Low Density Microarrays for Vaccine Related Protein Quantification, Potency Determination, and Efficacy Evaluation

Abstract

Methods for the quantification of influenza HA proteins and anti-influenza antibodies for the fields of vaccine-related protein quantification, potency determination, and efficacy evaluation are provided. According to the technology, quantification is achieved by providing capture agents attached to an array in a series of decreasing concentrations. Serial dilutions of a reference material also may be introduced. The reference material within each solution binds to the capture agents on the array and is labeled with a label agent capable of producing a detectable signal used to construct a calibration curve. A target material of unknown concentration is introduced to a separate identical array, and the target material binds to the capture agents and also is labeled by a label agent to produce a detectable signal. The calibration curve based on the reference material is then utilized to determine the concentration of the target material without the need to perform replicate experiments.

Claims

1-15. (canceled)

16. A system for quantification of an amount of influenza hemagglutinin (HA) target protein present in a sample, comprising: a solid support; a plurality of capture agents affixed to said solid support, wherein: said plurality of capture agents bind influenza HA, said plurality of capture agents are affixed to the solid support in a plurality of discrete areas in an array, said discrete areas each containing only a single unique capture agent; said plurality of capture agents comprise: a first anti-influenza A H1 antibody capture agent; a second anti-influenza A H3 antibody capture agent; and a third anti-influenza B antibody capture agent; or sialic acid glycopeptides or proteins; at least one label agent to produce a detectable signal indicative of binding between said plurality of capture agents and the influenza HA target.

17. (canceled)

18. The system of claim 16, wherein the at least one label agent binds target influenza hemagglutinin A H1N1 and A H3 and influenza B.

19. The system of claim 16, wherein at least one of said capture agents is a universal anti-influenza antibody and the at least one label agent binds target influenza hemagglutinin.

20. (canceled)

21. (canceled)

22. The system of claim 16, wherein said plurality of discrete areas are arranged in a configuration of decreasing concentration of said capture agents.

23. The system of claim 16, wherein the label agent is a fluorescent, colorimetric, electrical or magnetic label.

24. The system of claim 16, further comprising a calibration curve to quantify influenza HA in the sample from the detected signal.

25. The system of claim 24, wherein the calibration curve is based on a magnitude of detectable signal created by binding between a standard influenza antigen and the capture agents.

26. The system of claim 16, wherein said anti-influenza A H1 antibody capture agent is a monoclonal antibody specific to influenza A H1.

27. The system of claim 26, wherein the influenza A H1 is influenza A H1N1.

28. The system of claim 16, wherein said anti-influenza A H3 antibody capture agent is a monoclonal antibody specific to influenza A H3.

29. The system of claim 28, wherein the influenza A H3 is influenza A H3N2.

30. The system of claim 16, configured for use with a sample comprised of material from an influenza vaccine production process.

31. The system of claim 16, further comprising at least one positive control and at least one negative control affixed to the solid support.

32. The system of claim 16, wherein the capture agents comprise 2,6 and 2,3 sialic acid glycopeptides or proteins.

33. The system of claim 16, wherein the capture agents comprise: the first anti-influenza A H1 antibody capture agent; the second anti-influenza A H3 antibody capture agent; and the third anti-influenza B antibody capture agent.

34. The system of claim 16, comprising a plurality of label agent species, with each species specific to a unique target protein.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0016] A better understanding of the technology of the present application will be had upon reference to the following detailed description read in conjunction with the accompanying drawings. In the accompanying drawings, like reference characters refer to like parts throughout, and wherein:

[0017] FIG. 1 is a representative array layout of the current invention including serial dilutions of two unique capture sequences, a positive control, a negative control, and a spotting control

[0018] FIG. 2 is a schematic representation of the binding curves generated from reference material(s) and target used to construct a calibration curve and subsequently determine the unknown concentration of target

[0019] FIG. 3 illustrates a single capture event on an array involving an antibody as capture agent, antigen as target or reference material, and a fluorescently labeled antibody as a label agent

[0020] FIG. 4 is a fluorescence image of an array containing serial dilutions of an anti-human influenza A H3 antibody as capture agent, purified influenza HA H3 antigen as reference material, and a fluorescently labeled universal antibody as label agent

[0021] FIG. 5 is a binding curve obtained from the analysis of the detectable fluorescence signals obtained after exposing the array represented in FIG. 4 to 0.5 g/mL of H3 HA reference material.

[0022] FIG. 6 is a linear regression obtained by plotting the normalized maximum signal obtained for serial dilutions of HA reference material added to identical replicate arrays

[0023] FIG. 7 illustrates a single capture event on an array involving a glycopeptide or glycoprotein as capture agent, influenza HA from a vaccine as target or reference material, and a fluorescently labeled universal antibody or antibody fragment as a label agent

[0024] FIG. 8 illustrates a single capture event on an array involving HA antigen as capture agent, an anti-influenza antibody as target or reference material, and a fluorescently labeled universal antibody or antibody fragment as a label agent

DETAILED DESCRIPTION

[0025] As mentioned previously, the technology of the present application relates to methods for improved vaccine-related protein quantification, potency determination, and efficacy evaluation using an array-based format in which serial dilutions of an appropriate capture agent are printed. Detectable signals from replicate arrays contacted with different concentrations of a reference material are analyzed, and the maximum signal achieved for each concentration determined from a non-linear regression to the binding curve data is then used to construct a one-time calibration curve; the calibration curve can then be used to quantify a target material after a single concentration of said target material has been contacted with a replicate array and a detectable signal is produced. The technology of the present application provides significant advantages over the current state of the art methods in that a single concentration of target material(s) can be used to obtain the concentration of said target material(s) due to array encoded serial dilution of the capture agent, and that the quantification of multiple targets can be achieved in a single assay due to the multiplexing capability of an array-based approach. Moreover, while the technology of the present application is described in relation to influenza, one of ordinary skill in the art will understand on reading the present application that the technology may be used for many different viral proteins, and other protein biomarkers. Additionally, the below detailed description of the technology of the present application is provided with regard to certain exemplary embodiments. The word exemplary is used herein to mean serving as an example, instance, or illustration. Any embodiment described herein is not necessarily to be construed as preferred or advantageous over other embodiments. If a single exemplary embodiment is provided for completeness, it is not to be concluded that no other embodiments are possible. Moreover, all embodiments described herein should be considered exemplary unless otherwise stated.

[0026] For the purposes of the present application, an array refers to any solid support onto which a specific arrangement of capture agents can be placed onto one or more of its surfaces. The solid support can be constructed of but is not limited to glass, plastic, silicon-coated substrate, macromolecule-coated substrate, membrane or filter material, metal, particles or microparticles, beads or microbeads, magnetic or paramagnetic beads, or a variety of other materials known to those skilled in the art. In one embodiment of the current invention, the arrangement of capture agents upon said array are in discrete regions or locations, with each region or location containing only one specific capture agent, so as to create a specific pattern or configuration of capture agents. While provided in discrete regions or locations in the exemplary embodiments, in certain embodiments the capture agents may be provided in a contiguous region having delineated concentrations or the like.

[0027] In reference to the present application, a capture agent refers to anything that can be immobilized on the surface of said array that will capture or bind to a target material. For the purposes of the current invention, capture agents include any number of biological molecules including proteins, monoclonal and polyclonal antibodies, antisera, antigens, polypeptides, viral epitopes, cell membrane receptors, glycoproteins, glycopeptides, sugars, and other similar species known to those skilled in the art. In one embodiment of the technology, capture agents are designed to bind appropriate reference and target materials from a solution applied to the array for the purposes of detecting the presence and quantity of said reference and target materials.

[0028] For the purposes of the present application, reference material refers to any material of known concentration that can be used to construct a calibration curve based on the magnitude of detectable signals created by the binding event between capture agent(s) and reference material(s). As a non-limiting example, in the present application, reference material may refer to a standard influenza antigen from which a calibration curve of influenza hemagglutinin (HA) concentration can be created. As another non-limiting example, reference material may refer to standard anti-influenza antibody/antibodies from which a calibration curve of antibody concentration can be created.

[0029] A target material, for the purposes of the present application, is a material from the same family as the reference material (e.g. as a non-limiting example, both the reference and target materials are influenza HA antigens or are both anti-influenza antibodies) that is present at an unknown concentration and whose concentration can be quantified by utilizing a calibration curve constructed from a reference material.

[0030] For the purposes of the present application, a label agent is any species that can be utilized to detect the presence of target material on an array by exhibiting a detectable signal. For the purpose of the present application, a label agent could be an antibody capable of binding to the target agent that is either directly conjugated to a fluorescent molecule or entity, or conjugated to another moiety capable of subsequently binding to a fluorescent molecule or entity. In addition, a label agent could be a fluorescent molecule designed to be incorporated directly into the target agent by means known to those of ordinary skill in the art. In other embodiments of the technology, the detectable signal is based on a property other than fluorescence, including absorbance, chemiluminescence, electrical signal, or other signal types known to those skilled in the art.

[0031] The illustrative example shown in FIG. 1 details a typical layout of an array 100 of the present application. In one embodiment of the technology, a spotting control 102 is utilized to provide spatial orientation. Advantageously, the spotting control can also be utilized to normalize the detectable signals from the reference and target materials. In FIG. 1, with exception of the spotting control, all other capture agents 104 spotted on the array are spotted in triplicate (3 contiguous spots in a row). In another embodiment as shown in FIG. 1, the array 100 layout also contains a positive control 106 designed to validate the assay is functioning properly. In yet another embodiment as shown in FIG. 1, a negative control capture agent 108 (designed not to bind to the reference or target agents) is also included to determine if non-specific binding is occurring. In other words, if the negative control provides a detectable signal, the results of the array 100 are suspect. Advantageously, each dilution within a dilution series of a particular capture agent is spotted in triplicate in a defined configuration. FIG. 1 shows a non-limiting example in which two unique capture agents are spotted on the array. Each dilution within the series is spotted in triplicate. Advantageously, the dilution series of the capture agent(s) covers a broad concentration range that encompasses all key regions of a binding curve. In another embodiment of the technology, the array can be spotted within a flat-bottomed 96 well plate or other methods conventionally known to those of ordinary skill in the art for easy integration into existing laboratory systems. Regardless of the particular nature of the capture agent, reference, and target agents, a similar array layout can be used.

[0032] In current state of the art immunoassays, such as SRID or ELISA, the unknown target antigen concentration is determined from the linear portion of the calibration curve constructed from a serial dilution of a known, or standard, antigen concentration. The key mathematical relationships are described in Equations 1 and 2 below:

S.sub.kn=m.sub.knC.sub.kn+S.sub.o(Equation 1)

C.sub.unkS.sub.unk/m.sub.kn(Equation 2)

where in Equation 1, S.sub.kn is the detectable signal from a standard as a function of known concentration (C.sub.kn), m.sub.kn is the slope of the linear portion of the calibration curve, and S.sub.o is the background signal. Once the calibration curve is constructed, a serial dilution of the unknown is also analyzed to ensure that the signal is within the linear portion of the calibration curve. For those dilutions in the linear range, the unknown concentration can be obtained from the relationship shown in Equation 2, where C.sub.unk is the unknown antigen concentration, S.sub.unk is the signal for the unknown antigen concentration, and m.sub.kn is the slope of the linear portion of the calibration curve.

[0033] In contrast to the above mentioned SRID and ELISA methods, the technology of the present application provides a method for which the analysis of a single concentration of unknown target material results in a complete binding curve. Consider the binding curve obtained for a single concentration of target or reference material shown pictorially in FIG. 2A and described by Equation 3 below:

[00001]$\begin{array}{cc}S=S_o+\frac{S_{\max }}{1+{\left(C_{\mathrm{im}}\right)}^A}& \left(\mathrm{Equation}.Math..Math.3\right)\end{array}$

[0034] where S is the signal from the single concentration of target or reference material as a function of immobilized capture agent concentration (C.sub.im), S.sub.o is the background signal, S.sub.max is the maximum value of the signal obtained, and A is related to the slope of the binding curve. The maximum signal (S.sub.max) extracted from a non-linear regression to the data is directly proportional to the target or reference concentration and is used for quantification, rather than relying on the slope. Several dilutions of a reference material of known concentrations are prepared and applied to replicate arrays, and the binding curves for the reference material (dotted, dashed, and dash-dotted Reference material binding curves shown in FIG. 2A) are then used to construct a calibration curve by subsequently plotting S.sub.max versus C.sub.kn, as graphically illustrated in FIG. 2B. A single concentration of target material is then applied to a replicate array, a non-linear regression to the data is applied, and the maximum value (S.sub.max) obtained (solid black Target material binding curve in FIG. 2A). The equation of the calibration curve can then be used to solve for the unknown concentration of target material.

[0035] The technology of the present application is advantageous over the state of the art methods for a number of reasons. One reason is that all signals can be normalized to an internal reference (S.sub.iref) that is encoded on the array. As a non-limiting example, the spotting control shown in FIG. 1 can be used as S.sub.iref. Specifically, the S.sub.max value is divided by S.sub.iref (i.e., S.sub.max-norm=S.sub.max/S.sub.iref) to yield a signal normalized for random experimental variables (e.g., chip to chip variations). The ramification of this advantage is that the current method does not require a complete serial dilution of the standard for each batch of samples analyzed. In principle, for a given set of experimental conditions (e.g., influenza HA from recombinant baculovirus expression), a single serial dilution of the standard could be used to determine the concentration of large number of sample batches using S.sub.max-norm in a calibration curve (see FIG. 2B).

[0036] In another embodiment, numerous capture agents could be immobilized on the array to take advantage of multiplexing, allowing multiple target antigens (for example, HA antigens from influenza A H1N1, influenza A H3N2, and influenza B) could be quantified simultaneously in a multiplex analysis, thereby dramatically reducing the total number of assays required to quantify the targets of interest. This specific example could be utilized in potency determination in yearly trivalent influenza vaccines to speed the development time.

[0037] Several non-limiting examples follow to further explain and illustrate the advantages of the technology over the state of the art.

[0038] Quantification of Influenza HA Using Strain-Specific Capture Antibodies for Influenza Vaccine Potency Determination

[0039] In an illustrative example of the technology of the present application, subtype-specific monoclonal antibodies against influenza A H3 HA and influenza A H1 HA (Meridian, catalog #C01318M and #C86304M) were printed onto aldehyde-functionalized glass slides in the layout illustrated in FIG. 1, with the anti-H3 antibody represented by Capture Agent 1 (104, left-hand side of array layout) and the anti-H1 antibody represented by Capture Agent 2 (104, right-hand side or array layout). The general detection scheme for this example is schematically shown for a single binding event is shown in FIG. 3. For reference, FIG. 3 provides an exemplary array 300 consistent with the technology of the present application. Array 300 having a discretely located capture agent 302. The capture agent 302 binds in this exemplary embodiment to the HA antigen 304. An antibody label agent 306 binds the HA antigen 304 to a fluorescent label 308, which is capable of detection as is generally known in the art.

[0040] Serial dilutions of H3 hemagglutinin (HA) antigen from the influenza A H3N2 strain A/Wy/3/2003 (Protein Sciences Corporation, Meriden, Conn.) in phosphate buffer were each incubated on separate replicate microarrays at room temperature for 1 hr. After subsequent washing, the captured HA antigen was labeled with a universal biotinylated anti-HA antibody fragment (Sigma Aldrich, catalog # B9183) followed by a Cy3-labeled streptavidin at 1.2 g/mL. The universal antibody label utilized was raised against a universal HA peptide often used as a tag in recombinant proteins, and has demonstrated response to a conserved region of both native and denatured HA.

[0041] A representative fluorescence image for a single H3 HA concentration applied to the array (0.5 g/mL) is shown in FIG. 4. The normalized signal intensity from the fluorescence image as a function of the spotted anti-H3 antibody concentration was fit to Equation 3 using non-linear regression and the maximum signal achieved determined, as shown in FIG. 5. Only a limited range of HA concentrations were examined for this example, and the maximum signals determined for these different concentrations are plotted in FIG. 6. As expected, the extracted S.sub.norm value (plotted on the y-axis of FIG. 6) for this limited range of H3 HA concentrations is linear as determined by regression. It is anticipated from extrapolation that the quantification of the technology of the present application should be below 0.1 g/mL. Considering that the currently used SRID assay has a quantification limit of 2-5 g/mL, the technology of the present application would have an improved limit of detection over current state of the art methods and therefore provide benefits over the current state of the art to vaccine manufacturers.

[0042] Quantification of Influenza HA using Universal Capture Agent(s) for Influenza Vaccine Potency Determination

[0043] As previously mentioned, the traditional SRID assay requires the development and use of well characterized standard reference antibodies and antigens for each new strain of influenza produced. Since influenza viruses continually evolve, new standards must be produced in response to the emergence of each seasonal virus. Thus, the generation of these standard materials (e.g., antibodies and antigens) often represent a bottleneck in influenza vaccine development. Vaccine manufacturers must often wait to obtain reference materials from the Center for Biologics Evaluation and Research (CBER).

[0044] In one embodiment of the technology described herein, stable and universal standards used as capture agent(s) on an array for determination of influenza vaccine potency would streamline vaccine production by reduction of wait time for new reference antibodies and antigens and allow for improved quality control and assurance through historical trends with respect to a single reference standard (rather than relying on new unique standards each year for each strain of virus).

[0045] In another embodiment of the technology described herein, 2,6 and 2,3 sialic acid glyopeptides or proteins are used as capture agents to determine influenza vaccine potency. In the influenza viral infection process, influenza HA on the surface of the virus particle binds to sialic acid receptors on the host cell surface. It is well-known that influenza viruses from different host species vary in their affinity for sialic acid receptors with different linkages. Specifically, influenza viruses that replicate in humans selectively bind to the 2,6 sialic acid found on the surface of human respiratory epithelial cells, whereas influenza viruses that replicate in birds selectively bind to the 2,3 sialic acid found on the surface of epithelial cells found in the waterfowl gut.

[0046] Typical gold standard potency assays are based on the two irresolvable experimental parameters of concentration and binding constant. By utilizing the ratio of detectable signals produced on an array for the two types of receptors, the concentration and binding constant can be separated. As a non-limiting example, with 2,6 and 2,3 sialic acid glyopeptides or proteins, the relative binding strength of a target HA to both types of sialic acid glycopeptides or glycoproteins could be measured in a single assay. Mathematically, if we neglect the labeling step, the separation of variables can be shown by:

S.sub.max,2,6K.sub.2,6[C.sub.HA](Equation 4)

and

S.sub.max,2,3K.sub.2,3[C.sub.HA](Equation 5)

where S.sub.max is the maximum signal obtained from a binding curve as described in Equation 3, K.sub.x is the binding constant, and C.sub.HA is the concentration of HA in solution applied to the microarray. Since the concentration of HA for both is the same, the relationship below follows:

[00002]$\begin{array}{cc}\frac{S_{\max ,2,6}}{S_{\max ,2,3}}\frac{K_{2,6}}{K_{2,3}}& \left(\mathrm{Equation}.Math..Math.6\right)\end{array}$

[0047] This ratio may be a more direct measurement of vaccine potency, as a theoretical quantitative value can be determined from insight into cell receptor composition for each species (e.g. -2,6 for human, -2,3 for avian, and a mixture of receptors, therefore an intermediate ratio, for swine). As a non-limiting example, optimal potency of a human influenza vaccine would produce a high signal ratio in Equation 6 due to the much higher binding constant for HA to the human -2,6 sialic acid (K 2,6K 2,3).

[0048] To overcome the limitations associated with the current gold standard SRID assay, a sialic acid glycoprotein(s) or glycopeptide(s), in combination with a strain-independent label, can be developed, fully characterized, and used as a universal reference for determining influenza vaccine potency. The detection scheme for this non-limiting example is schematically illustrated in FIG. 7, where an immobilized glycopeptide or glycoprotein acts as capture agent. Serial dilutions of -2,6 and -2,3 sialic acid glyopeptide(s) or protein(s) are configured in an array. Influenza HA antigen is allowed to bind to the array and is subsequently labeled with a label agent. In one embodiment of the current invention, the label agent is a fluorescently tagged, strain-independent anti-HA antibody fragment (such as monoclonal anti-HA # H9037 from Sigma Aldrich). For reference, FIG. 7 provides an array 700 consistent with the technology of the present application. Discretely located on array 700 are a series of glycopeptides or glycoprotein capture agents 702 that capture or bind an associated HA antigen 704. An antibody label agent 706 binds the HA antigen 704 to a fluorescent label 708, which is capable of detection as is generally known in the art.

[0049] Hemagglutinin Inhibition Assay on an Array for Influenza Vaccine Efficacy Determination

[0050] As previously mentioned, the principle of the hemagglutinin inhibition (HI) assay is that antibodies will prevent the agglutination of red blood cells by influenza viruses. For influenza viruses, agglutination refers to the process whereby the virus binds to sialic acid receptors on cell surfaces and can cause the cells to aggregate around the virus. Aggregation leads to cell complexes that prevent red blood cells from settling to the bottom of a well. The assay is conducted by serial dilution of patient serum mixed with a specific concentration of virus and red blood cells whereby the highest dilution of the patient serum that prevents hemagglutination is the HI titer value.

[0051] To overcome the aforementioned limitations associated with the current gold standard HI assay for influenza vaccine efficacy, a reference standard of influenza hemagglutinin (HA) is used as a capture agent where serial dilutions of the HA standard(s) is/are configured onto an array under carefully controlled and reproducible conditions. The array of HA antigen(s) is then used to quantify antibodies in serum obtained from a patient that are developed in response to an influenza vaccination. The detection scheme for this non-limiting example of the current invention is illustrated in FIG. 8, where standard HA antigen is used as a capture agent. HA antigen is configured onto an array, antibodies produced in response to the vaccination from patient serum are captured on the array, and the captured antibodies are subsequently labeled with a label agent to produce a detectable signal. In the current non-limiting example, the label agent is a fluorescently tagged anti-human antibody. The patient produced antibodies are quantified by the value of S.sub.max-norm mapped to a calibration curve generated by serial dilutions of a reference antibody, similar to the process described previously and schematically represented in FIG. 2. Advantages of this example of the current invention are the quantitative nature of the assay where if the binding constant is known, the concentration determined can be expressed in absolute terms and compared to results from other common measurements of protein quantification (e.g. pg/mL or moles/mL). In addition, this example produces a rapid time to result, is automatable, and eliminates the use of red blood cells the assay. For reference, FIG. 8 provides an array 800 consistent with the technology of the present application. Discretely located on array 800 are a series of HA antigen capture agents 802 that capture or bind an associated target material 804, which is an antibody in this exemplary embodiment. An antibody label agent 806 binds the target material 804 to a fluorescent label 808, which is capable of detection as is generally known in the art. Unless otherwise indicated, all numbers or expressions, such as those expressing dimensions, physical characteristics, etc. used in the specification are understood as modified in all instances by the term approximately. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the claims, each numerical parameter recited in the specification or claims which is modified by the term approximately should at least be construed in light of the number of recited significant digits and by applying ordinary rounding techniques. Moreover, all ranges disclosed herein are to be understood to encompass and provide support for claims that recite any and all subranges or any and all individual values subsumed therein. For example, a stated range of 1 to 10 should be considered to include and provide support for claims that recite any and all subranges or individual values that are between and/or inclusive of the minimum value of 1 and the maximum value of 10; that is, all subranges beginning with a minimum value of 1 or more and ending with a maximum value of 10 or less (e.g., 5.5 to 10, 2.34 to 3.56, and so forth) or any values from 1 to 10 (e.g., 3, 5.8, 9.9994, and so forth).