Method for diagnosing diseases based on levels of anti-glycan antibodies

Abstract

Disclosed are methods for diagnosing Crohn's disease (CD) or anti-phospholipid Syndrome (APS) by measuring levels of antibodies to glycans in a biological sample.

1 . A method of diagnosing Crohn's disease in a subject, the method comprising 
 providing a test sample from said subject; and    determining whether at least one an anti-glycan antibody is present in said sample, wherein said at least one anti-glycan antibody is selected from the group consisting of an anti-Glc(β) antibody, an anti-Glc(β,1-4)Glc(β) antibody, an anti-Glc(β,1-3)Glc(p antibody, an anti-GlcNAc(β) 6-sulfate antibody, an anti-Dextran antibody, an anti-Xylan antibody, an anti-GlcNAc(β,1-4)GlcNAc(β) antibody, an anti-Gal 3-sulphate(β) antibody, an anti-GlcNAc(β,1-3)GalNAc(β) antibody, an anti-GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody, an anti-Gal(β) antibody, an anti-GalNAc(α) antibody, an anti-Glc(α) antibody, an anti-Gal(β,1-6)Gal(β) antibody, and an anti-GlcNAc(β,1-6)GalNAc(α) antibody,    wherein the presence of said antibody in said test sample indicates the subject has Crohn's disease.    
     
     
         2 . The method of  claim 1 , wherein said method further comprises comparing the levels of said at least one anti-glycan antibody in said test sample to the levels of said at least one anti-glycan antibody in a control sample, wherein said control sample is selected from the group consisting of one or more individuals known to have or not to have a gastrointestinal disorder other than Crohn's disease.  
     
     
         3 . The method of  claim 2 , wherein said control sample is from one or more individuals with a gastrointestinal disorder that is irritable bowel syndrome or ulcerative colitis.  
     
     
         4 . The method of  claim 2 , wherein said control sample is from one or more individuals that do not have a gastrointestinal disorder.  
     
     
         5 . The method of  claim 1 , wherein said method comprises detecting at least two of said antibodies.  
     
     
         6 . The method of  claim 1 , wherein said method comprises detecting at least four of said antibodies.  
     
     
         7 . The method of  claim 1 , wherein said method comprises detecting at least six of said antibodies.  
     
     
         8 . The method of  claim 1 , further comprising determining whether said test sample has an anti-Mannan (ASCA) antibody, wherein the presence of said anti-ASCA antibody in said sample indicates the subject has Crohn's Disease.  
     
     
         9 . The method of  claim 1 , further comprising determining whether said test sample has an anti-neutrophil cytoplasmic antibodies (ANCA), wherein the presence of said anti-neutrophil cytoplasmic antibodies (ANCA) indicates said subject does not have Crohn's Disease.  
     
     
         10 . The method of  claim 8 , further comprising determining whether said test sample has an anti-neutrophil cytoplasmic antibodies (ANCA), wherein the presence of said anti-neutrophil cytoplasmic antibodies (ANCA) indicates said subject does not have Crohn's Disease.  
     
     
         11 . The method of  claim 1 , wherein said method comprises detecting said anti-Glc(β,1-3)Glc(β) antibody, and one, two, or three of an anti-Man(α,1-3)Man(α) antibody, anti-Man(α,1-3)[Man(α,1-6)]Man(α) antibody, anti-Man(α,1-2)Man(α), anti-Man(α,1-6)Man(α), anti-Mannan (ASCA) antibody or anti-Gal(α) antibody.  
     
     
         12 . The method of  claim 1 , wherein said test sample is a biological fluid.  
     
     
         13 . The method of  claim 12 , wherein said biological fluid is whole blood, serum, plasma, urine, or saliva.  
     
     
         14 . The method of  claim 11 , wherein said wherein said biological fluid is serum.  
     
     
         15 . The method of  claim 1 , further comprising determining the isotype of said antibody.  
     
     
         16 . The method of  claim 15 , wherein said at least one antibody is an IgM type antibody.  
     
     
         17 . The method of  claim 15 , wherein said at least one antibody is an IgA type antibody.  
     
     
         18 . The method of  claim 15 , wherein said at least one antibody is an IgG type antibody.  
     
     
         19 . The method of  claim 18 , wherein said IgG antibody is an anti-Glc(β) antibody, an anti-Glc(β,1-3)Glc(β) antibody, an anti-Glc(β,1-4)Glc(β) antibody, an anti-GlcNAc(β) 6-sulfate antibody, or an anti-Xylan antibody.  
     
     
         20 . The method of  claim 1 , wherein said at least one anti-glycan antibody is detected using a fluorescent antibody.  
     
     
         21 . The method of  claim 1 , wherein said at least one anti-glycan antibody is detected using an enzyme-linked immunoabsorbent assay (ELISA).  
     
     
         22 . A method of diagnosing Crohn's disease in a subject, the method comprising 
 providing a test sample from a subject; and    determining whether an anti-glycan antibody is present in said test sample, wherein said at least one anti-glycan antibody is selected from the group consisting of an IgG Glc(β,1-3)Glc(β) antibody and an IgG anti-Man(α,1-3)Man(α) antibody,    wherein the presence of said at least one antibody in said test sample indicates the subject has Crohn's disease.    
     
     
         23 . The method of  claim 22 , wherein said method comprises detecting an IgG anti-Glc(β,1-3)Glc(β) antibody.  
     
     
         24 . The method of  claim 23 , wherein said method comprises detecting an IgG anti-Man(α,1-3)Man(α) antibody.  
     
     
         25 . The method of  claim 22 , wherein said method comprises detecting an IgG Glc(β,1-3)Glc(β) antibody and an IgG anti-Man(α,1-3)Man(α) antibody.  
     
     
         26 . The method of  claim 22 , wherein said method further comprises determining whether said sample has an IgG anti-Mannan or an IgA anti-Mannan antibody, wherein the presence of said IgG anti-Mannan or IgA anti-Mannan antibody in said sample indicates said subject has Crohn's disease.  
     
     
         27 . The method of  claim 26 , wherein said method comprises determining whether said sample has an IgG anti-Mannan antibody.  
     
     
         28 . The method of  claim 26 , wherein said method comprises determining whether said sample has an IgA anti-Mannan antibody.  
     
     
         29 . The method of  claim 26 , wherein said method further comprises determining whether said sample has an anti-neutrophil cytoplasmic antibodies (ANCA), wherein the absence of said antibody in said sample indicates said subject has Crohn's disease.  
     
     
         30 . A method of differentially diagnosing Crohn's disease or inflammatory bowel disease in a subject, the method comprising 
 providing a test sample from a subject; and    determining whether said sample has an antibody selected from the group consisting of an 
 anti-neutrophil cytoplasmic antibody (ANCA),  
 IgG anti-Glc(β,1-3)Glc(β)  
 IgG ASCA; and  
 IgA ASCA,  
   wherein the absence of ANCA and the presence of at least one of said IgG anti-Glc(β,1-3)Glc(β) IgG ASCA, and IgA ASCA antibodies in said test sample indicates the subject has Crohn's disease, and    wherein the presence of at least one of said antibodies in said test sample indicates the subject has inflammatory bowel disease (IBD).    
     
     
         31 . A method of differentially diagnosing Crohn's disease colitis and ulcerative colitis in a subject, the method comprising 
 providing a test sample from a subject; and    determining levels of at least one an anti-glycan antibody in said sample, wherein said at least one anti-glycan antibody is selected from the group consisting of    an IgG anti-Gal(α,1-4)GlcNAc(α) antibody,    an IgG anti-Gal(β,1-4)GlcNAc(13) antibody,    an IgG anti-GalNAc(α) antibody,    an IgG anti-Glc(α) antibody,    an IgG anti-Glc(β) antibody,    an IgG anti-GlcNAc(β,6-Sulphate) antibody,    an IgG anti-GlcNAc(β) antibody,    an IgG anti-GlcNAc(β,1-6)GalNAc(α) antibody,    an IgA anti-Gal(α,1-3)Gal(β,1-4)GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody,    an IgA anti-Gal(α,1-4)Gal(β,1-4), Glc(β) antibody,    an IgA anti-Gal(β) antibody,    an IgA anti-Gal(β,1-3)[GlcNAc(β,1-6)]GalNAc(α) antibody,    an IgA anti-Gal(β,1-3)GlcNAc(β) antibody,    an IgA anti-Gal(β,1-6)Gal(β) antibody,    an IgA anti-GalNAc(α) antibody,    an IgA anti-GalNAc(β) antibody,    IgA an anti-Glc(β) antibody,    an IgA anti-Glc(β,1-3)Glc(β) antibody,    an IgA anti-GlcNAc(β) antibody,    an IgA anti-GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody,    an IgA anti-GlcNAc(β,1-3)GalNAc(α) antibody,    an IgA anti-GlcNAc(β,1-4)GlcNAc(β) antibody,    an IgA anti-GlcNAc(β,1-6)GalNAc(α) antibody, and    an IgA anti-Xyl(β) antibody,    wherein the presence of said at least one antibody in said test sample indicates the subject has Crohn's disease colitis.    
     
     
         32 . The method of  claim 31 , wherein said method further comprises comparing the levels of said at least one anti-glycan antibody in said test sample to the levels of said at least one anti-glycan antibody in a control sample, wherein said control sample is selected from the group consisting of one or more individuals known to have or not to have Crohn's disease colitis or known to have or not to have ulcerative colitis (IC).  
     
     
         33 . The method of  claim 31 , further comprising 
 determining whether an additional anti-glycan antibody anti-glycan antibody is present in said sample, wherein said additional anti-glycan antibody is selected from the group consisting of    an IgG anti-Gal(α) antibody,    an IgG anti-Man(α) antibody,    an IgG anti-Man(α,1-3)Man(α,1-6)Man(β) antibody,    an IgG anti-Man(α,1-3)Man(α,1-6)Man(β) antibody,    an IgG anti-Man(α,1-3)Man(α) antibody,    an IgA anti-Man(α) antibody,    an IgA anti-Man(α,1-2)Man(α) antibody,    an IgA anti-Man(α,1-3)Man(α,1-6)Man(β) antibody,    an IgA anti-Man(β, 1-3)Man(α) antibody,    an IgA anti-Man(α,1-6)Man(α) antibody,    an IgA anti-Man(β) antibody, and    an IgA anti-X(α) antibody,    wherein the presence of said additional antibody in said test sample indicates the subject has Crohn's disease colitis.    
     
     
         34 . The method of  claim 31 , wherein said at least one antibody is the IgA anti-GlcNAc(β,1-4)GlcNAc(β) antibody.  
     
     
         35 . The method of  claim 33 , wherein said additional antibody is the IgG anti-Man(α,1-3)Man(α) antibody.  
     
     
         36 . The method of  claim 35 , wherein said at least one antibody is IgA anti-GlcNAc(β,1-4)GlcNAc(β) antibody.  
     
     
         37 . The method of  claim 31 , wherein said method comprises detecting at least two of said antibodies.  
     
     
         38 . The method of  claim 31 , wherein said method comprises detecting at least four of said antibodies.  
     
     
         39 . The method of  claim 31 , wherein said method comprises detecting at least six of said antibodies.  
     
     
         40 . The method of  claim 31 , wherein said test sample is a biological fluid.  
     
     
         41 . The method of  claim 31 , wherein said biological fluid is whole blood, serum, plasma, urine, or saliva.  
     
     
         42 . The method of  claim 31 , wherein said wherein said biological fluid is serum.  
     
     
         43 . A method for differentially diagnosing inflammatory bowel disease (IBD) or non-IBD digestive disease (NIC) in a subject, the method comprising 
 providing a test sample from a subject with symptoms of NIC or IBD;    determining if anti chitobioside (GlcNAc(β,1-4)GlcNAc(β)) carbohydrate Antibodies (ACCA) and anti-mannan (ASCA) antibodies are present in said sample,    wherein the presence of ACCA antibodies and the absence of ASCA antibodies in said sample indicates said subject has NIC.    
     
     
         44 . The method of  claim 43  where the determining if anti chitobioside (GlcNAc(β,1-4)GlcNAc(β)) carbohydrate Antibodies (ACCA) and anti-mannan (ASCA) antibodies are present in said sample is done by 
 comparing levels of said antibodies to levels of antibodies in a reference sample from a subject known to have IBD,    wherein a higher level of ACCA antibodies and a lower level of ASCA antibodies in said test sample relative to the said reference sample indicates said patient has NIC.    
     
     
         45 . The method of  claim 43 , further comprising determining whether said test sample has anti-laminarobioside (Glc(β,1-3)Glc(β)) Carbohydrate Antibodies (ALCA) antibodies, wherein the absence of ALCA antibodies in said sample indicates said subject has NIC.  
     
     
         46 . A kit for diagnosing Crohn's Disease, the kit comprising one or more reagents that specifically detect an antibody selected from the group consisting of an anti-Glc(β) antibody, an anti-Glc(β,1-4)Glc(β) antibody, an anti-Glc(β,1-3)Glc(β) antibody, an anti-GlcNAc(β) 6-sulfateantibody, an anti-Man(α,1-2)Man(α) antibody, an anti-Man(α,1-3)Man(α) antibody, an anti-Man(α,1-6)Man(α) antibody, an anti-Man(α) antibody, an anti-Man(α,1-3)[Man(α,1-6)]Man(α), an anti-Dextran antibody, an anti-Xylan antibody, an anti-GlcNAc(β,1-4)GlcNAc(β) antibody, an anti-Gal 3-sulphate(β) antibody, an anti-GlcNAc(β,1-3)GalNAc(β) antibody, and an anti-GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody.  
     
     
         47 . The kit of  claim 46 , further including instructions for using said kit.  
     
     
         48 . The kit of  claim 46 , wherein said kit further comprises one or more reagents that specifically detect an anti-Mannan (ASCA) antibodies or anti-neutrophil cytoplasmic antibodies (ANCA).  
     
     
         49 . The kit of  claim 46 , wherein said kit comprises a reagent or reagents that specifically detects an anti-Mannan (ASCA) antibody and a anti-neutrophil cytoplasmic antibodies (ANCA).  
     
     
         50 . The kit of  claim 46 , further comprising a reagent that specifically detects an IgG, IgM, or IgA-type antibody.  
     
     
         51 . The kit of  claim 46 , wherein said reagents are provided on an array.  
     
     
         52 . The kit of  claim 50 , wherein said kit comprises reagents that detect IgG Glc(β,1-3)Glc(β) antibody and an IgG anti-Man(α,1-3)Man(α) antibody.  
     
     
         53 . A kit for diagnosing Crohn's Disease, the kit comprising one or more reagents that specifically detect an antibody selected from the group consisting of at least one anti-glycan antibody is selected from the group consisting of 
 an IgG anti-Gal(α,1-4)GlcNAc(α) antibody,    an IgG anti-Gal(β,1-4)GlcNAc(β) antibody,    an IgG anti-GalNAc(α) antibody,    an IgG anti-Glc(α) antibody,    an IgG anti-Glc(β) antibody,    an IgG anti-GlcNAc(β,6-Sulphate) antibody,    an IgG anti-GlcNAc(β) antibody,    an IgG anti-GlcNAc(β,1-6)GalNAc(α) antibody,    an IgA anti-Gal(α,14)Gal(,1-4), Glc(β) antibody,    an IgA anti-Gal(β) antibody,    an IgA anti-Gal(β,1-3)[GlcNAc(β,1-6)]GalNAc(α) antibody,    an IgA anti-Gal(β,1-3)GlcNAc(β) antibody,    an IgA anti-Gal(β,1-6)Gal(β) antibody,    an IgA anti-GalNAc(α) antibody,    an IgA anti-GalNAc(β) antibody,    IgA an anti-Glc(β) antibody,    an IgA anti-Glc(β,1-3)Glc(β) antibody,    an IgA anti-GlcNAc(β) antibody,    an IgA anti-GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody,    an IgA anti-GlcNAc(β,1-3)GalNAc(α) antibody,    an IgA anti-GlcNAc(β,1-4)GlcNAc(β) antibody,    an IgA anti-GlcNAc(β,1-6)GalNAc(α) antibody, and    an IgA anti-Xyl(β) antibody.    
     
     
         54 . The kit of  claim 53 , further comprising one or more reagents that specifically detect an antibody selected from the group consisting of at least one anti-glycan antibody is selected from the group consisting of 
 an IgG anti-Gal(α) antibody,    an IgG anti-Man(α) antibody,    an IgG anti-Man(α,1-3)Man(α,1-6)Man(β) antibody,    an IgG anti-Man(α,1-3)Man(α,1-6)Man(β) antibody,    an IgG anti-Man(α,1-3)Man(α) antibody,    an IgA anti-Man(α) antibody,    an IgA anti-Man(α,1-2)Man(α) antibody,    an IgA anti-Man(α,1-3)Man(α,1-6)Man(β) antibody,    an IgA anti-Man(β, 1-3)Man(α) antibody,    an IgA anti-Man(α,1-6)Man(α) antibody,    an IgA anti-Man(β) antibody, and    an IgA anti-Xyl(α) antibody.    and IgA anti-Gal(α,1-3)Gal(β,1-4)GlcNAc(β) antibody.    an IgA anti-Gal(α,1-3)Gal(β,1-4)GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody,    
     
     
         55 . The kit of  claim 54 , further including instructions for using said kit.  
     
     
         56 . The kit of  claim 54 , wherein said kit further comprises one or more reagents that specifically detect an anti-Mannan (ASCA) antibodies or anti-neutrophil cytoplasmic antibodies (ANCA).  
     
     
         57 . The kit of  claim 56 , wherein said kit comprises a reagent or reagents that specifically detects an anti-Mannan (ASCA) antibody and anti-neutrophil cytoplasmic antibodies (ANCA).  
     
     
         58 . The kit of  claim 53 , further comprising a reagent that specifically detects an IgG, IgM, or IgA-type antibody.  
     
     
         59 . The kit of  claim 53 , wherein said reagents are provided on an array.  
     
     
         60 . A kit for differentially diagnosing Crohn's disease and inflammatory bowel disease in a subject, the kit comprising one or more reagents that detect an antibody selected from the group consisting of an anti-neutrophil cytoplasmic antibody (ANCA), IgG anti-Glc(β,1-3)Glc(β, IgG ASCA; and IgA ASCA.  
     
     
         61 . The kit of  claim 60 , further comprising instructions for using said kit.  
     
     
         62 . A kit for differentially diagnosing Crohn's disease colitis and ulcerative colitis in a subject, the kit comprising one or more reagents that detect at least one anti-glycan antibody selected from the group consisting of an IgG anti-Gal(α,14)GlcNAc(α) antibody, an IgG anti-Gal(β,1-4)GlcNAc(β) antibody, an IgG anti-GalNAc(α) antibody, an IgG anti-Glc(α) antibody, an IgG anti-Glc(β) antibody, an IgG anti-GlcNAc(β,6-Sulphate) antibody, an IgG anti-GlcNAc(β) antibody, an IgG anti-GlcNAc(β,1-6)GalNAc(α) antibody, an IgA anti-Gal(α,1-3)Gal(β,1-4)GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody, an IgA anti-Gal(α,1-4)Gal(β,1-4), Glc(β) antibody, an IgA anti-Gal(β) antibody, an IgA anti-Gal(β,1-3)[GlcNAc(β,1-6)]GalNAc(α) antibody, an IgA anti-Gal(β,1-3)GlcNAc(β) antibody, an IgA anti-Gal(β,1-6)Gal(β) antibody, an IgA anti-GalNAc(α) antibody, an IgA anti- GalNAc(β) antibody, IgA an anti-Glc(β) antibody, an IgA anti-Glc(β,1-3)Glc(β) antibody, an IgA anti-GlcNAc(β) antibody, an IgA anti-GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody, an IgA anti-GlcNAc(β,1-3)GalNAc(α) antibody, an IgA anti-GlcNAc(β,1-4)GlcNAc(β) antibody, an IgA anti-GlcNAc(β,1-6)GalNAc(O) antibody, and an IgA anti-Xyl(β) antibody.  
     
     
         63 . The kit of  claim 62 , further comprising instructions for using said kit.  
     
     
         64 . A kit for differentially diagnosing inflammatory bowel disease (IBD) or non- IBD digestive disease (MC) in a subject, the kit comprising one or more reagents that detect at least one anti chitobioside (GlcNAc(β,1-4)GlcNAc(β)) carbohydrate Antibodies (ACCA) and anti-mannan (ASCA) antibodies.  
     
     
         65 . The kit of  claim 64 , further comprising instructions for using said kit.  
     
     
         66 . An array comprising a plurality of carbohydrate reagents that specifically detect an antibody selected from the group consisting of an anti-Glc(β) antibody, an anti-Gal(α) antibody, an anti-Glc(β,1-4)Glc(β) antibody, an anti-Glc(β,1-3)Glc(β) antibody, an anti-GlcNAc(β) 6-sulfate antibody, an anti-Man(c, 1-2)Man(α) antibody, an anti-Man(α,1-3)Man(α) antibody, an anti-Man(α,1-6)Man(α) antibody, an anti-Man(α) antibody, an anti-Man(α,1-3)[Man(α,1-6)]Man(α), an anti-Dextran antibody, an anti-Xylan antibody, an anti-GlcNAc(β,1-4)GlcNAc(β) antibody, an anti-Gal 3-sulphate(p) antibody, an anti-aGlcNAc(β,1-3)GalNAc(β) antibody, an anti-GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody, and an anti-Gal(α,1-3)Gal(β,1-4)GlcNAc(β) antibody, wherein said reagents are attached at an addressable location on said array.  
     
     
         67 . The array of  claim 66 , further comprising a carbohydrate reagent or reagents that detect an anti-Mannan (ASCA) antibody or a anti-neutrophil cytoplasmic antibodies (ANCA).  
     
     
         68 . The array of  claim 66 , wherein said array comprises carbohydrate reagent or reagents that detect an anti-Mannan (ASCA) antibody and anti-neutrophil cytoplasmic antibodies (ANCA).  
     
     
         69 . The array of  claim 66 , wherein each of said glycans are attached to said array via a linker.  
     
     
         70 . The array of  claim 69 , wherein said linker includes at least one ethylene glycol derivative, at least two cyanuric chloride derivatives and an anilino group.  
     
     
         71 . The array of  claim 66 , wherein at least two of said reagent or reagents are provided at the same location on said addressable array.  
     
     
         72 . A glycan reagent for diagnosing CD, wherein said reagent specifically detects at least one anti-glycan antibody selected from the group consisting of an anti-Gal(α,1-4)GlcNAc(x) antibody, an anti-Gal(β,1-4)GlcNAc(β) antibody, an anti- GalNAc(α) antibody, an anti-Glc(β) antibody, an anti-Glc(α) antibody, an anti- GlcNAc(β,6-Sulphate) antibody, an anti-GlcNAc(β) antibody, an anti-GlcNAc(β,1-6)GalNAc(α) antibody, an anti-Gal(α,1-4)Gal(β,1-4), Glc(β) antibody, an anti-Gal(β) antibody, an anti-Gal(β,1-3)[GlcNAc(β,1-6)]GalNAc(α) antibody, an anti-Gal(β,1-3)GlcNAc(β) antibody, an anti-Gal(0,1-6)Gal(β) antibody, an anti-GalNAc(α) antibody, an anti-GalNAc(β) antibody, an anti-Glc(β) antibody, an anti-Glc(β,1-3)Glc(β) antibody, an anti-GlcNAc(β) antibody, an anti-GlcNAc(β,1-3)Gal(β,1-4)Glc(β) antibody, an anti-GlcNAc(β,1-3)GalNAc(α) antibody, an anti-GlcNAc(β,1-4)GlcNAc(β) antibody, an anti-GlcNAc(β,1-6)GalNAc(α) antibody, an anti-Xyl(β) antibody, and an anti-Xyl(α) antibody.