Assay with Synaptobrevin Based Moiety

Abstract

Compositions and methods for improved cell-based methods of characterizing botulinum neurotoxins are provided. Cells utilized in these methods include a reporting construct that is cleaved following uptake and processing of botulinum neurotoxin by the cell, resulting in proteolysis of the portion of the reporting construct that is released following cleavage. The released portion includes a fluorophore and amino acid substitutions or sequences that enhance the rate of proteolysis. A pair of reporting constructs can be utilized in which one member of the pair is modified to resist cleavage by the botulinum neurotoxin while co-localizing with the remaining member of the pair.

Claims

1. A pair of reporting peptides for characterizing botulinum serotype neurotoxin comprising: a first reporter peptide comprising a first membrane binding peptide configured to localize to a vesicle membrane, a first fluorescent peptide, and a first linking peptide interposed between the first membrane binding peptide and the first fluorescent peptide, wherein the first linking peptide is derived from synaptobrevin; and a second reporter peptide comprising a second membrane binding peptide configured to localize to a vesicle membrane, a second fluorescent peptide, and a second linking peptide interposed between the second membrane binding peptide and the second fluorescent peptide, wherein the second linking peptide is derived from synaptobrevin, wherein the first fluorescent peptide and the second fluorescent peptide are positioned such that no useful Forster resonance energy transfer (FRET) occurs between them.

2. The pair of reporting peptides of claim 1, wherein the first linking region comprises one or more mutations that decrease susceptibility to proteolysis by botulinum B neurotoxin.

3. The pair of reporting peptides of claim 2, wherein at least one of the one or more mutations is a point mutation of an amino acid that forms part of a botulinum serotype B neurotoxin cleavage site of synaptobrevin.

4. The pair of reporting peptides of claim 2, wherein at least one of the one or more mutations is a point mutation of an amino acid that forms part of an exosite of synaptobrevin that interacts with botulinum serotype B neurotoxin.

5. The pair of reporting peptides of claim 2, wherein at least one of the one or more mutations is a point mutation selected from the group consisting of D64N, D65N, D68N, and Q76V of synaptobrevin.

6. The pair of reporting peptides of claim 1, wherein the first fluorescent peptide and the second fluorescent peptide have distinguishably different emission frequencies.

7. The pair of reporting peptides of claim 1, wherein the first reporter peptide and the second reporter peptide are encoded by a single plasmid.

8. The pair of reporting peptides of claim 1, wherein the first reporting construct is encoded by a first plasmid and the second reporting construct is encoded by a second plasmid.

9. The pair of reporting peptides of claim 1, wherein at least one of the first fluorescent peptide and the second fluorescent peptide are derived from green fluorescent protein or a green fluorescent protein mutation.

10. The pair of reporting peptides of claim 1, wherein one of the first fluorescent peptide and the second fluorescent peptide comprise one or more mutations that increase the rate of intracellular proteolysis relative to an analogous peptide that does not incorporate the one or more mutations.

11. The pair of reporting peptides of claim 10, wherein the one or more mutations comprise a point mutation that replaces a native amino acid with a basic amino acid.

12. The pair of reporting peptides of claim 1, wherein the reporting construct is expressed in a cell.

13. The pair of reporting peptides of claim 12, wherein the cell is selected from the group consisting of Neuro2A cells, M17 cells, PC12 cells, SK-N-SH cells, LNCaP cells, immortalized murine astrocytes (for example, SV40T cells), human and/or murine hTERT immortalized cells, iPSC neurons, stem cell derived neurons, and primary neurons.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0018] FIG. 1 shows an exemplary arrangement of the components of a reporting construct of the inventive concept.

[0019] FIG. 2 shows an example of a reporting construct pair of the inventive concept.

[0020] FIG. 3 shows another example of a reporting construct pair of the inventive concept.

[0021] FIG. 4 shows an exemplary arrangement of the components of a reporting construct of the inventive concept.

[0022] FIG. 5 shows another exemplary arrangement of the components of a reporting construct of the inventive concept.

[0023] FIGS. 6A and 6B show a pMD0032 ORF encoding a YFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 1). The sequence shown in FIG. 6B continues from the sequence shown in FIG. 6A.

[0024] FIGS. 7A and 7B show a pMD0034 ORF encoding another YFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 3). The sequence shown in FIG. 7B continues from the sequence shown in FIG. 7A.

[0025] FIGS. 8A and 8B. show a different pMD0034 ORF, encoding a CFP-VAMP2 peptide (SEQ ID NO. 2). The sequence shown in FIG. 8B continues from the sequence shown in FIG. 8A.

[0026] FIGS. 9A and 9B show a pMD0071 ORF encoding for another YFP-VAMP2 peptide (SEQ ID NO. 5). The sequence shown in FIG. 9B continues from the sequence shown in FIG. 9A.

[0027] FIGS. 10A and 10B show a different pMD0071 ORF, encoding for an ECFP-synaptobrevin (VAMP2) (Q76V) peptide (SEQ ID NO. 4). The sequence shown in FIG. 10B continues from the sequence shown in FIG. 10A.

[0028] FIGS. 11A and 11B show a pMD0183 ORF encoding for a YFP-YFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 8), which incorporates two YFP peptides arranged sequentially. The sequence shown in FIG. 11B continues from the sequence shown in FIG. 11A.

[0029] FIGS. 12A and 12B show a pMD0185 ORF encoding for another YFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 7). The sequence shown in FIG. 12B continues from the sequence shown in FIG. 12A.

[0030] FIGS. 13A and 13B show a different pMD0185 ORF, encoding for a CFP-synaptobrevin (VAMP2) (D64N, D68N, Q76V) peptide (SEQ ID NO. 6). The sequence shown in FIG. 13B continues from the sequence shown in FIG. 13A.

[0031] FIG. 14 depicts a typical reporting construct utilized in the characterization of a BoNT from a serotype B Clostridium botulinum (BoNT/B).

[0032] FIGS. 15A and 15B schematically depict reporting construct pairs of the inventive concept. FIG. 15A shows a reporting construct pair that does not include a degron sequence position towards the N-terminus relative to a reporting fluorophore (e.g. YFP). FIG. 15B shows a reporting construct pair that includes a degron sequence position towards the N-terminus relative to a reporting fluorophore (e.g. YFP).

[0033] FIGS. 16A and 16B show the results of exposure of transformed cells carrying reporting construct pairs of the inventive concept to BoNT/B. FIG. 16A provides a photomicrograph of cells expressing a control (i.e. no degron sequence) reporting construct pair in the presence and absence of BoNT/B. FIG. 16B shows the overall fluorescence emission from cells such as those shown in FIG. 16A as characterized using a fluorescence plate reader.

[0034] FIGS. 17A to 17C show the results of fluorescence measurements made from non-transformed cells, cells transformed to express a control (i.e. not containing degron) reporting construct pair, and cells transformed to express reporting construct pairs in which the YFP-bearing construct included a degron sequence positioned towards the N-terminus relative to the YFP peptide. FIG. 17A shows measurements of YFP emission in the presence and absence of BoNT/B. FIG. 17B shows measurements of CFP emission in the presence and absence of BoNT/B. FIG. 17C shows results of measurements of YFP fluorescence:CFP fluorescence ratio in the presence and absence of BoNT/B.

[0035] FIGS. 18A to 18C shows results of studies similar to those of FIG. 17A to 17C, incorporating an additional cell population transformed to express a reporting construct pair with a degron sequence obtained from SNAP-25. FIG. 18A shows measurements of YFP emission in the presence and absence of BoNT/B. FIG. 18B shows measurements of CFP emission in the presence and absence of BoNT/B. FIG. 18C shows results of measurements of YFP fluorescence:CFP fluorescence ratio in the presence and absence of BoNT/B.

[0036] FIGS. 19A and 19B provide photomicrographs obtained from cells transformed with a control reporting construct pair that does not include a degron sequence and from cells transformed with reporting constructs that include a degron sequence. FIG. 19A shows brightfield, YFP emission, and CFP emission photomicrographs of transformed cells expressing a control reporting construct pair (containing no degron sequence) and transformed cells expressing reporting construct pairs that include degron sequences (specifically, Bonger or iNOS degron sequences) positioned N-terminally to the YFP peptide of the YFP-bearing member of the reporting construct pair. FIG. 19B shows the results of studies similar to those shown in FIG. 12A, but performed using cells carrying either the pMD0191 or pMD0192 reporting construct pairs, both of which show improved dynamic range on exposure to BoNT/B relative to control cell.

[0037] FIG. 20 shows results of application of BoNT/B at different concentrations to cells expressing a control BoNT/B-reactive construct pair lacking a degron sequence and cells expressing analogous BoNT/B-reactive construct pair where the YFP-bearing peptide includes a degron sequence.

DETAILED DESCRIPTION

[0038] The inventive subject matter provides compositions and methods in which reporting constructs and quantitation methods are described that are useful in characterizing botulinum B neurotoxin (BoNT/B) using cell based assays. Cells are transformed, either transiently or permanently to express a reporting construct that includes one or more fluorescing peptide domains. In instances where two or more fluorescing peptide domains are provided, they are arranged so that no useful Forster resonance energy transfer (FRET) occurs between fluorescing peptides (i.e. less than 25%, 20%, 15%, 10%, 5%, 2.5%, or 1% energy transfer). Such reporting constructs include a membrane targeting region derived from synaptobrevin, which is selective for vesicle membranes, thereby anchoring the reporting construct to a vesicle. A cleavage and recognition site that serves as a BoNT/B substrate is positioned such that BoNT/B light chain activity releases one or more fluorescent peptide portions of the reporting construct into the cytosol. Such reporting constructs are expressed in cells that include cell surface receptors that facilitate uptake of BoNT/B, and the resulting changes in fluorescence observed in such cells on exposure to BoNT/B can be utilized in characterization of the neurotoxin.

[0039] The following discussion provides many example embodiments of the inventive subject matter. Although each embodiment represents a single combination of inventive elements, the inventive subject matter is considered to include all possible combinations of the disclosed elements. Thus if one embodiment comprises elements A, B, and C, and a second embodiment comprises elements B and D, then the inventive subject matter is also considered to include other remaining combinations of A, B, C, or D, even if not explicitly disclosed.

[0040] As used herein, and unless the context dictates otherwise, the term “coupled to” is intended to include both direct coupling (in which two elements that are coupled to each other contact each other) and indirect coupling (in which at least one additional element is located between the two elements). Therefore, the terms “coupled to” and “coupled with” are used synonymously.

[0041] A reporting construct of the inventive construct can incorporate one or more amino acids or amino acid sequences (e.g. degron sequences) that enhance degradation of at least a portion of the reporting construct. For example, a reporting construct can include one or more degron sequence(s) positioned at or near the N-terminus of the reporting construct. A reporting peptide construct can, for example, produce a detectable signal (for example, a fluorescent peptide) from a region that is positioned adjacent to a degron sequence and is interposed between the degron sequence and a protease substrate sequence (which can be positioned at or near the C-terminus of the reporting construct). Such a protease substrate sequence can include one or more protease recognition sequences, one or more protease cleavage sites (which can be distinct from or essentially to the protease recognition sequences), and/or a localization sequence.

[0042] Alternatively, a localization sequence can be provided that is distinct from the protease substrate sequence and positioned between the protease substrate sequence and the C terminus of the reporting construct. Such a localization sequence serves to localize the intact reporting construct in a protected site, within which a reporting construct is protected or at least partially protected from an intracellular protein degradation system that interacts with a degron sequence of the reporting construct. On exposure to the protease activity being characterized a cleavage event occurs within the protease substrate sequence, release a fragment of the reporting construct that includes the degron sequence and the reporting peptide sequence from the protected site. Release from the protected site results in rapid degradation of the reporting peptide sequence (i.e. occurring at an elevated rate relative to the reporting sequence alone within the same intracellular environment), resulting in a rapid change in the observed detectable signal.

[0043] One should appreciate that the disclosed techniques provide many advantageous technical effects including providing highly sensitive testing for characterization of BoNT/B neurotoxin that provides a high degree of correlation to animal-based testing while relying on cultured cells. In addition, the disclosed methods and compositions provide reduced interference in such cell-based assay results from released, but undegraded, fragments of the reporting construct. This reduced interference can improve sensitivity and/or reduce time to first result in a cell-based assay.

[0044] The following discussion provides many example embodiments of the inventive subject matter. Although each embodiment represents a single combination of inventive elements, the inventive subject matter is considered to include all possible combinations of the disclosed elements. Thus if one embodiment comprises elements A, B, and C, and a second embodiment comprises elements B and D, then the inventive subject matter is also considered to include other remaining combinations of A, B, C, or D, even if not explicitly disclosed.

[0045] As used in the description herein and throughout the claims that follow, the meaning of “a,” “an,” and “the” includes plural reference unless the context clearly dictates otherwise. Also, as used in the description herein, the meaning of “in” includes “in” and “on” unless the context clearly dictates otherwise.

[0046] Unless the context dictates the contrary, all ranges set forth herein should be interpreted as being inclusive of their endpoints, and open-ended ranges should be interpreted to include only commercially practical values. Similarly, all lists of values should be considered as inclusive of intermediate values unless the context indicates the contrary.

[0047] Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. One or more members of a group can be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is herein deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.

[0048] One embodiment of the inventive concept is a reporting construct arranged as a single peptide that includes a first fluorescent peptide region, a synaptobrevin derived membrane binding region, a BoNT/B recognition and cleavage site, and a second fluorescent peptide. The first and second fluorescent peptide can have distinct excitation and emission spectra, and are arranged so that no significant FRET occurs between them. In a preferred embodiment the BoNT/B recognition and cleavage site is derived from synaptobrevin. Cleavage of the recognition and cleavage site results in release of one of the fluorescent peptides into the cytosol, where it can be subsequently degraded. In some embodiments one or both of the fluorescent peptides can include amino acid sequence modifications (such as incorporation of basic amino acids and/or degron sequences) that enhance degradation of the released peptide fragment on release into the cytosol. FIG. 1 shows an exemplary arrangement of the components of such a reporting construct.

[0049] In a preferred embodiment of the inventive concept a fluorescent peptide utilized in the construct is derived from green fluorescent protein (GFP) or a GFP mutation. Suitable GFP mutations include EGFP, EBFP, EBFP2. Azurite, mKalama1, CFP, ECFP, Cerulean, CyPet, mTurqoise, YFP, Citrine, Venus, and/or YPet. It should be appreciated that in some embodiments one member of the fluorescent peptide pair can be retained on the vesicle membrane on exposure of a cell expressing the construct to BoNT/B. In embodiments where one of the fluorescent peptides is retained on the vesicle membrane following proteolysis by BoNT/B light chain (or otherwise not degraded following exposure of the cell to a BoNT), emission measurement from the retained fluorescent peptide can be used to normalize emission measurements made from the release fluorescent peptide. For example, fluorescence emission from such a retained fluorescent peptide can be used to normalize results for differences in gene expression, cell number, and/or cell distribution within different test sites or test wells of an assay test fixture (such as a multiwell test plate). Alternatively, fluorescence emission from such a retained fluorescent peptide can be utilized as an identifying feature in an artificial vision system, for example an artificial vision system utilizing an algorithm that identifies specific features of interest (e.g. labeled cell and/or intracellular components) within an image obtained from a test area. In embodiments where both fluorescent peptides are released from the vesicle membrane by the action of BoNT/B light chain proteolytic activity data, similar normalization can be provided by the application of a reference dye (for example, a fluorescent cell membrane-binding dye with a distinguishable excitation and emission spectra).

[0050] In another embodiment of the inventive concept a pair of reporting constructs are utilized. In such an embodiment each member of the pair includes a synaptobrevin-derived membrane binding portion and a fluorescent peptide, with each member of the pair carrying a distinct fluorescent peptide. One member of the peptide pair includes a BoNT/B cleavage and recognition site (such as synaptobrevin or a synaptobrevin-derived peptide) interposed between the membrane binding portion and the fluorescent peptide. The remaining member of the peptide pair includes a peptide that is interposed between the membrane binding portion and the fluorescent peptide, but that does not act as a BoNT/B recognition and cleavage site. Such a peptide can be, for example, synaptobrevin or a synaptobrevin-derived peptide which includes amino acid substitutions at the BoNT/B proteolytic cleavage site and/or outlying BoNT/B recognition sites (e.g. exosites). As a result such a member of the peptide pair can retain localization, complex formation, and other characteristics of synaptobrevin, but is not cleaved by BoNT/B activity. As a result the associated fluorophore is retained on the vesicle membrane. It should be appreciated that, unlike BoNT peptides such as those reported in U.S. Pat. No. 9,624,529 (to Oyler and Tsai), use of such peptide pairs incorporating a non-cleavable member provides for an internal control useful in data normalization. In some embodiments significant (i.e. greater than 5% energy transfer) can occur between the fluorophores of a reporting construct pair. In other embodiments, while the different fluorescent peptides of the reporting construct can have distinct excitation and emission spectra the pair of fluorescent peptides is arranged such that no significant FRET occurs between them. It should be appreciated that such a lack of significant (i.e. greater than 5%) energy transfer between the fluorescent peptide can reduce or eliminate quenching effects associated with FRET, which in turn can improve the utility of a signal obtained from a retained (or otherwise non-labile) fluorescent peptide for data normalization. Cleavage of the BoNT/B recognition and cleavage site results in the release of one of the fluorescent peptides into the cytosol, where it is subsequently degraded. As noted above, such a released fluorescent peptide can be associated with amino acids and or amino acid sequences that enhance the rate of degradation on release into the cytosol (relative to a corresponding peptide that lacks a degradation-enhancing amino acid or amino acid sequence). FIG. 2 shows an example of such a reporting construct pair.

[0051] In another embodiment of the inventive concept a pair of reporting constructs are utilized. In such an embodiment each member of the pair includes a synaptobrevin-derived (i.e. corresponding to a portion of the synaptobrevin amino acid sequence and/or having greater than about 80% sequence identity with synaptobrevin) membrane binding portion, a BoNT/B recognition and cleavage site (for example, synaptobrevin or a synaptobrevin-derived peptide) and a fluorescent peptide, with each member of the pair carrying a distinct fluorescent peptide. One member of the peptide pair includes a BoNT/B cleavage and recognition site (such as synaptobrevin or a synaptobrevin-derived peptide) interposed between the membrane binding portion and the fluorescent peptide. While the distinct fluorescent peptides can have distinct excitation and emission spectra, the construct pair is arranged such that no significant FRET occurs between them, as noted above. Cleavage of the BoNT/B recognition and cleavage site results in the release of one or both of the fluorescent peptides into the cytosol, followed by degradation of the released peptide(s). As noted above, such released fluorescent peptides can include an amino acid or an amino acid sequence (e.g. a degron sequence) that enhances the rate of degradation following release into the cytosol relative to a corresponding peptide lacking such an amino acid or amino acid sequence. FIG. 3 shows an example of such a reporting construct pair.

[0052] In a preferred embodiment of the inventive concept a fluorescent peptide utilized in the construct is derived from green fluorescent protein (GFP) or a GFP mutation. It should be appreciated that in some embodiments one member of the fluorescent peptide pair can be retained on the vesicle membrane on exposure of a cell expressing the construct to BoNT/B. In embodiments where one of the fluorescent peptides is retained on the vesicle membrane following proteolysis by BoNT/B light chain, emission measurement from the retained fluorescent peptide can be used to normalize emission measurements made from the release fluorescent peptide. In embodiments where both fluorescent peptides are released from the vesicle membrane by the action of BoNT/B light chain proteolytic activity data normalization can be provided by the application of a reference dye (for example, a fluorescent cell membrane-binding dye with a distinguishable excitation and emission spectra).

[0053] In another embodiment of the inventive concept the reporting construct arranged as a single peptide that includes a synaptobrevin derived membrane binding region, a BoNT/B recognition and cleavage site, and a fluorescent peptide region. In a preferred embodiment the BoNT/B recognition and cleavage site is derived from synaptobrevin. Cleavage of the recognition and cleavage site results in release of the fluorescent peptide into the cytosol, where it can be subsequently degraded. In some embodiments the fluorescent peptide can include amino acid sequence modifications (such as incorporation of basic amino acids and/or a degron sequence) that enhance degradation on release into the cytosol relative to a corresponding peptide lacking such an amino acid or degron sequence. FIG. 4 shows an exemplary arrangement of the components of such a reporting construct.

[0054] In a preferred embodiment of the inventive concept a fluorescent peptide utilized in the construct is derived from green fluorescent protein (GFP) or a GFP mutation. In some embodiments data normalization can be provided by the application of a reference dye (for example, a fluorescent cell membrane-binding dye with a distinguishable excitation and emission spectra).

[0055] In another embodiment of the inventive concept the reporting construct arranged as a single peptide that includes a synaptobrevin derived membrane binding region, a BoNT/B recognition and cleavage site, and a fluorescent peptide region that includes at least two identical fluorescing peptides linked to one another by a spacer peptide. Such a spacer peptide is purely structural and does not fluoresce, does not act as a BoNT/B substrate, and does not have a membrane binding function. In a preferred embodiment the BoNT/B recognition and cleavage site is derived from synaptobrevin. Cleavage of the recognition and cleavage site results in release of the fluorescent peptide region into the cytosol, where it can be subsequently degraded. As noted above, such a released fluorescent peptide can include an amino acid or amino acid sequence (e.g. a degron sequence) that enhances the rate of degradation relative to a corresponding peptide lacking such an amino acid or amino acid sequence. In some embodiments one or more of the fluorescent peptides can include amino acid sequence modifications (such as incorporation of basic amino acids) that enhance degradation on release into the cytosol. FIG. 5 shows an exemplary arrangement of the components of such a reporting construct.

[0056] Reporting constructs as described above can be expressed in cells that have been transformed and/or transduced (e.g. utilizing a virus), either transiently or permanently. As such, they can be encoded on one or more plasmids. In some embodiments such plasmids can be incorporated and/or integrated into the genome of a bacterial, fungal, or eukaryotic cell. In embodiments of the inventive concept that utilize two different peptides, both peptides can be encoded on a single plasmid. In other embodiments that utilize two different peptides, each peptide can be encoded on different plasmids. In such an embodiment the plasmids can include identical regulatory elements, or can include different regulatory elements that permit differential expression of the peptides.

[0057] Cells suitable for use in methods of the inventive concept include cells that are susceptible to BoNT/B intoxication. Such cells can include cell surface receptors for BoNT/B. Suitable cells can be presented as cells in cell culture (either primary or as cultured cell lines), and can be neuronal cells or derived from neuronal cells (for example, from tumors derived from neuronal cells). Alternatively suitable cells can include non-neuronally derived cells that have been modified, permanently or transiently, to express or otherwise possess suitable cell surface receptors. Suitable cells can be of human or animal (e.g. murine or rat) origin, and can include retinoblastoma cells, Neuro2A cells, M17 cells, PC12 cells, SK-N-SH cells, LNCaP cells, immortalized murine astrocytes (for example, SV40T cells), human and/or murine hTERT immortalized cells, iPSC neurons, stem cell derived neurons, and/or primary neurons.

[0058] As noted above, constructs of the inventive concept can be encoded on plasmids, which can in turn be used in the temporary and/or permanent transformation of cells. In instances where the reporting construct system includes a pair of reporter peptides, both can be encoded on a single plasmid. Alternatively, in some embodiments of the inventive concept the peptides of a reporting construct system that utilizes a pair of reporter peptides can be encoded on different plasmids. Examples of suitable peptides are shown in FIGS. 6 to 13. A plasmid pMD0032 ORF (SEQ ID NO. 1) encodes for a YFP-synaptobrevin (VAMP2) peptide (FIGS. 6A and 6B). A plasmid pMD0034 ORF encodes for another YFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 3; FIGS. 7A and 7B) and another pMD0034 ORF encodes for a CFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 2; FIGS. 8A and 8B). A plasmid pMD0071 ORF encodes for another YFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 5; FIGS. 9A and 9B) and pMD0071 ORF encodes for an ECFP-synaptobrevin (VAMP2) (Q76V) peptide (SEQ ID NO. 4; FIGS. 10A and 10B, which is not cleaved by BoNT/B). A plasmid pMD0183 ORF encodes for a YFP-YFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 8; FIGS. 11A and 11B), which includes two YFP peptide sequences arranged in series. A plasmid pMD0185 ORF encodes for another YFP-synaptobrevin (VAMP2) peptide (SEQ ID NO. 7; FIGS. 12A and 12B) and another pMD0185 ORF encodes for a CFP-synaptobrevin (VAMP2) (D64N, D68N, Q76V) peptide (SEQ ID NO. 6; FIGS. 13A and 13B, which is not cleaved by BoNT/B).

[0059] In some embodiments of the inventive concept, a reporting construct is provided that includes signaling components that generate a detectable signal, one or more degrons that increase the rate of intracellular digestion of associated peptide sequences, a protease cleavage site that is recognized and cleaved by a protease of interest (for example, a BoNT), and a localization sequence that localizes the intact reporting construct in a region within a cell that is relatively protected from intracellular digestion. Such components can be arranged in the following order: N-terminus:degron sequence:signaling sequence:protease substrate site:localization sequence. In some embodiments the localization sequence is part of the protease substrate site. In other embodiments the localization sequence is separate and distinct from the protease substrate site. A depiction of a typical reporting construct utilized in the characterization of a BoNT from a serotype B Clostridium botulinum (BoNT/B) is shown in FIG. 14. It should be appreciated that in such an embodiment the BoNT/B sensitive site can be synaptobrevin or a fragment of synaptobrevin that includes BoNT/B recognition and/or cleavage sites and a membrane localization region. While FIG. 14 depicts a construct for characterization of BoNT/B, Inventors contemplate that reporting constructs of the inventive concept can be used in cell-based or non-cell-based assays for any suitable protease and/or protease activity.

[0060] A variety of degron sequences can be utilized in reporting constructs of the inventive concept. For example, an N-terminal amino acid can be selected that increases the rate of intracellular degradation according to the N-end rule. In other embodiments of the inventive concept the degron can be selected from degron sequences of degron-containing peptide substrates, as shown in Table 1.

TABLE-US-00001 TABLE 1 Bold amino acids represent phosphorylated  residues in phospho-degrons. Degron Containing Peptides Peptide Sequence Bonger  KTRGVEEVAEGVVLLRRRGNK (SEQ ID NO. 11) TAZ  KPFLNGGPYHSREQSTDSGLGLGSYK (SEQ ID NO. 12) HIF-α  ASADLDLEALAPYIPADDDFQLRK (SEQ ID NO. 13) iNOS  KEEKDINNNVKKTK (SEQ ID NO. 14) SRC3  DVQKADVSSTGQGIDSK (SEQ ID NO. 15) Cyclin D1  KAAEEEESLASTPTDVRDVDIK (SEQ ID NO. 16) IFNAR1  KKYSSQTSQDSGNYSNK (SEQ ID NO. 17) p53  KPLSSSVPSQKTYQGSYGFRLGK (SEQ ID NO. 18) β-catenin  KAWQQQSYLDSGIHSGATTTAPK (SEQ ID NO. 19)
It should be appreciated that the localization sequence of the reporting construct can be selected to provide protection from intracellular degradation processes mediated by the N-end amino acid, for example by localizing the intact reporting construct at or near a cell membrane. Surprisingly, the inventors have found that the presence of a localizing sequence (e.g. the membrane-binding portion of synaptobrevin) can effectively prevent intracellular degradation of the intact reporting construct.

[0061] Reporting constructs of the inventive concept can utilize any suitable signaling sequence. Suitable signaling sequences include green fluorescent peptide, cyan fluorescent peptide, yellow fluorescent peptide, other green fluorescent peptide mutations, and other fluorescent peptides. In preferred embodiments two or more signaling sequences in a reporting construct are arranged such that no useful FRET (i.e. less than about 5% energy transfer) occurs between them. In other embodiments two or more fluorescent peptides can be arranged as a FRET pair within a signaling sequence. Other suitable signaling sequences include luciferase, aequorin, and other light emitting sequences. As noted above, in some embodiments of the inventive concept a second signaling sequence can be associated with or coupled to the localization sequence of the reporting construct, such that the second signaling sequence remains within the protected region of the cell following cleavage of the reporting construct. In such embodiments the second signaling sequence can be used for normalization of the signal provided by the released signaling sequence, cell numbers between different test sites or wells, and distribution of cells within a test site or well.

[0062] Signaling sequences can directly adjoin a degron sequence located at or near the N-terminus of the reporting construct. Alternatively, a signaling sequence can be separated from the degron sequence by a spacer or linker region. Such a spacer or linker can be rigid, flexible, or include both rigid and flexible regions. Such a spacer can advantageously improve the access of components of intracellular protein degradation systems by relieving steric hindrance.

[0063] Reporting constructs of the inventive concept can utilize a wide variety of intracellular protease substrate sites. Suitable intracellular protease substrate sites include caspase sensitive sites, tetanus toxin sensitive sites, BoNT sensitive sites (i.e. sites that are susceptible to cleavage by BoNT/A, BoNT/B, BoNT/C, BoNT/D, BoNT/E, BoNT/F, and/or BoNT/G), and anthrax toxin sensitive sites. In some embodiments the protease substrate site can include both protease recognition sites (i.e. sites to which the protease has an affinity) and protease cleavage sites (i.e. the specific site at which the peptide chain is cleaved). Such protease recognition sites and protease cleavage sites can be a continuous or a discontinuous sequence. In some embodiments, for example a BoNT/B sensitive reporting construct, the protease substrate site can include a localization sequence that maintains the intact reporting construct at a protected location within the cell.

[0064] Reporting constructs of the inventive concept can utilize a wide variety of localization sequences that can localize the intact reporting construct at location within the cell that is protected or partially protected from intracellular protein degradative process that are mediated by the degron sequence. Such protected sites include cell membranes, such as the interior of the plasma membrane, rough ER membrane, smooth ER membrane, vesicle membranes, and nuclear membranes. For example, a localization sequence provided by a BoNT/B protease substrate sequence can localize the intact reporting construct to a vesicle surface where it is protected or partially protected from intracellular degradative processes. In some embodiments the localization sequence can be provided as part of a protease substrate sequence. In other embodiments the localization sequence can be a distinct and separate peptide sequence that is not directly related to the protease substrate sequence. In some embodiments a localization sequence from one intracellular protease substrate sequence (for example, a BoNT/A substrate sequence) can be utilized in a reporting construct having an unrelated second intracellular protease substrate sequence (for example, a BoNT/B substrate sequence, a caspase substrate sequence, or an anthrax toxin substrate sequence).

[0065] As noted, the above described reporting constructs can be utilized in cell-based assays. In such embodiments the reporting construct can be encoded on one or more plasmids utilized to transform, either permanently or transiently, cells utilized in such assays. In a preferred embodiment such a transformed cell would express one or more types of surface receptor that provides specific uptake of an analyte in culture media. Such an analyte could trigger production of the intracellular protease to be characterized or, alternatively can include the intracellular protease to be analyzed (for example, BoNTs). Such cells can be tumor derived or otherwise immortalized to provide cell lines suitable for use in cell-based assays. Alternatively, reporting constructs can be introduced into cells that do not encode for them by physical and/or chemical means, such as ultrasound, electroporation, or fusion with encapsulating vesicles. In a preferred embodiment the cells are neuronally-derived cells that include receptors for a specified BoNT neurotoxin, and that have been transformed to express a reporting construct that includes a corresponding BoNT substrate site.

[0066] Another embodiment of the inventive concept is a cell-based assay for protease activity. Such protease activity can be a result of the activity of an analyte after it is internalized by a cell, or can be associated with a protease that is produced by the cell in response to the presence of an analyte or another environmental condition. In such a cell-based assay one or more cells that include a reporting construct of the inventive concept are provided. Such cells are exposed to a culture medium, sample, and/or environmental condition that includes the analyte to be characterized. The cells can be observed for signal originating from the reporting construct prior to or immediately following exposure to the analyte in order to obtain a baseline signal. Following exposure to the analyte the cell or cells are monitored and additional signal data from the reporting construct obtained. Such monitoring can be continuous, intermittent, or include only a single observation that follows a defined time period. Comparison of the post-exposure to signal to the baseline signal can be used to characterize amount, activity, and/or other properties of the analyte. For example, exposure of a series of test sites containing suitable cells and exposed to a series of samples containing known concentrations of the analyte of interest can be used to derive a dose/response curve, which can subsequently be used to estimate concentration of the analyte in an unknown sample. Such assays can have particular utility in replacing animal studies of toxicity or pharmaceutical effect.

[0067] In another embodiment of the inventive concept, a population of cells susceptible to BoNT/B intoxication is genetically altered, either temporarily or permanently, to express at least one of the above described reporter constructs. Images are obtained of a field containing one or more of such cells at wavelengths corresponding to an emission wavelength of at least one of the fluorescent peptides that can be released by BoNT/B proteolytic activity, prior to the exposure of such transformed cells to BoNT/B. It should be appreciated that such cells are not generally positioned in a predetermined or ordered fashion, and can be distributed randomly or essentially randomly within the field. Such imaging takes place while illuminating the field at the excitation wavelength of the fluorescent peptide and recording the image at the emission wavelength of the fluorescing peptide. In embodiments where a fluorescent peptide is present that is not released by BoNT/B activity an additional image can be obtained while illuminating the field at the corresponding excitation wavelength and recording the image at the corresponding emission wavelength of this fluorescent peptide. Following the application of sample containing (or thought to contain) BoNT/B to the cells the same field is re-imaged at least once after a suitable time interval. Image recognition software is then applied to the image recorded prior to BoNT/B application to identify regions of the image that do show useful fluorescence (e.g. cell-free regions, cells that do not express a reporting construct) and to identify regions that exceed a pre-defined signal threshold (for example, a value representing CCD saturation and/or nonlinearity). Upon exclusion of such portions of the image the remaining regions represent a quantitation mask. This quantitation mask is applied to subsequent images obtained following exposure of the field to BoNT/B. In this fashion data is selectively obtained only from cells expressing the reporting construct at the desired level or within a desired range. Such selective collection of data from relevant portions of the test area can reduce interference from scatter and background fluorescence, and advantageously reduce variation and/or improve sensitivity.

[0068] A self-correcting intensity value can be obtained from images processed in this fashion by combining pixel intensity values with the total area included within the quantitation mask. For example, average pixel intensity throughout the quantitation mask can be multiplied by the area of the quantitation mask to derive a fluorescence intensity for that image. Fluorescence intensity values obtained from a given field after exposure to BoNT/B can be compared to fluorescence intensity values obtained prior to exposure to BoNT/B, and the result used to accurately estimate the effect of BoNT/B on the distribution and/or degradation of a fluorescent peptide released from the reporting construct by BoNT/B activity. Such values can be further normalized through the use of similar measurements obtained from fluorescent peptides that are not released by BoNT/B activity. Such an embodiment can be used in methods for quantifying or otherwise characterizing BoNT/B activity, for example by comparing results obtained from an unknown sample to results obtained from a set of samples containing known amounts of BoNT/B.

[0069] Alternatively, such a method can be used to identify cell lines and/or constructs that are suitably responsive to BoNT/B, with subsequent characterization of BoNT/B being carried out by methods that use such cell lines and/or constructs and acquire data using a conventional, non-imaging fluorometer. It should be appreciated that such a characterization method is generally applicable to cell-based assays and other assays where results are variable and localized to specific areas (which may or may not be randomly positioned within an observed field) within an image, and is not restricted to use with cells and/or BoNT/B. It should also be appreciated that such a characterization method can be effectively applied when only a portion of the potential test sites (for example, cells) are functional within the proscribed test parameters. For example, a characterization method of the inventive concept can be applied to a field containing transformed cells that express a reporting construct, where less than 90%, less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, or less than 10% of the cells in the field express the reporting construct at levels that are suitable for use in an assay.

[0070] In some embodiments of the inventive concept, a quantitation mask-based imaging method as described above can be used as a primary assay. In other embodiments of the inventive concept such a quantitation-mask based imaging method can be used to identify populations of cells, cell types, reporting construct configurations, or combination thereof that produce an acceptable result. Once identified such optimized cell-based reagents can be used as the basis of a non-imaging method where fluorescence data is gathered using a conventional (e.g. microwell plate) fluorometer that does not have imaging capability, but rather quantifies total fluorescence of a testing region.

EXAMPLES

[0071] A series of reporting peptide construct pairs were prepared, where each reporting peptide construct included a synaptobrevin (Vamp2) portion coupled to the carboxyl terminus of either a YFP peptide or a CFP peptide. This arrangement is shown schematically in FIG. 15A. Variations on this basic architecture inserted a degron sequence into a peptide sequence coupled to the N terminus of the YFP peptide (see FIG. 15B) to generate a series of degron-containing reporting constructs. Designations and degron content of the YFP-bearing constructs are shown in Table 2. The YFP constructs were paired with a common CFP-bearing construct (SEQ ID NO. 21) that did not include a degron sequence to provide the reporting peptide construct pairs. In this example the CFP-bearing construct (SEQ ID NO. 21) includes point mutations that prevent cleavage by BoNT/B (e.g. D64N, D65N, D68N, Q76V) while preserving the majority of the VAMP2 sequence and structure. As a result the CFP portion of the CFP-bearing construct remains localized in transformed cells and is not degraded at an accelerated rate following exposure to BoNT/B activity.

TABLE-US-00002 TABLE 2 Degron Sequence Designation None (Control) pMD0185 (SEQ ID NO. 20) Bonger pMD0189 (SEQ ID NO. 11; SEQ ID NO. 22) iNOS pMD0190 (SEQ ID NO. 23) p53 pMD0191 (SEQ ID NO. 9) SNAP-25 pMD0192 (SEQ ID NO. 10)

[0072] Neuro2A (neuroblastoma) cells were seeded in EMEM+10% FBS at 2.0×10.sup.4 cells per well in 96 well poly D-lysine coated tissue culture plates. The cells were allowed to recover for 18 (±2) hours. Cells were then washed with 100 μL serum-free EMEM following by a 30 minute incubation in serum-free EMEM (100 μL per well). Transfection reagents were prepared by preparing two 1.5 mL Eppendorf tubes as follows: Tube A—0.5 mL serum-free EMEM and 2.8 mg of plasmid DNA; Tube B— 0.5 mL serum-free EMEM and 7.0 μL of lipofectamine 2000™ (Life Technologies). Tubes A and B were incubated at room temperature for 5 minutes, then mixed with one another incubated for an additional 20 minutes. 25 μL of this transfection mixture was added to a well containing cells in order to provide a transient transfection.

[0073] Cells were incubated with the transfecting DNA for 18 hours, then treated with BoNT/B for 48 hours. Cells were imaged using a GE InCell™ automated cell imager at 10λ objective using brightfield, YFP, and CFP filter sets. Following this imaging the plates were washed with PBS in an automated plate washer and fluorophore emission intensities characterized using a Tecan F500™ plate reader.

[0074] FIG. 16A shows a photomicrograph of cells expressing the control (i.e. no degron sequence) reporting construct in the presence and absence of BoNT/B. Emissions from YFP and CFP fluorescent peptides are shown. In the absence of BoNT/B, YFP emission is localized in vesicles. In the presence of BoNT/B YFP emissions are re-localized, with diffusion of a YFP-containing peptide apparent throughout the cell. Localization of the CFP containing construct does not change due to the presence of point mutations that prevent cleavage by BoNT/B activity. FIG. 16B shows overall fluorescence emission from such cells as characterized using a fluorescence plate reader. Non-transfected cells were also characterized. As shown, YFP emission is sharply reduced in transformed cells exposed to BoNT/B, whereas CFP emission is relatively unaffected (the means of individual measurements at different BoNT/B concentrations falling within the variation of those measurements). As a result the results of YFP emission to CFP emission ratios parallel those of YFP emission.

[0075] FIGS. 17A to 17C show the results of fluorescence measurements made from non-transformed cells, cells transformed to express a control (i.e. not containing degron) reporting construct pair, and cells transformed to express reporting construct pairs in which the YFP-bearing construct included a degron sequence positioned towards the N-terminus relative to the YFP peptide. FIG. 17A shows the results of measurements of YFP emission in the presence and absence of BoNT/B. FIG. 17B shows the results of measurements of CFP emission in the presence and absence of BoNT/B. FIG. 17C shows the results of measurements of YFP fluorescence:CFP fluorescence ratio in the presence and absence of BoNT/B. Results are summarized below in Table 3. It is apparent that inclusion of degron sequences (e.g. iNOS and/or p53 degron sequences) positioned N-terminally from the YFP portion of the YFP-bearing member of the reporting construct pair can provide improved dynamic range in a BoNT/B cell-based assay, relative to cells transformed using an analogous construct pair lacking the degron sequence.

TABLE-US-00003 TABLE 3 Vehicle Only 100 nM BoNT/B Dynamic Construct (YFP:CFP ratio) (YFP:CFP ratio) Range pMD0185 3.90 1.78 2.20 (no degron) pMD0189 1.82 1.04 1.75 (Bonger) pMD0190 2.17 0.74 2.93 (iNOS) pMD0191 3.63 0.89 4.09 (p53) Dynamic Range = (YFP:CFP emission ratio with vehicle-only) ÷ (YFP:CFP emission ratio with vehicle + 100 nm BoNT/B)

[0076] FIGS. 18A to 18C show the results of similar studies performed using an additional set of cells transformed using a reporting construct pair that incorporates a degron sequence from SNAP-25 positioned towards the N-terminus relative to the YFP peptide. FIG. 18A shows the results of measurements of YFP emission in the presence and absence of BoNT/B. FIG. 18B shows the results of measurements of CFP emission in the presence and absence of BoNT/B. FIG. 18C shows the results of measurements of YFP fluorescence:CFP fluorescence ratio in the presence and absence of BoNT/B. Results are summarized below in Table 4. It is apparent that inclusion of degron sequences (e.g. iNOS, p53, and/or SNAP-25 degron sequences) positioned N-terminally from the YFP portion of the YFP-bearing member of the reporting construct pair can provide improved dynamic range in a BoNT/B cell-based assay, relative to cells transformed using an analogous construct pair lacking the degron sequence.

TABLE-US-00004 TABLE 4 Vehicle Only 100 nM BoNT/B Dynamic Construct (YFP:CFP ratio) (YFP:CFP ratio) Range pMD0185 3.80 1.99 1.91 (no degron) pMD0189 2.02 1.23 1.64 (Bonger) pMD0190 2.04 0.76 2.70 (iNOS) pMD0191 2.90 0.96 3.01 (p53) pMD0192 2.77 0.91 3.03 (SNAP-25) Dynamic Range = (YFP:CFP emission ratio with vehicle-only) ÷ (YFP:CFP emission ratio with vehicle + 100 nm BoNT/B)

[0077] Surprisingly, Inventors have found that inclusion of a degron sequence position N-terminally to a fluorescent peptide portion of a reporting construct can modify cytosolic relocalization of the fluorescent peptide on release from the reporting construct (for example, by proteolytic activity of a botulinum neurotoxin). This is evident in the photomicrographs shown in FIGS. 19A and 19B. FIG. 19A shows brightfield, YFP emission, and CFP emission from transformed cells expressing a control reporting construct pair (containing no degron sequence) and transformed cells expressing reporting construct pairs that include degron sequences (specifically, Bonger or iNOS degron sequences) positioned N-terminally to the YFP peptide of the YFP-bearing member of the reporting construct pair. Images were taken in the presence and in the absence of BoNT/B. The cells carrying the pMD0190 constructs (which showed improved dynamic range relative to control cells on exposure to BoNT/B) showed reduced YFP fluorescence and less cytosolic relocalization of YFP-bearing peptide than control cells following exposure to BoNT/B. FIG. 12B shows the results of similar studies performed using cells carrying either the pMD0191 or pMD0192 reporting construct pairs, both of which show improved dynamic range on exposure to BoNT/B relative to control cells. The cells carrying the pMD0191 and pMD0192 constructs also showed reduced YFP fluorescence and less cytosolic relocalization of YFP-bearing peptide than control cells following exposure to BoNT/B.

[0078] Results of application of BoNT/B at different concentrations to cells expressing a control BoNT/B-reactive construct pair lacking a degron sequence and cells expressing analogous BoNT/B-reactive construct pair where the YFP-bearing peptide includes a degron sequence are shown in FIG. 20. In such assays increasing BoNT/B concentrations are associated with a decreasing YFP emission, which results in a decreasing YFP emission:CFP emission ratio. As shown, cells expressing the control construct pair (pMD0185) reach maximum emission ratio (indicating assay saturation) at approximately 1 nM BoNT/B. Cells expressing a p53 degron-containing construct, however, do not reach assay saturation until approximately 10.sup.−2 nM BoNT/B, indicating a substantial improvement in sensitivity.

[0079] In some embodiments, methods described above can be performed manually. In other embodiments, certain aspects of a method (for example, sample and/or reagent dispensing, transportation of labware in and out of an incubator, etc.) can be performed in an automated fashion, while other aspects can be performed manually. In other embodiments a method of the inventive concept essentially all of the steps of the method can be performed in an automated fashion, for example through the use of a programmable laboratory robot.

[0080] It should be apparent to those skilled in the art that many more modifications besides those already described are possible without departing from the inventive concepts herein. The inventive subject matter, therefore, is not to be restricted except in the spirit of the appended claims. Moreover, in interpreting both the specification and the claims, all terms should be interpreted in the broadest possible manner consistent with the context. In particular, the terms “comprises” and “comprising” should be interpreted as referring to elements, components, or steps in a non-exclusive manner, indicating that the referenced elements, components, or steps may be present, or utilized, or combined with other elements, components, or steps that are not expressly referenced. Where the specification claims refers to at least one of something selected from the group consisting of A, B, C . . . and N, the text should be interpreted as requiring only one element from the group, not A plus N, or B plus N, etc.