Method and apparatus for labeling and analyzing cellular components
First Claim
1. In a set of labeled probes useful for optically marking a feature of an object, said set of labeled probes including at least one labeled probe that binds to said feature and generates a signal that can be used to identify said feature, any combination of labeled probes useful for marking the feature being uniquely optically discriminable, each labeled probe in said set of labeled probes comprising:
- (a) a binding element selectively binding to at least a portion of said feature; and
(b) at least one signaling component coupled to the binding element, so that;
(i) if only one binding element is bound to said feature, a plurality of signaling components that are optically discriminable, but need not be spatially discriminable are coupled to said binding element; and
(ii) if a plurality of binding elements are bound to said feature, at least one signaling component is coupled to each binding element to thereby bind a plurality of signaling components to the feature, said signaling components being optically discriminable, but not required to be spatially discriminable, when providing a unique optical signature that optically marks the feature.
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Abstract
A labeling method that labels an object or specific features of an object with labeled probes that provide a multiplexed signal that can be analyzed by spectral decomposition. This binary and higher encoding scheme can be employed to label components of biological cells. In each encoding scheme, labeled probes that selectively bind to a specific feature are required. The labeled probes include a binding element that binds to the feature, and at least one signaling component that generates a detectable signal, preferably a spectral signature. In one embodiment, adding multiple fluorescent dye molecules to each binding element provides the multiplexed signal. In another embodiment, adding only one signal compound to each binding element provides the multiplexed signal, such that some of the binding elements have a different signal compound added. The different signal compounds provide the multiplexed signal.
135 Citations
51 Claims
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1. In a set of labeled probes useful for optically marking a feature of an object, said set of labeled probes including at least one labeled probe that binds to said feature and generates a signal that can be used to identify said feature, any combination of labeled probes useful for marking the feature being uniquely optically discriminable, each labeled probe in said set of labeled probes comprising:
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(a) a binding element selectively binding to at least a portion of said feature; and
(b) at least one signaling component coupled to the binding element, so that;
(i) if only one binding element is bound to said feature, a plurality of signaling components that are optically discriminable, but need not be spatially discriminable are coupled to said binding element; and
(ii) if a plurality of binding elements are bound to said feature, at least one signaling component is coupled to each binding element to thereby bind a plurality of signaling components to the feature, said signaling components being optically discriminable, but not required to be spatially discriminable, when providing a unique optical signature that optically marks the feature. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
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9. A set of labeled probes useful for indicating one or more features of an object, comprising:
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(a) at least one binding element that selectively binds to a binding site of a feature; and
(b) a plurality of signaling components that are optically discriminable, but not required to be spatially discriminable and which together produce a signal indicative of the feature, said at least one binding element coupling to;
(i) two or more signaling components if the feature has only a single binding site to which said at least one binding element is bound; and
,(ii) at least one signaling component if the feature has a plurality of binding sites to which said at least one binding element is bound, so that at least a pair of the signaling components are coupled to the feature, providing a distinctive indication of the feature on the object. - View Dependent Claims (10, 11, 12, 13, 14, 15, 16, 18, 19, 20)
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17. A set of labeled probes useful for indicating different features of an object, comprising:
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(a) at least one binding element that binds to at least one of the different features; and
(b) at least one signaling component coupled to said at least one binding element and thus coupled to the feature to which said at least one binding element is bound, producing a uniquely discriminable optical signal, so that at least two different labeled probes of the set that bind to different features share at least one different signaling component in common, the signaling components bound to a feature not being required to be spatially discriminable.
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21. A set of labeled probes useful for indicating a presence of a plurality of different features of an object, said set of labeled probes comprising:
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(a) a plurality of different binding elements, each different binding element selectively binding to at least a portion of a feature of the object; and
(b) a plurality of signaling components, each different signaling component having a unique spectral signature, a number of different signaling components in said set being fewer than a number of the different binding elements in said set, such that at least two different labeled probes in the set that are capable of binding to different features share at least one different signaling component in common, labeled probes that are bound to a feature being optically discriminable, but not being required to be spatially discriminable. - View Dependent Claims (22, 25, 26, 27, 28, 29, 30)
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23. A set of probes useful for marking a plurality of different features associated with an object as a function of multiplexed optical signals that uniquely indicate each different feature, said set comprising:
a plurality of different labeled probes, each different labeled probe having a uniquely optically identifiable characteristic, a binding element that selectively binds to at least a portion of at least one feature of said plurality of different features, and at least one signaling component coupled to a feature by said binding element, each labeled probe providing a multiplexed optical signal enabling different features associated with an object to me identified, said multiplexed optical signal comprising a combination of optical signals produced by each signaling component that is coupled to the feature, said multiplexed optical signal being optically discriminable, but not required to be spatially discriminable, wherein the plurality of labeled probes comprises at least;
(a) a first labeled probe selected to bind to at least a portion of a first feature;
(b) a second labeled probe selected to bind to at least a portion of a second feature that is different than the first feature, such that said first and second labeled probes include at least one signaling component in common in the multiplexed optical signal that each produces to enable identification of the first and the second features.
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24. A system for marking and identifying at least one feature associated with an object, said system comprising:
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(a) a set of labeled probes useful for optically marking a feature of an object, said set of labeled probes including at least one labeled probe that binds to said feature and provides an optical signal that can be used to identify said feature, each different labeled probe in the set being uniquely optically discriminable and comprising a binding element selectively binding to at least a portion of said feature, and at least one signaling component coupled to the binding element, so that;
(i) if only one binding element is bound to said feature, a plurality of signaling components that are optically discriminable, but not spatially discriminable are coupled to said binding element; and
(ii) if a plurality of binding elements are bound to said feature, at least one signaling component is coupled to each binding element to thereby bind a plurality of signaling components to the feature, said signaling components being optically discriminable, but not spatially discriminable by the system, when providing a unique optical signature that marks the feature; and
(b) a light detector that detects the labeled probes bound to said at least one feature associated with the object, based upon the unique optical signature provided by the signaling components that are coupled to said at least one feature.
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31. A system for marking and identifying one or more features of an object, said system comprising:
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(a) a set of labeled probes useful for marking features of the object, each labeled probe of the set of labeled probes comprising;
(i) at least one binding element that binds to at least one feature; and
(ii) at least one signaling component coupled to said at least one binding element and thus coupled to the feature to which said at least one binding element is bound, producing a uniquely discriminable optical signal, so that at least two different labeled probes of the set that bind to different features share at least one different signaling component in common, the signaling components bound to a feature being optically discriminable, but not required to be spatially discriminable; and
(b) a cytometer for imaging the object and identifying each feature marked by at least one labeled probe of the set, by simultaneously detecting the uniquely discriminable optical signatures of any signaling components that are coupled to any feature of the object by said at least one binding element. - View Dependent Claims (32, 33, 35, 36, 37, 38, 39, 40, 41)
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34. A method for detecting a feature on an object using an imaging system, comprising the steps of:
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(a) providing at least one labeled probe that selectively binds to said feature, wherein said at least one labeled probe comprises a binding element that selectively binds to at least a portion of said feature, and at least one optical signaling component;
(b) exposing said object to said at least one labeled probe under conditions that cause said at least one labeled probe to bind to at least a portion of said feature, if said feature is associated with said object, such that a plurality of optical signaling components become bound to said feature;
(c) collecting light from said object along a collection path;
(d) focusing the collected light to produce an image corresponding to the object, locations of labeled probes bound to a feature included in the image being optically discriminated but not spatially discriminated in the image;
(e) detecting the image to produce a signal indicative of each optical signaling component bound to the feature on the object;
(f) analyzing the signal to determine if a spectral component due to the each optical signaling component bound to said feature is present in the image, thereby establishing that the feature is associated with the object.
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42. A method for probing an object with labeled probes to detect if any of a plurality of specific features is associated with the object, using an imaging system that does not spatially resolve locations of the labeled probes on any specific feature, the method comprising the steps of:
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(a) for each specific feature to be detected, providing at least one labeled probe that selectively couples to a corresponding specific feature, wherein each labeled probe comprises a binding element that selectively binds to at least a portion of the specific feature, and at least one optical signaling component that is bound to the specific feature by the binding element;
(b) exposing said object to said at least one labeled probe for each specific feature to be detected, under conditions that cause each labeled probe to couple to at least a portion of its corresponding specific feature, if that corresponding specific feature is associated with said object, such that at least two optical signaling components become bound to each specific feature associated with said object, each of said at least two optical signaling components that is bound to each specific feature being uniquely optically discriminable based upon a multiplex of the light from the optical signaling components, without spatially resolving a location of each labeled probe coupled to a specific feature;
(c) simultaneously detecting light from all optical signaling components associated with said object, producing a corresponding signal; and
(d) analyzing the signal to detect each optical signaling component bound to any specific feature associated with the object, thereby determining which specific feature is associated with the object. - View Dependent Claims (43, 44, 45, 46, 47, 48, 49, 50, 51)
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Specification