Patent Application
20210116462
Kawasaki disease is an acute, systemic vasculitis predominantly affecting young children. Clinical symptoms of Kawasaki disease include persistent fever not managed by antipyretic medications and antibiotics, rash, conjunctival infection, edema and erythema of the extremities, and oropharyngeal erythema.
The disease may impact the systemic vasculature, but the coronary arteries and cardiac tissue are particularly susceptible to damage. Inflammation of the coronary arteries and surrounding cardiac tissue may be mild and reversible or may be extensive, leading to cardiac artery aneurysms (ballooning) and stenosis (narrowing) of the arteries. An estimated 25% of Kawasaki disease subjects develop cardiac artery aneurysms or stenosis. While many subjects show recovery of cardiac functions and no angiographic evidence of cardiac artery aneurysms or stenosis following recovery, there can be evidence of continued endothelial and vascular dysfunction even years later. Subjects with larger aneurysms are at higher risk for myocardial infarct (MI) and other cardiovascular events later in life.
There is no specific test available to diagnose Kawasaki disease. Diagnosis largely is a process of ruling out diseases that cause similar signs and symptoms (http://www.mayoclinic.org/diseases-conditions/kawasaki-disease/basics/tests-diagnosis/con-20024663, Mar. 3, 2014).
Applicants have discovered that determination of levels or expression of particular biomarkers (e.g., protein levels, mRNA levels, glycan abundance, and/or the binding properties of IgG) in biological samples can be utilized to diagnose, prognose, and treat Kawasaki disease in subjects, and further to select subjects who would benefit from a Kawasaki disease therapy other than, or in addition to, IVIG treatment. Accordingly, the present invention encompasses methods and compositions that utilize these proteins for the diagnosis, prognosis, and treatment of Kawasaki disease.
In a first aspect, the invention features a method for diagnosing Kawasaki disease in a subject. This method includes the step of determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) proteins of Table 1 and/or Table 2 e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more and/or determining whether IgG in the sample binds to one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, forty, fifty, sixty, or more) peptides of Table 3.
According to this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of at least one protein of Table 1, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of at least one protein of Table 2, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or increased binding (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of IgG in said sample to a peptide of Table 3, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease) is indicative of the subject having Kawasaki disease.
In some embodiments, the method further includes the step of determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) additional biomarkers in the biological sample. In certain embodiments, the one or more additional biomarkers are a protein of Table 4, Table 5, Table 6, Table 7, Table 8, and/or Table 9; an mRNA of Table 10, Table 11, Table 12, and/or Table 13; and/or a glycan of Table 14, Table 15, Table 16, and/or Table 17.
By this method, a subject can be further diagnosed for a predisposition to develop a secondary Kawasaki disease symptom, e.g., a cardiac artery aneurysm or stenosis. According to this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of a protein of Table 4, Table 6, and/or Table 8, an mRNA of Table 10 or Table 12, and/or a glycan of Table 14 or Table 16, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease or a subject that has Kawasaki disease and responded positively to IVIG treatment) and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of a protein of Table 5, Table 7, and/or Table 9, an mRNA of Table 11 or Table 13, and/or a glycan of Table 15 or Table 17, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease or a subject that has Kawasaki disease and responded positively to IVIG treatment) is indicative of said subject having a predisposition to develop a secondary Kawasaki disease symptom, e.g., a cardiac artery aneurysm or stenosis.
In a second aspect, the invention features a method for diagnosing whether a subject has a predisposition to develop cardiac artery aneurysms or stenosis (e.g., without an initial biomarker-based Kawasaki disease diagnosis). This method includes the step of determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) biomarkers of Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Table 13, Table 14, Table 15, Table 16, and/or Table 17 in a biological sample obtained from the subject. According to this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of at least one protein of Table 4, Table 6, and/or Table 8, an mRNA of Table 10 or Table 12, and/or a glycan of Table 14 or Table 16, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of at least one protein of Table 5, Table 7, and/or Table 9, an mRNA of Table 11 or Table 13, and/or a glycan of Table 15 or Table 17, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease) is indicative of a subject having a predisposition to develop cardiac artery aneurysms or stenosis.
In a third aspect, the invention features a method for classifying a subject. Such classification includes predicting the response to a Kawasaki disease therapy in a subject, selecting a subject that may benefit from a Kawasaki disease therapy, selecting a subject who may benefit from IVIG therapy, or predicting the responsiveness of a subject to IVIG therapy. This method includes the step of determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) proteins of Table 1 and/or Table 2 in a biological sample obtained from the subject and/or determining whether IgG in the sample binds to one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, forty, fifty, sixty, or more) peptides of Table 3. According to this method, a subject is classified based on at least one or more of the proteins of Table 1 having an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more), as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or at least one or more of the proteins of Table 2 having a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less), as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or increased binding (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of IgG in said sample to a peptide of Table 3, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease).
In some embodiments, the method further includes the step of determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) additional biomarkers in the biological sample. In certain embodiments, the one or more additional proteins are any protein of Table 4, Table 5, Table 6, Table 7, Table 8, and/or Table 9; an m RNA of Table 10, Table 11, Table 12, and/or Table 13; and/or a glycan of Table 14, Table 15, Table 16, and/or Table 17. By this step a subject can be further classified (for example, by determining the likelihood of a subject to develop cardiac artery aneurysms or stenosis, predicting the response to a Kawasaki disease therapy, selecting a subject that may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy, or predicting the responsiveness of a subject to IVIG therapy) based on one or more of the proteins of Table 4, Table 6, and/or Table 8, one or more mRNA of Table 10 or Table 12, and/or one or more glycan of Table 14 or Table 16 having an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more), as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease or a subject that has Kawasaki disease and responded positively to IVIG treatment) and/or one or more of the proteins of Table 5, Table 7, and/or Table 9, one or more mRNA of Table 11 or Table 13, and/or one or more glycan of Table 15 or Table 17 having a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less), as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease or a subject that has Kawasaki disease and responded positively to IVIG treatment).
In a fourth aspect, the invention features a method for classifying a subject. Such classification includes determining the likelihood of a subject to develop cardiac artery aneurysms or stenosis, predicting the response to a Kawasaki disease therapy, selecting a subject that may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy, or predicting the responsiveness of a subject to IVIG therapy. The method includes: determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) biomarkers of Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Table 13, Table 14, Table 15, Table 16, and/or Table 17 in a biological sample. According to this method, a subject is classified based on at least one or more of the Table 4, Table 6, and/or Table 8, one or more mRNA of Table 10 or Table 12, and/or one or more glycan of Table 14 or Table 16 having an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more), as compared to a reference (e.g., a control, such as, a predetermined control value, or a sample from a subject that does not have Kawasaki disease or a subject that has Kawasaki disease and responded positively to IVIG treatment) and/or one or more Table 5, Table 7, and/or Table 9, one or more mRNA of Table 11 or Table 13, and/or one or more glycan of Table 15 or Table 17 having a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less), as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease or a subject that has Kawasaki disease and responded positively to IVIG treatment).
In a fifth aspect, the invention features a method for treating Kawasaki disease. The method includes: (a) determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) proteins from Table 1 or Table 2 in a biological sample obtained from the subject and/or determining whether IgG in the sample binds to one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, forty, fifty, sixty, or more) peptides of Table 3; and (b) administering a Kawasaki disease therapy to the subject if the level of the one or more proteins is indicative that the subject may benefit from a Kawasaki disease therapy (e.g., administration of IVIG). In this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of a protein of Table 1, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is indicative that the subject may benefit from a Kawasaki disease therapy, and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of a protein of Table 2, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or increased binding (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of IgG in said sample to a peptide of Table 3, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease) is indicative that the subject may benefit from a Kawasaki disease therapy.
In some embodiments, the method further includes, prior to the determining step, the step of selecting a subject having a fever and one or more of: red eyes; a red swollen tongue; red skin on the palms on the hands and/or soles of the feet; peeling skin on the hands and/or feet; a rash on the main part of the body and/or in the genital area; and swollen lymph nodes and/or the step of obtaining a biological sample from said subject.
In other embodiments, the method further includes, between step (a) and step (b), the step of comparing the level of said one or more proteins to a reference (e.g., a predetermined control value) and/or comparing the binding of IgG in the sample to a reference (e.g., a predetermined control value).
In some embodiments, the method further includes (c) determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) biomarkers from Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Table 13, Table 14, Table 15, Table 16, and/or Table 17 in a biological sample obtained from the subject; and (d) administering a Kawasaki disease therapy other than, or in addition to, IVIG therapy (e.g., a Kawasaki disease therapy including one or more anticoagulants such as enoxaparin and/or clopidogrel, an anti-inflammatory such as aspirin, and/or one or more immunosuppressant drugs such as infliximab, cyclosporine, and/or prednisone) to the subject if the level of the one or more biomarkers is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy. In this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of a protein of Table 4, Table 6, and/or Table 8, an mRNA of Table 10 or Table 12, and/or a glycan of Table 14 or Table 16 as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy (e.g., a Kawasaki disease therapy including one or more anticoagulants such as enoxaparin and/or clopidogrel, an anti-inflammatory such as aspirin, and/or one or more immunosuppressant drugs such as infliximab, cyclosporine, and/or prednisone); and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of a protein of Table 5, Table 7, and/or Table 9, an mRNA of Table 11 or Table 13, and/or a glycan of Table 15 or Table 17 as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy.
In a sixth aspect, the invention features a method of treating Kawasaki disease. The method includes: (a) determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) biomarkers from Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Table 13, Table 14, Table 15, Table 16, and/or Table 17 in a biological sample obtained from the subject; and (b) administering a Kawasaki disease therapy other than, or in addition to, IVIG therapy (e.g., a Kawasaki disease therapy including one or more anticoagulants such as enoxaparin and/or clopidogrel, an anti-inflammatory such as aspirin, and/or one or more immunosuppressant drugs such as infliximab, cyclosporine, and/or prednisone) to the subject if the level of the one or more biomarkers is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy. In this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of a protein of Table 4, Table 6, and/or Table 8, an mRNA of Table 10 or Table 12, and/or a glycan of Table 14 or Table 16 as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy (e.g., a Kawasaki disease therapy including one or more anticoagulants such as enoxaparin and/or clopidogrel, an anti-inflammatory such as aspirin, and/or one or more immunosuppressant drugs such as infliximab, cyclosporine, and/or prednisone); and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of a protein of Table 5, Table 7, and/or Table 9, an mRNA of Table 11 or Table 13, and/or a glycan of Table 15 or Table 17 as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy.
Any of the methods herein that rely upon protein measurement can also be adapted for use with the measurement of mRNA levels for the protein. Accordingly, in a seventh aspect, the invention features a method for diagnosing Kawasaki disease in a subject, diagnosing whether a subject has a predisposition to develop cardiac artery aneurysms or stenosis, classifying a subject, or treating Kawasaki disease. This method includes the step of determining the level of mRNA encoding one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) proteins of Tables 1-9 in a biological sample obtained from the subject. According to this method, increased level of mRNA (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) encoding a protein of Table 1, Table 4, Table 6, and/or Table 8 as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is a basis for classification of the subject and/or is indicative of the subject having Kawasaki disease, of the subject having a predisposition to develop cardiac artery aneurysms or stenosis, that the subject may benefit from a Kawasaki disease therapy, or that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy; and/or decreased mRNA level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of a protein of Table 2, Table 5, Table 7, and/or Table 9 as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is a basis for classification of the subject and/or is indicative of the subject having Kawasaki disease, of the subject having a predisposition to develop cardiac artery aneurysms or stenosis, that the subject may benefit from a Kawasaki disease therapy, or that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy.
In some embodiments, the method further includes the step of administering a Kawasaki disease therapy or a Kawasaki disease therapy other than, or in addition to, IVIG therapy if the mRNA level of the one or more proteins is indicative that the subject may benefit from a Kawasaki disease therapy or a Kawasaki disease therapy other than, or in addition to, IVIG therapy.
In other embodiments, the method further includes prior to determining the expression level, extracting mRNA from the biological sample and reverse transcribing the mRNA into cDNA to obtain a treated biological sample.
In certain embodiments, the mRNA level is determined by an amplification-based assay (e.g., PCR, quantitative PCR, or real-time quantitative PCR), amplification-free assay (e.g., Nanostring), microdroplet based assay, nanopore based assay, or bead based assays (e.g., Luminex, nanoparticles, Nanosphere).
Next generation sequencing methods may also be used with the methods of the invention. Next generation sequencing methods are sequencing technologies that parallelize the sequencing process, producing thousands or millions of sequences concurrently (see, for example, Hall, J. Exp. Biol. 209(Pt.9):1518-1525 (2007) for a review of next generation methods). Next generation sequencing methods include, but are not limited to, polony sequencing, 454 pyrosequencing, Illumina (Solexa) sequencing, SOLiD sequencing, Ion Torrent semiconductor sequencing, DNA nanoball sequencing, Heliscope single molecule sequencing, single molecule real time sequencing, nanopore DNA sequencing (see, for example, Dela Torre et al. Nanotechnology, 23(38):385308, 2012), tunneling currents DNA sequencing (see, for example, Massimiliano, Nanotechnology, 24:342501, 2013), sequencing by hybridization (see, for example, Qin et al. PLoS One, 7(5):e35819, 2012), sequencing with mass spectrometry (see, for example, Edwards et al. Mutation Research, 573(1-2):3-12, 2005), microfluidic Sanger sequencing (see, for example, Kan et al. Electrophoresis, 25(21-22):3564-3588, 2004), microscopy-based sequencing (see, for example, Bell et al. Microscopy and microanalysis: the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada, 18(5):1-5, 2012), and RNA polymerase sequencing (see, for example, Pareek et al. J. Applied Genetics, 52(4):413-415, 2011).
In an eighth aspect, the invention features a kit or device for selecting a subject that may benefit from a Kawasaki disease therapy. The kit or device includes a set of two or more (e.g., three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) distinct binding agents, each of the binding agents being capable of specifically binding to at least one protein from Table 1 and/or Table 2, wherein each binding agent binds a different protein and/or one or more peptides from Table 3.
In a ninth aspect, the invention features a kit or device for selecting a subject that may benefit from a Kawasaki disease therapy. The kit or device includes a set of two or more (e.g., three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) distinct reagents, each or the reagents being capable of detecting at least one mRNA that encodes a protein from Table 1 and/or Table 2, wherein each reagent detects a different mRNA that encodes a protein from Table 1 and/or Table 2.
Optionally the kit or device also includes instructions for use of the kit or device to determine the level of the proteins in a biological sample and/or instructions for use of the kit or device to determine the binding of IgG in the sample to the one or more peptides of Table 3.
In some embodiments of any of the foregoing kits or devices, the kit or device further includes a set of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) binding agents, each of the binding agents being capable of specifically binding to at least one protein, or the mRNA which encodes the protein, from Table 4, Table 5, Table 6, Table 7, Table 8, and/or Table 9; an mRNA or protein product of an mRNA of Table 10, Table 11, Table 12, and/or Table 13; and/or a glycan of Table 14, Table 15, Table 16, and/or 17.
In a tenth aspect, the invention features a kit or device for selecting a subject that may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy. The kit or device includes a set of two or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) binding agents, each of the binding agents being capable of specifically binding to at least one protein from Table 4, Table 5, Table 6, Table 7, Table 8, and/or Table 9; an mRNA or protein product of an mRNA of Table 10, Table 11, Table 12, and/or Table 13; and/or a glycan of Table 14, Table 15, Table 16, and/or 17 wherein each binding agent binds a different biomarker.
In an eleventh aspect, the invention features a kit or device for selecting a subject that may benefit from a Kawasaki disease therapy. The kit or device includes a set of two or more (e.g., three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) distinct reagents, each or the reagents being capable of detecting at least one mRNA that encodes a protein from Table 4, Table 5, Table 6, Table 7, Table 8, and/or Table 9 wherein each reagent detects a different mRNA that encodes a protein from Table 4, Table 5, Table 6, Table 7, Table 8, and/or Table 9.
In a twelfth aspect, the invention features a method for diagnosing Kawasaki disease in a subject. The method includes determining the level of one or more proteins in a biological sample obtained from the subject with any of the foregoing kits or devices, wherein an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of a protein of Table 1, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of a protein of Table 2, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or increased binding (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of IgG in said sample to a peptide of Table 3, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease) is indicative of the subject having Kawasaki disease.
In some embodiments, the method further includes the step of determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) additional biomarkers in the biological sample. In certain embodiments, the one or more additional biomarkers are any biomarker of Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Table 13, Table 14, Table 15, Table 16, and/or Table 17. A subject can be further diagnosed with a predisposition to develop cardiac artery aneurysms or stenosis based on one or more of the proteins of Table 4, Table 6, and/or Table 8, an mRNA of Table 10 or Table 12, and/or a glycan of Table 14 or Table 16 having an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more), as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease or a subject that has Kawasaki disease and responded positively to IVIG treatment) and/or one or more of the proteins of Table 5, Table 7, and/or Table 9, an mRNA of Table 11 or Table 13, and/or a glycan of Table 15 or Table 17 having a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less), as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease or a subject that has Kawasaki disease and responded positively to IVIG treatment) is indicative of the subject having a predisposition to develop cardiac artery aneurysms or stenosis.
In a thirteenth aspect, the invention features a method for diagnosing whether a subject has a predisposition to develop cardiac artery aneurysms or stenosis. This method includes the step of determining the level of one or more (e.g., two, three, four, five, six, seven, eight, nine, ten, twelve, fifteen, twenty, twenty-five, thirty, or more) biomarkers of Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Table 13, Table 14, Table 15, Table 16, and/or Table 17 in a biological sample obtained from the subject with any of the foregoing kits or devices. According to this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of at least one protein of Table 4, Table 6 and/or Table 8, and/or at least one glycan of Table 11, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of at least one protein of Table 5, Table 7, and/or Table 9, at least one mRNA of Table 11 or Table 13, and/or at least one glycan of Table 15 or Table 17, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease) is indicative of a predisposition to develop cardiac artery aneurysms or stenosis in said subject.
In a fourteenth aspect, the invention features a method for treating Kawasaki disease in a subject. The method includes the steps of (a) determining the level of one or more proteins in a biological sample obtained from the subject and/or binding of IgG in the sample to one or more peptides with any of the foregoing kits or devices; and (b) administering a Kawasaki disease therapy to the subject if the level of the one or more proteins is indicative that the subject may benefit from a Kawasaki disease therapy (e.g., administration of IVIG). In this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of a protein of Table 1, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is indicative that the subject may benefit from a Kawasaki disease therapy, and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of a protein of Table 2, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), and/or increased binding (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of IgG in said sample to a peptide of Table 3, as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease) is indicative that the subject may benefit from a Kawasaki disease therapy.
In a fifteenth aspect, the invention features a further method for treating Kawasaki disease in a subject. This method includes the steps of (a) determining the level of one or more biomarkers in a biological sample obtained from the subject with any of the foregoing kits or devices; and (b) administering a therapy other than, or in addition to, IVIG therapy to the subject if the level of the one or more proteins is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy. In this method, an increased level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5M-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more) of a protein of Table 4, Table 6, and/or Table 8, an mRNA of Table 10 or Table 12, and/or a glycan of Table 14 or Table 16 as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy (e.g., a Kawasaki disease therapy including one or more anticoagulants such as enoxaparin and/or clopidogrel, an anti-inflammatory such as aspirin, and/or one or more immunosuppressant drugs such as infliximab, cyclosporine, and/or prednisone); and/or a decreased level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less) of a protein of Table 5, Table 7, and/or Table 9, an mRNA of Table 11 or Table 13, and/or a glycan of Table 15 or Table 17 as compared to a reference (e.g., a control, such as a predetermined control value, or a sample from a subject that does not have Kawasaki disease), is indicative that the subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy.
In other embodiments of any of the foregoing methods, the Kawasaki disease therapy includes administration of IVIG to the subject (e.g., in high doses such as greater than 400 mg/kg, 500 mg/kg, 600 mg/kg, 700 mg/kg, 800 mg/kg, 900 mg/kg, 1 g/kg, 1.1 g/kg, 1.2 g/kg, 1.3 g/kg, 1.4 g/kg, 1.5 g/kg, 1.6 g/kg, 1.7 g/kg, 1.8 g/kg, 1.9 g/kg, 2.0 g/kg, 2.10 g/kg, 2.20 g/kg, 2.3 g/kg, 2.4 g/kg, 2.5 g/kg or more). In some embodiments, IVIG is administered to the subject between the fifth and ninth day after the appearance of symptoms. In other embodiments of any of the foregoing methods, the Kawasaki disease therapy includes administration of one or more anticoagulants (e.g., enoxaparin and/or clopidogrel or a pharmaceutically acceptable salt thereof) to the subject. In some embodiments of any of the foregoing methods, the Kawasaki disease therapy includes administration of an anti-inflammatory agent (e.g., aspirin). In other embodiments of any of the foregoing methods, the Kawasaki disease therapy includes administration of one or more immunosuppressant drugs (e.g., infliximab, cyclosporine, and/or prednisone).
In certain embodiments of any of the foregoing methods, the subject has one or more of: a fever; red eyes; a rash on the main part of the body and/or in the genital area; red, dry, cracked lips; a red, swollen tongue; swollen, red skin on the palms of the hands and/or soles of the feet; swollen lymph nodes; irritability; peeling of the skin on the hands and/or feet; joint pain; diarrhea; vomiting; and abdominal pain. For example, the subject may have a fever (e.g., a fever lasting more than four days) and one or more of: red eyes; a red swollen tongue; red skin on the palms of the hands and/or soles of the feet; peeling of the skin on the hands and/or feet; a rash on the main part of the body and/or in the genital area; and swollen lymph nodes.
In other embodiments of any of the foregoing methods, the subject exhibits the clinical symptoms of cardiac artery aneurysms and/or stenosis of the arteries. In yet other embodiments of any of the foregoing methods, the subject has not been diagnosed with cardiac artery aneurysms and/or stenosis of the arteries prior to determining the level of the one or more proteins. In certain embodiments of any of the foregoing methods, the subject has a white blood cell count and/or a C-reactive protein measurement that is not indicative of inflammation.
In some embodiments of any of the foregoing methods, the biological sample is obtained from the subject prior to the commencement of IVIG therapy. In other embodiments of any of the foregoing methods, the biological sample is obtained from the subject after commencement of IVIG therapy. In certain embodiments of any of the foregoing methods, the biological sample is obtained from the subject with 24 hours after commencement of IVIG therapy. In some embodiments of any of the foregoing methods, the biological sample is a tissue sample, whole blood, plasma, urine, saliva, pancreatic juice, bile, or serum sample. In certain embodiments of any of the foregoing methods, the biological sample is a plasma sample.
In some embodiments of any of the foregoing methods, the biological sample is processed prior to determining the level of the one or more the proteins, e.g., the biological sample is centrifuged, the biological sample is filtered, the biological sample is diluted, the biological sample is treated with reagents (e.g., digesting enzymes or reducing reagents), the biological sample is fractionated to remove more abundant proteins (e.g., proteins present at concentrations greater than 0.01 g/dL, greater than 0.02 g/dL, greater than 0.05 g/dL, greater than 0.1 g/dL, greater than 0.2 g/dL, greater than 0.5 g/dL, greater than 1.0 g/dL, greater than 2.0 g/dL, greater than 3.0 g/dL), such as, albumins, globulins (e.g., haptoglobulin, alpha2-macroglobulin, IgG, IgA, and IgM), alpha1-acid glycoprotein, apolipoprotein AI, apolipoprotein AII, complement C3, transthyretin, antitrypsin, transferrin, and fibrinogen and/or enrich for less abundant proteins, such as, any protein from Tables 1, 2, 4, or 5. In some embodiments, the biological sample is subjected to centrifugation to remove red blood cells. In certain embodiments, the biological sample is filtered (e.g., spin filtered). In some embodiments, the biological sample is diluted. In other embodiments, the biological sample is subjected to cold alcohol fractionation. In certain embodiments, the biological sample is subjected to chromatographic separation (e.g., using an immunoaffinity-based column). In some embodiments, the biological sample is concentrated. In other embodiments, the biological sample is buffer exchanged. In certain embodiments, the biological sample is treated with a digesting enzyme (e.g., trypsin).
In other embodiments any of the foregoing methods further include contacting the biological sample with one or more binding agents capable of specifically binding to the one or more proteins, one or more peptides of Table 3, one or more mRNAs of Table 10, Table 11, Table 12, and/or Table 13, and/or one or more glycans of Table 14, Table 15, Table 16, and/or Table 17.
In any of the aspects and embodiments described herein, the protein level and/or binding of IgG in the sample is determined by one or more of a hybridization assay, an immunoassay, liquid chromatography, mass spectrometry, and/or fluorescence in situ hybridization assay (e.g., Northern analysis, ELISA, immunohistochemical analysis, microarray, chip, microfluidic chip, sequencing, or Western blotting).
In certain embodiments of any of the foregoing methods, the subject is less than 18 years old (e.g., less than 17 years old, less than 16 years old, less than 15 years old, less than 14 years old, less than 13 years old, less than 12 years old, less than 11 years old, less than 10 years old, less than 9 years old, less than 8 years old, less than 7 years old, less than 6 years old, less than 5 years old, less than 4 years old, less than 3 years old, less than 2 years old, less than 1 year old, less than 6 months old). In some embodiments of any of the foregoing methods, the subject is Asian (e.g., Japanese or Korean) or Afro-Caribbean.
In other embodiments of any of the foregoing methods, the level of the one or more proteins and/or binding of IgG in the sample is determined at least twice within 365 days (e.g., twice within 180 days, within 90 days, within 60 days, within 30 days, within 14 days, within 7 days). In certain embodiments, the level of the one or more proteins and/or binding of IgG in the sample is determined at least once prior to the commencement of IVIG therapy and at least once after commencement of IVIG therapy.
In certain embodiments any of the foregoing kits or devices also include instructions for use of the kit or device to determine the level of the proteins in a biological sample, the binding of IgG to a peptide of Table 3, the expression level of an mRNA of Table 10, Table 11, Table 12, and/or Table 13, and/or the abundance of a glycan of Table 14, Table 15, Table 16, and/or Table 17.
In other embodiments of any of the foregoing methods, the method further includes the step of recording the result in a print or computer readable media. In other embodiments, the method further includes the step of informing (e.g., providing the results of the determining step on printable media) the subject that he or she has Kawasaki disease, may benefit from a Kawasaki disease therapy, may benefit from IVIG therapy, may have an increased likelihood to develop cardiac artery aneurysms and/or stenosis, may have a predisposition to develop cardiac artery aneurysms and/or stenosis, may benefit from a therapy other than, or in addition to, IVIG therapy, or may benefit from therapy that includes one or more anticoagulants, an anti-inflammatory agent, and/or one or more immunosuppressant drugs.
In some embodiments of any of the aspects described herein, the binding agent is an antibody. In other embodiments of any of the aspects described herein, one or more of the binding agents and/or peptides of Table 3 are provided on a solid support (e.g., as a microarray). In any of the aspects and embodiments described herein, the one or more proteins, one or more peptides of Table 3, one or more mRNAs of Table 10, Table 11, Table 12, and/or Table 13, one or more glycans of Table 14, Table 15, Table 16 and/or Table 17, and/or set of binding agents and/or peptides include or consist of any combination described herein. In any of the aspects and embodiments described herein, the one or more peptides of Table 3 may be attached to a solid support by a linker (e.g., an N-terminal or C-terminal cysteine, or an N-terminal or C-terminal cysteine-serine-glycine group).
Also provided herein are methods of monitoring a subject with Kawasaki disease. The diagnostic kits and methods disclosed herein can be used to determine an optimal treatment plan for a subject or to determine the efficacy of a treatment plan for a subject. For example, the subject can be treated for Kawasaki disease and the prognosis of the disease can be determined by the diagnostic kits and methods disclosed herein. In particular embodiments, a diagnostic kit or method is used to determine if a subject has Kawasaki disease. A diagnostic kit or method can include a screen for protein level and/or IgG binding profiles by any useful detection method (e.g., unlabeled, fluorescence, radiation, or chemiluminescence). A diagnostic test can further include one or more binding agents (e.g., one or more of probes, primers, peptides, small molecules, aptamers, or antibodies) to detect the level of these proteins or mRNAs encoding these proteins. In certain embodiments, the diagnostic kit includes the use of one or more proteins associated with Kawasaki disease and/or one or more peptides of Table 3 in a diagnostic platform, which can be optionally automated.
Also provided herein are general strategies to develop diagnostic tests which can be used to diagnose Kawasaki disease based on the level of proteins, binding of IgG to one or more peptides of Table 3, mRNAs of Table 10, Table 11, Table 12, and/or Table 13, one or more glycans of Table 14, Table 15, Table 16 and/or Table 17 disclosed herein. These strategies can be used to develop tests that use one or more of these proteins, peptides, mRNAs, and/or glycans, any combination of one or more of these proteins, peptides, mRNAs and/or glycans, one or more of these proteins, peptides, mRNAs, and/or glycans in combination with any other biomarkers found to be associated with Kawasaki disease, and/or one or more of these proteins, peptides, mRNAs, and/or glycans in combination with one or more reference biomarkers not associated with Kawasaki disease.
Also provided herein are methods of determining the likelihood of a subject to develop cardiac artery aneurysms or stenosis. Accordingly, the invention also includes methods of diagnosing a subject that would benefit from a therapy other than or in addition to, IVIG therapy by performing any of the methods or using any of the compositions or kits described herein.
Other features and advantages of the invention will be apparent from the following description and the claims.
As used herein, the term “about” means ±10% of the recited value.
The term “array” or “microarray,” as used herein refers to an ordered arrangement of hybridizable array elements, preferably protein probes (e.g., antibodies), on a substrate. The substrate can be a solid substrate, such as a glass slide, beads, or microfluidic chip, or a semi-solid substrate, such as nitrocellulose membrane.
The term “Afro-Caribbean” refers to a person of Caribbean descent (i.e., is from or has an ancestor from the Caribbean Region, as classified by the United Nations Department of Economic and Social Affairs) and has an ancestor that emigrated from Africa to the Caribbean Region in the period since 1492.
The term “anticoagulant” refers to a drug that works to prevent the coagulation of blood, such as coumarins, thienopyridines (e.g., clopidogrel), heparin, low molecular weight heparin (e.g., enoxaparin), inhibitors of factor Xa, or thrombin inhibitors.
The term “anti-inflammatory agent” refers to a drug that reduces inflammation in a subject, e.g., non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin, ibuprofen, and naproxen.
The term “Asian” refers to a person of Asian descent (i.e., is from or has an ancestor from the Eastern Asia or Southeastern Asia Regions, as classified by the United Nations Department of Economic and Social Affairs). For example, a person from, or having an ancestor from, Japan (i.e., someone who is Japanese); or a person from, or having an ancestor from, Korea (i.e., someone who is Korean) are Asian.
By a “binding agent” is meant any compound (e.g., a probe, primer, protein, small molecule, aptamer, or antibody) capable of specifically binding a target. By “specifically binds” is meant binding that is measurably different from a non-specific interaction. Specific binding can be measured, for example, by determining binding of a molecule compared to binding of a control molecule. For example, specific binding can be determined by competition with a control molecule that is similar to the target, for example, an excess of non-labeled target. In this case, specific binding is indicated if the binding of the labeled target to a binding agent is competitively inhibited by excess unlabeled target. The term “specific binding,” “specifically binding,” or “specifically binds to” a particular protein as used herein can be exhibited, for example, by a molecule having a KD for the target of 10−4 M or lower, alternatively 10−5 M or lower, alternatively 10−6 M or lower, alternatively 10−7 M or lower, alternatively 10−5 M or lower, alternatively 10−9 M or lower, alternatively 10−10 M or lower, alternatively 10−11 M or lower, alternatively 10−12 M or lower, or a KD in the range of 10−4 M to 10−12 M or 10−6 M to 10−10 M or 10−7 M to 10−9 M. As will be appreciated by the skilled artisan, affinity and KD values are inversely related. A high affinity for a target is measured by a low KD value. In one embodiment, the term “specific binding” refers to binding where a binding agent binds to a particular protein, mRNA, or glycan without substantially binding to any other protein, mRNA, or glycan.
By “biological sample” or “sample” is meant a fluid or solid sample from a subject. Biological samples may include cells; nucleic acid, protein, or membrane extracts of cells; or blood or biological fluids including (e.g., plasma, serum, saliva, urine, bile). Solid biological samples include samples taken from feces, the rectum, central nervous system, bone, breast tissue, renal tissue, the uterine cervix, the endometrium, the head or neck, the gallbladder, parotid tissue, the prostate, the brain, the pituitary gland, kidney tissue, muscle, the esophagus, the stomach, the small intestine, the colon, the liver, the spleen, the pancreas, thyroid tissue, heart tissue, lung tissue, the bladder, adipose tissue, lymph node tissue, the uterus, ovarian tissue, adrenal tissue, testis tissue, the tonsils, and the thymus. Fluid biological samples include samples taken from the blood, serum, plasma, pancreatic fluid, CSF, semen, prostate fluid, seminal fluid, urine, saliva, sputum, mucus, bone marrow, lymph, and tears. Samples may be obtained by standard methods including, e.g., venous puncture and surgical biopsy. In certain embodiments, the biological sample is a blood, plasma, or serum sample.
By “classifying a subject” is meant predicting a response to a Kawasaki disease therapy by a subject; selecting a subject that may benefit from a Kawasaki disease therapy; selecting a subject who may benefit from IVIG therapy; predicting the responsiveness of a subject to IVIG therapy; determining the likelihood of a subject to develop cardiac artery aneurysms or stenosis; or selecting a subject that may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy.
By “diagnosing” is meant identifying a molecular or pathological state, disease or condition, such as the identification of Kawasaki disease or cardiac artery aneurysm and/or stenosis, or to refer to identification of a subject having Kawasaki disease who may benefit from a particular treatment regimen.
By “determining the level of a protein, mRNA, or glycan” is meant the detection of a protein, mRNA, or glycan by methods known in the art either directly or indirectly. “Directly determining” means performing a process (e.g., performing an assay or test on a sample or “analyzing a sample” as that term is defined herein) to obtain the physical entity or value. “Indirectly determining” refers to receiving the physical entity or value from another party or source (e.g., a third party laboratory that directly acquired the physical entity or value). Methods to measure protein level generally include, but are not limited to, western blotting, immunoblotting, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, immunofluorescence, surface plasmon resonance, chemiluminescence, fluorescent polarization, phosphorescence, immunohistochemical analysis, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, liquid chromatography (LC)-mass spectrometry, microcytometry, microscopy, fluorescence activated cell sorting (FACS), and flow cytometry, as well as assays based on a property of a protein including, but not limited to, enzymatic activity or interaction with other protein partners. Methods to measure mRNA and glycan levels are known in the art. Exemplary methods are provided herein.
By “determining the binding of IgG” is meant the detection of binding of IgG in a sample (e.g., a plasma sample) to a binding agent (e.g., a peptide of Table 3) by methods known in the art. “Directly determining” means performing a process (e.g., performing an assay or test on a sample or “analyzing a sample” as that term is defined herein) to obtain the physical entity or value. “Indirectly determining” refers to receiving the physical entity or value from another party or source (e.g., a third party laboratory that directly acquired the physical entity or value). Methods to measure binding generally include, but are not limited to, western blotting, immunoblotting, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), immunoprecipitation, immunofluorescence, surface plasmon resonance, chemiluminescence, fluorescent polarization, phosphorescence, immunohistochemical analysis, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, liquid chromatography (LC)-mass spectrometry, microcytometry, microscopy, fluorescence activated cell sorting (FACS), flow cytometry, peptide arrays, protein arrays and microarrays.
The term “immunosuppressant drug,” as used herein refers to a drug that inhibits or prevents activity of the immune system including glucocorticoids such as prednisone, cytostatics such as methotrexate, antibodies such as infliximab, drugs acting on immunophilins such as cyclosporine.
By “informing a subject” is meant providing the subject or the parent or legal guardian of the subject the results of the determining step and/or analysis of the results verbally and/or on printable media.
The term “IVIG” as used herein refers to intravenous immunoglobulin, a blood product containing pooled, polyvalent IgG extracted from the plasma of over one thousand blood donors. The term “IVIG therapy” refers to a treatment including the administration of IVIG to a subject, e.g., in high doses, such as, 2 g/kg.
By “Kawasaki disease therapy” is meant any therapy in the art for the treatment of Kawasaki disease, such as, therapeutic agents or modalities for Kawasaki disease. Common treatments for Kawasaki disease include administration of IVIG (i.e., IVIG therapy); salicylates (e.g., aspirin); corticosteroids (e.g., prednisone); IL-1 receptor antagonists; anticoagulants (e.g., enoxaparin and/or clopidogrel); anti-TNF agents (e.g., infliximab); or any combination thereof.
The terms “kit or device,” as used herein, refer to a set of articles and/or equipment, such as reagents, instruments, and systems, intended for use in diagnosis or prognosis of disease or other conditions, including determination of the state of health, in order to cure, mitigate, treat, or prevent disease or its sequelae. The kits and devices of the invention are intended for use in the collection, preparation, and/or examination of biological samples taken from the subject. For example, the kits and devices of the invention may be used for biochemical estimation or the qualitative detection of a protein. The kits and devices of the invention may include general purpose reagents and analyte specific reagents. A “general purpose reagent” refers to a chemical reagent that has general laboratory application, used to collect, prepare, and/or examine specimens from the human body for diagnostic purposes, and is not labeled or otherwise intended for a specific diagnostic application. An “analyte specific reagent” refers to antibodies, both polyclonal and monoclonal, specific receptor proteins, ligands, nucleic acids, and other binding agents which, through specific binding or chemical reaction with substances in a biological sample, are intended for use in a diagnostic application for identification and quantification of an individual chemical substance or ligand in biological samples. The kits and devices of the invention may include a label which states the name of the kit or device, the intended use or uses of the device (e.g., the diagnosis of Kawasaki disease), a statement of warnings or precautions for users of any hazardous substances contained in the kit or device and any other warnings appropriate to user hazards, the established name of the reagents, quantity, proportion, or concentration of all active ingredients and for reagents derived from biological activity, the source and measure of its activity, storage instructions, and/or instructions for manipulation of products requiring mixing or reconstitution. The kit may also include instructions for detection read out and interpretation.
By “level” is meant a level of a protein, glycan, or mRNA, as compared to a reference. The reference can be any useful reference, as defined herein. By a “decreased level” or an “increased level” of a protein is meant a decrease or increase in protein level, as compared to a reference (e.g., a decrease or an increase by about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 100%, about 150%, about 200%, about 300%, about 400%, about 500%, or more; a decrease or an increase of more than about 10%, about 15%, about 20%, about 50%, about 75%, about 100%, or about 200%, as compared to a reference; a decrease or an increase by less than about 0.01-fold, about 0.02-fold, about 0.1-fold, about 0.3-fold, about 0.5-fold, about 0.8-fold, or less; or an increase by more than about 1.2-fold, about 1.4-fold, about 1.5-fold, about 1.8-fold, about 2.0-fold, about 3.0-fold, about 3.5-fold, about 4.5-fold, about 5.0-fold, about 10-fold, about 15-fold, about 20-fold, about 30-fold, about 40-fold, about 50-fold, about 100-fold, about 1000-fold, or more). A level of a protein may be expressed in mass/vol (e.g., g/dL, mg/mL, μg/mL, ng/mL) or percentage relative to total protein, glycan, or mRNA in a sample. By “protein level profile” is meant one or more protein level values determined for a sample.
By “processing a sample” is meant any process carried out on the sample prior to the determination of the level or expression of the protein. Exemplary processing steps include, but are not limited to, centrifugation of the sample, fractionation of the sample, treatment with reagents (e.g., digesting enzymes or reducing reagents), and/or dilution of the sample. By “fractionation of a sample” is meant the general processes of separating the various components of a sample. For example, the components of the sample may be separated by chromatography (e.g., ion exchange chromatography). In some cases, the most abundant proteins, such as, proteins present at greater than 0.01, greater than 0.02, greater than 0.05, greater than 0.1 g/dL (e.g., greater than 0.2 g/dL, greater than 0.5 g/dL, greater than 1.0 g/dL, greater than 2.0 g/dL, greater than 3.0 g/dL) are depleted from the sample by chromatography to enhance the sensitivity for less abundant proteins, such as, proteins present at less than 0.2 g/dL (e.g., less than 0.1 g/dL, less than 0.05 g/dL, less than 0.01 g/dL). Columns/kits for the depletion of abundant proteins are known in the art, for example, MARS Human-6 and Human-7 from Agilent Technologies deplete the 6 and 7 most abundant proteins from human plasma.
By “reagent” is meant a polynucleotide sequence or polypeptide sequence capable of detecting a target sequence, or a fragment thereof.
By a “reference” is meant any useful reference used to compare protein or mRNA levels related to Kawasaki disease and/or binding of IgG to a peptide of Table 3. The reference can be any sample, standard, standard curve, or level that is used for comparison purposes. The reference can be a normal reference sample or a reference standard or level. A “reference sample” can be, for example, a control, e.g., a predetermined negative control value such as a “normal control” or a prior sample taken from the same subject; a sample from a normal healthy subject, such as a normal cell or normal tissue; a sample (e.g., a cell or tissue) from a subject not having Kawasaki disease; a sample from a subject that is diagnosed with cardiac artery aneurysms or stenosis; a sample from a subject that has been treated for Kawasaki disease; or a sample of a purified protein (e.g., any described herein) at a known normal concentration. By “reference standard or level” is meant a value or number derived from a reference sample. A “normal control value” is a pre-determined value indicative of non-disease state, e.g., a value expected in a healthy control subject. Typically, a normal control value is expressed as a range (“between X and Y”), a high threshold (“no higher than X”), or a low threshold (“no lower than X”). A subject having a measured value within the normal control value for a particular biomarker is typically referred to as “within normal limits” for that biomarker. A normal reference standard or level can be a value or number derived from a normal subject not having Kawasaki disease; a subject that is diagnosed with cardiac artery aneurysms or stenosis; a subject that has been treated for Kawasaki disease. In preferred embodiments, the reference sample, standard, or level is matched to the sample subject sample by at least one of the following criteria: age, weight, sex, disease stage, and overall health. A standard curve of levels of a purified protein, e.g., any described herein, within the normal reference range can also be used as a reference.
“Response” as used herein indicates a subject's response to a Kawasaki disease therapy, e.g., a response can be a positive response such that symptoms will be alleviated as a result of the Kawasaki disease therapy.
By “selecting a subject” is meant to choose a subject directly or indirectly in preference to others based on an analysis, e.g., analysis of results of the methods of the invention or clinical evaluation. Directly selecting means performing a process (e.g., performing an analysis) to choose a subject. Indirectly selecting refers to receiving the results of an analysis from another party or source (e.g., a third party laboratory that directly performed the analysis).
By “solid support” is meant a structure capable of storing, binding, or attaching one or more binding agents.
By “subject” is meant a human (e.g., a child less than 18 years old, less than 13 years old, less than 8 years old, less than 5 years old, less than 4 years old, less than 3 years old, less than 2 years old, or less than 1 year old). A subject to be treated with a pharmaceutical composition described herein may be one who has been diagnosed by a medical practitioner as having such a disease or condition (e.g., Kawasaki disease) or one at risk for developing a disease or condition (e.g., cardiac artery aneurysm or stenosis).
By “target sequence” is meant a portion of a gene or a gene product, including the mRNA and related cDNA.
By “therapeutic agent” is meant any agent that produces a healing, curative, stabilizing, or ameliorative effect.
A “therapeutically effective amount” of a compound may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the compound to elicit a desired response in the individual. A therapeutically effective amount encompasses an amount in which any toxic or detrimental effects of the compound are outweighed by the therapeutically beneficial effects. A therapeutically effective amount also encompasses an amount sufficient to confer benefit, e.g., clinical benefit.
By “treating” is meant administering a composition (e.g., a pharmaceutical composition) for therapeutic purposes or administering treatment to a subject already having a condition or disorder to improve the subject's condition or to reduce the likelihood of a condition or disorder. By “treating a condition or disorder” is meant that the condition or disorder and/or the symptoms associated with the condition or disorder are, e.g., alleviated, reduced, cured, or placed in a state of remission. By “reduce the likelihood of” is meant reducing the severity, the frequency, and/or the duration of a disorder (e.g., cardiac artery aneurysms and/or stenosis) or symptoms thereof. Reducing the likelihood of cardiac artery aneurysms and/or stenosis is synonymous with prophylaxis or the chronic treatment of cardiac artery aneurysms and/or stenosis.
Other features and advantages of the invention will be apparent from the following Detailed Description and the claims.
There is no specific test available to diagnose Kawasaki disease. Diagnosis largely is a process of ruling out diseases that cause similar signs and symptoms, including: scarlet fever; juvenile rheumatoid arthritis; Stevens-Johnson syndrome; toxic shock syndrome; measles; certain tick-borne illnesses. A doctor may do a physical examination and perform other tests to help in the diagnosis or prognosis. These tests may include urine tests, blood tests, electrocardiogram, and echocardiogram. (http://www.mayoclinic.org/diseases-conditions/kawasaki-disease/basics/tests-diagnosis/con-20024663, Mar. 3, 2014).
The present invention relates to the identification of biomarkers (e.g., protein levels, mRNA levels, glycan abundance, or IgG binding) that identify subjects having Kawasaki disease and/or being predisposed to develop Kawasaki disease-related cardiac artery aneurysms or stenosis. Such differential levels of proteins, mRNAs, glycans, and/or differential binding of IgG in samples can be used to diagnose, prognose, and classify subjects with Kawasaki disease and/or a predisposition to develop cardiac artery aneurysms or stenosis from healthy controls. Accordingly, the kits and methods described herein are useful for treating or diagnosing Kawasaki disease and/or related cardiac artery aneurysms or stenosis. Also described herein are diagnostic kits (e.g., on a solid support, such as an array or chip) which can be used to perform such methods.
Applicants have discovered that the levels of certain proteins can be utilized to diagnose, prognose, and treat Kawasaki disease, as well as to select subjects who would benefit from either IVIG therapy or a Kawasaki disease therapy other than, or in addition to, IVIG therapy. Proteins, the levels of which are of interest in the methods and compositions of the invention, include those in Table 18.
As indicated above, proteins useful for diagnosing Kawasaki disease, or selecting or classifying a subject that may benefit from a Kawasaki disease therapy include those in Tables 1 and 2. Proteins useful for selecting or classifying a subject that may benefit from a therapy other than, or in addition to, IVIG therapy include those in Tables 4, 5, 6, and 7.
Applicants have discovered that the level of binding of IgG in samples to certain proteins can be utilized to diagnose, prognose, and treat Kawasaki disease, as well as to select subjects who would benefit from a Kawasaki disease therapy. Proteins, the binding of which are of interest in the methods and compositions of the invention, include those comprising an amino acid sequence of any one of SEQ ID NOs:1 to 68.
Applicants have discovered that the mRNA expression levels of certain genes can be utilized to diagnose, prognose, and treat Kawasaki disease, as well as to select subjects who would benefit from either IVIG therapy or a Kawasaki disease therapy other than, or in addition to, IVIG therapy. Genes, the mRNA levels of which are of interest in the methods and compositions of the invention, include those in Table 19.
As indicated above, genes useful for selecting or classifying a subject that may benefit from a therapy other than, or in addition to, IVIG therapy include those in Table 10, Table 11, Table 12, and/or Table 13.
Applicants have discovered that the levels of certain glycans on IgG and IgA can be utilized to diagnose, prognose, and treat Kawasaki disease, as well as to select subjects who would benefit from either IVIG therapy or a Kawasaki disease therapy other than, or in addition to, IVIG therapy. Glycans, the levels of which are of interest in the methods and compositions of the invention, include those in Table 20.
G; N-glycans, P; plasma, fraction #, LA; low abundant fraction, HA; high abundant fraction. Glycan annotations according to Oxford Symbol nomenclature. All N-glycans have two core GlcNAcs; F at the start of the abbreviation indicates a core a(1-6)fucose linked to inner GlcNAc; Mx, number (x) of mannose on core GlcNAcs; Ax, number of antenna (GlcNAc) on trimannosyl core; A2, biantennary with both GlcNAcs as b(1-2) linked; A3, triantennary with a GlcNAc linked b(1-2) to both mannose and a third GlcNAc linked b(1,4) to the a(1-3) linked mannose; A3′; triantennary with a GlcNAc linked b(1-2) to both mannose and the third GlcNAc linked b(1-6) mannose; B, bisecting GlcNAc linked b(1-4) to b(1-3) mannose; Gx, number (x) of b1-4 linked galasose on the antenna; Fx, number (x) of linked fucose on antenna, (4) or (3) after the F indicates that the Fuc is a(1-4) or a(1-3) linked to the GlcNAc; Sx, number (x) sialic acids linked to galactose; the number 3 or 6 in parenthesis after S indicates whether the sialic acid is in an a(2-3) or a(2-6) linkage. See Harvey et al. Proposal for a standard system for drawing structural diagrams of N- and O-linked carbohydrates and related compounds. Proteomics 2009, 9:3796-801.
As indicated above, glycans useful for diagnosing Kawasaki disease, selecting or classifying a subject that may benefit from a Kawasaki disease therapy and/or selecting or classifying a subject that may benefit from a therapy other than, or in addition to, IVIG therapy include those in Table 14, Table 15, Table 16, and/or Table 17.
The present invention features methods and compositions to diagnose Kawasaki disease. The kits and methods of the invention may be used alone or as a companion diagnostics with other diagnostic or therapeutic approaches, as an early molecular screen to distinguish Kawasaki disease from other diseases and disorders with similar symptoms. More specifically, alterations in the level of one or more proteins described herein (e.g., proteins of Table 1 and/or Table 2) and/or binding of IgG to a protein of Table 3 in a test sample as compared to a normal reference can be used to diagnose Kawasaki disease and/or distinguish Kawasaki disease from diseases or disorders with similar symptoms, thereby allowing subject classification.
Further, the present invention features methods and compositions useful in determining the likelihood of a subject to develop cardiac artery aneurysms and/or stenosis. For example, the methods and compositions of the invention may be used to determine if a subject may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy, by determining the levels of one or more biomarkers of Table 4, Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11, Table 12, Table 13, Table 14, Table 15, Table 16, and/or Table 17.
The methods of the invention can be used to diagnose, prognose, or classify a subject, for example, an increase in the level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more, as compared to a reference) of the biomarker(s) (e.g., a protein of Table 1) may indicate a subject has Kawasaki disease and/or may benefit from a Kawasaki disease therapy. Similarly, a decrease in the level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less, as compared to a reference) of the biomarker(s) (e.g., a protein of Table 2) may indicate a subject has Kawasaki disease and/or may benefit from a Kawasaki disease therapy. An increase (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more, as compared to a reference) in binding of IgG in a sample to a protein comprising an amino acid sequence of Table 3 may indicate a subject has Kawasaki disease and/or may benefit from a Kawasaki disease therapy.
Alternatively, an increase in the level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more, as compared to a reference) of the biomarker(s) (e.g., a protein of Table 4) may indicate a subject is predisposed to develop cardiac artery aneurysms or stenosis and/or may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy. Similarly, a decrease in the level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less, as compared to a reference) of a biomarker(s) (e.g., a protein of Table 5) may indicate a subject is predisposed to develop cardiac artery aneurysms or stenosis and/or may benefit from a Kawasaki disease therapy other than, or in addition to, IVIG therapy.
To carry out the methods of the invention, a sample can be obtained by any method known in the art. For instance, samples from a subject may be obtained by venipuncture, resection, bronchoscopy, fine needle aspiration, bronchial brushings, or from sputum, pleural fluid, urine, or blood, such as serum or plasma. Proteins can be detected in these samples. By screening such biological samples, a simple early diagnosis or differential diagnosis can be achieved for Kawasaki disease. In addition, the progress of therapy can be monitored by testing such biological samples for target proteins and/or binding of IgG to a protein of Table 3. Furthermore, the prediction of outcome or response to therapy can similarly be tested using such biological samples for target proteins and/or binding of IgG to a protein of Table 3.
In certain embodiments, the sample may be contacted with an antibody specific for the target protein under conditions sufficient for an antibody-protein complex to form, and detection of the complex. The presence of the biomarker may be detected in a number of ways, such as by Western blotting or ELISA procedures using any of a wide variety of tissues or samples, including plasma or serum. A wide range of immunoassay techniques using such an assay format are available, see, e.g., U.S. Pat. Nos. 4,016,043, 4,424,279, and 4,018,653. These include both single-site and two-site or “sandwich” assays of the noncompetitive types, as well as traditional competitive binding assays. These assays also include direct binding of a labeled antibody to a target biomarker.
Another method involves immobilizing the target biomarkers (e.g., on a solid support) and then exposing the immobilized target to a specific antibody, which may or may not contain a label. Depending on the amount of target and the strength of the label's signal, a bound target may be detectable by direct labeling with the antibody. Alternatively, a second labeled antibody, specific to the first antibody is exposed to the target-first antibody complex to form a target-first antibody-second antibody tertiary complex. The complex is detected by the signal emitted by a label, e.g., an enzyme, a fluorescent label, a chromogenic label, a radionuclide containing molecule (i.e., a radioisotope), or a chemiluminescent molecule.
Variations on the forward assay include a simultaneous assay, in which both sample and labeled antibody are added simultaneously to a bound antibody. These techniques are well known to those skilled in the art, including any minor variations as will be readily apparent. In a typical forward sandwich assay, a first antibody having specificity for the biomarker is either covalently or passively bound to a solid surface (e.g., a glass or a polymer surface, such as those with solid supports in the form of tubes, beads, discs, or microplates), and a second antibody is linked to a label that is used to indicate the binding of the second antibody to the molecular marker.
In alternative methods, the expression of a protein in a sample may be examined using immunohistochemistry (“IHC”) and staining protocols. IHC staining of tissue sections has been shown to be a reliable method of assessing or detecting presence of proteins in a sample. IHC and immunofluorescence techniques use an antibody to probe and visualize cellular antigens in situ, generally by chromogenic or fluorescent methods. The tissue sample may be fixed (i.e., preserved) by conventional methodology (see, e.g., “Manual of Histological Staining Method of the Armed Forces Institute of Pathology,” 3rd edition (1960) Lee G. Luna, HT (ASCP) Editor, The Blakston Division McGraw-Hill Book Company, New York; The Armed Forces Institute of Pathology Advanced Laboratory Methods in Histology and Pathology (1994) Ulreka V. Mikel, Editor, Armed Forces Institute of Pathology, American Registry of Pathology, Washington, D.C.). One of skill in the art will appreciate that the choice of a fixative is determined by the purpose for which the sample is to be histologically stained or otherwise analyzed. By way of example, neutral buffered formalin, Bouin's or formaldehyde, may be used to fix a sample. Generally, the sample is first fixed and is then dehydrated through an ascending series of alcohols, infiltrated and embedded with paraffin or other sectioning media so that the tissue sample may be sectioned. Alternatively, one may section the tissue and fix the sections obtained. The primary and/or secondary antibody used for immunohistochemistry typically will be labeled with a detectable moiety, such as a radioisotope, a colloidal gold particle, a fluorescent label, a chromogenic label, or an enzyme-substrate label.
Alternatively, the levels of biomarkers may be detected without the use of binding agents. In some instances, biological samples as described herein are analyzed, for example, by one or more, enzymatic methods, chromatographic methods, mass spectrometry (MS) methods, chromatographic methods followed by MS, electrophoretic methods, electrophoretic methods followed by MS, nuclear magnetic resonance (NMR) methods, and combinations thereof. In some instances, the biological sample is treated with one or more enzymes (e.g., trypsin). Exemplary chromatographic methods include, but are not limited to, Strong Anion Exchange chromatography using Pulsed Amperometric Detection (SAX-PAD), liquid chromatography (LC), high performance liquid chromatography (HPLC), ultra performance liquid chromatography (U PLC), thin layer chromatography (TLC), amide column chromatography, and combinations thereof. Exemplary mass spectrometry (MS) include, but are not limited to, tandem MS, LC-MS, LC-MS/MS, matrix assisted laser desorption ionisation mass spectrometry (MALDI-MS), Fourier transform mass spectrometry (FTMS), ion mobility separation with mass spectrometry (IMS-MS), electron transfer dissociation (ETD-MS), Multiple Reaction Monitoring (MRM), and combinations thereof. Exemplary electrophoretic methods include, but are not limited to, capillary electrophoresis (CE), CE-MS, gel electrophoresis, agarose gel electrophoresis, acrylamide gel electrophoresis, SDS-polyacrylamide gel electrophoresis (SDS-PAGE) followed by Western blotting using antibodies that recognize specific glycan structures, and combinations thereof. Exemplary nuclear magnetic resonance (NMR) include, but are not limited to, one-dimensional NMR (1 D-NMR), two-dimensional NMR (2D-NMR), correlation spectroscopy magnetic-angle spinning NMR (COSY-NMR), total correlated spectroscopy NMR (TOCSY-NMR), heteronuclear single-quantum coherence NMR (HSQC-NM R), heteronuclear multiple quantum coherence (HMQC-NMR), rotational nuclear overhauser effect spectroscopy NMR (ROESY-NMR), nuclear overhauser effect spectroscopy (NOESY-NMR), and combinations thereof.
Any of the methods herein that rely upon protein measurement can also be adapted for use with the measurement of mRNA levels for the protein. The level of mRNA can be determined using methods known in the art. Methods to measure mRNA levels generally include, but are not limited to, sequencing, northern blotting, RT-PCR, gene array technology, and RNAse protection assays.
Binding Agents
Any binding agent that specifically binds a target biomarker may be used in the methods of the invention. The binding agent may be, e.g., a protein (e.g., an antibody), small molecule, or aptamer capable of specifically binding a target.
Preferably, each binding agent specifically binds to one biomarker in a sample. For determining the level of a biomarker, the measurement of antibodies specific to a biomarker of the invention in a subject may be used for the diagnosis of Kawasaki disease. The binding agent may optionally contain a label, such as a radioisotope, a colloidal gold particle, a fluorescent label, a chromogenic label, an enzyme-substrate label, or a chemiluminescent label.
Sample Processing
In some embodiments of any of the foregoing methods, the biological sample is processed prior to determining the level of the one or more the biomarkers, e.g., the biological sample is centrifuged, the biological sample is filtered, the biological sample is diluted, the biological sample is treated with reagents (e.g., digesting enzymes or reducing reagents), the biological sample is fractionated to remove more abundant proteins (e.g., proteins present at concentrations greater than 0.01 g/dL, greater than 0.02 g/dL, greater than 0.05 g/dL, greater than 0.1 g/dL, greater than 0.2 g/dL, greater than 0.5 g/dL, greater than 1.0 g/dL, greater than 2.0 g/dL, greater than 3.0 g/dL), such as, albumins, globulins (e.g., haptoglobulin, alpha2-macroglobulin, IgG, IgA, and IgM), alpha1-acid glycoprotein, apolipoprotein AI, apolipoprotein AII, complement C3, transthyretin, antitrypsin, transferrin, and fibrinogen and/or enrich for less abundant proteins, such as, any protein from Tables 1, 2, 4, and/or 5.
For example, a blood sample may be obtained, and prior to determining the level of one or more proteins, the sample may be centrifuged to remove red blood cells (i.e., to provide a plasma sample). The plasma sample may be spin filtered and diluted. Subsequently, the sample may be chromatographically separated using an immunoaffinity-based column to remove more abundant proteins (e.g., the 10-20, e.g., 10, 12, 14, 16, 18, 20 most abundant proteins) and enrich for less abundant proteins. The enriched sample may be concentrated and buffer exchanged, followed by treatment with a digesting enzyme, e.g., trypsin. Determination of protein levels may then be carried out on the processed sample.
The invention further features methods for predicting response to a Kawasaki disease therapy in a subject before or after administration of one or more Kawasaki disease therapies. These methods may be carried out generally as described above or as known in the art with respect to sample collection and assay format. For example, these methods may be carried out by collecting a sample, e.g., a blood or plasma sample from a subject; measuring the level of one or more biomarkers described herein (e.g., proteins of Table 1, 2, 4, 5, 6, 7, 8, and/or 9, genes of Table 10, Table 11, Table 12, and/or Table 13, and/or glycans of Table 14, Table 15, Table 16, and/or Table 17) in the sample and/or determining the binding of IgG in the sample to a protein comprising an amino acid sequence of Table 3; comparing to a control sample; and making a prediction about whether the subject will be responsive to a Kawasaki disease therapy. The method also can be used to predict whether a subject, who has been diagnosed with Kawasaki disease, will respond positively to a Kawasaki disease therapy such as a therapeutic (e.g., IVIG) or a combination of therapeutics (e.g., IVIG and one or more anticoagulants, an anti-inflammatory agent, and/or one or more immunosuppressant drugs).
A prediction of a positive response refers to a case where the Kawasaki disease symptoms will be alleviated and/or the risk of mortality will be reduced as a result of the Kawasaki disease therapy.
In the methods of predicting response to a Kawasaki disease therapy, the level of the protein(s) binding of IgG, gene(s), and/or glycan(s) can be determined relative to a control value. A control value can be a range or average value from a normal subject or a population of normal subjects; a value from a sample from a subject or population of subjects who have undergone a Kawasaki disease therapy and have reduced symptoms following therapy; a value from the same subject before the subject was diagnosed or before the subject started treatment.
The methods of the invention can be used to predict whether a subject will be responsive to a Kawasaki disease therapy, for example, an increase in the level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more, as compared to a reference) of the biomarker(s) (e.g., a protein of Table 1) may indicate a positive response to a Kawasaki disease therapy. Similarly, a decrease in the level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less, as compared to a reference) of the biomarker(s) (e.g., a protein of Table 2) may indicate a positive response to a Kawasaki disease therapy. Also, increased binding (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more, as compared to a reference) of IgG in the sample may indicate a positive response to a Kawasaki disease therapy.
Alternatively, an increase in the level (e.g., an increase by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more, or an increase by more than 1.2-fold, 1.4-fold, 1.5-fold, 1.8-fold, 2.0-fold, 3.0-fold, 3.5-fold, 4.5-fold, 5.0-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 100-fold, 1000-fold, or more, as compared to a reference) of the biomarker(s) (e.g., a protein of Table 4) may indicate a poor response to a Kawasaki disease therapy. Similarly, a decrease in the level (e.g., a decrease by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400%, 500%, or more; or a decrease by less than 0.01-fold, 0.02-fold, 0.1-fold, 0.3-fold, 0.5-fold, 0.8-fold, or less, as compared to a reference) of the biomarker(s) (e.g., a protein of Table 5) may indicate a poor response to a Kawasaki disease therapy.
The methods of the invention can be used to predict a subject's response to a Kawasaki disease therapy and classify the subject as a “responder,” e.g., a subject with protein levels and/or binding of IgG indicative of a positive response to a Kawasaki disease therapy (e.g., IVIG), or a “non-responder,” e.g., a subject with protein levels and/or binding of IgG indicative of a poor response to a Kawasaki disease therapy (e.g., a subject that may benefit from a therapy other than, or in addition to, IVIG therapy).
The prediction can be made prior to administration of a first Kawasaki disease therapy. Alternatively, the prediction can be made after administration of the first Kawasaki disease therapy, or after administration of a first Kawasaki disease therapy but before a second Kawasaki disease therapy. Furthermore, the prediction can be made at any time during the course of a Kawasaki disease therapy.
The methods described herein can also be used to monitor Kawasaki disease status (e.g., progression or regression) during therapy or to optimize dosage of one or more therapeutic agents for a subject. For example, alterations (e.g., an increase or a decrease as compared to either the positive reference sample or the level diagnostic for Kawasaki disease) can be detected to indicate an improvement in Kawasaki disease status. In this embodiment, the levels of the protein(s), binding of IgG, gene(s), and/or glycan(s) may be measured repeatedly as a method of not only diagnosing disease, but also monitoring the treatment, prevention, or management of the disease.
In order to monitor the status of Kawasaki disease in a subject, subject samples may compared to reference samples taken early in the diagnosis of the disorder. Such monitoring may be useful, for example, in assessing the efficacy of a particular therapeutic agent (e.g., IVIG) in a subject, determining dosages, or in assessing disease progression or status. For example, levels of any of the proteins, genes, and/or glycans described herein, and/or binding of IgG, or any combination thereof can be monitored in a subject, and as the levels or activities increase or decrease, relative to control, the dosage or administration of therapeutic agents may be adjusted.
The invention also features a method for treatment of Kawasaki disease in a subject by contacting a biological sample from the subject with one or more binding agents capable of specifically binding one or more biomarkers (e.g., one or more proteins of Table 6); determining if the level in said biological sample is changed relative to a control value; predicting a response to a Kawasaki disease therapy in said subject based on the level of one or more of said biomarkers; and, if the prediction is positive, administering a Kawasaki disease therapy.
The methods can also be used to determine the proper dosage (e.g., the therapeutically effective amount) of a therapeutic agent for the subject, the proper type of therapeutic agent, or whether a therapy should be administered.
Several therapeutic agents have been used in the treatment of Kawasaki disease. These include, without limitation, administration of IVIG (i.e., IVIG therapy); salicylates (e.g., aspirin); corticosteroids (e.g., prednisone); IL-1 receptor antagonists; anticoagulants (e.g., enoxaparin and/or clopidogrel); infliximab; or any combination thereof. Approximately 25% of subjects do not respond to IVIG treatment. These predisposed subjects are at a higher risk for developing cardiac artery aneurysms or stenosis. These subjects, as classified herein, may be administered low molecular weight heparin (LMWH), such as enoxaparin, in addition to IVIG, for an extended period of time, e.g., weeks to months. Other therapies that may be administered in addition to IVIG, include, but are not limited to, anti-TNF agents (e.g., adalimumab, infliximab, or etanercept); anti-IL treatment (e.g., anti-IL-1a, IL-1 b, IL-1 RA); statins (e.g., atorvastatin, pravastatin); corticosteroids (e.g., prednisolone, methylprednisolone); immunomodulators (e.g., cyclosporine A, methotrexate), anti-CD20 therapy (e.g., rituximab); plasma exchange, warfarin, and fibrinogen receptor glycoprotein IIb/IIIa, such as Abciximab.
The invention also provides test kits and devices. For example, a diagnostic test kit can include one or more binding agents and, if desired, components for detecting and/or evaluating binding between the binding agent and a biomarker. For detection, one or more of binding agents may be labeled. In further embodiments, one or more of the binding agents may be substrate-bound, such that a biomarker-antibody interaction can be established by determining the amount of label attached to the substrate following binding between the antibody and the biomarker. A conventional ELISA is a common, art-known method for detecting antibody-substrate interaction and can be provided as the kit of the invention.
A kit that determines an alteration in the level of a protein, binding of IgG, to a peptide, gene, and/or glycan relative to a reference, such as the level present in a normal control, is useful as a diagnostic kit in the methods of the invention. Such a kit or device may further include a reference sample or standard curve indicative of a positive reference or a normal control reference.
Desirably, the kit will contain instructions for the use of the kit. In one example, the kit contains instructions for the use of the kit for the diagnosis of Kawasaki disease. In yet another example, the kit contains instructions for the use of the kit to monitor therapeutic treatment or dosage regimens. In yet another example, the kit contains instructions for the use of the kit to predict outcome, response to therapy, or disease recurrence. In a further example, the instructions include one or more metrics (e.g., metrics to be used as references).
The following examples are intended to illustrate the invention. They are not meant to limit the invention in any way.
Plasma Proteomics
Proteomics on human plasma samples were carried out as follows. In order to enhance sensitivity for less abundant species, the top 14 most abundant proteins were depleted from plasma samples prior to proteomics analysis using the Agilent MARS column. Briefly, 50 μl of human plasma was spin filtered and diluted with the sample buffer and applied to a MARS column. Two fractions, eluted from the column, were collected: fraction 1 representing less abundant proteins (LA Frn1) and fraction 2 representing highly abundant serum proteins (HA Frn2). Both fractions were concentrated and buffer exchanged. LA Frn1 was digested by trypsin, followed by proteomics analysis. Lower abundant fraction-1 tryptic digests were subjected to nano-LC-MS/MS analysis. Separations were carried out using an Ultimate3000 RSLCnano system. Chromatography was carried using analytical EASY-Spray PepMap RSLC, 25 cm×75 μm id, C18, 2 μm and 100 Å nano column thermostatically controlled at 50° C. and at 300 nL/min with a linear gradient from 1% to 38% acetonitrile/water both containing 0.1% (v/v) FA for a total duration of 150 minutes. The separation step was followed by a 30 minute washing step with 99% acetonitrile/water followed by a 20 minute equilibration step with 99% water/acetonitrile both containing 0.1% (v/v) FA. 1.0 μg of each sample was injected into the column. Data dependent MS-MS was performed on the top 25 precursor ions from the full MS scan on the Orbi-Velos MS instrument.
1 μg protein from each sample was injected into the nano-LC-MS/MS system. The data quality was reproducible across all samples. Proteome discoverer with Sequest search engine was used for database searching of each sample against Uniprot human protein database. ˜450 proteins were identified from each sample. The distribution of peptide spectral matches (PSM) was plotted for each sample, and the overall assessment indicated that most samples contained equivalent numbers of PSM as observed.
Overall, ca. 440 protein signatures were acquired per sample using the set criteria.
Log ratios were calculated from the average normalized spectral counts from pairwise comparisons to get the fold change of proteins across the groups. T-test was conducted to determine the significance of the change. Further, the data were filtered to include changes with less than or equal to 0.05 T-test value.
Soluble Plasma Proteins
The concentrations of plasma IgG and IgA were determined using the Total Human IgG Immunoenzymetric Assay and the Human Immunoglobulin A Immunoenzymetric Assay from Cygnus Technologies (Southport, N.C.). The Human FcγR3B ELISA Kit from MyBioSource (San Diego, Calif.) was used to quantify the concentration of soluble CD16 in the patient samples. The concentration of α2,6-sialyltransferase (ST6GALI) in the plasma samples was quantified using the α2,6-Sialyltransferase Assay Kit from Immuno-Biological Laboratories (Minneapolis, Minn.). The plasma samples were diluted in diluents provided with each ELISA. The manufacturer's instructions supplied with the assay kits were followed for the quantitation of each analyte. Absorbance readings for all assays were determined using a SpectraMax M2 spectrophotometer (Molecular Devices, Sunnyvale, Calif.) and analysis was performed using SoftMax Pro 5.2 software (Molecular Devices).
IgG and IgA Glycomics
Methods for glycosylation analysis of Ig proteins is known in the art, for example, as described in Pucic et al, Molecular and Cellular Proteomics, 2011 October(10): 1-15.
Tryptic digests of Protein G enriched plasma fraction were subjected to nano-LC-MS/MS analysis. Two IVIg samples were used along with the KD samples as controls throughout the sample prep and data analysis. All separations were carried out using an Ultimate3000 RSLCnano system. Chromatography was carried using analytical EASY-Spray PepMap RSLC, 25 cm×75 μm id, C18, 2 μm and 100 Å nano column thermostatically controlled at 50° C. and at 300 nL/min with a linear gradient from 1% to 38% acetonitrile/water both containing 0.1% (v/v) FA for a total duration of 70 minutes. The separation step was followed by a 30 minutes washing step with 99% acetonitrile/water followed by a 20 minutes equilibration step with 99% water/acetonitrile both containing 0.1% (v/v) FA. 1.0 ug of each sample was injected on column. Data dependent MS-MS was performed on top 25 precursor ions from the full MS scan on the Orbi-Velos MS instrument.
Data analysis was performed using Xcalibur software—Qual and Quan browser. Area of each of the glycopeptides (IgG1, IgG2, IgG3/4 and IgA) was extracted from the base peak chromatogram. All the glycopeptide species m/z and retention time were captured in a processing method that was used for quantitation across all the samples. Peak integration was manually checked for accuracy in the quan browser. The raw abundances/area of all the glycopeptides for all the 30 KD samples and two IVIg controls was then exported in excel. The data was normalized based on the total glycopeptide abundance for each specific IgG (1, 2, 3/4) and IgA protein within the sample. Based on these data analysis, we reported the relative abundance of each of the IgG1, IgG2, IgG3/4, and IgA glycopeptide species per sample. Up to this point the samples were all blinded. Once we had the measurement values, then for interpretation we used the unblinded sample description wherein we could group the samples as Febrile controls, Acute phase KD, IVIg treated, and LMWH treated patient samples.
Total Plasma Glycome
To low- and high-abundant protein plasma fractions (25 μL) were added: 2 μL of sample buffer (0.625 mL of 0.5M Tris, pH 6.6, 1 mL of 10% SDS, and 3.375 mL of water), 2 μL of water, and 1 μL of 0.5M dithiothreitol (DTT), followed by incubation at 65° C. for 15 min. The samples were then alkylated by adding 1 μL of 100 mM iodoacetamide and incubated for 30 min in the dark at room temperature. The samples were then set into gel blocks by adding 22.5 μL of 30% (w/w) acrylamide/0.8% (w/v) bis-acrylamide stock solution (37.5:1.0, Protogel, National Diagnostics, Hessle, Hull, UK), 11.25 μL of 1.5M Tris (pH 8.8), 1 μL of 10% SDS, 1 μL of 10% ammonium peroxodisulfate (APS), and finally 1 μL of N,N,N,N′-tetramethyl-ethylenediamine (TEMED), mixed, and then left to set. The gel blocks were transferred to a filter plate and washed with 1 mL of acetonitrile with vortexing on a plate mixer (Sarstedt, Leicester, UK) for 10 min, followed by removal of the liquid. Washing procedure was repeated twice with 1 mL of 20 mM NaHCO3(pH 7.0) followed by 1 mL of acetonitrile. N-glycans were released by adding 50 μL of 0.1 U/mL PNGaseF (Prozyme, CA, USA) in 20 mM NaHCO3 (pH 7.0) to each sample and incubating overnight at 37° C. The released glycans were collected by washing the gel pieces with 3×200 μL of water, 200 μL of acetonitrile, 200 μL of water, and finally 200 μL of acetonitrile. The released glycans were dried, 20 μL of 1% formic acid was added, and the mixture was incubated at room temperature for 40 min and then re-dried. Samples were labeled by adding 5 μL of 2AB labeling solution, vortexed, incubated for 30 min at 65° C., vortexed again, and incubated for a further 90 min. Excess 2AB was removed using Whatman 3 MM chromatography paper cleanup: 1-cm square pieces of prewashed, dried Whatman 3 MM chromatography paper were folded into quarters and placed into a filter plate (Whatman protein precipitation plate prewashed with 200 μL of acetonitrile followed by 200 μL of water). The 5 μL of 2AB-labeled samples were applied to the paper and left to dry/bind for 15 min. The excess 2AB was washed off the paper by vortexing with 1.8 mL of acetonitrile for 15 min and then removing the acetonitrile using a vacuum manifold; this procedure was repeated four times. The labeled glycans were eluted from the paper by vortexing with 900 μL of water for 30 min and then collected by vacuum into a 2-mL 96-well plate. This was repeated with a further 900 μL of water. The eluates were dried and re-constituted in H2O/ACN (v/v 30/70). Released and labeled glycans were subsequently fractionated by normal phase chromatography. Ultra Performance Hydrophilic interaction liquid chromatography (UPLC-HILIC) was carried out on a 1.7 μm Waters BEH Glycan (150 mm×2.1 mm) column as detailed in Mittermayr et al. “Multiplexed analytical glycomics: Rapid and confident IgG N-glycan structural elucidation,” J. Prot. Res. 2011:10:3820-9 with retention times expressed as glucose units (GU) with the following conditions: Solvent A was 50 mM formic acid adjusted to pH 4.4 with ammonia solution. Solvent B was acetonitrile. The column temperature was set to 30° C. The 30 min method was used with a linear gradient of 30-47% with solvent A (=70-53% solvent B) at 0.56 mL/min for 23 min followed by 47-70% solvent A and finally reverting back to 30% solvent A to complete the run method. Samples were injected in 60% acetonitrile. Samples were run once and peaks were identified by their GU values which were compared with the GlycoBase 3.1 structural library for serum N-Glycans (http://glycobase.nibrt.ei).
Glycan HILIC data represent the relative percentage areas from HILIC profiles. Therefore, the data are compositional, and convey the relative amounts of glycan structures in a sample rather than the absolute quantities. Compositional data are subject to an awkward constant sum constraint, that is, the values sum to a constant value such as one or one hundred percent. For this reason, the logit transform was used to map the data onto real space.
Gene Expression
RNA was purified from whole blood collected in Paxgene tubes. Reverse transcription was performed on 0.5 μg of RNA with random hexamer priming (Invitrogen) and reverse transcriptase (New England Biolabs). Expression analysis of 48 genes was performed by Real Time-Quantitative Polymerase Chain Reaction (RT-qPCR) performed on the Roche LightCycler 480 II. The ΔΔCp method (Pfaff) 2001) was used to quantify transcripts using the average Cp value of housekeeping genes ACTB, GUSB and RPS14 to normalize each sample. −ΔCp was used as an arbitrary unit measure of transcript quantity.
Study Design
Subject samples selected for this study were between 2 to 33 months of age, Hispanic, males treated for Kawasaki Disease at Kawasaki Disease Center at Rady Children's Hospital.
Thirty subject samples, consisting of blood plasma, DNA, and RNA were used in the study. The Kawasaki Disease group consisted of 3 subjects that received IVIG and LOVENOX® treatment (Note: Subject 1 also received a second dose of IVIG 14 days after the first dose); and 5 subjects that received IVIG. A control group was selected consisting of 5 age and sex matched non-Kawasaki, febrile infants.
Samples were categorized according to the stage of disease or treatment into:
Group A—acute Kawasaki
Group B—sub-acute, post IVIG
Group C—on LOVENOX®;
Group D—convalescent
Febrile controls have only acute samples available.
All samples were randomized and blinded for each analytical platform that was applied.
The subject's clinical information, including treatment information, is provided in Table 21.
Shot-gun proteomics identified ˜450 unique proteins on average per sample. In the targeted comparison of Kawasaki disease subjects at the acute stage (1A-8A) with the febrile control (9A-13A), 39 proteins were differentially expressed with 22 down-regulated and 17 up-regulated with a p-value <0.05 as a filter. These differentially expressed proteins belong to: inflammatory response pathway (S100A9, ORM1 ↑), Statin pathway (Apolipoproteins↑), Complement/Coagulation cascades (CFH, Serpin A1, C1), and Autophagy (GSN ↑), and they were among those altered in Kawasaki compared to the Febrile control.
A list of proteins that were found to be significantly different between the Kawasaki disease group (1A-8A) and the febrile control group (9A-13A) are shown in Table 23.
SERPINA3 protein is an example of a measurement that separates Febrile Controls and Acute Kawasaki Disease. SERPINA3 is considered to be an acute phase response protein observed to be increased during certain types of inflammatory response. CRP is another protein that belongs to the acute phase response group. However, CRP does not appear to consistently separate Febrile Controls from Acute Kawasaki Disease subjects. IVIG treatment appears to reduce levels of both of these proteins as evidenced by reduced levels after IVIG treatment.
Current standard of care for Kawasaki disease is treatment with IVIG/ASA at the time of diagnosis at the acute stage. As there is no test or diagnostic tool to identify subjects “at risk” for developing cardiac aneurysm at the acute stage, the aneurysm treatment (LOVENOX®) is generally delayed until echocardiogram imaging is provided later in the course of disease, often when a coronary artery aneurysm has already occurred. A test or diagnostic tool that identifies subjects “at risk” earlier could prevent the development of coronary artery aneurysms and the resulting long term effects (e.g., increased risk of heart attack and other cardiovascular events later in life).
To identify proteins indicative of development of cardiac artery aneurysms or stenosis, a group of Kawasaki disease subjects (1A, 2A, 3A) who were subjected to IVIG/LOVENOX® treatment (based on the clinical outcome) was compared with a group of subjects that were treated with IVIG only (4A, 5A, 6A, 7A, 8A). All subjects in the IVIG/LOVENOX® group developed coronary aneurysm. These subjects may be genetically predisposed to developing coronary artery aneurysm even with the appropriate standard of care treatment.
Ten proteins were significantly altered in the high risk group: three were up-regulated (PROC, F11, APOF) and seven down-regulated (CD44, ANKRD26, LAMP2, BCAM, MMRN1, TGFBI, TET2). The differential levels of these proteins in subjects that developed coronary artery aneurysms or stenosis indicates these proteins are useful for selecting or classifying subjects predisposed to coronary artery aneurysms or stenosis. This early selection may allow for treatment with anticoagulants (e.g., enoxaparin and/or clopidogrel) or other therapies (e.g., infliximab, cyclosporine, and/or prednisone) to begin before the development of coronary artery aneurysms or stenosis, rather than in response to their development as is the current practice.
These protein identifiers were mapped to the following functions:
A list of proteins that were found to be significantly different between the IVIG/Lovenox® group (1A-3A) and the IVIG only group (4A-8A) are shown in Table 19.
In an effort to identify further proteins indicative of development of cardiac artery aneurysms or stenosis, a group of Kawasaki disease subjects (1, 2, 3, 4, and 6) who developed aneurysms based on electrocardiogram imaging was compared with a group of subjects that either did not develop aneurysms or were only dilated and not considered to have developed full aneurysms (5, 7, and 8). The subjects that developed aneurysms may be genetically predisposed to developing coronary artery aneurysm even with the appropriate standard of care treatment.
Student's t-test were used to determine if any significant differences were observed between aneurysm and non-aneurysm groups. Of the 647 measurements, 10 and proteins had a p-value less than 0.05 (see Table 25).
A 10K random peptide array was tested for IgG reactivities in plasma samples of KD. A total of 68 out of 10,000 peptides were found to have significantly different binding to plasma IgG between acute KD and febrile control (p<0.05).
Using the 68 peptides, an agglomerative hierarchical clustering technique (via Ward's minimum variance method) was used to naturally break the data into a hierarchy of “similar” clusters. Here, the natural break created two clusters. The 68 peptides identified have the sequences of SEQ ID NOs: 1-68, provided in Table 3, supra. The 68 peptides were attached to the microarray by cysteine-serine-glycine linkers. The peptides (including the linker sequence) are listed in Table 26.
The predisposition for development of aneurysms can also be examined by looking at the difference in gene expression between the aneurysm group (Subjects 1 and 2) and the non-aneurysm group (Subjects 3-8). Measurements that show persistently different values in the Sub-acute samples in Subjects 1 and 2 were identified by selecting those measurements where the absolute value of the standard normal deviate was greater than 2.58 for both subjects. (Z=2.58 is the critical value for the two-tailed 99% confidence interval of the normal distribution). Sixty three measurements were observed to be persistently perturbed, either up or down, in subjects 1 and 2 at the sub-acute phase as shown in Table 27.
PRO, protein from shot-gun proteomics; ELISA, soluble plasma protein; GE, gene expression; GLY, serum protein glycans; GP, fraction number; HA, high-abundant fraction; LA, low abundant fraction.
Measurements made on samples from KD subjects were analyzed to examine the effect of IVIG treatment. Acute phase samples were compared to samples collected after IVIG treatment.
A total of 690 analytes per sample from 21 biological samples with the complete data sets was used for the analysis. Samples were divided into an “Acute Disease” group and a “Sub-acute” group. Differences between the two groups were examined by Student's t-tests after variance stabilizing transformation. Transformations were performed by analytic: plasma proteomics, log2; RT-qPCR −ΔCp, none; plasma protein ELISA, none; plasma glycans, log2; Ig glycopeptides, logit. A total of 157 measurements with P≤0.01 were considered to be significantly different between the two groups (Acute Value vs. Sub-acute Value) and are listed in table 28.
While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features herein before set forth.
All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 62067123 | Oct 2014 | US | |
| 61987907 | May 2014 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 15308114 | Nov 2016 | US |
| Child | 16841575 | US |
