Proximity assay for in situ detection of targets

• US 9,663,814 B2
• Filed: 03/11/2014
• Issued: 05/30/2017
• Est. Priority Date: 03/12/2013
• Status: Active Grant

• Current Assignee: Ventana Medical Systems Incorporated (Roche Holding AG)
• Original Assignee: Ventana Medical Systems Incorporated (Roche Holding AG)
• Inventors: Farrell, Michael, Hong, Rui, Jiang, Zeyu
• Primary Examiner(s): Cheu, Jacob
• Application Number:
  US14/769,892
• Publication Number:
  US 20160002701A1
• Time in Patent Office: 1,176 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/25 involving enzymes not classifiable in groups C12Q1/26 - C12Q1/66
• CPC Class Codes: G01N 2333/9015 Ligases (6)
• CPC Class Codes: G01N 2440/32 biotinylation
• CPC Class Codes: G01N 33/535 with enzyme label or co-enzymes, co-factors, enzyme inhibitors or enzyme substrates
• CPC Class Codes: G01N 33/581 with enzyme label (including co-enzymes, co-factors, enzyme inhibitors or substrates)

Abstract

A proximity detection method is described that utilizes enzymatic biotinylation to detect targets in a sample, particularly formalin fixed paraffin embedded samples using automated staining platforms. One disclosed embodiment comprises contacting the sample with a first conjugate comprising a biotin ligase and a first specific binding moiety that binds proximally to the first target; contacting the sample with a second conjugate comprising a biotin ligase substrate and a second specific binding moiety that binds proximally to the second target; subjecting the sample to conditions that allow biotinylation of the biotin ligase substrate by the biotin ligase when the first target and the second target have a proximal arrangement; and detecting biotinylation of the biotin ligase substrate. The conditions that allow biotinylation of the substrate include addition of biotin and ATP. The method also may comprise contacting the sample with a streptavidin-enzyme conjugate. Signal amplification also can be used.

Claims

1. A method for analyzing a sample to determine whether a first target is proximal to a second target, the method comprising:

contacting a sample with a first conjugate comprising a biotin ligase and a first binding moiety specific for the first target;

contacting the sample with a second conjugate comprising a biotin ligase peptide substrate and a second binding moiety specific for the second target;

contacting the sample with biotin and ATP so that the biotin ligase labels the biotin ligase peptide substrate with biotin if the first target is proximal to the second target; and

detecting the biotin label;

wherein the first and second binding moieties are selected from an antibody, an antibody fragment, or an antibody derivative or an antibody mimetic.

2. The method according to claim 1, wherein labeling the first target includes contacting the sample with a first primary antibody specific to the first target and labeling the second target includes contacting the sample with a second primary antibody specific to the second target.

3. The method according to claim 2, wherein the first primary antibody is labeled with a first hapten and labeling the first target includes contacting the sample with a first secondary antibody specific to the first hapten.

4. The method according to claim 3, wherein the second primary antibody is labeled with a second hapten and labeling the second target includes contacting the sample with a second secondary antibody specific to the second hapten.

5. The method according to claim 2, wherein the first primary antibody is derived from a first species and labeling the first target includes contacting the sample with a first secondary anti-species antibody specific to the first species.

6. The method according to claim 5, wherein the second primary antibody is derived a second species and labeling the second target includes contacting the sample with a second secondary anti-species antibody specific to the second species.

7. The method according to claim 2, wherein labeling the first target includes contacting the sample with a first amplification reagent selected from a tyramide conjugate or a quinone methide precursor conjugate.

8. The method according to claim 2, wherein labeling the second target includes contacting the sample with an amplification reagent selected from a tyramide conjugate or a quinone methide precursor conjugate.

9. The method of according to claim 1, wherein the first target and the second target are dimerized proteins.

10. The method of according to claim 1, wherein the first target is a first nucleic acid target, wherein labeling the first target comprises contacting the sample with a first nucleic acid probe.

11. The method according to claim 10, wherein the second target is a second nucleic acid target, wherein labeling the second target comprises contacting the sample with a second nucleic acid probe.

12. The method according to claim 10, wherein the first nucleic acid probe is labeled with a third hapten, wherein labeling the first target comprises contacting the sample with a third secondary antibody specific to the third hapten.

13. The method of according to claim 1, wherein detecting the biotin comprises contacting the sample with a conjugate comprising a biotin binding antibody, avidin, or streptavidin conjugated to one or more enzymes.

14. The method of claim 13, wherein detecting the biotin comprises contacting the sample with a chromogen.

15. The method of according to claim 1, wherein detecting the biotin comprising contacting the sample with an amplification reagent selected from a tyramide conjugate or a quinone methide precursor conjugate.

16. The method of according to claim 1, wherein the sample is a formalin fixed paraffin embedded tissue.

17. The method of according to claim 1, wherein the first target is proximal to a second target if is less than about 100 nm, less than about 50 nm, less than about 20 nm apart, less than about 10 nm, less than about 5 nm, or less than about 2 nm apart.

18. The method according to claim 1, wherein labeling the first target or labeling the second target includes contacting the sample with a reagent comprising a linker.

19. The method according to claim 18, wherein the linker has from about 2 to about 20 PEG units.

20. The method according to claim 18, wherein the linker is selected from PEG₂, PEG₃, PEG₄, PEG₅, PEG₆, PEG₇, PEG₈, PEG₉, PEG₁₀, PEG₁₁, PEG₁₂, PEG₁₃, PEG₁₄, PEG₁₅, PEG₁₆, PEG₁₇, PEG₁₈, PEG₁₉, PEG₂₀, 1,4-diaminohexane, xylylenediamine, terephthalic acid, 3,6-dioxaoctanedioic acid, ethylenediamine-N,N-diacetic acid, 1,1′

-ethylenebis(5-oxo-3-pyrrolidinecarboxylic acid), 4,4′

-ethylenedipiperidine, succinimidyl-6-hydrazino-nicotinamide(S-HyNic, HyNic-NHS), N-succinimidyl-4-formylbenzoate (S-4FB, 4-FB-NHS), maleimide HyNic (MHPH), maleimide 4FB (MTFB), succinimidyl-[(N-maleimidopropionamido)-octaethyleneglycol] ester (Mal-PEG₈-NHS), succinimidyl-[(N-maleimidopropionamido)-tetraethyleneglycol] ester (Mal-PEG₄-NHS), 4-FB-PEG₄-PFP, azidobenzoyl hydrazide, N-[4-(p-azidosalicylamino)butyl]-3′

-[2′

-pyridyldithio]propionamid), bis-sulfosuccinimidyl suberate, dimethyladipimidate, disuccinimidyltartrate, N-maleimidobutyryloxysuccinimide ester, N-hydroxy sulfosuccinimidyl-4-azidobenzoate, N-succinimidyl[4-azidophenyl]-1,3′

-dithiopropionate, N-succinimidyl[4-iodoacetyl]aminobenzoate, glutaraldehyde, and succinimidyl-4-[N-maleimidomethyl]cyclohexane-1-carboxylate, 3-(2-pyridyldithio)propionic acid N-hydroxysuccinimide ester (SPDP), and 4-(N-maleimidomethyl)-cyclohexane-1-carboxylic acid N-hydroxysuccinimide ester (SMCC).

21. An automated method, comprising using an automated staining apparatus to perform one or more steps associated with a method of testing a formalin fixed paraffin embedded tissue sample for the presence of a first target and a second target in close proximity, the method comprising:

contacting the sample with a first set of reagents so that the first target is recognized by a first binding moiety specific for the first target and that results in the conjugation or deposition of a biotin ligase proximally to the first target;

contacting the sample with a second set of reagents so that the second target is recognized by a second binding moiety specific for the second target and that results in the conjugation or deposition of a biotin ligase substrate proximally to the second target;

contacting the sample with biotin and biotinylation reagents so that the biotin ligase biotinylates the biotin ligase substrate if the first target and the second target are in close proximity; and

detecting the biotin;

wherein the first and second binding moieties are selected from an antibody, an antibody fragment, an antibody derivative or an antibody mimetic.