Method for Diagnosing Prognosing Inflammatory Bowel Disease and Crohn's Disease

Abstract

Disclosed are methods for diagnosing and prognosing Inflammatory Bowel disease or Crohn's disease (CD) by measuring levels of antibodies to glycans in a biological sample.

1 . A method for diagnosing severe Crohn's disease in a subject, the method comprising,
 providing a test sample from a subject with symptoms of Crohn's disease; and   determining whether said sample includes an antibody selected from an antibody selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody,   wherein the presence of said antibodies in said test sample indicates the subject has severe Crohn's disease.   
     
     
         2 . The method of  claim 2 , wherein said method includes determining whether said sample includes two antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         3 . The method of  claim 2 , wherein said method includes determining whether said sample includes three antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         4 . The method of  claim 2 , wherein said method includes determining whether said sample includes four antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         5 . The method of  claim 2 , wherein said method includes determining whether said sample includes five antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         6 . The method of  claim 2 , wherein said method includes determining whether said sample includes an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         7 . The method of  claim 1 , further comprising determining whether said sample includes an antibody selected from the group consisting of an anti mannan antibody (gASCA) and an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         8 . The method of  claim 7 , wherein said method comprises determining whether said sample includes two antibodies selected from the group consisting of an anti mannan antibody (gASCA) and an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         9 . The method of  claim 7 , wherein said method comprises determining whether said sample includes three antibodies selected from the group consisting of an anti mannan antibody (gASCA) and an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         10 . The method of  claim 7 , wherein said method comprises determining whether said sample includes four antibodies selected from the group consisting of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         11 . The method of  claim 7 , wherein said method comprises determining whether said sample includes an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         12 . The method of  claim 7 , further comprising determining whether said sample includes an anti-neutrophil cytoplasmic antibody (ANCA). 
     
     
         13 . The method of  claim 1 , further comprising determining whether said subject has a CARD15 allele associated with Crohn's disease. 
     
     
         14 . The method of  claim 7 , wherein said method comprises determining whether said subject has the R702W, G908R, or 1007fs CARD15 allele. 
     
     
         15 . The method of  claim 7 , further comprising determining whether said subject with severe Crohn's disease has strictures or fistulas. 
     
     
         16 . The method of  claim 5 , further comprising treating said subject with said antibodies for symptoms associated with severe Crohn's disease. 
     
     
         17 . The method of  claim 5 , wherein said treatment is surgery. 
     
     
         18 . The method of  claim 5 , wherein said anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, said anti-α-GalNAc antibody (AGCA), and said anti-laminarin antibody are IgG antibodies and said anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and said anti-β-GalNAc antibodies are IgA antibodies. 
     
     
         19 . The method of  claim 7 , wherein said (gASCA) antibody, anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and anti-α-Man antibody (AMA) are IgG antibodies. 
     
     
         20 . The method of  19 , the anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, the anti-α-GalNAc antibody (AGCA), the anti-β-GalNAc, and the anti-laminarin antibody are IgG antibodies and the anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and the anti-β-GalNAc antibody are IgA antibodies 
     
     
         21 . The method of  claim 1 , wherein said test sample is serum. 
     
     
         22 . The method of  claim 1 , wherein the presence of antibodies in said sample are determined using an enzyme-linked immunosorbent assay (ELISA). 
     
     
         23 . The method of  claim 4 , wherein said subject is determined to have severe Crohn's disease if when said anti-β-GalNAc is above S, said anti-Glc(β1,6)Glc(β) antibody is above T, said ALCA level is above W, said AGCA is above X, said anti-laminarin antibody is above Y, and said ACCA level is above Z,
 wherein S, T, W, X, Y, and Z are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.   
     
     
         24 . The method of  claim 6 , wherein said subject is determined to have severe Crohn's disease, if when said gASCA level is above U, and said AMCA is above V,
 wherein U and V are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.   
     
     
         25 . The method of  claim 4 , wherein said method comprises determining the aggregate amount of ALCA, anti-Glc(β1,6)Glc(β) antibody, AGCA, anti-β-GalNAc anti-laminarin antibodies and ACCA, wherein the subject is determined to have severe Crohn's disease if the aggregate amount of said antibodies is greater than R. 
     
     
         26 . The method of  claim 11 , wherein said method comprises determining the aggregate amount of ALCA, anti-Glc(β1,6)Glc(β) antibody, AGCA, anti-β-GalNAc anti-laminarin antibodies and ACCA, wherein the subject is determined to have severe Crohn's disease if the aggregate amount of said antibodies is greater than R. 
     
     
         27 . The method of  claim 25 , wherein said method further comprises determining the aggregate amount of gASCA, AMCA, AMBA, AMNA and AMA antibodies, and said subject is determined to have severe Crohn's disease if the aggregate amount of said antibodies is greater than R. 
     
     
         28 . A method for assessing the prognosis of Crohn's disease complications in a subject, the method comprising
 providing a test sample from a subject with symptoms of Crohn's disease; and   determining whether said sample includes an antibody selected from an antibody selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, an anti-Glc(α1,6)Glc(α) antibody, and an anti-laminarin antibody,   wherein the presence of said antibodies in said test sample indicates a severe Crohn's disease prognosis for said subject.   
     
     
         29 . A method for assessing the prognosis of Crohn's disease complications in a subject, the method comprising
 providing a test sample from a subject with symptoms of Crohn's disease; and   determining whether said sample includes an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-Man(α1,3)Man(α) antibody (AMBA), and an anti-Mannan antibody,   wherein the presence of said antibodies in said test sample indicates a severe Crohn's disease prognosis for said subject.   
     
     
         30 . A method for differentiating inflammatory bowel disease (IBD) from a disease other than IBD in subject, the method comprising
 providing a test sample from a subject with symptoms of IBD; and   determining whether said sample includes determining whether said sample includes an antibody selected from an antibody selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody,   wherein the presence of said antibodies in said test sample indicates the subject has inflammatory bowel disease.   
     
     
         31 . The method of  claim 30 , wherein said method includes determining whether said sample includes two antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         32 . The method of  claim 30 , wherein said method includes determining whether said sample includes three antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         33 . The method of  claim 30 , wherein said method includes determining whether said sample includes four antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         34 . The method of  claim 30 , wherein said method includes determining whether said sample includes five antibodies selected from the group consisting of an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         35 . The method of  claim 30 , wherein said method includes determining whether said sample includes an anti-Glc(β1,3)Glc(β) antibody (ALCA), an anti-Glc(β1,6)Glc(β) antibody, an anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA), an anti-α-GalNAc antibody (AGCA), an anti-β-GalNAc antibody, and an anti-laminarin antibody. 
     
     
         36 . The method of  claim 30 , further comprising determining whether said sample includes an antibody selected from the group consisting of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA), an anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and anti-α-Man antibody (AMA). 
     
     
         37 . The method of  claim 36 , wherein said method comprises determining whether said sample includes two antibodies selected from the group consisting of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, an anti-Man(α1,6)Man(α) antibody (AMBA), an anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         38 . The method of  claim 36 , wherein said method comprises determining whether said sample includes three antibodies selected from the group consisting of an anti mannan antibody (gASCA) and an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         39 . The method of  claim 36 , wherein said method comprises determining whether said sample includes four antibodies selected from the group consisting of an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         40 . The method of  claim 36 , wherein said method comprises determining whether said sample includes an anti mannan antibody (gASCA), an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), and an anti-α-Man antibody (AMA). 
     
     
         41 . The method of  claim 30 , wherein said method further comprises determining whether said sample includes an anti-neutrophil cytoplasmic antibody (ANCA). 
     
     
         42 . The method of  claim 30 , further comprising determining whether said subject has a CARD15 allele associated with Crohn's disease. 
     
     
         43 . The method of  claim 42 , wherein said method comprises determining whether said subject has the R702W, G908R, or 1007fs CARD15 allele. 
     
     
         44 . The method of  claim 30 , further comprising determining whether said subject with inflammatory bowel disease has strictures or fistulas. 
     
     
         45 . The method of  claim 30 , further comprising treating said subject with said antibodies for symptoms associated with severe Crohn's disease. 
     
     
         46 . The method of  claim 45 , wherein said treatment is surgery. 
     
     
         47 . The method of  claim 30 , wherein said anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, said anti-α-GalNAc antibody (AGCA), said anti-β-GalNAc, and said anti-laminarin antibody is an IgG antibody and said anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) or said anti-β-GalNAc antibody is an IgA antibody. 
     
     
         48 . The method of  claim 36 , wherein said (gASCA) antibody, an anti-Man(α1,3)Man(α) antibody (AMCA) antibody, anti-Man(α1,6)Man(α) antibody (AMBA), anti-Man(α1,2)Man(α) antibody (AMNA), or anti-α-Man antibody (AMA) is an IgG antibody. 
     
     
         49 . The method of  claim 35 , wherein said anti-Glc(β1,3)Glc(β) antibody (ALCA), anti-Glc(β1,6)Glc(β) antibody, said anti-α-GalNAc antibody (AGCA), said anti-β-GalNAc antibody, and said anti-laminarin antibody are IgG antibodies and said anti-GlcNAc(β1,4)GlcNAc(β) antibody (ACCA) and said anti-β-GalNAc antibodies are IgA antibodies. 
     
     
         50 . The method of  claim 30 , wherein said test sample is serum. 
     
     
         51 . The method of  claim 30 , wherein the presence of antibodies in said sample are determined using an enzyme-linked immunosorbent assay (ELISA). 
     
     
         52 . The method of  claim 30 , wherein said subject is determined to have severe Crohn's disease if when said ALCA level is above W, said AGCA is above X, said anti-laminarin antibody is above Y, and said ACCA level is above Z,
 wherein W, X, Y, and Z are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.   
     
     
         53 . The method of  claim 30 , wherein said subject is determined to have severe Crohn's disease, if when said gASCA level is above U, and said AMCA is above V,
 wherein U and V are independently selected to achieve an optimized clinical parameter selected from the group consisting of: sensitivity, specificity, negative predictive value, positive predictive value and overall agreement.   
     
     
         54 . The method of  claim 30 , wherein said method comprises determining the aggregate amount of ALCA, AGCA, anti-laminarin antibodies and ACCA, wherein the subject is determined to have severe Crohn's disease if the aggregate amount of said antibodies is greater than T.