in a swellable material comprises permeating one or more monomers or other precursors throughout the sample and polymerizing and/or crosslinking the monomers or precursors to form the swellable material or polymer. In this manner the sample of interest is embedded in the swellable material.
  • a a sample of interest, or a labeled sample is permeated with a composition comprising water soluble precursors of a water swellable material and reacting the precursors to form the water swellable material in situ.
  • the sample of interest can, optionally, be treated with a detergent prior to being contacted with the one or more swellable material precursors.
  • a detergent can improve the wettability of the sample or disrupt the sample to allow the one or more swellable monomer precursors to permeate throughout sample.
  • the sample is permeated with one or more monomers or a solution comprising one or more monomers or precursors which are then reacted to form a swellable polymer.
  • a solution comprising the monomers sodium acrylate and acrylamide, and the cross-linker N,N-methylenebisacrylamide are perfused throughout the sample.
  • the solution is activated to form sodium polyacrylate.
  • the solution comprising the monomers is aqueous.
  • the solution is preferably at high concentration, such as about 50% or more saturation (defined herein as the percentage of solids present in the aqueous solvent in the same ratio as would result in precipitation under the conditions of permeation).
  • the solution is preferably at high concentration, such as about 75% or more saturation, more preferably 90% or more saturation.
  • the sample e.g., a labeled sample
  • the sample is anchored or crosslinked to the swellable material before expansion. This can preferably be accomplished by chemically crosslinking a tag or label with the swellable material, such as during or after the polymerization or in situ formation of the swellable material.
  • the sample is, optionally, subjected to a disruption of the endogenous biological molecules (or the physical structure of the sample of interest, where the sample is other than a biological material), leaving the tags or fluorescent dye molecules intact and anchored to the swellable material. In this way, the mechanical properties of the sample-swellable material complex are rendered more spatially uniform, allowing isotropic expansion with minimal artifacts.
  • the "disruption of the endogenous biological molecules" of the sample of interest generally refers to the mechanical, physical, chemical, biochemical or, preferably, enzymatic digestion, disruption or break up of the sample so that it will not resist expansion.
  • a protease enzyme is used to homogenize the sample- swellable material complex. It is preferable that the disruption does not impact the structure of the swellable material but disrupts the structure of the sample. Thus, the sample disruption should be substantially inert to the swellable material. The degree of digestion can be sufficient to compromise the integrity of the mechanical structure of the sample or it can be complete to the extent that the sample-swellable material complex is rendered substantially free of the sample.
  • sample-swellable material complex is then isoptropically expanded.
  • a solvent or liquid is added to the complex which is then absorbed by the swellable material and causes swelling.
  • the swellable material is water swellable, an aqueous solution can be used.
  • the addition of water allows for the embedded sample to expand 4x to 5x (e.g., 4.5x) or more its original size in 3-dimensions.
  • the sample can be increased 100-fold or more in volume. This is because the polymer is embedded throughout the sample, therefore, as the polymer swells (grows) it expands the tissue as well. Thus, the tissue sample itself becomes bigger.
  • the anchored tags maintain their relative spacial relationship.
  • the swollen material with the embedded sample of interest can be imaged on any optical microscope, allowing effective imaging of features below the classical diffraction limit. Since the resultant specimen is preferably transparent, custom microscopes capable of large volume, wide field of view, 3-D scanning may also be used in conjunction with the expanded sample.
  • Fig. 1 is a flowchart depicting steps in an exemplary embodiment of the method of the invention.
  • Anchor-able dye system DNA sequences were ordered with 5' amine modification (Integrated DNA Technologies) and conjugated to secondary antibodies (Jackson ImmunoResearch) using a commercial kit (Solulink, Antibody-Oligonucleotide All-in-One Conjugation Kit). For the tertiary DNA/dye staining molecule, the
  • complementary oligonucleotides are ordered with a 3 ' amine modification and a 5 ' Acrydite modification (Integrated DNA Technologies) and conjugated to dyes (Life Technologies and Sigma Aldrich) modified with NHS-ester chemistry per the
  • Conjugated DNA molecules were purified via reverse-phase HPLC, lyophilized and re-suspended in ddH 2 0.
  • HEK293-FT cells were fixed in 3% formaldehyde/0.1% glutaraldehyde (Electron Microscopy Sciences) for 10 minutes, followed by quenching in lOOmM glycine for 10 minutes and reduction with 0.1% NaBH4 for 7 minutes. Cells were permeabilized with 0.2% Triton for 15 minutes at room temperature and blocked with 5% normal donkey serum for one hour. Specimens were incubated with primary antibodies in blocking buffer at a concentration of lOug/mL for 1-4 hours, and then washed in PBS three times for 5 minutes each.
  • Specimens were incubated with DNA-labeled secondary antibodies in DNA hybridization buffer (2x SSC buffer, 10% Dextran sulfate, lmg/mL yeast tRNA, 5% normal donkey serum) at a concentration of approximately lOug/mL for 1-4 hours, then washed in PBS as for primary. Specimens were incubated with dye-labeled DNA tertiaries in hybridization buffer at a concentration of 0.5ng/uL overnight, then washed three times in 2x SSC.
  • DNA hybridization buffer 2x SSC buffer, 10% Dextran sulfate, lmg/mL yeast tRNA, 5% normal donkey serum
  • Thyl-YFP-expressing mice were anesthetized with isoflurane and perfused transcardially with ice cold 4%
  • Slices were incubated with primary antibodies in slice blocking buffer at a concentration of lOug/mL for 6-12 hours, and then washed in slice blocking buffer four times for thirty minutes each wash.
  • Slices were incubated with DNA-labeled secondary antibodies in hybridization buffer at a concentration of approximately lOug/mL for 6-12 hours, then washed in slice blocking buffer as for primary.
  • Specimens were incubated with dye-labeled DNA tertiaries in hybridization buffer at a concentration of Ing/uL for 6-12 hours, then washed in slice blocking buffer as for primary.
  • Imaging was performed on a Deltavision OMX SIM microscope. Stained cells were imaged within Culturewell Chambered Coverglass with SlowFade Gold antifade reagent (Invitrogen) for suppression of photobleaching and refractive index matching.
  • SlowFade Gold antifade reagent Invitrogen
  • Post-expansion imaging was performed on a Perkin Elmer Spinning disk confocal or a Zeiss Laser Scanning Confocal (LSM 710). Briefly, expanded gels were placed in glass-bottom six well plates (In Vitro Scientific) and held in place with low- melting point agarose. Images were taken at with 1 Airy unit and Nyquist sampling on the LSM 710.
  • Figs. 2A-B present an example.
  • Fig. 2A Standard confocal image with
  • magnification is being achieved in part by the physical expansion of the sample.
  • FIG. 3A Structured Illumination
  • Fig. 3B Post Expansion 4.5x imaging on spinning disk confocal, lOOx, 1.40 NA. Note that features smaller than the diffraction limit of light can be imaged on the confocal.
  • Sodium acrylate, a monomer used to produce super-absorbent materials, along with the co-monomer acrylamide and the crosslinker N-N'-methylenebisacrylamide were infused into chemically fixed and permeabilized brain tissue (Fig. 4B).
  • APS ammonium persulfate
  • TEMED tetramethylethylenediamine
  • the tissue-polymer composite was treated with protease to homogenize its mechanical characteristics.
  • dialysis in water resulted in a 4.5-fold linear expansion, without distortion at the level of gross anatomy (Fig. 4C). Digestion was uniform throughout the slice. Expanded specimens were transparent as they consist largely of water. Thus, polyelectrolyte gel expansion is possible when the polymer is embedded throughout a biological sample.
  • a fluorescent label compatible with the proteolytic treatment and subsequent tissue expansion described herein, was incorporated directly into the polymer network.
  • the label was tri-functional, comprising a methacryloyl group capable of participating in free radical polymerization, a chemical fluorophore for visualization, and an oligonucleotide that can hybridize to a complementary sequence attached to an affinity tag (e.g., a secondary antibody) (Figs. 4E and F).
  • an affinity tag e.g., a secondary antibody
  • Fluorescence imaging was performed using expansion microscopy (ExM) of the present invention, examining microtubules in fixed HEK293 cells labeled with the tri-functional label and imaged with confocal laser scanning micros-copy pre- vs. post- ExM processing.
  • the post-ExM image (Fig. 5B) was registered to the pre-ExM image (Fig. 5A) via a similarity transformation resulting in visually indistinguishable images.
  • Pre-ExM conventional super-resolution images was compared to post-ExM confocal images.
  • Features traditionally used to characterize the performance of super- resolution microscopes, including microtubules and clathrin coated pits were labeled and imaged with a super-resolution structured illumination microscope (SR-SIM) pre-ExM, and a spinning disk confocal post-ExM.
  • SR-SIM super-resolution structured illumination microscope
  • Microtubule networks were more sharply resolved in ExM (Fig. 5G) than with SR-SIM (Fig. 5F).
  • Tri-functional labels with different colors and oligonucleotides were synthesized to enable multicolor ExM.
  • Bassoon and Homerl staining form overlapping spots at each synapse (Fig. 6F)
  • the post-ExM image Fig. 6G shows clearly distinguishable pre- and post-synaptic labeling.
  • the distance between the Bassoon and Homerl scaffolds, as measured by ExM was quantified.
  • the Bassoon-Homerl separation was 169 ⁇ 32.6 nm (Fig. 6J, n 277 synapses from 4 cortical slices).

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PCT/US2015/016788 2014-02-21 2015-02-20 Expansion microscopy WO2015127183A2 (en)

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WO2020199328A1 (zh) * 2019-03-29 2020-10-08 华中科技大学 膨胀切削显微成像方法及适用于该方法的超吸水水凝胶
US10995361B2 (en) 2017-01-23 2021-05-04 Massachusetts Institute Of Technology Multiplexed signal amplified FISH via splinted ligation amplification and sequencing
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