Patent Application
20220128545
Hemostasis is a dynamic process driven by regulated events that culminate in the arrest of bleeding. Specialized surface receptors are at the forefront of this process contributing to platelet adhesion, activation, and aggregation. Flow cytometric analysis of platelets stained with receptor-specific monoclonal antibodies conjugated to fluorescent probes (fluorescence flow cytometry or FFC) is traditionally used in clinical and research settings to study changes in these platelet surface receptors as a means of assessing platelet activation and diagnosing patients with platelet disorders. A major drawback of FFC is that the number of parameters that can be simultaneously analyzed is inherently limited by emission spectra overlap.
Mass cytometry (MC) is a next generation flow cytometry platform that enables simultaneous phenotypic and functional analysis of multiple parameters on individual cells. MC overcomes the limitations associated with FFC by employing probes (e.g. antibodies, lectins, RNA probes, intercalators) that are conjugated to heavy metal isotopes, flow cytometric analysis of single-cells, and time-of-flight mass spectrometry as a detection technique. This enables mass cytometry to simultaneously detect a significantly greater number of cellular parameters than is possible by FFC. Consequently, MC can be used to subtype platelets in greater detail and to identify subpopulations of platelets that are common to healthy subjects and unique to particular platelet disorders or diseases.
In one aspect the invention provides a method of simultaneously detecting one or more biomarkers associated with one or more platelets in a platelet sample, the method comprising: contacting the sample with one or more metal-tagged probes or mixtures thereof that bind the one or more biomarkers; washing the sample to remove unbound probes; and analyzing the sample by MC to simultaneously detect binding of the one or more metal-tagged probes or mixtures thereof to one or more biomarkers associated with the one or more platelets; thereby simultaneously detecting the one or more biomarkers associated with the one or more platelets.
In another aspect the invention provides a method of identifying one or more subpopulations of platelets in a platelet sample, the method comprising: contacting the sample with one or more probes or mixtures thereof that bind one or more biomarkers associated with one or more platelets; washing the sample to remove unbound probes; analyzing the sample by MC to simultaneously detect binding of the one or more metal-tagged probes to the one or more biomarkers associated with platelets in the sample, thereby simultaneously detecting one or more biomarkers associated with one or more platelets in the sample; and classifying the platelets into one or more subpopulations based on the biomarkers detected; thereby identifying one or more subpopulations of platelets in a platelet sample.
In another aspect the invention provides a method of diagnosing a subject for a disease characterized by platelet abnormalities, the method comprising: contacting a platelet sample of the subject with one or more probes or mixtures thereof that bind one or more platelet biomarkers characteristic of the disease; washing the sample to remove unbound antibodies, ligands or mixtures thereof; and analyzing the sample by MC, thereby determining a level of the one or more biomarkers; and diagnosing the subject as having a disorder based on the level of the one or more biomarkers relative to one or more corresponding reference levels. In one embodiment, the method further comprises identifying in the subject a risk factor for a disease or complication thereof characterized by platelet abnormalities based on the level of one or more biomarkers relative to one or more reference levels.
In another aspect the invention provides a method for performing MC on a platelet sample, the method comprising contacting the sample with a panel comprising one or more probes or mixtures thereof that bind to one or more biomarkers associated with platelets in the sample; washing the sample to remove unbound probes; and analyzing the sample by MC.
In another aspect the invention provides a method of differentiating among two or more populations of platelets in a mixture of platelets wherein each population is derived from a different source, the method comprising: contacting a first population of platelets derived from a first source with a first set of one or more metal-tagged probes or mixtures thereof that bind to one or more biomarkers associated with the platelets in the first population; washing the first population of platelets to remove unbound probes or mixtures thereof; analyzing the first population of platelets by MC, thereby detecting the one or more biomarkers in the population of platelets; assigning a first biomarker profile to the first population of platelets; contacting a second population of platelets derived from a second source with a second set of one or more metal-tagged probes or mixtures thereof that bind to one or more biomarkers associated with the platelets in the second population; washing the second population of platelets to remove unbound probes or mixtures thereof; analyzing the second population of platelets by MC, thereby detecting the one or more biomarkers in the second population of platelets; assigning a second biomarker profile to the second population of platelets; contacting a mixture of the first and second population of platelets derived from different sources with the first and second set of one or more metal-tagged probes or mixtures thereof that bind to one or more biomarkers associated with the platelets in mixture; washing the mixture to remove unbound probes or mixtures thereof; analyzing the mixture by MC, thereby detecting one or more biomarkers in a mixture of platelets; and comparing the first and second biomarker profiles with a profile of the biomarkers detected in the mixture; thereby differentiating among two or more populations of platelets in a mixture of platelets wherein each population is derived from a different source.
In various embodiments the method further comprises differentiating between platelets received by transfusion and endogenous platelets in a platelet sample of a subject transfused with platelets, wherein the first population of platelets is derived from a sample of blood of the subject prior to transfusion, the second population of platelets is derived from a sample of platelets to be transfused, and the mixture of the first and second or populations of platelets is derived from a sample of blood of the subject post-transfusion; thereby differentiating between the platelets received by transfusion and the endogenous platelets in a platelet sample of a subject transfused with platelets.
In another aspect, the invention provides a method of assessing the suitability of a population of platelets for transfusion into a subject, the method comprising contacting a population of platelets to be transfused with one or more metal-tagged probes that bind to one or more biomarkers associated with the platelets; washing the population of platelets to remove unbound antibodies, ligands or mixtures thereof; analyzing the population of platelets by MC, thereby detecting the one or more biomarkers associated with the platelets to be transfused; assigning one or more classifications to the population of platelets in the sample based on the biomarkers detected to create a classified pre-transfusion sample; transfusing the subject with the classified pre-transfusion sample; obtaining a post-transfusion sample from the subject; identifying in the post-transfusion sample the platelets having one or more classifications assigned pre-transfusion; and comparing the level of metal-tagged platelets in the pre-transfusion sample with the level of metal-tagged platelets in the post-post transfusion sample; thereby assessing the suitability of a population of platelets for transfusion into a subject.
In various embodiments the biomarkers are present on the surface of the platelets.
In various embodiments the biomarkers are intracellular.
In various embodiments MC simultaneously detects binding of the probes to 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more or 14 or more biomarkers.
In various embodiments the probes bind one or more biomarkers selected from the group consisting of CD9, CD29, CD31, CD36, CD41, CD42a, CD42b, CD61, CD62P, CD63, CD107a, CD154, GPVI, activated integrin αIIbβ3 and mixtures thereof.
In various embodiments the method further comprises activating the platelets with thrombin receptor activating peptide (TRAP), thrombin, adenosine diphosphate (ADP), collagen, collagen-related peptide (CRP-XL), arachidonic acid, epinephrine, serotonin, histamine, convulxin, U46619, podoplanin or combinations thereof.
In various embodiments the sample is obtained from a subject after the subject receives a transfusion of platelets.
In various embodiments the method further comprises obtaining the sample from a subject.
In various embodiments the subject is a mammal.
In various embodiments the subject is a human.
In various embodiments the subject is a human subject exhibiting symptoms associated with a disease characterized by thrombosis or abnormal bleeding.
In various embodiments in the disease is selected from the group consisting of Glanzmann's thrombasthenia (GT), Hermansky-Pudlak syndrome (HPS),
In various embodiments the disease is GT and the characteristic biomarkers comprise CD41, CD61 and activated integrin αIIbβ3.
In various embodiments the method further comprises treating the subject having been diagnosed with GT.
In various embodiments treating the subject comprises providing the subject with factor VIIa.
In various embodiments the disease is HPS.
In various embodiments the method further comprises treating the subject having been diagnosed with HPS.
In various embodiments the method further comprises contacting the platelet sample of the subject with a panel comprising two or more metal-tagged probes that bind one or more biomarkers characteristic of the disorder.
In various embodiments the subject is a mammal.
In various embodiments the subject is a human.
In various embodiments the biomarkers comprise human leukocyte antigen (HLA) and/or human platelet antigen (HPA).
In another aspect the invention provides a composition comprising one or more metal-tagged probes that bind to one or more biomarkers selected from the group consisting of CD9, CD29, CD31, CD36, CD41, CD42a, CD42b, CD61, CD62P, CD63, CD107a, CD154, GPVI, activated integrin αIIbβ3 and mixtures thereof.
In various embodiments the one or more probes bind at least two biomarkers selected from the group consisting of CD9, CD29, CD31, CD36, CD41, CD42a, CD42b, CD61, CD62P, CD63, CD107a, CD154, GPVI, activated integrin αIIbβ3 and mixtures thereof.
In various embodiments the one or more probes bind at least three biomarkers selected from the group consisting of CD9, CD29, CD31, CD36, CD41, CD42a, CD42b, CD61, CD62P, CD63, CD107a, CD154, activated integrin αIIbβ3 and mixtures thereof.
In various embodiments the one or more probes bind each of the group consisting of CD9, CD29, CD31, CD36, CD41, CD42a, CD42b, CD61, CD62P, CD63, CD107a, CD154, GPVI, activated integrin αIIbβ3 and mixtures thereof.
In various embodiments the one or more metal-tagged probes bind to CD41, CD61 and activated integrin αIIbβ3.
In various embodiments, the one or more probes comprise IgM antibodies. In certain embodiments, the IgM is PAC1 (Shattil S J, Hoxie J A, Cunningham M, Brass L F. “Changes in the platelet membrane glycoprotein IIb-IIIa complex during platelet activation.” J. Bio. Chem. 1985; 260: 11107-14.) In certain embodiments, the IgM is conjugated to a metal-chelating polymer using a Maxpar Antibody Labeling Kit (http://maxpar.fluidigm.com/product-catalog-maxpar.php). In certain embodiments, the probe is PAC1-159Tb.
In various embodiments the invention provides a panel comprising two or more metal-tagged probes described herein or mixtures thereof.
In various embodiments the invention provides a method of making the panel, comprising labeling the two or more probes or mixtures thereof with a metal tag and assembling the labeled probes in an array.
In various embodiments the invention provides a kit comprising the panel and instructions for use.
In various embodiments the abnormalities are associated with an increased risk of thrombosis.
In various embodiments the abnormalities are associated with an increased risk for bleeding.
In various embodiments the disease is a metabolic disorder (e.g., diabetes), a cardiovascular disease, immune thrombocytopenia, sickle cell disease, a vascular anomaly, or cancer.
In various embodiments the platelet sample is obtained from a subject receiving at least one therapeutic agent.
In various embodiments the at least one therapeutic agent is a platelet inhibitor selected from the group consisting of abciximab, eptifibatide, tirofiban, aspirin, indomethacin, prostaglandin E1, theophylline, vorapaxar, clopidogrel and active metabolites thereof, prasugrel and active metabolites thereof, ticagrelor and active metabolites thereof, cangrelor and active metabolites thereof and mixtures thereof.
In various embodiments the method further comprises conducting the analyzing step before and after contact of the platelet sample with the therapeutic agent and assessing the difference in the presence or absence of biomarkers before and after contact with the therapeutic agent.
In various embodiments the one or more probes comprise one or more of an antibody, a ligand, a Fab fragment of an antibody, a chimeric or engineered antibody, lectins, an adhesive glycoprotein, a nucleotide or derivative thereof, an RNA probe, a reactive oxygen species or a phospholipid binder.
In various embodiments the phospholipid binder is annexin V or lactadherin.
In various embodiments the adhesive glycoprotein is selected from the group consisting of fibrinogen, fibronectin and von Willebrand factor.
In various embodiments, the one or more probes comprise IgM antibodies. In certain embodiments, the IgM is PAC1. In certain embodiments, the IgM is conjugated to a metal-chelating polymer. In a specific embodiment, the probe is PAC1-159Tb.
In another aspect, the invention provides PAC1-159Tb. In a related aspect, the invention provides a probe comprising PAC1-159Tb.
The following detailed description of various embodiments of the invention will be better understood when read in conjunction with the appended drawings. Certain embodiments are shown in the drawings for the purpose of illustrating the invention. It should be understood, however, that the invention is not limited to the precise arrangements and instrumentalities of the embodiments shown in the drawings.
Sub-populations:
A: CD62P−/CD154−/CD31−
B: CD62P−/CD154−/CD31+
C: CD62P−/CD154+/CD31+
D: CD62P+/CD154−/CD31−
E: CD62P+/CD154−/CD31+
F: CD62P+/CD154+/CD31−
G: CD62P+/CD154+/CD31+
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although any methods and materials similar or equivalent to those described herein can be used in the practice for testing of the present invention, certain advantageous materials and methods are described herein. In describing and claiming the present invention, the following terminology will be used.
It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
“About” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or ±10%, more preferably ±5%, even more preferably ±1%, and still more preferably ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.
“Biomarker” as used herein is a biological molecule found in blood, other body fluids, or tissues that is a sign of/characteristic of/associated with a normal or abnormal process, or of a condition or disease. A biomarker can be used to diagnose a subject as having a particular disease, disorder or complication thereof; to assess a subject as being a risk of developing a particular disease, disorder or complication thereof; and/or to see how well the body responds to a treatment for a disease, disorder, condition or complication thereof. Biomarkers as used herein are located on the surface of a cell or intracellularly, and include molecular markers, signature molecules, receptors, etc.
“Diagnosing” as used herein includes the identification of a disease/disorder from which a subject is suffering, predicting a certain clinical outcome, and/or identifying a subject as being at risk of developing a disease/disorder and/or complication thereof; e.g., identifying which patients with coronary artery disease are at increased risk of thrombosis; which patients may benefit from treatment with a specific drug; which patients are at risk of developing a disease/disorder or complication thereof, etc.
The term “platelet” as used herein includes naturally occurring platelets and synthetic or engineered platelets and platelet like particles, whether naturally occurring or synthetic/engineered.
As used herein, the term “probe” means a molecule that binds a biomarker and provides a detectable signal upon binding of a biomarker. By way of non-limiting example, the probe can be an antibody (natural or synthetic; e.g., chimeric or engineered), fragments thereof, a ligand and/or mixtures thereof that bind an intra- or extracellular molecule (e.g., receptor). The probes used herein can be metal tagged, meaning that they contain one or more heavy metal atoms that can be detected by MC. By way of non-limiting example, the heavy metal atom can be a lanthanide.
An “individual”, “patient” or “subject”, as that term is used herein, includes a member of any animal species including, but are not limited to, birds, humans and other primates, and other mammals including commercially relevant mammals such as cattle, pigs, horses, sheep, cats, and dogs. Preferably, the subject is a human.
“Instructional material,” as that term is used herein, includes a publication, a recording, a diagram, or any other medium of expression which can be used to communicate the usefulness of the composition and/or compound of the invention in a kit. The instructional material of the kit may, for example, be affixed to a container that contains the compound and/or composition of the invention or be shipped together with a container which contains the compound and/or composition. Alternatively, the instructional material may be shipped separately from the container with the intention that the recipient uses the instructional material and the compound cooperatively. Delivery of the instructional material may be, for example, by physical delivery of the publication or other medium of expression communicating the usefulness of the kit, or may alternatively be achieved by electronic transmission, for example by means of a computer, such as by electronic mail, or download from a website.
The term to “treat,” as used herein, means reducing the frequency with which symptoms are experienced by a subject or administering an agent or compound to reduce the frequency and/or severity with which symptoms are experienced. As used herein, “alleviate” is used interchangeably with the term “treat.”
As used herein, “treating a disease, disorder or condition” means reducing the frequency or severity with which a symptom of the disease, disorder or condition is experienced by a subject. Treating a disease, disorder or condition may or may not include complete eradication or elimination of the symptom.
As used herein, “biomarker profile” refers to a pattern of the levels of a set of biomarkers present in a population or sub-population of platelets that can be used to distinguish the platelets.
Values indicated throughout this disclosure can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range.
Without wishing to be limited by theory, the invention is based in part on the first use of MC to evaluate platelet surface glycoproteins and function. Since its introduction 30 years ago, FFC has been the gold-standard analytical tool to measure platelet surface antigens. The number of parameters simultaneously detected by FFC is, however, inherently limited by spectral overlap of fluorophore emissions. MC overcomes these limitations by employing metal-tagged antibodies and time-of-flight mass spectrometry to simultaneously analyze on individual cells an order of magnitude more platelet surface antigens than FFC. The invention provides a novel MC metal-tagged antibody panel for simultaneous analysis of 14 different platelet surface antigens. As shown in example 1, this panel and method were validated by (i) direct comparison against data obtained using FFC, (ii) changes in reactivity with agonist-stimulated vs. unstimulated platelets, (iii) inhibition with specific blocking reagents and (iv) reactivity with platelets genetically deficient in integrin αIIbβ3 (GT platelets). The optimized panel was used to study activation-dependent changes in surface antigen expression on healthy donor and GT patient platelets. MC revealed previously unappreciated subpopulations of platelets in healthy donors and novel alterations in surface glycoproteins on GT platelets.
Previous studies have tended to treat platelets as a single population. However, circulating platelets differ one from another with respect to their size, surface receptor expression glycosylation, granule content, response to agonist stimulation, and participation in thrombus formation. The factors contributing to this variability may include heterogeneity among platelet-producing megakaryocytes, differences relating to platelet age, and differences in exposure to local, in vivo activating conditions which may lead to changes in expression of surface molecules and desensitization to further activation. In patients with immune thrombocytopenia, increased surface P-selectin on some circulating platelets and decreased numbers of platelets that become positive for surface P-selectin and activated integrin αIIbβ3 is associated with more severe bleeding scores. Recent studies demonstrated a subpopulation of platelets that lack endothelial nitric oxide synthase (eNOS), fail to produce nitric oxide, and have a down-regulated soluble guanylate cyclase signaling pathway. As a result, this subpopulation of platelets showed greater adhesion to collagen, activation of αIIbβ3, and formed larger aggregates than eNOS-positive platelets.
Thus, ample evidence exists for variability among platelets in health and disease. However, until now, it has been difficult to determine whether variation in one platelet parameter corresponded to variation in other parameters, thereby defining distinct platelet subpopulations. This is primarily due to the inherent limitations of FFC, whereby the use of fluorescent probes restricts the number of parameters that can be simultaneously analyzed. The utility of MC and a custom platelet-specific metal-tagged antibody panel for identifying platelet subsets in healthy individuals is demonstrated in example 1 and the associated figures. After activation, most platelets, as expected, stained intensely for activated integrin αIIbβ3, CD62P and CD63, yet a subset of these platelets differed with respect to CD31 expression (
GT platelets were used to validate MC for assessing platelet function and to demonstrate the platform's power as a research tool. In agreement with previous findings, both MC and FFC demonstrated CD41, CD61 and activated αIIbβ3 expression to be significantly reduced on GT platelets compared to control platelets under both non-stimulating and stimulating conditions. MC enabled us to survey an array of additional surface antigens and, in agreement with previous reports, CD29, CD36, CD62P, and CD107a membrane expression was found to be similar on GT and control platelets following agonist stimulation.
CD9 levels on GT platelets have previously been reported to be similar to levels on healthy donor platelets. MC revealed significantly elevated CD9 surface expression on platelets from the GT patient cohort following agonist stimulation (0.5 μM ADP and 20 μM TRAP) compared to healthy donor platelets (
CD63 was significantly elevated on GT platelets compared to healthy control platelets following TRAP stimulation. CD63 is found on dense granule and lysosomal membranes of resting platelets and upon activation becomes expressed on the plasma membrane, where it associates with the integrin αIIbβ3-CD9 complex and with the actin cytoskeleton via αIIbβ3. Similar to CD9, CD63 expression may be limited by membrane protein crowding, and in the absence of αIIbβ3 there would be less crowding. Interestingly, studies have shown that some GT patient platelets show increased surface expression of CD63, but not CD107a or CD62P following FcγRIIA crosslinking. The investigators of these studies hypothesized that increased dense granule exocytosis was responsible for the increased surface expression of CD63.
ADP-induced CD31 surface expression was observed to be significantly reduced on GT platelets compared to healthy control platelets. A previous study showed no difference in CD31 in GT patients, but this study immunoblotted whole platelet lysates, thus measuring total platelet CD31 levels not platelet surface expression of CD31. As expected, CD42a and CD42b surface expression on GT and healthy control platelets were relatively comparable in the present study; although subtle, yet significant, differences in surface levels of CD42a were seen with 20 μM TRAP treatment, which may be attributable to donor-to-donor variation in surface expression patterns.
TRAP- and ADP-induced dose-dependent increases in integrin αIIbβ3 activation and P-selectin expression, as determined by MMI or MFI, were highly correlated (R2=0.9186 or 0.8995, respectively). Although this finding may be largely expected, it should be noted that the monoclonal antibody used to detect activated αIIbβ3 is an IgM and the labeling of an IgM with the metal chelating polymer has not previously been reported. In fact, the manufacturer recommendation is that IgM not be labeled using this procedure. Nevertheless, purified PAC1 labeled in-house with 159Tb using the identical procedure recommended for IgG antibodies demonstrated high-affinity binding to platelets, which was activation dependent and could be blocked by the integrin αIIbβ3 antagonist eptifibatide. Other technical hurdles which were overcome during development of the MC procedure for platelets include optimization of sample volume, sample type (whole blood was used to avoid pre-analytical artifacts associated with isolation of platelet-rich plasma), fixative solutions and washing conditions (washing is not required for FFC but is required for MC in order to avoid exposure of the mass spectrometer to damaging salts). Platelet recovery after fixation and wash procedures was determined to be >80%.
In one aspect, the invention provides a method of simultaneously detecting one or more biomarkers associated with one or more platelets in a platelet sample, by contacting the sample with one or more metal-tagged probes; washing the sample to remove unbound probes; and analyzing the sample by mass cytometry; thereby simultaneously detecting the one or more biomarkers associated with the one or more platelets. The step of contacting the sample with one or more metal-tagged probes will vary in terms of the solvent used, concentration of the probe and the length of incubation time. A skilled person will understand that the step of contacting is to facilitate binding of the probe to the biomarker and accordingly will vary the conditions to facilitate binding. The step of washing removes excess probe from the sample prior to analysis in order to inter alia, protect the mass spectrometer or to improve signal-to-noise ratio by reducing non-specific binding. The specifics of the washing step will vary according to the type of probe employed. Any appropriate method of MC may be selected to detect the presence and level of the biomarkers. A skilled person in possession of this disclosure is able to select appropriate conditions, instruments and data processing methods to perform the step of analyzing the sample by MC. Simultaneous detection of the biomarkers refers to the high dimensionality and simultaneous detection possible when employing MC.
In another aspect, the invention provides a method of identifying one or more subpopulations of platelets in a platelet sample, by performing the steps described above and classifying the platelets into one or more subpopulations based on the biomarkers detected; thereby identifying one or more subpopulations of platelets in a platelet sample.
In another aspect, the invention provides a method of diagnosing a subject for a disease characterized by platelet abnormalities, by performing the steps described above and diagnosing the subject as having a disorder based on the level of the one or more biomarkers relative to one or more corresponding reference levels. In various embodiments, the disease is selected from the group consisting of GT, HPS, metabolic disorders (e.g., diabetes) cardiovascular disease, immune thrombocytopenia, sickle cell disease, a vascular anomaly, or cancer. In various embodiments, the disease is GT and the characteristic biomarkers comprise CD41, CD61 and activated integrin αIIbβ3. In various embodiments, the method further comprises treating the subject for the disease diagnosed. In various embodiments, the method further comprises treating the subject having been diagnosed with GT. In various embodiments, the method further comprises treating the subject comprises providing the subject with factor VIIa. In various embodiments, the method further comprises contacting the platelet sample of the subject with a panel comprising two or more metal-tagged probes that bind one or more biomarkers characteristic of the disorder. In various embodiments, the biomarkers comprise human leukocyte antigen (HLA) and/or human platelet antigen (HPA). In various embodiments, the abnormalities are associated with an increased risk of thrombosis. In various embodiments, the abnormalities are associated with an increased risk for bleeding. The methods of the invention may also be used to track the efficacy of treatment with a therapeutic agent by following the presence and level of biomarkers associated with the subject's platelets. Accordingly, in various embodiments, the platelet sample is obtained from a subject receiving at least one therapeutic agent.
In another aspect the invention provides a method for performing MC on a platelet sample, the method comprising contacting the sample with a panel comprising one or more probes that bind to one or more biomarkers associated with platelets in the sample; washing the sample to remove unbound probes; and analyzing the sample by MC. In various embodiments, the invention provides an improved method of MC in which the sample is a platelet sample.
In another aspect the invention provides a method of differentiating among two or more populations of platelets in a mixture of platelets wherein each population is derived from a different source, the method by contacting a first population of platelets derived from a first source with a first set of one or more metal-tagged probes or mixtures thereof that bind to one or more biomarkers associated with the platelets in the first population; washing the first population of platelets to remove unbound probes or mixtures thereof; analyzing the first population of platelets by MC, thereby detecting the one or more biomarkers in the population of platelets; assigning a first biomarker profile to the first population of platelets; contacting a second population of platelets derived from a second source with a second set of one or more metal-tagged probes or mixtures thereof that bind to one or more biomarkers associated with the platelets in the second population; washing the second population of platelets to remove unbound probes or mixtures thereof; analyzing the second population of platelets by MC, thereby detecting the one or more biomarkers in the second population of platelets; assigning a second biomarker profile to the second population of platelets; contacting a mixture of the first and second population of platelets derived from different sources with the first and second set of one or more metal-tagged probes or mixtures thereof that bind to one or more biomarkers associated with the platelets in mixture; washing the mixture to remove unbound probes or mixtures thereof; analyzing the mixture by MC, thereby detecting one or more biomarkers in a mixture of platelets; and comparing the first and second biomarker profiles with a profile of the biomarkers detected in the mixture; thereby differentiating among two or more populations of platelets in a mixture of platelets wherein each population is derived from a different source. In various embodiments, the method comprises differentiating between platelets received by transfusion and endogenous platelets in a platelet sample of a subject transfused with platelets, wherein the first population of platelets are derived from a sample of blood of the subject prior to transfusion, the second population of platelets are derived from a sample of platelets to be transfused, and the mixture of the first and second or populations of platelets are derived from a sample of blood of the subject post-transfusion; thereby differentiating between the platelets received by transfusion and the endogenous platelets in a platelet sample of a subject transfused with platelets.
In another aspect, the invention provides a method of assessing the suitability of a population of platelets for transfusion into a subject, the method comprising by contacting a population of platelets to be transfused with one or more metal-tagged probes that bind to one or more biomarkers associated with the platelets; washing the population of platelets to remove unbound antibodies, ligands or mixtures thereof; analyzing the population of platelets by MC, thereby detecting the one or more biomarkers associated with the platelets to be transfused; assigning one or more classifications to the population of platelets in the sample based on the biomarkers detected to create a classified pre-transfusion sample; transfusing the subject with the classified pre-transfusion sample; obtaining a post-transfusion sample from the subject; identifying in the post-transfusion sample the platelets having one or more classifications assigned pre-transfusion; and comparing the level of metal-tagged platelets in the pre-transfusion sample with the level of metal-tagged platelets in the post-post transfusion sample; thereby assessing the suitability of a population of platelets for transfusion into a subject.
The usual metrics for platelet transfusion are recovery at 1 hour post transfusion and survival (e.g., the number of platelets surviving in the circulation after 24 hours. Advantageously, a minimum of 60% is achieved. A standard method for assessing recovery and survival of the transfused platelets is using radioactivity to label the platelets. However, the this method does not permit analysis of the function of the radiolabeled platelets separate from the recipient's non-radioactive platelets.
Use of MC in accordance with the methods described herein can not only distinguish the transfused platelets from the recipient's platelets and, using the quantitative method described herein, determine the recovery and survival but also allows for functional analysis of the transfused and native platelet populations.
In various embodiments, the biomarkers are present on the surface of the platelets.
The methods described herein may also be used to investigate intracellular markers (e.g., phospho-proteins, cytokines, chemokines, etc.) in platelets and other cell types. Specifically, following staining of surface markers, samples can be fixed, gently permeabilized, and a panel of metal-tagged antibodies or other probes to intracellular markers is added. Accordingly, in various embodiments, the biomarkers are intracellular.
The methods described herein can be used to simultaneously evaluate a significant number of biomarkers. Accordingly, in various embodiments the above described methods may simultaneously detect 7 or more, 8 or more, 9 or more, 10 or more, 11 or more, 12 or more, 13 or more or 14 or more biomarkers. In various embodiments, the probes bind one or more biomarkers selected from the group consisting of CD9, CD29, CD31, CD36, CD41, CD42a, CD42b, CD61, CD62P, CD63, CD107a, CD154, GPVI, activated integrin αIIbβ3 and mixtures thereof.
In various embodiments, it may be advantageous to activate the platelets with one or more reagents prior to analysis. Accordingly, the methods described herein may further comprise activating the platelets with thrombin receptor activating peptide (TRAP), thrombin, adenosine diphosphate, collagen, arachidonic acid, epinephrine, serotonin, histamine, convulxin, U46619, Podoplanin or combinations thereof.
In various embodiments, the methods described herein further comprise obtaining the sample from a subject. The sample can be obtained by any appropriate technique known to a person of skill in the art. In various embodiments, the subject is a mammal. In various embodiments, the subject is a human. In various embodiments, the human subject exhibits symptoms associated with a disease characterized by thrombosis or abnormal bleeding.
In various embodiments, the probes include one or more of an antibody, a ligand, a Fab fragment of an antibody, a chimeric or engineered antibody, lectins, adhesive glycoproteins, fibrinogen, fibronectin, von Willebrand factor, a derivative of a nucleotide, RNA probes, reactive oxygen species probes, a phospholipid binder and mixtures thereof. In various embodiments, the phospholipid binder is annexin V or lactadherin.
Compositions Comprising Probes for the Mass Cytometric Analysis of Platelets
In another aspect, the invention provides a composition comprising one or more metal-tagged probes that bind to one or more biomarkers selected from the group consisting of CD9, CD29, CD31, CD36, CD41, CD42a, CD42b, CD61, CD62P, CD63, CD107a, CD154, GPVI, activated integrin αIIbβ3 and mixtures thereof. In various embodiments, the composition may include probes that bind to two, three or all of these biomarkers. In various embodiments, the one or more probes bind to CD41, CD61 and activated integrin αIIbβ3. In various embodiments, the one or more probes include IgM antibodies.
In various embodiments, the invention provides a panel comprising two or more metal-tagged probes. In various embodiments, the invention provides a method of making the panel by labeling two or more probes with a metal tag and assembling the labeled probes in an array. In various embodiments, the invention provides a kit including the panel and instructions for use to facilitate the practice of the methods described herein.
The invention is further described in detail by reference to the following examples. This example is provided for purposes of illustration only and is not intended to be limiting unless otherwise specified. Thus, the invention should in no way be construed as being limited to the following example, but rather, should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.
Metal-conjugated monoclonal antibodies were from Fluidigm Corporation (San Francisco, Calif.): anti-CD9-171Yb (clone SN4 C33A2), anti-CD31-145Nd (clone WM59), anti-CD61-165Ho (clone VI-PL2); from Longwood Medical Area Antibody Core (Boston, Mass.): anti-CD36-150Nd (clone 5-271), anti-CD42b-163Dy (clone HIP1), anti-CD41-149Sm (clone HIP8), anti-CD62P-172Yb (clone AK4), anti-CD63-161Dy (clone H5C6), anti-CD107a-166Er (clone H4A3), anti-CD154-154Sm (clone 24-31); or labeled in-house (described below): anti-CD29-176Yb (Biolegend, San Diego, Calif., clone TS2/16), anti-CD42a-155Gd (BD Biosciences, San Jose, Calif., clone ALMA.16), anti-GPVI-152Sm (EMD Millipore, Billerica, Mass., polyclonal IgG), anti-activated αIIbβ3 (PAC1)-159Th (BD Biosciences, San Jose, Calif., clone PAC1). Fluorescent-conjugated monoclonal antibodies were from BD Biosciences (San Jose, Calif.): anti-CD41-PE (clone HIP8), anti-CD42b-PE-Cy5 (clone HIP1), anti-CD62P-PE (clone AK4), anti-activated αIIbβ3 (PAC1)-fluorescein isothiocyanate (FITC) (clone PAC1); or Agilent (Santa Clara, Calif.): anti-CD61-FITC (clone Y2/51). MaxPAR X8 Antibody Labeling Kits, Iridium 191/193 Cell-ID DNA Intercalator, and EQ Four Element Calibration Beads were from Fluidigm Corporation (San Francisco, Calif.). Antibody Stabilization Buffer was from Candor Biosciences (GmbH, Wangen, Germany). Amicon 3 kDa (Cat #UFC500396) and 50 kDa (Cat #UFC505096) centrifugal filter units were from EMD Millipore (Burlington, Mass.). Bovine serum albumin, sodium azide, HEPES [N-(2-Hydroxyethyl) piperazine-N′-(2-ethanesulfonic acid)], and tris(2-carboxyethyl)phosphine (TCEP) bond breaker were from Sigma Aldrich (St. Louis, Mo.). Protease-activated receptor 1 (PAR1) thrombin receptor-activating peptide (TRAP, SFLLRN-NH2) was from Bachem (Torrance, Calif.). Adenosine 5′-diphosphate (ADP) was from Chrono-log Corporation (Havertown, Pa.). Vacutainer® 3.2% sodium citrate blood collection tubes were from BD Biosciences (San Jose, Calif.). HEPES-Tyrode's buffer with 0.35% bovine serum albumin (HT-BSA; henceforth known as vehicle) (10 mM HEPES, 137 mM sodium chloride, 2.8 mM potassium chloride, 1 mM magnesium chloride, 12 mM sodium hydrogen carbonate, 0.4 mM sodium phosphate dibasic, 5.5 mM glucose, and 0.35% w/v bovine serum albumin, pH 7.4) was made with reagents from Sigma Aldrich (St. Louis, Mo.). All other chemicals or reagents were from Sigma Aldrich.
Blood was collected by venipuncture with a 21-gauge butterfly needle into evacuated tubes containing 3.2% sodium citrate. Blood was drawn from healthy volunteers or GT patients who were free from antiplatelet agents and non-steroidal anti-inflammatory drugs for 10 days prior to the donation. The blood draws were performed by the same phlebotomist. Complete blood cell counts were performed in a Sysmex XN-1000 Hematology Analyzer.
Anti-CD29, anti-CD42a, anti-GPVI, and anti-activated αIIbβ3 (PAC1) were conjugated to chelating polymers loaded with lanthanide metals (176Yb, 155Gd, 152Sm and 159Tb, respectively) using a MaxPAR X8 Antibody Labeling Kit and Fluidigm buffers (Buffer L, R, and W) according to the manufacturer's protocol. The supplied chelating polymer was loaded with the lanthanide metal of choice by co-incubation in Buffer L at 37° C. for 30-40 minutes. Separately, the antibodies were partially reduced in Buffer R solution plus 4 mM TCEP bond breaker solution at 37° C. for 30 minutes and then purified by buffer exchange using a 50 kDa Amicon filter. The metal-loaded polymers were concentrated in a 3 kDa Amicon filter, added to the reduced antibody, and incubated at 37° C. for 1-2 hours for conjugation to occur. Conjugated antibodies were washed free of unreacted polymer and metal ions using Buffer W, quantified by measuring absorbance at 280 nm on a NanoDrop 2000 Spectrophotometer (ThermoFisher Scientific, Waltham, Mass.), resuspended at a concentration of 0.5 mg/mL in Antibody Stabilization Buffer, supplemented with 0.05% sodium azide and stored long term at 4° C. Each antibody was titrated to optimal staining concentrations using healthy donor platelets.
A panel of metal-labeled antibodies directed against platelet antigens of interest was assembled (
Whole blood FFC analysis of platelet activation was performed as previously described. Three color analysis was performed using two cocktails of fluorescently labeled antibodies: PE-conjugated anti-CD62P, FITC-conjugated PAC1 (directed against the high affinity conformation of integrin αIIbβ3) and PE-Cy5-conjugated anti-CD42b; or PE-conjugated anti-CD41a, FITC-conjugated anti-CD61 and PE-Cy5-conjugated anti-CD42b (see Table 2 for antibody information). Citrate-anticoagulated whole blood was treated with vehicle, TRAP or ADP at the indicated concentrations in the presence of the appropriate fluorescently labeled antibody cocktail for 30 minutes at ambient temperature. Samples were fixed in 1% formaldehyde/HEPES-saline buffer for 30 minutes prior to analysis in a FACSCalibur flow cytometer (BD Biosciences, San Jose, Calif.). Platelets were gated based on forward light scatter, side light scatter and CD42b expression (see
Data were analyzed using GraphPad version 5.0 software (GraphPad Software, La Jolla, Calif.) and are presented as mean±standard error of the mean. An extra sum-of-squares F test was performed to determine differences in EC50 values between dose-response curves constructed using FFC and MC. Data used for statistical analysis was tested using a 1-way ANOVA in conjunction with a Dunnett multiple comparison test/Bonferroni post-test or a 2-way ANOVA with a Bonferroni post-test.
In contrast to other MC protocols that use isolated fresh or frozen peripheral blood mononuclear cells, the methods of the invention use fresh whole blood, platelet rich plasma, washed platelets or other platelet containing solutions. Fixation solutions were optimized for stabilizing platelets and maximizing platelet recovery after washing. Centrifugation speeds and times were also optimized to achieve the highest recovery without inducing platelet-platelet clumping.
Also, in contrast to other MC preparation procedures, the methods disclosed herein provide for quantitative analysis of the number of total platelets and the number of platelets in each subpopulation of platelets present in the starting sample. For example, as shown in the examples below, the quantitative analaysis starting samples were “spiked” with a known number of platelets that were pre-labeled with a near saturating concentration of a metal-tagged antibody with a unique mass. For example, a CD61 antibody was labeled with an isotope different from the mass used for the CD61 antibody probes. Test samples spiked with a known concentration of these labeled antibodies were stained with the metal-tagged antibody panel, fixed and washed as usual and analyzed by MC.
The spiked platelets labeled with the different mass marker on CD61 are easily distinguishable from the test platelets. After collection of a total of ˜30,000 total CD61 positive platelet events, the number of spiked platelets was determined. From the original concentration of spiked platelets, the volume of sample analyzed could be determined. (for example, for a sample of test platelets spiked to a concentration of 50,000 spike platelets per 10 μL of whole blood, could be stained with the 14-antibody panel, fixed, washed and analyzed. If 30,000 total platelets were analyzed, and 5000 of those had the CD61 label identifying them as spiked platelets, then the volume of sample analyzed can be calculated as 10 μL/50,000 platelets time 5,000 platelets=1 μL. Then, the concentration of platelets in the test whole blood sample would be calculated as 30,000 platelet analyzed, minus 5,000 spike platelets, =25,000 test platelets/1 μL.
To compare the MC and FFC platforms for platelet analysis a novel metal-tagged MC antibody panel was designed to target well-established surface markers on platelets (
MC and FFC platforms were compared for evaluating platelet activation by incubating platelets with CD62P-172Yb and PAC1-159Tb antibodies or with their fluorescent antibody counterparts, CD62P-PE and PAC1-FITC with and without various concentrations of TRAP or ADP. Agonist-induced increases in platelet surface activated αIIbβ3 and P-selectin using MC and FFC platforms were similar and the results were highly correlated (R2≥0.9,
MC Enables an Order of Magnitude More Cellular Parameters than FFC to be Assessed Simultaneously During Platelet Activation
Identification of Platelet Subpopulations by High-Dimensional viSNE Analysis
To accomplish this, viSNE analysis was used to visualize high-dimensional single-cell data obtained from a healthy donor across 3 separate blood donations (
viSNE analysis demonstrated heterogeneity in circulating platelets by identifying subpopulations of platelets with unique antigen expression profiles (
Using viSNE analysis platelet subpopulations that were common between different healthy donors were identified, as well as subpopulations that were unique to particular donors (see
GT platelets were used to validate the use of MC as a research tool by comparing data obtained using MC with that obtained using FFC. Both MC and FFC analysis platforms showed, as expected, greatly reduced surface expression of CD41, CD61 and activated integrin αIIbβ3 on GT platelets, both without and with ex vivo stimulation (0.5 or 20 μM ADP or 1.5 or 20 μM TRAP) compared to that on healthy control platelets (
Platelet surface P-selectin (CD62P) expression following stimulation with ADP (0.5 or 20 μM) or TRAP (1.5 or 20 μM) as measured by both MC and FFC platforms was similar on platelets from GT patients and non-GT controls (
Visual Stochastic Neighbor Embedding (viSNE) is based on the t-distributed Stochastic Neighbor Embedding (tSNE) algorithm and analyzes expression levels of all markers on all cells within a sample. Cells are grouped into clusters (subpopulations) based on shared similarities between expression patterns of all markers. The distance between populations of cells is inversely proportional to how closely related those populations are in terms of marker expression and characteristics. (
The disclosures of each and every patent, patent application, and publication cited herein are hereby incorporated herein by reference in their entireties.
Although the invention has been described herein with reference to specific embodiments, it is apparent that other embodiments and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such embodiments and equivalent variations.
This application is a national stage filing under 35 U.S.C. § 371 of international PCT application PCT/US2019/040480, filed on Jul. 3, 2019, which claims the benefit of priority under 35 U.S.C. § 119(e) to U.S. provisional application Ser. No. 62/694,571, filed on Jul. 6, 2018, the entire contents of each of which are incorporated by reference herein. This application may also contain subject matter that is related to copending U.S. provisional application Ser. No. 62/696,311, filed on Jul. 10, 2018, entitled “Methods and Compositions for Analyzing Immortalized Megakaryocyte Progenitor Cell Lines and Platelet-like Particles” (attorney docket no. 368665-3331P1(00017), the entire disclosure of which is incorporated herein by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US19/40480 | 7/3/2019 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62694571 | Jul 2018 | US |
