CA2452162A1 - Diabetogenic epitope from a .alpha./.beta.-gliadin a-ii precursor, .alpha./.beta.-gliadin mm1 precursor or g1b1 - Google Patents

Abstract

The present invention provides nucleotide and amino acid sequences of diabetogenic epitopes, and proteins comprising diabetogenic epitopes. Also provided are kits comprising diabetogenic epitopes, methods of identifying subjects comprising antibodies to diabetogenic epitopes and foodstuffs modified to remove or reduce diabetogenic epitopes or proteins comprising diabetogenic epitopes.
Diabetogenic epitopes and proteins comprising diabetogenic epitopes from .alpha./.beta.-gliadin A-II
precursor, .alpha./.beta.-gliadin MM1 precursor, or Glb1 are also disclosed.

Description

FIELD OF INVENTION
The present invention relates to proteins which are antigenic/immunogenic in pathological conditions.
BACKGROUND OF THE INVENTION
Type 1 diabetes is an autoimmune disease that results when a chronic inflammatory process of unknown origin destroys most of the insulin-producing (3-cells in the pancreatic islets of Langerhans. Genetic susceptibility to diabetes is inherited and there is evidence that environmental co-factors strongly influence disease expression:
<30% pairwise concordance in identical twins, 3.0% annual increase in global incidence since 1960 (Onkamo, P., et al,. (1999) Diabetologia 42, 1395-1403.), 'wide geographic variation and results from numerous studies in animals showing environmental factors can modify the development of spontaneous autoimmune diabetes (Scott, F. W. (1996) Diabetes/Metabolism Reviews 12, 341-359;
Akerblom, H. K., and M. Knip. (1998) Diabetes/Metabolism Reviews 14, 31-67). A major unresolved issue is the identification of the environmental factors that promote the development of type 1 diabetes. This task has proven difficult because of the multifactorial nature of the disease, difficulty in linking past exposures to development of diabetes, lack of knowledge of the environmental antigens, and.
the large number of predisposing genes in individuals at risk (Field, L. L. (2002) Diabetologia 45, 21-35).
The two most studied environmental factors are viruses and diet. Enteroviruses may be involved but as yet, a diabetes-inducing enterovirus has not been identified.

-2-Epidemiological evidence of infectious hotspots or traceable routes of infection is lacking and there are conflicting data with respect to the presence of candidate viruses in the pancreas or immune cells of diabetic patients (Juhela, S. et al. (2000) Diabetes 49,1308-1313; Foulis, A. K., et al.. (1997) Diabetologia 40, 53-61; Buesa-Gomez, J., et al. (1994) J Med Virol 42,193-197). The highest incidence of spontaneous diabetes in Biobreeding (BB) rats and non obese diabetic (NOD) mice occurs when they are maintained in ultraclean conditions and gnotobiotic animals still develop diabetes. If animals that are maintained in strict viral-antibody-free conditions still develop diabetes, that leaves diet as the major environmental stimulus.
Although bovine proteins have been a central focus, a recent blinded, mufti-center study demonstrated that a milk-free, wheat-based diet produced the highest diabetes frequency in diabetes-prone BB rats and NOD mice in three widely separate locations (Beales, P. et al., (2002) Diabetologia 45, 1240-1246), confirming numerous reports that the highest incidence of spontaneous diabetes occurs in animals fed mixed plant-based diets in which wheat is the major component. Defined' diets in which wheat is the sole protein source are potent inducers of diabetes in BB rats (Scott, F. W. (1996) Diabetes/Metabolism Reviews 12, 341-359; Scott, F. W.et al. (1988) Adv Exp Med Biol 246, 277-285).
In a different model of diabetes, the NOD mouse, wheat-based diets also resulted in high diabetes frequency (Coleman, D. L. et al., (1990) Diabetes 39, 432-436;
Karges, W., et al., (1997) Diabetes 46, 557-564; Hoorfar, J., et al., (1993) Br J Nutr 69, 597-607; Funda, D. P., et al., (1999} Diabetes Metab Res Rev 15, 323-327). In addition, an unusual.lyhigh proportion of patients with type 1 diabetes (2-10%) have wheat gluten sensitive enteropathy (celiac disease, CD) (Lampasona, V., et al., (1999) Diabetologia 42, 1195-1198), a rate that is 10-33 times that in the normal population and about 1/3 of diabetes ____._ F~,. . .._ _.___.__~..,.~-__~____. _ r____

-3-patients have antibodies against the CD autoantigen, tissue transglutaminase.
Other reports indicate that increased peripheral blood T cell reactivity to wheat gluten was more frequent in newly diagnased patients than in controls. These data are consistent with the involvement of dietary wheat proteins in diabetes pathogenesis.
Although considered to 'be a T cell mediated disease, studies of the prediction and pathogenesis of type 1 diabetes in humans rely heavily on serum autoantibodies as biomarkers of the destructive process. The humoral immune response to selected autoantigens correlates with histologic damage in the pancreas of newly diagnosed to patients (Imagawa, A., et al., (2001) Diabetes 50, 1269-1273.).
The 64 kDa autoantigen originally reported in BB rat and human islets was identified in patients concordant for both the neurologic disease, Stiff man syndrome and 'type 1 diabetes, as glutamic acid decarboxylase (GAD), a major autoantigen in type 1 diabetes (Baekkeskov, S., et al,, (1990) Nature 347, 151-156). Despite continued i5 progress, the antigens that initiate and maintain the pracess leading to (3-cell destruction remain poorly understood.
The development of autoimmune type 1 diabetes involves complex interactions among several genes and environmental agents. Human patients with type 1 diabetes show an unusually high frequency of wheat gluten-sensitive enteropathy, T cell 2o response to wheat proteins is increased in some patients and high concentrations of wheat antibodies in blood have been reported. In both major models of spontaneous type 1 diabetes, the BB rat and NOD mouse, at least half of the cases are diet-related.
In studies of BB rats fed defined semipurified diets, wheat gluten was a potent diabetes-inducing protein source. A major limitation in understanding how wheat or

-4- -other dietary antigens affect type 1 diabetes has been the difficulty identifying specific diabetes-related dietary proteins.
There is a need in the art to identify proteins and nucleotide sequences encoding proteins which are diabetogenic in animals. Further, there is a need in the art to identify proteins, for example foodstuff proteins that are highly antigenic in overt diabetic animals. 'There is also a need in the art to develop screening processes to identify foodstuff proteins that are antigenic/immunogenic in subjects.
Further, there is a need in the art to develop screening processes to identify subjects that may be at risk for developing a pathological condition due to consuming a foodstuff comprising l o an antigenic/immunogenic protein. There is also a need in the art to produce foods and foodstuffs in which one or more antigenic/immunogenic proteins are reduced or eliminated.
SUMMARY OF THE INVENTION
The present invention relates to proteins which are antigenic/immunogenic in 15 pathological conditions.
According to the present invention there is provided an amino acid sequence comprising a diabetogenic epitope from a protein selected from the group consisting of od[3-gliadin A-II precursor, aJ(3-gliadin MMl precursor, or Glbl. In a preferred embodiment which is not meant to be limiting in any manner, the diabetogenic 20 epitope comprises the amino acid sequence EEQLRELRRQ from Glb 1.
Also according to the present invention, there is provided a diabetogenic epitope as defined above comprising part of a larger peptide or protein that does not occur naturally in nature. In addition it is contemplated that the diabetogenic epitope is . $ ., attached to a carrier protein, non-carrier protein, macromolecule or support.
The support may comprise but is not limited to a bead, plate, dish, cover slip, slide, multiwell assay plate, or bio-assay chip.
The present invention also provides a nucleotide sequence encoding a diabetogenic epitope from a/(3-gliadin A-II precursor, al (3-gliadin MM 1 precursor, or Glb 1. In an embodiment of the present invention, which is not meant to be limiting the diabetogeic epitope is EEQLRELRRQ from Glbl.
Also provided by the present invention, there is provided nucleotide sequence complementary to a sequence encoding a diabetogenic epitope or a portion thereof.
The nucleotide sequence encoding a diabetogenic epitope, protein comprising a diabetogenic epitope or sequence complementary thereto may comprise part of a larger nucleotide sequence, for example a cloning vector or the like. The larger nucleotide sequence may comprise one or more regulatory sequences, for example, but not limited to express a nucleotide sequence encoding a diabetogenic epitopf;, protein comprising a diabetogenic epitope, or a sequence complementary thereto.. The present invention further contemplates portions of nucleotide sequences encoding diabetogenic epitopes or proteins comprising diabetogenic epitopes or nucleotide sequences coplementary thereto, for example, but not limited to as probes. It is also possible that such probes may be labeled with any label known in the art.
2o The present invention also provides an isolated antibody capable of binding to Glbl, al(3-gliadin precursor, or a/(3-gliadin MM-1 precursor. Preferably the isolated antibody is capable of binding to a diabetogenic epitope of Glbl, a/(3-gliadin precursor, or a/(3-gliadin MM-1 precursor. In a preferred embodiment, the antibody binds to the diabetogenic epitope EEQLRELRRQ from Glb 1.
Also provided by the present invention is an antibody as defined above which is a monoclonal antibody. In a further embodiment, the monoclonal antibody is an Ig;G
antibody. The antibody may be produced in the serum of an animal, for example, but not limited to a diabetogenic animal, or an asyrnptomatic diabetic animal.
Also provided by the present invention is a kit comprising one or more of 1) a diabetogenic epitope, 2) a protein or peptide comprising a diabetogenic epitope, 3) a non-protein carrier or macromolecule comprising the diabetogenic epitope, 4) a to support comprising the diabetogenic epitope, 5) a diabetogenic epitope attached to a non-covalent association agent 6) a nucleotide sequence encoding a diabetogenic epitope or peptide or protein comprising the diabetogenic epitope 7) a nucleotide sequence complementary to a nucleotide sequence encoding a diabetogenic epitope, 8) a nucleotide sequence complementary to a portion of a nucleotide sequence encoding 15 a diabetogenic protein, or a combination thereof. In a preferred embodiment of the present invention, the diabetogenic epitope is from oc/a-gliadin A-II
precursor, oe/(3-gliadin MMl precursor, or Glbl. In a further embodiment, which is not meant to be limiting, the diabetogenic epitope may be EEQLRELRRQ from Glbl.
The kit as defined above may further comprise one or more beads, plates, dishes, 2o coverslips, slides, multi-well assay plates, bioassay chips, which may be attached or unattached to the diabetogenic epitope, protein or peptide comprising the diabetogenic epitope, nucleotide sequence encoding the diabetogenic epitope, sequence complementary thereto, or fragment thereof.
_.~_ . . ... _.

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Further, it is contemplated that the kit as defined above may also comprise one or more primary antibodies capable of binding to the diabetogenic epitope, or protein comprising the diabetogenic epitope, one or more secondary antibodies that are capable of binding to the primary antibody, solutions, reagents, enzymes, or a combination thereof.
The present invention also provides for a method of screening foodstuffs to identify proteins in the foodstuff which are antigenic/immunogenic in a subject, or group of subjects comprising a pathological condition, the method comprising the steps of:
a) processing the foodstuff to produce separated proteins, and;
1o b) screening the separated proteins from step a) with an antibody containing mixture derived from one or more subjects having the pathological condition to identify proteins that are antigenic/immunogenic in the subject and that are present in the foodstuff.
In an alternate embodiment of the present invention, which is not meant to be limiting in any manner there is provided a method of screening foodstuffs to identify antigenic/immunogenic proteins common in at least two subjects, or groups of subjects wherein each subject or group of subjects comprise different pathological conditions, the method comprising the steps of a) processing the foodstuff to produce separated proteins;
2o b) screening the separated proteins from step a) with a first antibody containing mixture derived from one or more subjects having a first pathological condition;

_$_ c) screening the separated proteins from step a) with a second antibody containing mixture derived from one or more subjects having a second pathological condition;
d) comparing proteins binding to the first antibody containing mixture with proteins binding to the second antibody mixture to identify proteins common in at least two subjects, or groups of subjects with different pathological conditions, t:he proteins also present in the foodstuff.
The present invention also provides a foodstuff modified to reduce or eliminate one or more diabetogenic epitopes or proteins comprising diabetogenic epitopes. In an 1 o embodiment of the present invention the foodstuff is modified to reduce ox eliminate Glbl, aJ[3-gliadin precursor or od(3-gliadin MM1 precursor, or a diabetogenic epitope thereof. For example, but not to be limiting in any manner, the foodstuff may be a genetically modified plant comprising a knockout of one or more diabetic epitopes or proteins comprising said. one or more diabetic epitopes. Tn an embodiment, the genetically modified plant is a wheat plant.
Also contemplated by the present invention is a foodstuff which comprises an inhibitory RNA nucleotide sequence that reduces or eliminates the production of one or more proteins comprising one or more diabetogenic epitopes.
This summary of the invention does not necessarily describe all features of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS
These and other features of the invention will become more apparent from the following description in which reference is made to the appended drawings wherein:
Figure 1 shows the modification of diabetes development in diabetes-prone BB
rats by wheat-based diets. Survival cuives and final diabetes incidence (inset) in BBdp rats fed from weaning a mixed, cereal-based, mainly wheat-based, NTP-2000 (National Toxicology Program, NTP) diet, or two semipurified, isocaloric, isonitrogenous diets in which the sole amino acid source was either hydrolyzed casein (HC) or wheat proteins (WP) plus supplemental sulphur amino acids. Animals fed the NTP-2000 diet had the highest incidence, 65.3 ~ 14.9 % (n=6 experiments, total of 169 rats, Figure l; ~, denotes p< 10~ vs. HC). Thexe were more cases of diabetes in BBdp rats fed WP diets (n=12 experiments, total of 282 rats, 50.6 ~ 11.1 %) than those fed a protective HC
diet (n=14 experiments, total of 322 rats, 18.8 ~ I0.6%, 14 experiments; t denotes p=10-

5) Figure 2 shows examples of (A) plaque lifts of clones screened with serum from diabetic, asymptomatic or control rats; (B) antibody reactivity to three clones and (C) frequency of antibody reactivity to the wheat proteins. Figure 2A shows plaque lifts of clones WP5212, WP 1211 l, WP23112 and WPCON screened with serum from five diabetic, asymptomatic or control rats. Figure 2B shows .mean antibody reactivity (intensity/pixel) ~ SD to the recombinant wheat proteins screened with diabetic (cross-hatch), asymptomatic (hatched) or control (open) BB rats are shown. Individual values for diabetic (diamonds), asymptomatic (squares) or control (circles) rats are shown. Figure 2C shows the frequency of diabetic (cross-hatched), asymptornatic (hatched), and control (open) BB rats with positive antibody reactivity to the wheat proteins is shown. A

-lo-positive antibody level was defined as an antibody reactivity greater than the mean intensity of WPCON screened with control rat serum plus two SD. (ANOVA/LSD; '~
indicates significant difference vs control rats, p<_0.02; * indicates significant vs asymptomatic rats, p<_0.02).
Figure 3 shows antibody reactivity to the Glb 1 clone is strongly asociated with pancreatic inflammation or insulitis. The correlation between the percent of islets infiltrated (left column) or insulitis score (right column) and antibody reactivity (mean intensity/pixel) to three recombinant wheat proteins in diabetic (diamonds), asyrnptomatic (squares) or to control (circles) rats are shown. The Pearson Product-Moment correlation r and p values are indicated.
Figure 4 shows 1D Western analysis of wheat proteins probed with serum collected prospectively from BB rats at different risk of developing diabetes. 1 D
Western blots of ~s wheat proteins probed with serum from prediabetic or asyrnptomatic BB rats at 50 d, 70 d and necropsy are shown in Figure 4A. The mean intensity ~ SD of each wheat protein band is shown for the prediabetic period (70 d) or at necropsy for asymptomatic (open bars) or diabetic (filled bars) in Figure 4B; (ANOVA/LSD; t, p=0.02; ~, p=0.006).
20 Figure 5 shows 1D and 2D Western analysis of antibody binding to wheat proteins in patients and HLA-DQ matched controls. Figure SA shows 1 D Western blots of wheat proteins probed with serum samples from diabetic children and control children without diabetes. Figure SB shows the mean absorbance + SD of (each) wheat protein band probed with serum from diabetic children (filled bars) and HLA-DQ-matched controls (open bars) (ANOVA/LS:D; * indicates p=0.005). Figure SC shows 2D Western blot of wheat proteins probed with pooled serum samples from newly diagnosed diabetic children (left) or control children (right). Wheat storage globulin, Glbl, was bound by antibodies in serum from children with diabetes but there was no binding using serum from non-diabetic controls.
Figure 6 shows identification of wheat storage globulin, Glb 1, by in-gel tryptic digestion and capLC-MS/MS analysis. Figure 6A shows the MS/MS spectrum of the doubly protonated ion (MFI22+) at m/z 514.8 corresponding to the Glb 1 tryptic peptide, 1 o VAIMEVNPR. The sequence of this peptide can be determined from the y-ion series (i.e., fragment ions that originate from the C-terminus of the peptide) as is indicated on the spectrum. Figure 6B.
Figure 7 shows increased IgG reactivity to wheat proteins in adult T 1 D
patients. 2D
Western blots of patients with type 1 diabetes (average age 24.6+/- 6.8 y, n--7) and controls (27.5+l- 5.8y, n=12) are shown. WG extract was resolved using 2D-electrophoresis and bloti;ed onto nitrocellulose. Proteins were probed with serum from patients and IgG binding was detected using enhanced chemiluminescence. The filled spots represent proteins that were more frequently antigenic in T1D patients compared with controls (p<0.05). Diabetic patients Dl to D7 are age and sex matched to controls 2o C1 to C7; additional unmatched controls are included in the analysis.
Figure 8 shows increased IgG reactivity to wheat proteins in children with T1D. 2D
western blots from two vpatients (age 8y) with T1D. The filled spots represent proteins that were more frequently antigenic in TID patients (n=9) compared with controls.

... ....... ....._...,_"._...."mr_..- N~,..=,..~,:zq,7r.-w..~s.~F~..uAm.m.Twau~...."..n.~,..,r., ,a."~.,e,-.-."a..~....r.rmw...~.-. _--.,............. ,........

Figure 9 shows proliferation of PBMC from T1D patient to chymotrypsin-treated WG.
Figure 20 shows cloning of TID WG-reactive cells by flow sorting. PBMC from a patient were stained with CFSE and cultured in the presence of 6.25 ~.g/ml chymotrypsin treated WG. CeIIs were harvested at day 9, stained with anti-CD3-ECD antibody and sorted. The gates show % CD3+CFSE~°"'~ (WG reactive T cells) and %
CD3+CFSE~'Ign~
(unresponsive T cells) before and after sorting.
Figure 11 shows the predicted three dimensional structure of WP5212.
Figure 12 shows a potential three dimensional structure of the antigenic epitope of WP5212 as shown by the arrow.

DETAILED DESCRIPTION
The following description is of a preferred embodiment, which is not meant to be limiting in any manner.
Peptide Sequences According to an embodiment of the present invention, there is provided a peptide or protein sequence comprising at least one diabetogenic epitope.
By the term "diabetogenic epitope" it is meant a sequence of amino acids which is capable of being bound by an antibody produced by a subject, for example, but not to limited to a human subject, the antibody involved in an autoimmune reaction associated with diabetes or diabetes pathogenesis. The epitope may comprise a linear sequence of amino acids which is recognized by the antibody, or the epitope may adopt a higher ordered structure, for example, a three dimensional structure as is known in the art, and the antibody may bind to the three dimensional structure of the epitope.
In an embodiment of the present invention which is not meant to be considered limiting in any manner, the peptide sequence comprises a diabetogenic epitope from al j3-gliadin A-II precursor, a/(3-gliadin MMl precursor, or Glbl. The nucleotide sequence of WP5212 and amino acid sequences of these proteins are shown in Tables 1 and 2.
In a further embodiment of the present invention the diabetogenic epitope is EEQLRF;LRRQ
(shown from N-terminus to C-terminus) from Glbl.

Table 1: Wheat gene senuences Gene Name Database Nucleotide Sequence and ID No.

(HomologueWheat AAGCCTTCTCTTCGCCGCGGCTGTTTCGGCCTCCCATGACGAGGAGGAGG
to globulin Gene indexACAGGCGCGGTGGGCGCTCGCTTCAGCGGTGCGTGCAGCGGTGCCAGCA
Begl precursor GGACCGGCCGCGGTACTCTCATGCCCGGTGCGTGCAGGAGTGCCGGGACG

TC1039161) ACCAGCAGCAGCACGGAAGGCACGAGCAGGAGGAGCAGGGCCGCGGGCA

TGGCCGGCACGGCGAGGGGGAGCGTGAGGAGGAGCAGGGCCGTGGCCGT

GGGCGGCGCGGCCAGGGAGAGCGTGAGGAGGAGCAGGGCCGTGGACGTG

GGCGGCGCGGCGAGGGAGAGCGTGATGAGGAGCACGGGGATGGCCGGCG

GCCGTACGTGTTCGGCCCGCGCAGCTTCCGCCGCATCATCCGGAGCGACC

ACGGGTTCGTCAAGGCCCTTCGCCCGTTCGACGAAGTGTCCAGG<:TCCTC

CGGGGCATCAGGAACTACCGTGTCGCCATCATGGAGGTGAACCCGCGCGC

GTTCGTCGTGCCGGGACTCACGGACGCAGACGGCGTCGGCTACGTCGCTC

AAGGCGAGGGGGTGCTGACGGTGATCGAGAACGGCGAGAAGCGGTCCTA

CACCGTCAGGCAAGGCGATGTGATCGTCrGCGCCGGCGGGGTCCATCATGC

ACCTGGCCAACACCGACGGCCGGAGGAAGCTGGTCATCGCCAAGATTCTC

CACACCATCTCCGTCCCCGGCAAGTTCCAGTATTTCTCGGCCAAGCCTCTC

CTCGCTAGTTTGAGCAAACGCGTGCTCACAGCGGCGTTAAAGACCTCGGA

TGAGCGGCTGGGTAGTCTCTTGGGCAGCCGCCAAGGCAAGGAGCTAGGAG

GAGAAGTCCATCTCCATCGTCCGCGCGTCAGAGGAGCAGCTCCGCGAGCT

GCGTCGCCAGGCGTCCGAGGGTGACCAGGGCCACCACTGGCCTCTCCCCC

CGTTCCGCGGCGACTCGCGCGACACCTTCAACCTCCTGGAGCAGCGCCCC

AAGATCGCCAACCGCCATGGCCGCCTCTACGAGGCCGACGCCCGTAGCTT

CCACGCCCTCGCCCAACACGACGTCCGCGTCGCCGTGGCCAACATCACGC

CGGGTTCTATGACCGCGCCCTACCTGAACACCCAGTCGTTCAAGCTCGCC

GTCGTGCTGGAAGGCGAGGGCGAGGTGGAGATCGTCTGCCCGCACCTCG

GCCGCGACAGCGAGCGCCGCGAGCAAGAGCACGGCAAGGGCAGGTGGAG

GAGCGAGGAAGAGGAGGACGACCGGCGGCAGCAACGCCGACGCGGGTCC

GGCTCCGAGTCGGAGGAGGAGCAGGACCAGCAGAGGTACGAGACGGTCC

GCGCGCGGGTGTCGCGCGGCTCGGCGTTCGTGGTGCCCCCCGGCCACCCG

GTGGTGGAGATCGCCTCGTCCCGCGGCAGCAGCAACCTCCAGGTGGTGTG

CTTCGAGATCAACGCCGAGAGGAACGAGCGGGTGTGGCTCGCCGGGAGG

AACAACGTGATCGCCAAGCTGGACGACCCCGCCCAGGAGCTCGC;CTTCGG

CAGGCCCGCGAGGGAGGTGCAGGAGGTGTTCCGCGCCAAGGATCAGCAG

GACGAGGGCTTCGTCGCCGGACCCGAGCAGCAGCAGGAGCATGAGCGCG

GGGACCGCCGCCGTGGTGACCGCGGGCGCGGCGACGAAGCCGTGGAGGC

GTTCCTGAGGATGGCAACCCrCCGCGCTCTGAGGCGGCAAGGCCGCTGTTG

TTAAGTGAATGTGTGAGCTGGAGCCCGTGCCATTTGAGAGCTGAACTTGT

ATGTGTGTGTAAGTTTGTCAGTACGCGGGAGTAGCATAAATAAGTCGTGG

CACGCrGCTCAGTACGATGATGTAAGTTGCGTACCTACCTTCTACCAAGGC

ATGCATGCCCAACATAAATAAACACAAGGGCGTTGCGCCTCTTTTTCAGT

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.... ___._ Table 2: Wheat protein sequences Protein DatabaseAmino Acid Sequence Name and ID
No.

WP5212z n/a MATRGRATIPLLFLLGTSLLFAAAVSASHDEEEDRRGGRSLQRCVQ

RCQQDRPRYSHARCVQECRDDQQQHGRHEQEEQGRGHGRHGEGE

REEEQGRGRGRRGQGEREEEQGRGRGRRGEGERDEEHGDGRRPY

VFGPRSFRRIIRSDHGFVKALRPFDEVSRLLRGIRNYRVAIMEVNPR

AFVVPGLTDADGVGYVAQGEGVLTVIENGEKRSYTVRQGDVIVAP

AGSIMHLAN'TDGRRKLVIAKILHTISVPGKFQYFSAKPLLASLSKRV

LTAALKTSDERLGSLLGSRQGKEEEEKSISIVRASEEQLRELRRQAS

EGDQGHHWPLPPFRGDSRDTFNLLEQRPKIANRHGRLYEADARSF

HALAQHDVRVAVANITPGSMTAPYLNTQSFKLAVVLEGEGEVEIV

CPHLGRDSERREQEHGKGRWRSEEEEDDRRQQRRRGSGSESEEEQ

DQQRYETVRARVSRGSAFVVPPGHPWEIASSRGSSNLQVVCFEIN

AERNERVWLAGRNNVIAKLDDPAQELAFGRPAREVQEVFRAKDQ

QDEGFVAGPEQQQEHERGDRRRGDRGRGDEAVEAFLRMATAAL

alpha/beta-NCBI mktfpilallaivattattavrvpvpqlql qnpsqqqpqeqvplvqeqqfqgqqqpfppq gliadin qPYPqPqpfpsqqpYlqlqpfpqpqlpypq pqpfrpqqpypqpqpqysqpqqpisqqqqq A-II

precursor qqqqqqqqqqilqqilqqqlipcrdwlqq hniahgssqvlqestyqlvqqlccqqlwqi P04722 peqsrcqaihnw haiilhqqhhhhqqqqq qqqqqplsqvsfqqpqqqypsgqgffqpsq qnpqaqgsfqpqqlpqfeeirnlalqtlpa mcnvyippyctiapfgifgtn alphalbeta-NCBI mktflilallaivattariavrvpvpqlqp qnpsqqqpqeqvplvqqqqfpgqqqpfppq gliadin qpYpqpqpfpsqqpYlqlqpfpqpqlpypq pqlpypqpqlpypqpqpfrpqqpypqsqpq precursor YsqPqqpisqqqqqqqqqqqqkqqqqqqqq ilqqilqqqliperdwlqqhsiaygssqv P18573 lqqstyqlvqqlccqqlwqipe qsrcqaih nwhaiilhqqqqqqqqqqqqple~qvsfqq pqqqypsgqgsfqpsqqnpqaqgsvqpqql pqfeeirnlaletlpamcnvyipp:yctiap vgifgtn 'Recently a new EST was submitted to the TIGR Wheat Gene Index that matched exactly the sequence for 'VVP5212, referred to as Glb. l 2The expected translation of the open reading frame of WP5212.

It is also contemplated that the diabetogenic epitope may comprise part of a larger peptide or protein. For example, but not wishing to be limiting in any manner, one or more amino acids may be attached via one or more peptide bonds to the diabetogenic epitope at the N-terminal amino acid, the C-terminal amino acid or both. Further, the diabetogenic epitope may be attached covalently or non-covalently to a carrier protein, for example, but not limited to serum albumin such as BSA, KLH or other suitable earner. It is also contemplated that the ~iiabetvgenic epitope may be attached in series to form a homopolymer for example, but not limited to EEQLItELRRQEEQLRELRRQ. In the event that the diabetogenic epitope is attached to a carrier protein or other peptide or amino acid sequence, preferably it is attached via a covalent bond, for example a peptide bond or other covalent bond.
It is also contemplated that the diabetogenic epitope, peptide comprising the diabetogenic epitope, or carrier protein attached thereto may comprise a purification tag, for example, but not limited to a hexahistidine tag to facilitate purification, an amino acid spacer sequence for example, but not limited to reduce steric hindrance during binding of the diabetogenic epitope to an antibody or the tike, a non-covalent association agent such as, but not limited to biotin to promote association between the diabetogenic epitope and avidin or avidin-like molecule, for example, but not limited to streptavidin.
The diabetogenic epitope also may be covalently attached or non-covalently associated with a non-protein carrier or macromolecule for example, but not limited to polyethylene glycol, dextran or the like, or it may be covalently attached or non-covalently associated with a support for example, but not limited to a bead, plate, dish, cover slip, slide, multiwell assay plate, bio-assay chip, and the like manufactured from any suitable material known in the art. Representative examples of such materials may include, but are not limited to glass, and plastic for example, but not limited to polystyrene, polypropylene, and the like. A variety of methods exist in the art to attach, couple, bind or associate the diabetogenic epitope with a non-protein earner or support, and any such method is meant to be encompassed within the scope of the present invention.
As indicated previously, the diabetogenic epitope may form part of a larger protein or macromolecule. Preferably, the larger protein or macromolecule does not naturally occur in nature. Also, it is preferred that the diabetogenic epitope is sterically unhindered such that it is capable of being bound by an antibody. More preferably, the diabetogenic epitope forms part of a surface region such that an antibody specific for such a sequence is capable of binding to it under about normal physiological conditions, for example conditions similar to those in which an antibody binds to an antigen in an organism from which the antibody is naturally produced.
The diabetogenic epitope alone or attached to a carrier protein, non-protein carrier, 1 s macromolecule, support or combination thereof may be prepared according to a variety of methods known in the art. For example, proteins or peptides comprising the diabetogenic epitope may be prepared using standard techniques in molecular biology, for example by 1) transforming a suitable cell with an expression vector comprising a nucleotide sequence encoding the diabetogenic epitope or a peptide or protein comprising the 2o diabetogenic epitope, and 2) expressing the protein or peptide in the cell.
Alternatively, a diabetogenic epitope, peptide comprising the diabetogenic epitope, or protein comprising the diabetogenic epitope may be prepared by peptide chemistry for example, 'but not limited to solid phase or solution phase peptide synthesis. Preferably the diabetogenic epitope, or protein comprising the diabetogenic epitope is relatively short, for example, .~m..~~,....~.__ _ ..~.~.._.~_ _.___.__ ...._._-..._,_~.~...~.~___.___.._._ ...._._...;...___.____ _ j$ -but not limited to less than about 50 amino acids in length, more preferably less than about 30 amino acids in length, and still more preferably less than about 20 amino acids in length. Macromolecules, non-protein carriers, supports and the like may be prepared by standard techniques known in the art and any method known in the art to attach a diabetogenic epitope or protein comprising a diabetogenic epitope thereto may be employed in the present invention. It is also contemplated that a combination apI>roach using molecular biology and other techniques may be employed.
The amino acid sequence of the diabetogenic epitope, or protein comprising the diabetogenic epitope may be used to screen for animals or humans that develop one or more antibodies that bind to the diabetogenic epitope. In this manner it may be possible to screen for animals have diabetes or that are at risk or predisposed to developing diabetes.
For example, the diabetogenic epitope, or protein comprising the diabetogenic epitope may be contacted with immune serum from an animal. Binding of an antibody in the sera of an animal to the diabetogenic epitope is indicative that the animal may be at risk for developing type 1 diabetes.
Nucleotide Seauences The present invention also.contemplates a nucleotide sequence encoding a diabetogenic epitope, or a portion thereof, the diabetogenic epitope derived from a protein selected from the group consisting of, but not limited to a/(3-gliadin A-II precursor, oc/(3-gliadin 2o MM1 precursor, and Glbl. In an embodiment of the present invention, which is not meant to be limiting in any manner, the nucleotide sequence encodes an epitope defined by the amino acid sequence EEQLRELRRQ. As will be evident to a person of skill in the art, a particular protein sequence may be encoded by numerous DNA sequences due to the degeneracy of the genetic code and thus multiple nucleotide sequences may encode 1s the same diabetogenic epitope. All such nucleotide sequences are meant to be encompassed by the present invention.
In an alternate embodiment of the present invention, the nucleotide sequence m,ay be complementary to a sequence encoding a diabetogenic epitope or a portion thereof. The complementary nucleotide sequence may be employed as a probe to identify sequences of DNA in organisms such as, but not limited to plants which may encode proteins comprising diabetogenic epitopes. Alternatively, but without wishing to be limiting, the complementary nucleotide sequence may be employed as a primer, for example in PCR
reactions and the like. In an embodiment of the present invention, the complementary 1 o nucleotide sequence comprises greater than about 10 nucleotides, preferably greater than about 17 nucleotides, more preferably greater than about 21 nucleotides. In still another embodiment, the complementary nucleotide sequence may be longer, for example, but not limited to in the range of about 50 to about 150 nucleotides.
The nucleotide sequence of the present invention also encompasses nucleotide sequences encoding diabetogenic epitopes such as but not limited to EEQLRELRRQ and complementary nucleotide sequences or portions thereof which hybridize under stringent hybridization conditions (see Maniatis et al., in Molecular Cloning (A
Laboratory Manual), Cold Spring Harbor Laboratory (1982) p 387 to 389). An example of one such stringent hybridization condition may be hybridization at 4XSSC at 65°C, followed by 2o washing in O.1XSSC at 65°C for an hour. Alternatively an exemplary stringent hybridization condition could be in 50% formamide, 4XSSC at 42°C.
It is also contemplated that the nucleotide sequence encoding a diabetogenic epitope may form part of a larger nucleotide sequence, for example, but not limited to a vector that further comprises one or more regulatory sequences including, but not lirr~ited to promoter elements, basal (core) promoter elements, elements that are inducible in response to an external stimulus, elements that mediate promoter activity such as negative regulatory sequences or txanscriptional enhancers. Regulatory sequences may also comprise elements that are active following transcription, for example, regulatory s sequences that modulate gene expression such as translational and transcriptional enhancers, translational and transcriptional repressors, upstream activating sequences, and mRNA instability determinants. Several of these latter elements may be located proximal to the coding region. In the context of this disclosure, the regulatory sequence typically refers to a sequence of DNA, usually, but not always, upstream (5') to the coding sequence of a structural gene, which controls the expression of the coding region by providing the recognition for RNA polymerise and/or other factors required for transcription to start at a particular site. However, it is to be understood that other nucleotide sequences, located within introns, or 3' of the sequence may also contribute to the regulation of expression of a coding region of interest. An example of a regulatory sequence that provides for the recognition for RNA polymerise or other transcriptional factors to ensure initiation at a particular site is a promoter sequence. A
promoter sequence comprises a basal promoter sequence, responsible for the initiation of transcription, as well as other regulatory sequences {as listed above) that modify gene expression.
2o 'There are also several types of regulatory sequences, including those that are developmentally regulated, inducible and constitutive. A regulatory sequence that is developmentally regulated, or controls the differential expression of a gene under its control, is activated within certain organs or tissues of an organ at specific times during the development of that organ or tissue. However, some regulatory sequences 'that are developmentally regulated may preferentially be active within certain organs or tissues at specific developmental stages, they may also be active in a developmentally regulated manner, or at a basal level in other organs or tissues within the plant as well.
An inducible regulatory sequence is one that is capable of directly or indirectly activating transcription of one or more DNA sequences or genes in response to an inducer.
In the absence of an inducer the DNA sequences or genes will not be transcribed.
Typically the protein factor, that binds specifically to an inducible sequence to activate transcription, may be present in an inactive form which is then directly or indirectly converted to the active form by the inducer. However, the protein factor may also be absent.
The inducer 1 o can be a chemical agent such as a protein, metabolite, growth regulator, herbicide or phenolic compound or a physiological stress imposed directly by heat, cold, salt, or toxic elements or indirectly through the action of a pathogen or disease agent such as a virus.
Any regulatory sequence known in the art may comprise part of the nucleotide sequence encoding a diabetogenic epitope as described herein. Further, as it is equally contemplated that the nucleotide sequence encoding a diabetogenic epitope may be produced by a variety of cells, for example, but not limited to bacterial cells, yeast cells, insect cells, or mammalian cells, the present invention contemplates the use of any regulatory element known in the art, for example, but not limited to promoter;
terminator, upstream activation sequence, erdlancer, origin of replication, or any combination thereof 2o in the nucleotide sequence of the present invention.
The nucleotide sequence encoding a diabetogenic epitope may also comprise a label for example, but not limited to a radiolabel, heavy metal particle, for example, but not limited to gold, silver or the like, a fluorescent group, or the like to facilitate identification of the sequence during use. Any label lrnown in the art is meant to be encompassed by the present invention.
Nucleotide sequences encoding a diabetogenic epitope or protein may be employed for mass production of such proteins or epitope sequences. Alternatively, the nucleotide sequences complementary thereto may be employed i.n a method to identify DNA
in organisms that may be translated to produce potentially diabetogenic proteins.
For example, but not wishing to be limiting in any manner, a food plant, such as, but not limited to wheat rnay be screened to determine whether the plant may comprise DNA that produces a diabetogenic protein.
1 o Antibodies The present invention also provides an isolated antibody capable of binding to Glb l, a/[3 gliadin precursor, or a/(3 gliadin MM-1 precursor. Preferably, the antibody binds to a diabetogenic epitope of a,/(3 gliadin precursor, a/(3 gliadin MM-1 precursor, or GIb l, for example, but not limited to the amino acid sequence EEQLRELRRQ. In a preferred embodiment, the antibody is a monoclonal antibody, more preferably an Ig-G
monoclonal antibody. The antibody may be derived from any antibody producing species, for example, but not limited to mouse, rat, human, goat, rabbit, etc. Further; the antibody may be produced by immunizing an animal, with the diabetogenic epitope, peptide or protein comprising the diabetogenic epitope, or non-protein Garner comprising a 2o diabetogenic epitope. The production of antibodies may be performed bya person of skill using any one of a variety of methods known in the art, for example, but not limited to Harlow and Lane, "Antibodies a laboratory manual", (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1988). Alternatively, the isolated antibody may be obtained from the serum of an animal that comprises one or more antibodies specific for a diabetogenic epitope. A variety of methods are known in the art for purifying antibodies and any such method may be employed in the present invention.
Kits The present invention also contemplates a kit comprising one or more of: 1) a diabetogenic epitope, 2) a protein or peptide comprising a diabetogenic epitope, 3) a non-protein carrier or macromolecule comprising the diabetogenic epitope, 4) a support comprising the diabetogenic epitope, 5) a diabetogenic epitope attached to a non-covalent association agent, 6) a nucleotide sequence encoding a diabetogenic epitope orpeptide or 1 o protein comprising the diabetogenic epitope, 7) a nucleotide sequence complementary to a nucleotide sequence encoding a diabetogenic epitope, 8) a nucleotide sequence complementary to a portion of a nucleotide sequence encoding a diabetogenic protein, or any combination thereof.
In an embodiment of the present invention which is not meant to be limiting in any manner, the diabetogenic epitope is from a/(3-gliadin A-II precursor, al(3-gliadin MM1 precursor, or Glbl. In a specific embodiment of the present invention the diabetogenic epitope is EEQLRELRRQ from Glb 1.
It is also contemplated that the kit may comprise a protein or peptide comprising a diabetogenic epitope, for example, but not limited to the a/~3-gliadin A-lI
precursor , a/(3-gliadin MM1 precursor peptide or Glbl. The kit may also comprise combinations of these proteins.
As disclosed earlier, any nucleotide sequence defined above may be part of a larger nucleotide sequence, for example, but not limited to cloning vector or the like. The larger nucleotide sequence, for example, cloning vector or the like may comprise additional nucleotide sequences for example, but not limited to regulatory sequences.
Also the nucleotide sequence as disclosed above may comprise a label, for example, but not limited to P-32 label to aid in identification of the sequence.
The kits of the present invention may also comprise one or more beads, plates, dishes, coverslips, slides, mufti-well assay plates, bioassay chips, which may be attached or unattached to the diabetogenic epitope, protein or peptide comprising the diabetogenic epitope, nucleotide sequence encoding the diabetogenic epitope, sequence complementary thereto, or fragment thereof .
to The kits of the present invention may further comprise other components, for example, but not limited to one or more primary antibodies capable of binding to the diabetogenic epitope, or protein comprising the diabetogenic epitope. Preferably the primary antibody binds to the diabetogenic epitope. The kits may also comprise a secondary antibody which is capable of binding to the primary antibody. It is also possible that the kit may comprise a tertiary antibody, (or higher order antibodies) which is capable of binding the secondary antibody. The secondary, tertiary or higher order antibodies may be labeled for example, but not limited to provide a signal to aid in identification of binding.
The kit may also comprise one or more solutions, reagents, enzymes or combinations thereof For example, the kit may comprise protein or nucleotide sequence binding 2o solutions, washing solutions, blocking solutions, substrate solution, for example but not limited to enzyme substrate solutions and solutions permitting chemiluminescence. The kit may also comprise assay instructions for example, but not limited to any method as disclosed herein.

The kit comprising one or more diabetogenic proteins, peptides or fragments thereof may be used to identify subjects that comprise one or more antibodies against a diabetogenic epitope or protein comprising a diabetogenic epitope. For example, the one or more diabetogenic proteins, peptides or fragments thereof may be contacted with immune serum from an animal or human. Further, the kits may be employed in screens to identify animals or humans at risk or predisposed to developing diabetes. Binding of an antibody in the sera of an animal or human to a diabetogenic protein, peptide, more preferably a diabetogenic epitope in the protein or peptide may be indicative that the animal or human is prone to diabetes. The kits also may be employed to identify foodstuffs which comprise proteins that comprise diabetogenic epitopes, or nucleotide sequences that may encode proteins comprising diabetogenic epitopes.
Methods According to the present invention there is provided a method of screening foodstuffs to 1 s identify proteins in the foodstuff which are antigeriic/immunogenic in a subject, or groups of subjects comprising a pathological condition, the method comprising the steps of a) processing the foodstuff to produce separated proteins, and;
b) screening the separated proteins from step a) with an antibody containing mixture derived from one or more subj ects having the pathological condition to identify proteins 2o that are antigenic/immunogenic in the subject and that are present in the foodstuff.
By the term "foodstuffs" it is meant any food component that may be consumed by a subject. The foodstuffs may include foods such as food plants that are cultivated or occur naturally, for example, but not limited to wheat, soybean, corn, and the like.
Similarly, the foodstuffs may include foods derived from animals or products of animals, for example, but not limited to meats, milk, eggs and the like, for example but not limited to from cows, pigs, lambs, chicken, fish, seafood and the like. Any plant or any animal that may be consumed as a food may be considered a foodstuff within the context of the present invention. In addition, the term "foodstuff' is meant to include any food component, or group or mixture of food components that is processed physically or chemically for example, but not limited to by cooking, curing, preserving, fermenting, pasteurizing, canning, sterilizing, irradiating and the like.
By the phrase "proteins in the foodstuff which are antigenic/immunogenic in a subject" it 1o is meant one or more proteins in a foodstuff which may be bound by one or more antibodies in a subject having a pathological condition. The one or more antibodies in a subject that bind to a foodstuff may be present in the serum of a subject with the pathological condition.
By the term "pathological condition" it is meant an unnatural condition or disease which is is detrimental to the subject if left untreated. Tn this manner the pathological condition may be clinical or subclinical. A subject with a subclinical pathological condition may be asymptomatic at a particular time, but may develop clinical signs of the pathological condition later on. In an embodiment of the present invention, the subject or group of subjects may comprise diabetes as a pathological condition. In an alternate embodiment 20 of the present invention, the subject or group of subjects may comprise celiac disease as a pathological condition. In another embodiment of the present invention the subject or group of subjects may comprise both diabetes and celiac disease as pathological bonditions.

By the term "subjects" it is meant any mammalian subj ect, for example, but not limited to rat, mouse, hamster, guinea pig, rabbit, chimpanzee or human. In a preferred embodiment, the subject is a human.
By the term "processing the foodstuff' it is meant separating proteins contained in the foodstuff by any method known in the art, for example, but not limited to 1 D
electrophoresis, 2D electrophoresis, chromatography, for example, but not limited to gel filtration, anion exchange, cation exchange, affinity chromatography, hydrophobic interaction, reverse phase and the like. In a preferred embodiment, the foodstuff is processed by 2D gel electrophoresis to separate proteins in the foodstuff, for example, but to not limited to as described in the Examples. In this manner, a majority of the protein components in the foodstuff are separated from each other.
The processing of a foodstuff may also comprise one or more other processing steps including, but not limited to dialysis, extractions for example, alkali, acid, alcohol or organic chemical for example, but not limited to chloroform, methylene chloride, ethanol, methanol, butanol or a combination thereof, multiphase extractions, precipitations, or any combination thereof. In an embodiment of the present invention, which is not meant to be limiting in any manner, the method comprises a chromatographic step, extraction, precipitation or dialysis step prior to an electrophoresis processing step, for example, but not limited to two dimensional electrophoresis.
According to an alternate embodiment of the present invention there is provided a method of screening foodstuffs to identify antigenic/immunogenic proteins common in at Ieast two subjects, or groups of subjects wherein each subject or group of subjects comprise different pathological conditions, the method comprising the steps of a) processing the foodstuff to produce separated proteins;
b) screening the separated proteins from step a) with a first antibody containing mixture derived from one or more subjects having a first pathological condition;
c) screening the separated proteins from step a) with a second antibody containing mixture derived from one or more subjects having a second pathological condition;
d) comparing proteins binding to the first antibody containing mixture with proteins binding to the second antibody mixture to identify proteins common in at least two to subjects, or groups of subjects with different pathological conditions, the proteins also being present in the foodstuff.
Several variations of the method as disclosed above may also be employed in the present invention. For example, the step of processing the foodstuff in step a) may be performed 1 s in duplicate or higher, for example, but not limited to be under identical conditions. The steps of screening as described in b) and c) may each be performed on distinct samples of processed foodstuffs, preferably processed under identical conditions to ensure that all antigenic sequences in the foodstuff are available for binding by each antibody containing mixture. Further, one or more control subjects may be employed in the method of the 2o present invention to further aid in the identification, of proteins that are antigenic/irnmunogenic in a subject and that are present in the foodstuff.

The method of the present invention may further comprise a step of isolating and optionally sequencing the one or more proteins that are antigenic/immunogenic in the subject and present in the foodstuff. Further, the method of the present invention may comprise subjecting the one or more proteins to mass spectroscopy, or epitope mapping, for example, but not limited to as described in the Examples section.
Modified Foods and Foodstuffs The present invention also contemplates foodstuffs, for example, but not limited to plants, animals, or processed foodstuffs therefrom, that are modified to reduce or eliminate proteins which are antigenic/immunogenic in a subject or group of subjects comprising a pathological condition. Alternatively, the foodstuffs may be modified to reduce or eliminate antigeniclimmunogenic epitopes of foodstuff proteins which are antigenic/immunogenic in a subject or group of subjects. In an embodiment of the present invention there is provided a foodstuff modified to reduce or eliminate Glb l, a/j3-gliadin precursor or a/(3 -gliadin MM1 precursor, or a diabetogenic epitope thereof.
Proteins other than those listed above are also meant to be included by the present invention.
Foodstuffs may be modified to reduce or eliminate proteins by a variety of methods: For example, a plant or animal foodstuff may be genetically modified to "knockout"
a gene of interest or portion thereof encoding a protein. Such methods are well known to those of skill in the art in molecular biology. Alternatively, techniques of RNAi maybe employed to reduce or eliminate proteins. For example, but not wishing to be limiting in any manner, a region of the WP5212 cDNA clone may be amplified from cv. AC Barrie and inserted into the RNAi silencing vector, pHellsgate which has been used to transform wheat cells.

It is also contemplated that the foodstuffs comprising proteins may be processed to remove or reduce proteins that may be antigenic/immunogenic in a subject, for example, but not limited to by chemical or protease treatment. Such treatments may modify or hydrolyze proteins at specific sequences and may destroy epitopes in proteins which are antigenic/immunogenic in a subject.
Wheat protein diets can modulate diabetes outcome Animals fed a non-purified, defined, mainly wheat-based NTP-2000 diet showed the highest incidence of diabetes (n=6 experiments, total of 169 rats, 65.3 ~ 14.9 %, Figure 1). When comparing only defined, isocaloric and isonitrogenous semi-purified diets with 1 o amino acids from wheat gluten or hydrolyzed casein, there were more cases of diabetes in BBdp rats fed wheat protein (WP) diets (n=12 experiments, total of 282 rats, 50.6 ~
11.1%) compared with BBdp rats fed a protective hydrolysed casein (HC) diet (n=14 experiments, total of 322 rats,18.8 ~ 10.6% Figure l; ANOVA/LSD, p< 1 x 10-5).
When fed to diabetes-prone BB rats, diets in which wheat gluten was the sole protein source induced nearly three times as many cases of diabetes as a hydrolyzed casein-based diet (Figure 2). To analyze as many potential diabetes-related wheat proteins as possible, more than one million recombinant phage from a wheat cDNA expression library were translated and screened with pooled sera from diabetic rats. Positive clones were subjected to nucleotide sequencing. One of the clones termed WP5212 was bound 2o strongly by antibodies in sera from diabetic rats. Nucleotide and translated BLAST
searches of Genbank ( NCBI. (2002) in http://www.ncbi.nlm.nih.gov/BLAST/, National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA) and TIGR Wheat Gene Index (TIGRWheatDatabase. (2001) in http://www.tigr.org/tdb/tagi/, Institute for Genomic Research, Rockville, MD, USA) databases revealed high similarity at the nucleotide and translated amino acid level with the wheat storage globulin protein, Glbl . Clone WP5212 contained a 1890 base pair (bp) open reading frame (ORF), including 95 by of the LacZ gene. It shared 90%
identity across 1387 nucleotides with the T~iticum aestivum wheat storage protein (Glbl) gene (Acc. No. M81719.1 ). The expected translated amino acid sequence was 629 amino acids in length and shared 80% identity across 642 amino acids with the T. aestivum wheat storage protein (Acc. No. AAA34269.1), Glbl. IgG reactivity against Glbl was strain-specific, highest in overt diabetic, lower in asymptomatic BB rats and lowest in non-diabetes-prone BBc rats.
l0 Clones WP 12111 and WP23112 also exhibited reactivity when the cDNA was translated and screened with pooled sera from diabetic rats. The open reading frame for cDNA
clone WP12111 was 789 by coding for a putative product of 262 amino acids. The nucleotide sequence shared 96% identit~~ across 138 nucleotides with clone CNW03PL453 ITEC CNW from a wheat powdery mildew resistant line library (Acc.
No.
BE401554) and 63% identity across 144 amino acids with an unknown Arabidopsis thaliana protein (Acc. No. AAK25945).
Clone WP23112 had an ORF of 624 by coding for a putative product of 207 amino acids.
WP23112 shared 96% identity across 542 nucleotides with the BAC clone T 16L24 from . A. thaliana DNA chromosome 3 (Acc. No. 6899943) and 62% identity across 62 amino acids with the gene product, a putative A. thaliana protein (Acc. No.
CAB75463.1).
Clone WP23112 also shared 100% identity across 511 nucleotides with a clone from a Brevor mature wheat embryo ABA library (Acc. No. WHE0606).

Diabetic rats have increased frequency and intensity of antibody reactivity to wheat rop teins Antibody reactivity to translated sequences from a wheat cDNA library, for example, but not limited to cDNA clones WP5212, WP 12111 and WP23112 was assayed by screening with serum antibodies from individual diabetic (n=7), asymptomatic (n=10) and control (n=9) BB rats (Figure 2, panel A and B). Antibody reactivity was measured by densitometry and is reported as intensity/pixel. Antibody reactivity to WP5212 in diabetic rats was significantly higher than in asymptomatic (p=0.005) and control (p=10-

6) rats.
Asymptomatic BBdp rats also had increased antibody reactivity to WP5212 compared to with control rats (p=0.0004). Diabetic rats also exhibited higher antibody reactivity to WP12111 than asymptomatic rats (p=0.02). Diabetic rats had increased antibody reactivity to WPCON compared with asymptomatic and control rats. Antibody reactivity in serum from BB control rats was not different among any of the proteins analysed, suggesting that this level represented nonspecific antibody reactivity.
The frequency of rats with antibodies to wheat proteins was determined (Figure 2, panel C). A positive antibody level was defined as an antibody reactivity value greater than the mean intensity plus 2 SD for WPCON screened with control serum. More diabetic (p=0.009) and asymptomatic (p=0.02) rats had antibodies to WP5212 than control rats.
Similar data from a human patient who has both type 1 a diabetes and celiac disease indicated that antibodies from this highly wheat-sensitive individual bind strongly to the Glb 1 protein, similar to the pattern we observed in diabetes-prone rats.
Antibody reactivity to a Glb 1 protein correlates with islet inflammation and damage The autoimmune process involves progressive infiltration into the (3-cell-containing core of the islets by mononuclear cells and macrophages, a process called insulitis. The severity and prevalence of insulitis or its sequelae (end stage islets) reflect the extent of damage in the pancreas. When sera from individual rats at different risk of developing diabetes were used, IgG reactivity against the Glbl clone showed a remarkably close correlation with overall islet infiltration and damage (insulitis rating), as well as inflammation of individual islets. To determine if antibody reactivity to the cloned wheat proteins correlated with damage to the target tissue, the proportion of islets infiltrated with mononuclear cells was calculated, as well as the mean insulitis score. A
relationship to with diabetogenesis was considered to occur when both percent infiltration (degree of inflammation) and mean insulitis score showed a significant correlation with antibody intensity on the dot blots. Diabetic rats had significantly fewer islets than both asymptomatic and control rats. Diabetic rats had a higher percent of infiltrated islets and mean insulitis score compared with both asymptomatic (p=0.02 and p=0.0001 ) and i5 control (p= 10-6 and p< 10-~) rats. In asymptomatic rats, the percent of infiltrated islets was higher, as was the mean insulitis score compared with control rats (p=0.0001 and p=0.002). A positive correlation was observed between antibody intensity to WP5212 and percent of infiltrated islets (Figure 3, panel A, r = 0.81, p =10~) and mean insulitis score (Figure 3, panel B, r = 0.78, p = 3 x 10-6). These results demonstrated not only a strong 2o immune reaction against the Glb 1 protein in wheat-fed, diabetes-prone BB
rats, but also a close link with the diabetogenic process in the target tissue.
In patients with type 1 diabetes, the presence of autoantibodies to either GAD
or islet antigen (IA)-2 has been shown to be closely correlated with in situ pancreatic islet inflammation (insulitis) andlor hyperexpression of MHC class I antigens in islets Imagawa, A., et al., (2001) Diabetes 50, 1269-1273.). Similarly, antibodies from BBdp and diabetic rats showed strong reactivity to the Glbl protein, arid this immunoreactivity correlated closely with the destructive immune process that targets the pancreatic islet (3-cells in the pancreas. The close correlation between antibody reactivity to Glb 1 and islet inflammation in BB diabetes-prone and diabetic rats, represents a new association between a previously unidentified wheat antigen and the target tissue. The fact that higher immunoreactivity to Glb 1 was observed in patients compared with HLA-DQ
matched non-diabetic children suggests that wheat may also be involved in the pathogenesis of human type 1 diabetes.
l0 Increased humoral immune reactivity to low molecular weight wheat proteins in pre-diabetic rats To examine whether differences in antibody binding to wheat proteins were associated with the development of disease, Western blots of wheat gluten proteins were probed with serum obtained prospectively at 50 and 70 d from BB rats at different risk of developing diabetes. Western blots of wheat proteins showed antibody reactivity increased with age in BBdp rats (Figure 4, panel A). At day 50 the level of antibodies in asymptomatic and pxe-diabetic rats was similar. Compared with animals that remained asymptomatic, higher signal intensity was detected for wheat proteins around 46 kDa (p=0.02, Figure 4 panel B) in prediabetic animals at approximately day 70. At necropsy, animals with overt diabetes had stronger reactivity to 36 kDa wheat proteins compared with asymptomatic rats (p=0.006). Blots probed with BB control rat serum at 1:600 showed low antibody binding to wheat proteins (data not shown). The frequency of rats reacting to these wheat proteins did not differ when comparing BBc, BBdp or overt diabetic animals.

1 D and 2D Western blots show increased LAG binding to wheat.proteins in patient serum;
Glb 1 protein is bound by antibodies from patients but not controls 1D Western blots were used to investigate antibody binding to wheat proteins (Figure 5, panel A). Signal intensity for several proteins, for example, but not limited to the 33 kDa proteins was higher in patients than in controls in 19 of the 23 case-control comparisons (about 83%).
2D Western blots of wheat proteins probed with pooled sera from the same patients also 1 o showed IgG antibody binding to several wheat proteins (Figure 5, panel C).
As in the case of diabetic BB rats, binding of antibodies to wheat proteins was widespread and more intense compared with controls. Wheat storage globulin, GIb 1, consists of two subunits with a molecular weight of 49 kDa (pI 6.6) and 35 kDa {pI 6.9) (Marcone, M.
F., et al., (1998) Food Chemistry 62, 27-47). One of the proteins bound by antibodies from diabetic children (but not controls) displayed a MW of 50 kDa and pI of 6.5.
When the nature of this protein was determined using LC-MS/MS, it was found to have peptides homologous to both Glb 1 and WP5212. The expected (theoretical) peptide fragments of Glb 1 and WP5212 and the experimental fragmentation detected by mass spectrometry are shown in Figure 6.
The prospective Western analysis showed a marked humoral response to certain low molecular weight (36 and 46 kDa) wheat proteins, particularly in animals that later developed overt diabetes. These bands are similar in size to the 35 and 49 kDa subunits of Glbl. Higher antibody binding to the 33 kDa band was present in 83% of diabetic children. This indicates a broad response to wheat proteins for example, but not limited to Glb 1.
2D blots also showed higher antibody binding in diabetic children to several other wheat proteins (Figure 5, panel A and C). Glbl was among these proteins, but absent in the 2D blots probed with control serum in keeping with the result of the 1 D analysis (Figure 5, panel A). Without wishing to be bound by theory these results support the interpretation that diabetic patients have unique patterns of immune reactivity, some of which include for example, but not limited to Glbl . Increased peripheral blood T
cell reactivity to wheat proteins was seen in 24% of newly diagnosed patients with 1 o type 1 diabetes, compared with only 5°/~ of non-diabetic controls ( Klemetti, P., et al., (1998) Scand J Immunol 47, 48-53). Without wishing to be bound by theory, these data are consistent with the proposition that wheat antigens are a target of inappropriate immune responses in certain individuals who are genetically susceptible to develop autoimmune diabetes.
In order to identify additional diabetogenic wheat proteins, additional proteomic analyses of IgG antibody reactivity to wheat proteins subjected to 2D
electrophoresis and Western blotting (See attached Figure 7) were performed. Blots were probed with serum from 7 T1D patients (age 24.6 ~ 6.8 years) and 12 controls (27.5 ~ 5.8 years), seven of whom were age and sex-matched. None of the sera was tissue 2o transglutaminase positive suggesting the subjects did not have subclinical celiac disease. T1D patients had stronger and more frequent reactivity to several WG
proteins, for example, but not limited to 36-42 kDa proteins. LC-MS/MS
analysis tentatively identified some of these proteins as a/~i-gliadin isoforms. Four of these proteins were more frequently antigenic in T1D patients {Figures 7 and Figure 8, filled spots, p<0.05). Two of these proteins were identified as the a,/(3-gliadin A-II precursor and cc/(3 -gliadin MMl precursor, the latter contained the celiac immunostimulatory 33-mer peptide [Shan et al., Science 297:2275-2279, 2002] (Without wishing to be bound by theory, a,/(3-gliadin precursor (peptide 1) and ec/(3 -gliadin precursor (peptide 2) are proteins that may come from the same protein (cx/(3 -gliadin precursor). Five out of seven T1D patients reacted strongly to the proteins mentioned above. Three out of 12 controls (C3, C5, C7) reacted to some of the proteins identified by T1D
serum.
Analysis of spot frequency revealed that immune reactivity to specific wheat gluten proteins is increased significantly in a relatively large subset of T1D
patients (p<0.05).
Refernng now to Figure 8, there is shown an analysis of wheat reactivity in two T1D
children (8 y). Both showed reactivity to several wheat proteins, for example, but not limited to gliadin isoforms. One of these proteins was a/(3-gliadin A-II
precursor.
This suggests that increased immune reactivity to certain gliadin isoforms and gliadin proteins is present in young patients and in those with diabetes of long duration.
In a subset of T1D patients (n=8) and controls (n=4), proliferation of T cells in response to wheat gluten was investigated using a recently described method of cell labeling with CFSE (Turcanu et al., J Clin Invest 111:121:908-916, 2003). This 2o method was developed to monitor proliferation of cells that represent a small proportion of the total population in peripheral blood. When cells that are labelled with CFSE divide, they lose half of the fluorescent label, and this process is repeated with each cell division. Therefore, cells that are proliferating undergo more divisions and become CFSE~°"'. This method enabled us to monitor chymotrypsin-treated WG

_..._.._.._, ~ ..~ ._..~n~_ ~.~mM>,~r~,~ ~~J~,;~,_~..~" .~._. _._ ..._ _..__..~.w ~. . m..~~P__._.._ stimulation of PBMC that were CD3+ (T cells), and sort them by flow cytometry into CD3+ CFSEI°W (WG-reactive) and CD3~ CFSEh'~' (WG-non-reactive) cells (Figures 9 and Figure 10).
The proliferative response to WG measured as percent of CD3+ CFSE~°W
cells was larger in some T1D patients. All controls showed very low reactivity to wheat, 0.4 ~
0.7% (mean ~ standard deviation (SD)). In the T1D group, WG responders were defined as those having a percentage of WG-reactive T cells (minus background) higher than the mean of the control group value + 3 SD. Four out of eight T1D
l0 patients (50%) were declared responders and their mean response (~ SD) was 27.2 ~
8.8 % (p<0.0009). Without wishing t~ be bound by theory, these results suggest that a subset of T1D patients exists that is WG-responsive. This is higher than the frequency reported by Klemetti et al., who found 24% WG-responders using standard proliferation assays Scand.J.Immunol. 47:48-53, 1998. They observed gluten-induced proliferation more frequently in newly diagnosed patients whereas most of our patients were insulin-treated and with diabetes of longer duration. Thus, without wishing to be bound by theory or limiting in any manner, the sensitivity of the CFSE
method may be an important factor in detecting WG-responsive subjects.
The preliminary data suggest that wheat reactivity, both humoral and cellular is enhanced in a large subset of TlD patients compared with controls. If wheat causes diabetes in some T1D individuals, it should be possible to either modify it to be less diabetogenic, avoid it in the diet or develop tolerizing regimes so the risk for wheat-induced T1D is minimized Although it is possible to identify individuals at high risk for T1D, there is no safe intervention or treatment to offer them at this time. Dietary protein modification could be a safe, economical and effective means of preventing the development of islet autoimmunity and diabetes.
Epitope Mapping of Diabetes-Related Wheat Proteins The antigenic epitopes of diabetes related wheat proteins, for example, but not limited to WP5212 (Glb-1) may be performed as described in Example 11. Without wishing to be limiting in any manner or bound by theory, defining the antigenic epitopes of may be useful for a number of reasons: 1) epitope peptides may be easier to express; 2) epitope peptides can be synthesized; 3) epitope peptides can be used to immunize animals for the production of WP5212 specific antibodies; 4) epitope sequences rnay be homologous to self proteins providing evidence for cross-reactivity and potential molecular mimicry; and 5) antigenic epitopes may be more indicative of disease outcome and/or state.
To determine the antigenic epitopes of WP5212, a library of random, overlapping inserts expressed by transformed cells was screened by colony immunoscreening by using serum from an anti-Glb 1 antibody positive patient with both type 1 diabetes and celiac disease.
2o Bacterial colonies expressing immunoreactive peptides were selected and plasmid inserts were sequenced by using primers complementary to flanking regions of the cloning site in pSCREEN T-vector. The amino acid sequences from expressed WP5212 peptides were deduced. One clone contained a WP5212 fragment spanning nucleotides 937-967 of the original WP5212 clone was expressed in the correct reading frame with the T7 gene 10 fizsion protein. It translates to a 10 amino acid sequence (EEQLRELRRQ), which shares 100% (10/10) identity with the expected translated protein sequence of WP5212 (amino acids 309-318). It shares 90% (9/10) identity and 100% (/0/10) positives with the protein sequence of wheat storage globulin Glbl; there is a conserved change from Q to E at position 10.
Of particular note, the Glbl epitope shares 90% (9/10) identity and 100%
(10/10) positives with the protein sequence for desmin from human, cow, chicken and pig and there is a conserved amino acid change from Q to E at position three. It also shares 80%
(8/10) identity and 100% (10/10) positives with the protein sequence for desmin from to mouse, rat and hamster; there is a conserved amino acid change from Q to E
at position three and L to M at position four.
Desmin is a marker of activated pancreatic stellate cells, which are involved in the development of fibrosis in chronic, alcohol induced and autoirnmune pancreatitis (Bachem, M.G., et al., Gastroenterology, 1998. 115(2): p. 421-32; Haber, P.S., et al., Am J Pathol, 1999. 155(4): p.1087-95; Apte, M.V., et al., Gut, 1999. 44(4): p.
534-41).
Pancreatic stellate cells have also been associated with fibrosis in acinar tissue during diabetes development (Taniyama, H., et al., J Vet Med Sci, 1999. 61(7): p. 803-10;
Fehsel, K., et al., Lab Invest, 2003. 83(4): p. 549-59; Bach, J.F., Endocr Rev,1994. 15(4):
p. 516-42.) During an inflammatory process such as insulitis, immune mediators 2o including interferon-y, tumor necrosis factor a or production of nitric oxide can damage or destroy ~-cells as well as neighboring cells (Bach, J.F., Endocr Rev, 1994.
15(4): p.
516-42.). This 'bystander death' can result in the release of normally sequestered antigens from cells (Back, J.F., Endocr Rev, 1994. 15(4): p. 516-42.). Without wishing to be bound by theory, it may be that stellate cells present in the islets or in surrounding acinar area are being destroyed in this manner resulting iri antibody production to stellate cell proteins such as desmin and thus the homology between the Glb 1 peptide and desmin may therefore represent a form of molecular mimicry.
The antigenic epitope of WP5212 also shares 80% (8110) identity and 100%
(10/10) positives with the protein sequence for vimentin, an intermediate filament protein found in cells of mesenchymal origin. There is a conserved amino acid change from Q
to E at position three and L to M at position four. The homology is between WP5212 and vimentin from mouse, rat, hamster, viper and puffer fish.
To determine the three-dimensional structure WP5212, the translated amino acid to sequence was submitted to SWISS-MODEL (see Example 11). The SWISS-MODEL
program superimposes the sequence of interest onto related solved three-dimensional structures from the RCSB Protein Databank (PDB). The amino acid sequence for WP5212 was aligned with template three-dimensional structures of canavalin from Sack bean (Canavalia ensiformis; PDB identification 2CAV and 2CALT) and beta-conglycinin from soybean (Glycine max; PDB identification lIPJ and lIPK). 'The expected three-dimensional structure of WP5212 based on these templates can be seen in Figure 11.
Without wishing to be limiting or bound by theory, the antigenic epitope sequence appears to form part of an alpha-helix on an external hydrophilic portion of the protein as shown in (Figure 12) Expression of Diabetogenic Epitopes and Proteins comprising Diabetogenic Epitopes In an embodiment of the present invention there is provided a method of producing one or more diabetogenic epitopes or proteins comprising one or more diabetogenic epitopes in a transgenic cell comprising the steps of transforming the transgenic cell with a nucleotide construct comprising a promoter functional in the cell, the promoter driving the expression of a nucleotide sequence encoding a diabetogenic epitope or protein comprising a diabetogenic epitope. In an aspect of an embodiment, the transgenic cell may be a bacterial cell, for example, but not limited to an E. coli cell, an insect cell, a yeast cell, a plant cell in culture, a transgenic plant, a mammalian cell, for example, but not limited to a rat, mouse, goat or human cell.
The present invention will be further illustrated in the following examples, which are not meant to limit the scope of the invention in any way.
1 o EXAMPLE 1: Human Blood Samples Blood samples for serum were obtained from Finnish children newly diagnosed with type 1 diabetes but not yet treated with insulin (n= 23; mean age 9.8 + 3.4 yr.) and non-diabetic control children (n=37; mean age 9.9 + 3.5 yr.), matched for age, sex and HLA-DQ MHC class II haplotype. Permission for blood sampling and ethics approval were obtained from the local ethics committee at the University of Turku.
Example 2: Animals Male and female diabetes-prone BioBreeding (BBdp) and control BB rats (BBc) were obtained from the Animal Resources Division of Health Canada. The animals are maintained in laminar flow protected cages under specific pathogen-free conditions. The mean incidence of diabetes in BBdp rats from this colony fed a standard cereal-based diet (Rao, G. N. (1996) Fundam Appl Toxicol 32, 102-108) has remained constant over the past 5 years at 65.3 ~ 14.9 % (mean ~ Standard deviation (SD)). This colony is directly descended from the original diabetic rats discovered at BioBreeding laboratories near Ottawa in 1974 and transferred to Health Canada in 1977. The colony is not completely inbred, but has remained a closed colony for the past 2~ years and recent genotyping for selected markers indicates the animals are about 80% identical at the DNA
level. These animals carry the same mutation at the Iddmlllyp locus as BB/W rats that is attributable to a frameshift deletion in a novel member of the Immune-Associated Nucleotide (TAN)-related gene family, IanS (MacMurray, A. J., et al. (2002) Genome Res 12, 1029-1039).
BBc rats are derived from an early subline of animals from the original BB rat colonythat does not spontaneously develop diabetes. Tests in sentinel animals indicate the colony is antibody-free with respect to Sendai virus, pneumonia virus of mice, rat corona l0 virus/sialodacryoadenitis virus, I~ilham rat virus, Toolan's H-1 virus, reovirus type 3, and Mycoplasma pulmonis. Animals were weaned at 23 days of age, caged in banks. of wire-bottom cages, and given free access to food and water. The principles of laboratory animal care as described by the Canadian Council on Animal Care were followed.
Animals were tested twice weekly for glucose in urine using Testape (Lily, Toronto, Ontario) after 60 days of age. Those with a value greater than 2+ were fasted overnight, and blood glucose in tail blood was measured the next morning using a glucometer.
Diabetes was diagnosed when fasting blood glucose was greater than about 11.1 rrunol/l.
Diabetic animals were killed within 24 h of diagnosis by exsanguination while under anesthesia with 3% halothane in oxygen.
EXAMPLE 3: Insulitis Scores All histological analyses were performed on coded samples. Hematoxylin and eosin stained sections of pancreas fixed in Bouin's solution were evaluated at 1 OOx magnification, and confirmed at 200x magnification using an Axiolab microscope (Zeiss, Mississauga, Ontario). Subjective overall rating of pancreatic islet inflammation (insulitis (Hoorfar, J., Scott, F. W., and Cloutier, H. E. (1991 ) J Nutr 121, 908-916)) was performed using the following scale: 0, normal islet appearance;
1, infiltration in islet periphery only; 2, infiltration concentrated in islet periphery with infiltration in the islet core; 3, infiltration concentrated in one third of the islet core; 4, infiltration concentrated in up to one half of the islet core; 5, end stage islets with widespread (3-cell destruction and/or core filled with infiltrating mononuclear cells.
The mean of 10 islets per animal was used for an overall insulitis score.
Inflamrr~ation of the islets was also measured as the percent of infiltrated islets.
to EXAMPLE 4: DIETS
NTP-2000 (NTP~ diet The NTP-2000 diet (Zeigler Bros., Gardners, PA), is an open formula (the percentage composition is known), nonpurified diet for rodents developed by the U.S.
National Toxicology Program of the National Institute of Environmental Health Sciences.
NTP-2000 does not contain any milk protein. This is a mainly plant-based (milk-free) diet with wheat as the major component (37%), followed by corn, soybean meal, alfalfa meal, oat hulls, fish meal and cellulose. The diet contains approximately 14.6%
protein, 8.2%
fat, 9.9% crude fiber, 52% carbohydrate, 10.7% moisture; the remainder is native and added micronutrients. The NTP-2000 diet used in these studies was irradiated, and 2o contained low levels of chemical and microbial contaminants (Rao, G. N. ( 1996) Fundam Appl Toxicol 32, 102-108).
Wheat Protein ~WP) diet WP semipurified diets were made up of 22.5% wheat gluten (ICN Biochemicals, Cleveland, OH), 50.2% corn starch, 12.0% sucrose, 5.0% corn oil, 5.0% fiber (Solka-___._ ,..__.__ ,~~~~~_~... 3._~~~._~._.__ __.___~__~_.~. ~..~....~~~..__.._ _..__.,__.. ~

Floc), 3.5% AIN-76 (or AIN-93G) mineral mix (ICN), 1.0% AIN-76A (or AIN~-93G) vitamin mix (ICN), supplemented with 0.2% choline bitartrate, 0.02% DL-methionine, 0.5% L-lysine, and 0.08% L-threonine to compensate for low sulfur amino acids in wheat proteins.
Hydrolyzed casein (HC) diet HC diets contained 51.0% corn starch, 12.0% sucrose, 20.0% casein hydrolyzate (pancreas S enzymatic hydrolyzate, Redstar Bioproducts, Mississauga, Ontario),

7.0%
soybean oil, 5.0% fiber, 3.5% AIN-76 (or AIN-93G) mineral mix, 1.0% AIN-76A
(or l0 AlN-93G) vitamin mix, 0.2% choline bitartrate, and 0.3% L-cystine. Both semipurified diets were isocaloric and isonitrogenous.
EXAMPLE 5: Wheat cDNA library construction and probing for antigenic proteins Total RNA was isolated (Venvoerd, T. C., et al. (1989) Nucleic Acids Res 17, 2362) from hard red spring wheat, AC Barrie, provided by Dr. V. Burrows, Eastern Cereal Oilseed Research Centre" of Agriculture and Agri-Food Canada, Ottawa.
Caryopse;s were .
harvested at approximately 10-20 d after pollination, total RNA was prepared and sent to Stratagene (La Jolla CA) to construct a ZAP Express~ Custom cDNA library. The cDNA
2o was inserted into the EcoR IlXho I cloning site in the amino-terminal region of the lacZ
gene in the ZAP Express vector (Stratagene).
XL1-Blue-MRF' Escherichia coli were infected with 3.5 x 104 pfu per plate (150 mm x 15 mm) of phage from the wheat ZAP Express Custom cDNA library following the 2s manufacturer's instructions (Stratagene). Protein expression was induced by the addition of 15 ~,l of 2 M isopropyl-1-thio-(3-D-galactopyranoside per 600 ~1 ofE. coli.
Plaque lifts were performed and the nitrocellulose membranes were screened following the manufacturer's instructions (Stratagene, La Jolla CA). The primary antibody (diluted 1:200 in SMP-TBS) consisted of pooled sera from 7 diabetic BB rats fed a wheat protein (WP) diet from weaning. The BB rat antibodies were pre-absorbed with E. coli phage lysate. The secondary antibody, alkaline phosphatase-conjugated AffmiPure goat anti-rat IgG, Fcy fragment specific antibody (Jackson Irnmuno Research Laboratories Inc", West Grove PA), was diluted 1:5000 in SMP-TBS. Antibody binding was detected. using alkaline phosphatase development solution ( 100 mM Tris-HCI, pH 9.5,100 mM
1'daCl, 5 mM MgCl2) containing nitroblue tetrazolium chloride (0.3 mg/ml) and 5-bromo-4-1o chloro-3-indolyl phosphate (0:15 mg/ml). Positive clones were detected as dark purple plaques and cored from the agar.
The agar plugs were placed in 500 ~,1 of SM buffer ( 100 mM NaCl, 8 mM MgS04~
7H20, 50 mM Tris-HCl (pH 7.5), 0.01 % (w/v) gelatin) containing 20 ~1 chloroform and stored at 4°C. Screening was repeated until the positive phage reached clonality. Single; clone excision was performed to allow in vivo excision and recircularization of the cloned insert, according to the manufacturer's instructions (Stratagene). Resistance to kanamycin indicated the presence of the pBK-CMV phagemid.
Phagemid DNA was prepared for sequencing using a Plasmid Midi Kit (Cliagen, Mississauga ON). The "DNA inserts were sequenced at the University of Ottawa Biotechnology Research Institute on a 373 Stretch sequencer (Applied Biosystems, Foster City CA) using standard T3 forward and T7 reverse primers. For clone WP5212, internal primers were designed to sequence the full eDNA insert (Forward: S'-ACCACGGGTTCGTCAAGG-3', Reverse: 5'-AACACCTCCTGCACCTCC-3'.
Nucleotide and translated BLAST (Altschul, S. F., et al. (1997) Nucleic Acids Research 25, 3389-3402) searches of the Genbank (NCBI. (2002;) in http://www.ncbi.nlm.nih.gov/BLAST/, National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA) and TIGR Wheat Gene l:ndex TIGRWheatDatabase. {2001) in http://www.tigr.org/tdb/tagi/, Institute for Genomic Research, Rockville, MD, USA) databases were performed for each sequence.
to EXAMPLE 6: Probing wheat clones for antibody reactivity using serum from individual rats fed WP-based diets Serum (diluted 1:200 in SMP-TBS) from individual diabetic (n=7), asymptomatic (no clinical symptoms of diabetes by 150 d; n=10) BBdp, and BBc (n=9) rats was used to screen the wheat clones in the same manner as for the library screening.
Densitometric analysis of regions of interest on nitrocellulose blots of wheat clones was performed using a Kodak Digital ScienceTM image station 440CF. The mean intensity/pixel for each region of interest was tabulated. A clone was randomly chosen from the library to represent background antibody binding. This clone, WPCON, had an ORF 366 lbp long and an expected expression product size of 121 amino acids. WPCON shared 91%
2o identity across 326 nucleotides with barley ascorbate peroxidase mRNA
(Hordeum vulgare, Acc. No. AF411228.1) and shared 96% identity across 86 amino acids with the ascorbate peroxidase protein (H. vulgare, Acc. No. AAL08496.I).

EXAMPLE 7: 1D Western immunoblotting of wheat proteins Proteins were extracted from wheat gluten powder (ICN) using lysis buffer as described previously (Gorg, A., Postel, W., and Gunther, S. (1988) Electrophoresis 9, 531-546).
Samples were electrophoresed in 10% SDS-PAGE gels (Laemmli, U. K. (1970) :Nature 227, 680-685), transferred to nitrocellulose, and blocked with 5% (w/v) skim milk powder in Tris-buffered saline {SMP-TBS, pH 7.5). Blots were incubated with sera diluted in SMP-TBS: I :600. Samples were from rats at different risk of diabetes and fed WP diet: control BBc (n=10), asymptomatic BBdp (no clinical symptoms of diabetes by 120 d, n=7) and pre-diabetic BBdp animals (developed overt diabetes before I20 d, n=7 or animals with overt diabetes, BBd). Sera from individual patient (n=23) and non-diabetic HLA-DQ-matched control children (n=37) was diluted I :50. Following 5 x 5 min washes with TBS containing 1% (v/v) Tween 20, the membrane was exposed to horseradish peroxidase-conjugated goat anti-rat IgG (Fcy-fragment specific;
Cedarlane Laboratories, Hornby, Ontario) or rabbit anti-human total IgG antibody (Dako), diluted 1:2000 with SMP-TBS. Bands were visualized using enhanced chemiluminescence (ECL) according to the manufacturer's instructions {ECL-Western blotting detection, Amersham Pharmacia Biotech, Buckinghamshire UK) and quantified by densitometry.
Digital images of the Western blot films were acquired using the Kodak Digital ScienceTM
image station 440CF (Rochester NYC and analyzed using the Kodak Digital Science 1 D
image software (New Haven CT).
EXAMPLE 8: 2D Western immunoblotting of Wheat Proteins 150 pg of wheat gluten proteins in lysis buffer were added to the IEF buffer (4% CHAPS, 7 M urea, 2 M thiourea, 40 mM Trizma base, 2 mM tributylphosphine and 0.4% Bio-lyte 3/10 (BioRad)) and applied to rehydrated Ready Strips (BioRad) with an immobilized linear pH gradient (IPG) from pH 3-10. Wheat proteins were focused at 21°C for a total of 100,000 Volt hours on the Protean IEF cell (BioRad); reduced with 20 mg/ml of dithiothreitol and alkylated with 25 mg/ml iodoacetamide. Proteins were separated in the second dimension in 10% SDS-PAGE gels by electrophoresis at 30 mA for 15 rain and 60 mA for 2 h, transferred to nitrocellulose membrane and blocked using SM:P-TBS
overnight at 4°C. Serum was pooled from the 23 patients and 37 controls, diluted 1:500 in SMP-TBS buffer, and used to probe 2D Western blots (1 hour at 4°C).
The secondary antibody, rabbit anti-human total IgG conjugated with horseradish peroxidase (:Dako), was diluted to 1:2000 with SMP-TBS buffer and incubated with the membranes for l0 min at 4°C. Antibody binding was visualized using ECL as recommended by the manufacturer (Amersham Pharmacia, Baie d'Urfe, Quebec) and analyzed using 2D
analysis software (PDQuest, BioRad, Toronto, Ontario).
EXAMPLE 9: Mass spectrometry analysis 2D gels of wheat gluten proteins were stained with a non-fixing silver stain (Gharahdaghi, F., et al.. (1999) Electrophoresis 20, 601-605.). Excised gel plugs were digested overnight at 37°C with 200 ng of modified sequencing grade trypsin (Pxomega) in the ProGestTM automatic digester (Genomic Solutions, Ann Arbor MI) as described (Gharahdaghi, F., et al., (1999) Electrophoresis 20, 601-605.). Rapid capillary LC-2o MS/MS (capLC-MS/MS) was performed using a Waters CapLC liquid chromatograph (Waters, Milford MA) coupled to a Q-TOF 2 mass spectrometer (Micromass, Manchester UK) with an electrospray ionization interface. The digest extracts were redissolved in 5%
(v/v) acetonitrile, 0.5% acetic acid and 10 p,L was loaded onto a 0.3 x 5 mm Cl~; micro pre-column cartridge (DionexlLC-Packings) for each analysis. Rapid peptide elutiion was achieved using a linear gradient of 5 to 60% acetonitrile, 0.2% formic acid in 6 .minutes _ _ ~... _.,~.~ ~.__~a__ .r...,_ ~ ~,~~~,R ~ _____ _ _.w__-.-.. w.~ ",~r.~.»,-...,.-....-__.. _ _ T_ (flow rate of 1 ~,I,/min). The mass spectrometer was operated in data dependent acquisition mode.
EXAMPLE 10: Statistical analysis Comparisons between sample populations were made using one-way ANOV'A and Scheffe or LSD post hoc tests (STATISTICA Version 4.5, StatSoft Inc., 1993., Tulsa OK). Fisher's Exact test (2-tailed) was used to compare the frequency of individuals with antibody reactivity to wheat proteins. Pearson Product-Moment correlation was used to determine r and p values. Survival analysis using the log-Rank test was used to compare l0 the effect of different diets on diabetes incidence (STATISTICA).
EXAMPLE 11: Construction of the WP5212 epitope library.
The Novatope Library Construction System (Novagen, Madison, WI) for characterizing B
cell epitopes within antigenic polypeptides was used to map sites of antibody Minding r5 within WP5212. Plasmid DNA was introduced into E. coli NovaBlue (DE3) cel'.ls, and transformants were selected with ampicillin. DNase I digestion of the WP5212/pETl7b expression construct containing the complete ORF of WPS212 was performed using the DNase Shotgun Cleavage kit (Novagen} following the manufacturer's instructions. The DNase I digestion reaction was set up by adding 10 pg of WP5212/pET 17b plasmid DNA
2o to DNase I (0.0015, 0.001, 0.0007 or 0.0005 U/p,l), DNase I buffer (0.05 M
Tris-HCI
pH7.5, 0.05 mg/ml BSA), 10 mM MnCl2 in a total volume of 10 p.l. The reactions were incubated at room temperature for 10 min, after which 2 p,l of 6X Stop Buffer (100 mM
EDTA, 30% glycerol and tracking dye) was added. Samples were analyzed by agarose gel electrophoresis on 2% gel. The samples containing DNA fragments ranging in si2;e from 25 SO-150 by were pooled and run on a 2% agarose gel. The band corresponding to :50-150 -$1-by fragments was excised from the gel and equilibrated by adding 1X volume of the gel of lOX agarose buffer (100 mM Bis Tris-HCl pH 6.5, 10 mM Na2EDTA) to make I%
gel. The gel was melted at 65°C for 10 min. The sample was cooled to 42"C and incubated with molten agarose with 2 U per 200 ~l 1% agarose for 1 h. The; DNA
solution was extracted sequentially with one volume TE-buffered phenol, one volume of 1:24:1 phenol:chloroform:isoamyl alcohol (phenol:CIAA) and 1 volume CIAA. The DNA was precipitated by adding 0.1 volume of 3 M NaOAc and 2 volumes ethanol.
The sample was placed at -70°C for 1 h. It was centrifuged at 12,000 X g for 15 min, washed once with 1 volume of 70% ethanol, centrifuged at 12,000 X g for 5 min and the pellet 1o was dried. The DNA was resuspended in 30 ~1 TE buffer. The DNA
concentration was determined at A26o.
The resulting oligonucleotides (ranging 50-150 by in length) were blunt-ended and tailed with a single dATP using the Single dA Tailing Kit (Novagen). The DNA ends were I5 blunted by combining 1 ~.g ofthe DNA with flushing buffer (0.05 M Tris-HCl pH 8.0, 5 mM MgCl2, 0.1 mg/mI BSA), 0.1 rnM dCTP, dGTP and dTTP, 1 mM dATP, 5 ml'vI DTT
and 1 U T4 DNA polymerase in a total volume of 25 ~,1. The reaction was mixed gently and incubated at 11°C far 20 min. The reaction was stopped by heating to 75°C for 10 min. A single 3' dA residue was added to the blunt ends by adding l OX dA
tailing buffer 20 ( 100 mM Tris-HCl pH 9.0, 0.5 M KCI, 0.1 % gelatin; 1 % Triton X-I 00) and 1.25 L:f of Tth DNA polymerase to the entire flushing reaction and bringing the reaction volume to 85 ~I. A positive dA tailing control was set up by adding 100 ng of a positive control 36mer to flushing buffer (0.05 1VI Tris-HCl pH 8.0, 5 mM MgCl2, 0.1 mg/ml BSA), 0.1 mM
dCTP, dGTP and dTTP, 1 mM dATP, I OX dA tailing buffer and 0.75 U Tth polymerase in a total reaction volume of 42.55 ~.1. The reactions were incubated at 70°C for 15 min.
One volume of CIAA was added, the sample was vortexed for 60 s and centrifuged at 12,000 X g for 1 min. The aqueous phase was added to a fresh tube.
The oligonucleotides were ligated into the pSCREEN T-vector. The ligation reaction was made by adding 6 ng sample DNA to 5 mM DTT, 0.5 mM ATp, 50 ng pSCRE;EN T-vector, 2 U T4 DNA ligase in a total reaction volume of 10 ~,1. The sample was mixed gently and incubated overnight at 16°C. The DNA was transformed into NovaBlue; (DE3) competent cells following the protocol provided. In brief, 1 p.l of the ligation reaction was added to 20 pl of cells and stirred gently. The samples were placed on ice for 30 min. The l0 samples were heated for 30 s at 42°C and then placed on ice for 2 min. Cells were grown for 1 h at 37°C with shaking at 250 rpm. 50 ~.1 of each transformation was spread on LB
agar plates containing 50 ~g/ml ampicillin and 15 ~,g/ml tetracycline. The platea were inverted and incubated overnight at 37°C.
Screening the WP5212 epitope library 15 The library of random, overlapping inserts expressed by transformed cells was screened by colony immunoscreening with anti=WP5212 antibody positive serum from a highly wheat sensitive female patient with both type 1 diabetes and celiac disease (age 26 years).
The epitope library was plated at a density of approximately 1000 colony forming units (cfu) on LB plates containing 50 p.g/~.1 ampicillin and grown overnight at 37°C. The 2o plates were overlaid with. nitrocellulose filters (VWR). The orientation of the filter on the plate was marked by an I 8 gauge needle dipped in India ink. After one min of contact, the membranes were carefully lifted off and placed in a chloroform vapor chamber :.for cell lysis. The chamber was sealed with Saran wrap and left for 15 min at room temperature.

The membranes were removed from the chamber and placed colony side up on a piece of Whatman paper saturated with colony denaturing solution (20 mM Tris-HCl pH
7.9, 6 M
urea, 0.5 M NaCI) for I 5 min at room temperature. The membranes were placed in TBST
containing 5% w/v nonfat skim milk powder and incubated with shaking for 30 min. The membranes were washed twice for 15 min each with TBST and placed in the primary antibody diluted in blocking buffer for 30 min. Colonies were immunoscreened for protein expression using anti-WP5212 positive serum from a T1D/CD patient (1:.2000).
The membranes were washed 3 times for 10 min each with TBST and placed in secondary antibody, anti-human IgG conjugated to alkaline phosphatase (1:20,000) for 30 1o min. The membranes were washed three times for 10 rnin each with TBST and placed in AP developer. Dark purple colonies were determined to be positive.
Identification of epitopes.
Bacterial colonies expressing immunoreactive peptides were selected and plasmid inserts were sequenced by using primers complementary to flanking regions of the cloning site in pSCREEN T-vector. Positive colonies were picked and grown overnight at 37°C with shaking. Plasrnid DNA was prepared using the Wizard Plus SV miniprep kit following the manufacturers instructions (Promega). Sequencing of the inserts was performed by the Ottawa Genorne Centre DNA Sequencing Facility (Ottawa, ON). Insert sequences were aligned with the OFtF WP5212 sequence using Align Plus 5, version 5.01 software from the Clone Manager Professional Suite (Scientific and Educational Software, Durham, NC).
Protein modeling The translated amino acid sequence of WP5212 was submitted to SWISS-MODEL
(httir//www.expasy.or~/swissmod/SWISS-MODEL.html) for three-dimensional rendering (Peitsch, M.C., Bio/Technology, 1995. 13: p. 658-660; Peitsch, M.C., Biochem Soc Trans, 1996. 24(1): p. 274-9; Guex, N. and M.C. Peitsch, Electrophoresis., 1997.
18(15): p. 2714-23).
EXAMPLE 12: Method of Screening cDNA library with Sera from Tl''.D/CD
patients:
To identify and characterize T1D-related wheat proteins, a large number, for example, but not wishing to be limiting, about 1 million recombinant wheat proteins from a wheat cDNA expression library are screened with IgG antibodies in pooled sera from patients with T1D and T1D/CD. Candidate clones are also screened with sera from two control groups (CD patients and healthy controls).
An approach similar to that used to identify and characterize Glb-1 and other proteins is employed to screen a wheat cDNA expression library with IgG antibodies in pooled sera from patients with T1D and T1D/CD. Sera from patients with CD alone is used to screen the clones identified by Group 1 and 2 sera to identify wheat antigens chat are common to T1D, T1D/CD and CD patients. A control group of age and sex-matched subjects is inchaded. To eliminate proteins that are not diabetes-relatedL, 2o candidate clones are probed with sera from the control group and positive clones are eliminated from further analysis. Clones identified by screening the library with pooled serum from T1D and T1D/CD are probed with antibodies from individual subjects in the four groups to determine what proportion reacts to each protein.
Candidate clones are expressed in insect cells as described below.

Wheat protein expression in insect cells Glb I (WP5212) is provided as an example. However, a person of skill in the art will understand that other diabetogenic proteins and peptides may be expressed in such cells.
IPLB-SfZl insect cell like: Insect Spodoptera fiNugiperda (SfZI, BD
Biosciences) cells are maintained in Grace's insect cell culture medium, plus 10~/o fetal bovine serum (Sigma), penicillin (50 units/ml), and streptomycin (50 ~.g/ml) at 27°C. Insect 1o Ti~ichoplusia ni (High-Fi.veTM, Invitrogen, Carlsbad, CA) cells are maintained in Express-FiveTM SFM medium at 27°C. For protein expression, High-Five cells are maintained in suspension cultures.
PCR amplification and subclonin~ of the FLAG-ta~y~ed WP52I2 into pBacPak9:
transfer vector The WP5212 sequence is amplified by PCR. The forward PCR primer is designed to include an Eco RI restriction enzyme site, a start codon followed by the FLAGT"' (Sigma, Oakville, ON) epitope sequence in frame with the WP5212 cDNA. The reverse primer is designed to include an Eco RI restriction enzyme site (Sigma 2o Genosys). The 1.9 kb WP5212 PCR product is cloned into the pCR~2.1 plasmid using the TOPO~ TA-cloning kit (Invitrogen). Plasmid DNA from clones containing inserts is prepared using the Wizard Plus S~ Miniprep kit (Promega). WP5212 is clonf;d into the Bam HIlXho I restriction enzyme sites of the pBacPak9 transfer vector (BD

Biosciences). The presence of WP5212 is confirmed by restriction digests with Eco RI and sequencing using Bacl and Bac2 primers (BD Biosciences).
Generation of a recombinant BacPak6 baculovirus Glbl (WP5212) expression s sy tem Transfected insect cells with the recombinant virus containing Glbl (untagged) Jzas been performed and the protein has been identified in lysates of High Five cells by Western blot analysis with BB rat serum. Purification of Glb 1 may be performed according to a variety of methods known in the art. Recombinant baculovirus is generated using the Bac-PAKbaculovirus expression system (Clontech). SfZI
cells 1o are co-transfected with fVP5212-pBakPAK9 and BacPAK6 viral DNA (Clontech) using Bacfectin (Clontech) following the manufacturer's instructions.
Recombinant virus is isolated, propagated and amplified in Sf21 cells. High-Five cells are cultured in Express-FiveTM SFM medium (invitrogen) at 27°C and infected with the recombinant virus. After infection and protein production, cells are harvested and 15 lysed and insoluble fractions are removed by centrifugation. The expression of FLAG-tagged WP5212 is confirmed by Western blot analysis of insect cell lysate.
Samples are diluted in 2X sample loading buffer arid electrophoresed in 10% SDS-PAG)=~, gels and electrotransferred to nitrocellulose membranes. For immunoblotting, memtmanes are incubated in blocking buffer, followed by incubation in mouse anti-FLAGTM

2o monoclonal antibody (Sigma) diluted in blocking buffer. Membranes are washed, incubated in the secondary antibody, rabbit anti-mouse polyvalent immunoglobulins monoclonal antibody conjugated to alkaline phosphatase (Sigma) diluted in blocking buffer. Antibody binding is detected using alkaline phosphatase solution.
Recombinant protein is purified by anti-FLAGTM M2 agarose (Sigma) affinity chromatography. The FLAG tag is removed from purified recombinant protein urith enterokinase and enterokinase is removed using the enterokinase removal kit (Sigma).
Disease-specific clones are isolated from the library by screening with sera from T1D
and T1D/CD patients. Screening the clones with control serum reveals non-specific clones and those that are positive with CD serum aids differentiation of CD-specific versus T1D-specific proteins (or identify shared antigenic proteins). These clones are sequenced and identified on the basis of homology to known wheat proteins.
Recombinant wheat proteins for use in in vitro T-cell assays may be produced to~
further elucidate the role of these proteins in T1D.
l0 Identify T1 D-related proteins b~proteomic analysis of wheat lg uten protein extracts An analysis of antibody reactivity to wheat using 2D Western blots may be performed in parallel with the library screening. WG protein extracts are probed with IgG
antibodies from each individual patient and control as described above.
Candidate proteins may be characterized using a capillary liquid chromatograph coupled to a 15 QTOF-2 mass spectrometer (LC-MS/MS), or other chromatography and/or mas:9 spectroscopy system.
2-D electrophoresis and Western blot (Isoelectric Focusing (IEF)) Immobilized pH gradient strips (IPG; BioRad; broad range pI 3-10) are rehydrat:ed 20 overnight with 150 ~g of WG proteins in BioRad ReadyPrep Sequential Extraction Reagent 3 and 0.002 M 'Tributylphosphine. Proteins are then focused for 95,000 Vh on a Protean IEF Cell apparatus (Bio-Rad) at 23°C.
SDS-PAGE
The focused wheat proteins on the IPG strip are reduced with dithiothreitol and alkylated with iodoacetarnide. The proteins are resolved on 10%
polyacrylarnide gradient gels at 40 mA in a Tris-glycine-SDS running buffer.
Western immunoblottin~ and Mass Spectroscopy Wheat proteins are transferred onto nitrocellulose membranes. Non-specific antibody binding is blocked with 5% skim milk powder in Tris-buffered saline at 4°C.
Membranes are probed with serum from individual patients or controls (1:50 dilution) for 1 hour at 23°C. An HRP-anti-total IgG secondary antibody (1:50,000 dilution), is used to detect antibody-bound wheat proteins using Enhanced Chemiluminescence l0 (Amersham). Results are analyzed using 2D analysis software (PDQuest, BioRad).
Proteins are resolved on a polyacrylamide gel and visualized using a non-fixing silver stain. Gel plugs with proteins of interest are excised from the gel for trypsin digestion and mass spectrometry (MS) analysis, as described previously. Rapid capillary LC-MS/MS is performed using a CapLC Liquid chromatograph (Waters, Milford, MA) coupled to a Q-TOF2 MS. Database searching is performed automatically using MascotTM (Matrix Science, London, U.K.), which searches for homologous sequences in the peptide MS/MS spectra files and protein and nucleotide sequence databases. In cases where the spectra cannot be matched, sequencing is performed manually;
sequences are used to search the SwissProt, NCBI and other protein sequence 2o databases using MS-Seq (Protein ProspectorTM, Mass Spectrometry Facility, UCSF, San Francisco, CA) or NCBI's BLAST searching algorithms.
Produce recombinant candidate wheat proteins and determine anri_genic/immuno~enicity in human T cells Candidate wheat proteins may be expressed in insect or other cells and purified, Candidate proteins and peptides are tested in human PBMC and wheat-reactive 'T
cell lines from a variety of T 1D patients and HLA matched controls for ability to stimulate T cell proliferation, alter gene and protein expression of inflammatory mediators or response to T1D autoantigens such as insulin or GAD.
This research (1) identifes specific wheat proteins that are differentially immunoreactive in T1D (and T1D/CD) patients, (2) determines what proportion of T1D patients show increased antibodies and T cell responses to these proteins, a.nd (3) identifies the T cells being stimulated.
is A subset of a control patient group and T1D patient group are HLA matched and analyzed for T cell reactivity to WG, and other food antigens, controls and identified candidate proteins or gliadin peptides. Analysis of small populations of antigen-specific T-cells using flow cytometry of cells labeled with CFSE is performed.
Cells 15 that proliferate are characterized by a decreasing fluorescent signal;
these cells can be isolated by FACS on the basis of this characteristic, allowing further analysis to confirm specificity and determine phenotype. Our studies demonstrate that this method can be used for the isolation of WG-responsive T-cell populations.
2o CFSE labeling and cell culture Blood is collected in heparin-treated vacutainers, diluted 1:1 in sterile PBS
and PBMC
are isolated by density-gradient using Histopaque-1077 (Sigma Diagnostics). As described {Turcanu et al., J. Clin invest 111:1065-1072, 2003) PBMC are resuspended in 1 ml sterile PBS and stained for 10 min at 37°C with 2u.M of CFSE.
Cells are;
25 washed once with RPMI-1640 supplemented with 10°,~0 (v/v) pooled human senzm, 2.0 uM L-glutamine, 50 mM 2-mercaptoethanol, 100 U/ml penicillin and 100 ~,g;/ml streptomycin (RP-10) followed by a second wash in X-Vivo 15 medium. PBMC are plated at 2x106/2 ml X-Vivo-15 in 24 well-plates and stimulated with medium (control), 2.5 wg/ml PHA, I l,tM ovalbumin protein (OVA), 2~.g/ml ~.-lactoglobulin or varying concentrations of chymotrypsin-digested WG (12.5, 6.25 or 3.1 wg/ml).
Proliferation of CFSE labeled T cells to WG and generation of WG-reactive T
cell lines.
Both CD4+ and CD8+ T cells play a role in T1D and thus both of these populations to may be examined. 1x10 CFSE-Labeled cells cultured in the presence of chymotrypsin-WG, gliad.in peptides, other diabetogenic peptide (or protein) or control antigens (ovalbumin, Iactalbumin, PHA (positive control), KLH, (negative control) are stained with human anti-CD3-ECD to monitor the proliferation of all T
lymphocytes (CD4 and CD8 lymphocytes). Double-stained T cells are analyzed.
for 15 cell division by FACS. CD3+T cells show reduced CFSE signal due to proliferation (CD3+CFSEI°"') and are gated as WG-reactive T cell population. To generate WG-reactive T cells lines, WG-expanded cells are harvested and sorted by flow into CD3+CFSE~°"' and CD3+CFSEh'~'cells. Single cell clones are generated from CD3+CFSEi°W population by flow sorting using 96 well plates with one cell per well.
20 Single clones are cultured in X-Vivo 15 medium containing 10 I(J/ml of hIL-2. After expansion, single cell clones are tested against candidate proteins or immunoreactive gliadin (or other) peptides to examine clone WG-specificity.
Phenotyping of PBMC.
25 To compare PBMC from T1D patients to cells from controls, 1x106 PBMC are resuspended in 100 N,1 FACS buffer and stained with anti-CD19, anti-CD83 and anti-CD3 (Pharmingen) to monitor the expression of B cell, DC and T cell surface markers respectively on resting cells.
Specificity and phenotype of WG-reactive T cells.
2 x 104 cells / well of WG-reactive T cells obtained by flow sorting plus 2 x irradiated autologous APCs are plated in 96-well plates and stimulated with varying concentrations of chymotrypsin treated-WG (or test antigens) in X-Vivo 15 medium or control antigens. After 5 d, the cells are pulsed with 1 p:Ci per well of 3H-thymidine (Amersham.Pharmacia Biotech) for an additional day. Cells are harvested onto glass fiber filters (Packard) and radioactivity is measured. To determine the proportion of CD4 and CD8 cells comprising WG-reactive T cells (CD3+CFSEI°"'), sorted T cells are double stained with anti-CD4-PE and anti-CD8-Cy5 and analyzed by flow cytometry.
HLA typin .
1x106 PBMC are cultured in X-Vivo-15 medium in the presence of 2.5 ~Cg/ml PIMA.
At d 5, Sx106 cells are harvested and sent to the Biochemistry, Ottawa Hospital for HLA DR and DQ typing.
WG-induced , e~ ne expression in T1D PBMC.
Gene expression in WG-reactive T cells obtained from T1D patients is analyzed by an array technique. 5x106 sorted WG-reactive T cells are stimulated with PMA/ionomycin for.6 hours. Cells are harvested for total RNA preparation using Trizol (Life Technologies). 2-5 pg total RNA are analyzed for inflammatory cyi:okine, cytokine receptors, chemokines and growth factor gene expression using the Q
sf;ries of common human cytokines and interleukin receptor microarray membranes (SuperArray Bioscience Corporation, Frederick, MD). Superarray membranes contain up to 96 cDNA fragments from genes associated with specific biological pathways.
~okine profile of WG-reactive T cells.
2x104 cells/well of WG-reactive T cells from T1D patients obtained as above, plus 2 x 105 irradiated autologous APCs in 200 N.l are stimulated with varying concentrations of WG or other test antigen in X-Vivo 15 medium or control antigens. At d7 pos;t-stimulation, cell free supernatants are harvested for Thl/Th2 cytokine profile analysis to by capture ELISA. ELISA experiments are performed using OptEIA human IFN-y (Thl-associated cytokine) and IL-5 (Th2-specific cytokine) kits (BD
Biosciences) using a modified protocol.
Flow cytometry facilitates phenotype determination of the WG-reactive immune cells (CD4, CD8). Without wishing to be limiting or bound by theory, the predominant T-i s cell phenotype may be CD4~ IFN- y secreting cells as in CD. The cytokine expression data will facilitate the determination of whether the Thl/Th2 cytokine balance of the wheat-responsive cells favours an inflammatory response (Thl predominant), (Th2) or is tolerizing (Th3). As part of the specificity testing, the capacity of T1D
autoantigens, GAD and insulin, to stimulate proliferation and cytokine production may be 20 evaluated. This study will facilitate identification of specific, potentially diabetogenic proteinslpeptides responsible for triggering the abnormal immune response in patients and aid in the determination as to which types) of immune cells (CD4, CD8) in T1D patients are WG-reactive.

_ __..._.___~....____ All citations are hereby incorporated by reference.
The present invention has been described with regard to one or more embodiments.
However, it will be apparent to persons skilled in the art that a number of variations and modifications can be made without departing from the scope of the invention as defined in the claims.

SEQUENCE LISTING
(1) GENERAL INFORMATION:
(i) APPLICANT:
(A) NAME: Ottawa Health Research Institute (B) STREET: Technology Transfer Office, 725 Parkdale Avenue (C) CITY: Ottawa (D) STATE: Ontario (E) COUNTRY: Canada (F) POSTAL CODE (ZIP): K1Y 4E9 (ii) TITLE OF INVENTION: Diabetogenic Epitopes (iii) NUMBER OF SEQUENCES: 8 (iv) COMPUTER READABLE FORM:
(A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS
(D) SOFTWARE: PatentIn Release #1.0, Version #1.30 (EPO) (2) INFORMATION FOR SEQ ID NO: 1:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 10 amino acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID N0: 1:
Glu Glu Gln Leu Arg Glu Leu Arg Arg Gln (2) INFORMATION FOR SEQ ID NO: 2:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 2018 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 2:

AAACGCGTGC

TTCAGTAAAAP~~~AAP.AAAAAAAAAAAAAAAAAAAAAA 2 (2) INFORMATION FOR SEQ ID NO: 3:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 588 amino acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID N0: 3:
Met Ala Thr Arg Gly Arg Ala Thr Ile Pro Leu Leu Phe Leu Leu Gly Thr Ser Leu Leu Phe Ala Ala Ala Val Ser Ala Ser His Asp Glu Glu Glu Asp Arg Arg Gly Gly Arg Ser Leu Gln Arg Cys Val Gln Arg Cys Gln Gln Asp Arg Pro Arg Tyr Ser His Ala Arg Cys Val Gln Glu Cys Arg Asp Asp Gln Gln Gln His Gly Arg His Glu Gln Glu Glu Gln Gly Arg Gly His Gly Arg His Gly Glu Gly Glu Arg Glu Glu Glu Gln Gly Arg Gly Arg Gly Arg Arg Gly Gln Gly Glu Arg Glu Glu Glu Gln Gly Arg Gly Arg Gly Arg Arg Gly Glu Gly Glu Arg Aap Glu Glu His Gly Asp Gly Arg Arg Pro Tyr Val Phe Gly Pro Arg Ser Phe Arg Arg Ile Ile Arg Ser Asp His Gly Phe Val Lys Ala Leu Arg Pro Phe Asp Glu Val Ser Arg Leu Leu Arg Gly Ile Arg Asn Tyr Arg Val Ala Ile Met Glu Val Asn Pro Arg Ala Phe Val Val Pro Gly Leu Thr Asp Ala Asp Gly Val Gly Tyr Val Ala Gln Gly Glu Gly Val Leu Thr Val Ile Glu Asn Gly Glu Lys Arg Ser Tyr Thr Val Arg Gln Gly Asp Val Ile Val Ala Pro Ala Gly Ser Ile Met His Leu Ala Asn Thr Asp Gly Arg Arg Lys Leu Val Ile Ala Lys Ile Leu His Thr Ile Ser Val Pro Gly Lys Phe Gln Tyr Phe Ser Ala Lys Pro Leu Leu Ala Ser Leu Ser Lys Arg Val Leu Thr Ala Ala Leu Lys Thr Ser Asp Glu Arg Leu Gly Ser Leu Leu Gly Ser Arg Gln Gly Lys Glu Glu Glu Glu Lys Ser Ile Ser Ile Val Arg Ala Ser Glu Glu Gln Leu Arg Glu Leu Arg Arg Gln Ala Ser Glu G1y Asp Gln Gly His His Trp Pro Leu Pro Pro Phe Arg Gly Asp Ser Arg Asp Thr Phe Asn Leu Leu Glu Gln Arg Pro Lys Ile Ala Asn Arg His Gly Arg Leu Tyr Glu Ala Asp Ala Arg Ser Phe His Ala Leu Ala Gln His Asp Val Arg Val Ala Val Ala Asn Ile Thr Pro Gly Ser Met Thr Ala Pro Tyr Leu Asn Thr Gln Ser Phe Lys Leu Ala Val Val 3g5 390 395 400 Leu Glu Gly Glu Gly Glu Val Glu Ile Val Cys Pro His Leu Gly Arg Asp Ser Glu Arg Arg Glu Gln Glu His Gly Lys Gly Arg Trp Arg Ser Glu Glu Glu Glu Asp Asp Arg Arg Gln Gln Arg Arg Arg Gly Ser Gly Ser Glu Ser G1u Glu Glu Gln Asp Gln Gln Arg Tyr Glu Thr Val Arg Ala Arg Val Ser Arg Gly Ser Ala Phe Val Val Pro Pro Gly His Pro Val Val Glu Ile Ala Ser Ser Arg Gly Ser Ser Asn Leu Gln Val Val Cys Phe Glu I1e Asn Ala Glu Arg Asn Glu Arg Val Trp Leu Ala Gly Arg Asn Asn Val Ile Ala Lys Leu Asp Asp Pro Ala Gln Glu Leu Ala Phe Gly Arg Pro Ala Arg Glu Val Gln Glu Val Phe Arg Ala Lys Asp Gln Gln Asp Glu Gly Phe Val A1a Gly Pro Glu Gln Gln Gln Glu His Glu Arg Gly Asp Arg Arg Arg Gly Asp Arg Gly Arg Gly Asp Glu Ala Val Glu Ala Phe Leu Arg Met Ala Thr Ala Ala Leu (2) INFORMATION FOR SEQ ID NO: 4:

GCGGGAGTAG

(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 290 amino acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 4:
Met Lys Thr Phe Pro Ile Leu Ala Leu Leu Ala Ile Val Ala Thr Thr Ala Thr Thr Ala Val Arg Val Pro Val Pro Gln Leu Gln Leu Gln Asn Pro Ser Gln Gln Gln Pro Gln Glu Gln Val Pro Leu Val Gln Glu Gln Gln Phe Gln Gly Gln Gln Gln Pro Phe Pro Pro Gln Gln Pro Tyr Pro Gln Pro Gln Pro Phe Pro Ser Gln Gln Pro Tyr Leu Gln Leu Gln Pro Phe Pro Gln Pro Gln Leu Pro Tyr Pro Gln Pro Gln Pro Phe Arg Pro Gln Gln Pro Tyr Pro Gln Pro Gln Pro Gln Tyr Ser Gln Pro Gln Gln Pro Ile Ser Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Ile Leu Gln Gln Ile Leu Gln Gln Gln Leu Ile Pro Cys Arg Asp Val Val Leu Gln Gln His Asn Ile Ala His Gly Ser Ser Gln Val Leu Gln Glu Ser Thr Tyr Gln Leu Val Gln Gln Leu Cys Cys Gln Gln Leu Trp Gln Ile Pro Glu Gln Ser Arg Cys Gln Ala Ile His Asn Val Val His Ala Ile Ile Leu His Gln Gln His His His His Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Pro Leu Ser Gln Val Ser Phe Gln Gln Pro Gln Gln Gln Tyr Pro Ser Gly G1n Gly Phe Phe Gln Pro Ser Gln Gln Asn Pro Gln Ala Gln Gly Ser Phe Gln Pro Gln Gln Leu Pro Gln Phe Glu Glu Ile Arg Asn Leu Ala Leu Gln Thr Leu Pro Ala Met Cys Asn Val Tyr Ile Pro Pro Tyr Cys Thr Ile Ala Pro Phe Gly Ile Phe Gly Thr (2) INFORMATION FOR SEQ ID N0: 5:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 307 amino acids (B) TYPE: amino acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID N0: 5:
Met Lys Thr Phe Leu Ile Leu Ala Leu Leu Ala Ile Val Ala Thr Thr Ala Arg Ile Ala Val Arg Val Pro Val Pro Gln Leu Gln Pro Gln Asn Pro Ser Gln Gln Gln Pro Gln Glu Gln Val Pro Leu Val Gln Gln Gln Gln Phe Pro Gly Gln Gln Gln Pro Phe Pro Pro Gln Gln Pro Tyr Pro Gln Pro Gln Pro Phe Pro Ser Gln Gln Pro Tyr Leu Gln Leu Gln Pro Phe Pro Gln Pro Gln Leu Pro Tyr Pro Gln Pro Gln Leu Pro Tyr Pro Gln Pro Gln Leu Pro Tyr Pro Gln Pro Gln Pro Phe Arg Pro Gln Gln Pro Tyr Pro Gln Ser Gln Pro Gln Tyr Ser Gln Pro Gln Gln Pro Ile Ser Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Lys Gln Gln Gln Gln Gln Gln Gln Gln Ile Leu Gln Gln Ile Leu Gln Gln Gln Leu Ile Pro Cys Arg Asp Val Val Leu Gln Gln His Ser Ile Ala Tyr Gly Ser Ser Gln Val Leu Gln Gln Ser Thr Tyr Gln Leu Val Gln Gln Leu Cys Cys Gln Gln Leu Trp Gln Ile Pro Glu Gln Ser Arg Cys Gln Ala Ile His Asn Val Val His Ala Ile Ile Leu His Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Gln Pro Leu Ser Gln Val Ser Phe Gln Gln Pro Gln Gln Gln Tyr Pro Ser Gly Gln Gly Ser Phe Gln Pro Ser Gln Gln Asn Pro Gln Ala Gln Gly Ser Val Gln Pro Gln Gln Leu Pro Gln Phe Glu Glu Ile Arg Asn Leu Ala Leu Glu Thr Leu Pro Ala Met Cys Asn Val Tyr Ile Pro Pro Tyr Cys Thr Ile Ala Pro Val Gly Ile Phe Gly Thr Asn (2) INFORMATION FOR SEQ ID N0: 6:
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Glu Glu Gln Leu Arg Glu Leu Arg Arg Gln Glu Glu Gln Leu Arg Glu Leu Arg Arg Gln (2) INFORMATION FOR SEQ ID NO: 7:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID N0: 7:

(2) INFORMATION FOR SEQ ID NO: 8:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8:

Claims (32)

WHAT IS CLAIMED IS:

1. An amino acid sequence comprising a diabetogenic epitope selected from the group consisting of, but not limited to .alpha./.beta.-gliadin A-II precursor, .alpha./.beta.-gliadin MM1 precursor, or Glb1.

2. The amino acid sequence of claim 1, wherein said diabetogenic epitope comprises EEQLRELRRQ from Glb1.

3. The diabetogenic epitope of claim 1, comprising part of a larger peptide or protein that does not occur naturally in nature.

4. The diabetogenic epitope of claim 3, wherein said epitope is attached to a Garner protein, non-carrier protein, macromolecule or support.

5. The diabetogenic epitope of claim 4, wherein said diabetogenic epitope is attached to a support, said support comprising a bead, plate, dish, cover slip, slide, multiwell assay plate, or bio-assay chip.

6. A nucleotide sequence encoding a diabetogenic epitope from .alpha./.beta.-gliadin A-II
precursor, .alpha./.beta.-gliadin MM1 precursor, or Glb1.

7. The nucleotide sequence of claim 6, wherein said diabetogeic epitope is EEQLRELRRQ from Glb1.

8. A nucleotide sequence complementary to a sequence encoding a diabetogenic epitope or a portion thereof.

9. The nucleotide sequence of claim 6, said sequence comprising part of a larger nucleotide sequence.

10. The larger nucleotide sequence of claim 9, comprising one or more regulatory sequences.

11. The larger nucleotide sequence of claim 9, comprising a cloning vector.

12. The nucleotide sequence of claim 8, wherein said nucleotide sequence is part of a larger nucleotide sequence.

13. The larger nucleotide sequence of claim 12 comprising one or more regulatory sequences.

14. An isolated antibody capable of binding to Glb1, .alpha./.beta. gliadin precursor, or .alpha./.beta.
gliadin MM-1 precursor.

15. An isolated antibody capable of binding to a diabetogenic epitope of Glb1, .alpha./.beta.
gliadin precursor, or .alpha./.beta. gliadin MM-1 precursor.

16. The antibody of claim 15, wherein said diabetogenic epitope is EEQLRELRRQ.

17. The antibody of claim 14, said antibody comprising a monoclonal antibody.

18. The monoclonal antibody of claim 17, said antibody comprising an IgG
antibody.

19. The antibody of claim 14, said antibody produced in the serum of an animal.

20. The antibody of claim 19, wherein said animal is a diabetic animal.

21. A kit comprising one or more of 1) a diabetogenic epitope, 2) a protein or peptide comprising a diabetogenic epitope, 3) a non-protein carrier or macromolecule comprising the diabetogenic epitope, 4) a support comprising the diabetogenic epitope, 5) a diabetogenic epitope attached to a non-covalent association agent 6) a nucleotide sequence encoding a diabetogenic epitope or peptide or protein comprising the diabetogenic epitope 7) a nucleotide sequence complementary to a nucleotide sequence encoding a diabetogenic epitope, 8) a nucleotide sequence complementary to a portion of a nucleotide sequence encoding a diabetogenic protein, or a combination thereof.

22. The kit of claim 21, wherein said diabetogenic epitope is from .alpha./.beta.-gliadin A-II
precursor, .alpha./.beta.-gliadin MM1 precursor, or Glb1.

23. The kit of claim 22, wherein said diabetogenic epitope is EEQLRELRRQ from Glb1.

24. The kit of claim 21, further comprising one or more beads, plates, dishes, coverslips, slides, multi-well assay plates, bioassay chips, which may be attached or unattached to the diabetogenic epitope, protein or peptide comprising the diabetogenic epitope, nucleotide sequence encoding the diabetogenic epitope, sequence complementary thereto, or fragment thereof.

25. The kit of claim 21, further comprising one or more primary antibodies capable of binding to the diabetogenic epitope, or protein comprising the diabetogenic epitope, one or more secondary antibodies that are capable of binding to the primary antibody, solutions, reagents, enzymes, or a combination thereof.

26. A method of screening foodstuffs to identify proteins in the foodstuff which are antigenic/immunogenic in a subject, or group of subjects comprising a pathological condition, the method comprising the steps of:
a) processing the foodstuff to produce separated proteins, and;

b) screening the separated proteins from step a) with an antibody containing mixture derived from one or more subjects having the pathological condition to identify proteins that are antigenic/immunogenic in the subject and that are present in the foodstuff.

27. A method of screening foodstuffs to identify antigenic/immunogenic proteins common in at least two subjects, or groups of subjects wherein each subject or group of subjects comprise different pathological conditions, the method comprising the steps of a) processing the foodstuff to produce separated proteins;
b) screening the separated proteins from step a) with a first antibody containing mixture derived from one or more subjects having a first pathological condition;
c) screening the separated proteins from step a) with a second antibody containing mixture derived from one or more subjects having a second pathological condition;
d) comparing proteins binding to the first antibody containing mixture with proteins binding to the second antibody mixture to identify proteins common in at least two subjects, or groups of subjects with different pathological conditions, the proteins also present in the foodstuff.

28. A foodstuff modified to reduce or eliminate one or more diabetogenic epitopes or proteins comprising diabetogenic epitopes.

29. The food or foodstuff of claim 28 modified to reduce or eliminate Glb1, .alpha./.beta.-gliadin precursor or .alpha./.beta.-gliadin MM1 precursor, or a diabetogenic epitope thereof.

30. The foodstuff of claim 28, said foodstuff comprising a genetically modified plant comprising a knockout of one or more diabetic epitopes or proteins comprising said one or more diabetic epitopes.

31. The foodstuff of claim 30, wherein said genetically modified plant comprises a wheat plant.

32. The foodstuff of claim 28, wherein said foodstuff comprises an inhibitory RNA
nucleotide sequence that reduces or eliminates the production of one or more proteins comprising one or more diabetogenic epitopes.