U.S. patent application number 14/630004 was filed with the patent office on 2017-10-19 for epitopes related to coeliac disease.
This patent application is currently assigned to BTG International Limited. The applicant listed for this patent is BTG International Limited. Invention is credited to Robert Anderson, Tim Beissbath, Jason Tye Din.
Application Number | 20170296651 14/630004 |
Document ID | / |
Family ID | 56973853 |
Filed Date | 2017-10-19 |
United States Patent
Application |
20170296651 |
Kind Code |
A9 |
Anderson; Robert ; et
al. |
October 19, 2017 |
EPITOPES RELATED TO COELIAC DISEASE
Abstract
The invention herein disclosed is related to epitopes useful in
methods of diagnosing, treating, and preventing coeliac disease.
Therapeutic compositions which comprise at least one epitope are
provided.
Inventors: |
Anderson; Robert; (Victoria,
AU) ; Beissbath; Tim; (Heidelberg, DE) ; Din;
Jason Tye; (Victoria, AU) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BTG International Limited |
London |
|
GB |
|
|
Assignee: |
BTG International Limited
London
GB
|
Prior
Publication: |
|
Document Identifier |
Publication Date |
|
US 20160279233 A1 |
September 29, 2016 |
|
|
Family ID: |
56973853 |
Appl. No.: |
14/630004 |
Filed: |
February 24, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13541864 |
Jul 5, 2012 |
9017690 |
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14630004 |
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11568428 |
Jul 9, 2008 |
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PCT/GB05/01621 |
Apr 28, 2005 |
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13541864 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A23L 33/18 20160801;
A61K 39/001 20130101; C12N 15/8251 20130101; A61K 39/35 20130101;
C07K 14/415 20130101; A23L 33/17 20160801; G01N 33/564 20130101;
A23L 33/185 20160801; C12N 15/8258 20130101; G01N 2333/415
20130101; G01N 2800/06 20130101 |
International
Class: |
A61K 39/35 20060101
A61K039/35; A23L 33/17 20060101 A23L033/17; G01N 33/564 20060101
G01N033/564; A23L 33/18 20060101 A23L033/18; C07K 14/415 20060101
C07K014/415; C12N 15/82 20060101 C12N015/82; A23L 33/185 20060101
A23L033/185; A61K 39/00 20060101 A61K039/00; C12N 15/82 20060101
C12N015/82 |
Foreign Application Data
Date |
Code |
Application Number |
Apr 28, 2004 |
AU |
2004201774 |
Feb 11, 2005 |
AU |
2005900650 |
Claims
1. A method of preventing or treating coeliac disease comprising
administering to an individual at least one agent selected from:
(a) a peptide comprising at least one epitope comprising a sequence
selected from the group consisting of SEQ ID NOs: 1-1927, and
equivalents thereof; and (b) an analogue of (a) which is capable of
being recognised by a T cell receptor that recognises the peptide
of (a) and which is not more than 50 amino acids in length.
2. A method of claim 1 wherein the agent is HLA-DQ2-restricted.
3. A method of claim 1 wherein the agent is HLA-DQ8-restricted.
4. A method of claim 1 wherein one agent is HLA-DQ2-restricted and
a second agent is HLA-DQ8-restricted.
5. A method of claim 1 wherein the agent comprises a wheat
epitope.
6. A method of claim 1 wherein the agent comprises an oat
epitope.
7. A method of claim 1 wherein one agent comprises a wheat epitope
and one agent comprises an oat epitope.
8. A method of preventing or treating coeliac disease comprising
administering to an individual a pharmaceutical composition
comprising an agent as defined in claim 1 and a pharmaceutically
acceptable carrier or diluent.
9. A method of preventing or treating coeliac disease comprising
administering to an individual a pharmaceutical composition
comprising an antagonist of a T cell which has a T cell receptor as
defined in claim 1, and a pharmaceutically acceptable carrier or
diluent.
10. A method of preventing or treating coeliac disease comprising
administering to an individual a composition for tolerising an
individual to a gluten protein to suppress the production of a T
cell or antibody response to an agent as defined in claim 1, which
composition comprises an agent as defined in claim 1.
11. A method of preventing or treating coeliac disease comprising:
diagnosing coeliac disease in an individual by either: a)
contacting a sample from the host with at least one agent selected
from: i) a peptide comprising at least one epitope comprising a
sequence selected from the group consisting of: SEQ ID NOS: 1-1927,
and equivalents thereof; and ii) an analogue of i) which is capable
of being recognised by a T cell receptor that recognises i) and
which is not more than 50 amino acids in length; and determining in
vitro whether T cells in the sample recognise the agent;
recognition by the T cells indicating that the individual has, or
is susceptible to, coeliac disease; or b) administering an agent as
defined in claim 1 and determining in vivo whether T cells in the
individual recognise the agent, recognition of the agent indicating
that the individual has or is susceptible to coeliac disease; and
administering to an individual diagnosed as having, or being
susceptible to, coeliac disease a therapeutic agent for preventing
or treating coeliac disease.
12. Use of an agent for the preparation of a medicament for
treating or preventing coeliac disease, wherein the agent
comprises: (a) a peptide comprising at least one epitope comprising
a sequence selected from the group consisting of SEQ ID NOs: 1-1927
and equivalents thereof; and (b) an analogue of (a) which is
capable of being recognised by a T cell receptor that recognises
the peptide of (a) and which is not more than 50 amino acids in
length.
13. A use of claim 12 wherein the agent is HLA-DQ2-restricted.
14. A use of claim 12 wherein the agent is HLA-DQ8-restricted.
15. A use of claim 12 wherein one agent is HLA-DQ2-restricted and a
second agent is HLA-DQ8-restricted.
16. A use of claim 12 wherein the agent comprises a wheat
epitope.
17. A use of claim 12 wherein the agent comprises an oat
epitope.
18. A use of claim 12 wherein one agent comprises a wheat epitope
and one agent comprises an oat epitope.
19. A use of claim 12 wherein the agent is present within a
pharmaceutical composition comprising a pharmaceutically acceptable
carrier or diluent.
20. A use of claim 12 wherein the agent is present within a
pharmaceutical composition comprising an antagonist of a T cell
which has a T cell receptor as defined in claim 12, and a
pharmaceutically acceptable carrier or diluent.
21. A use of claim 12 wherein the agent is present within a
composition for tolerising an individual to a gluten protein to
suppress the production of a T cell or antibody response to an
agent as defined in claim 1.
22. An agent as defined in claim 1, optionally in association with
a carrier, for use in a method of treating or preventing coeliac
disease by tolerising T cells which recognise the agent.
23. An antagonist of a T cell which has a T cell receptor as
defined in claim 1, optionally in association with a carrier, for
use in a method of treating or preventing coeliac disease by
antagonising such T cells.
24. An agent as defined in claim 1 or an analogue that binds an
antibody that binds to an epitope of an agent as defined in claim 1
for use in a method of treating or preventing coeliac disease in an
individual by tolerising the individual to prevent the production
of such an antibody.
25. A protein that comprises a sequence which is able to bind to a
T cell receptor, which T cell receptor recognises an agent as
defined in claim 1, and which sequence is able to cause antagonism
of a T cell that carries such a T cell receptor.
26. An agent as defined in claim 1 or an antagonist as defined in
claim 9.
27. A pharmaceutical composition comprising an agent as defined in
claim 1 or an antagonist as defined in claim 9 and a
pharmaceutically acceptable carrier or diluent.
28. A composition for tolerising an individual to a gluten protein
to suppress the production of a T cell or antibody response to an
agent as defined in claim 1, which composition comprises an agent
as defined in claim 1.
29. A composition for antagonising a T cell response to an agent as
defined in claim 1, which composition comprises an antagonist as
defined in claim 9.
30. A mutant gluten protein whose wild-type sequence can be
modified by a transglutaminase to a sequence which is an agent as
defined in claim 1, which mutant gluten protein comprises a
mutation which prevents its modification by a transglutaminase to a
sequence which is an agent as defined in claim 1; or a fragment of
such a mutant gluten protein which is at least 7 amino acids long
and which comprises the mutation.
31. A polynucleotide that comprises a coding sequence that encodes
a protein or fragment as defined in claim 25 or 30.
32. A polynucleotide according to claim 31 that additionally
comprises one or more regulatory sequences operably linked to the
coding sequence, which regulatory sequences are capable of securing
the expression of the coding sequence in a cell.
33. A polynucleotide according to claim 32 wherein the regulatory
sequence(s) allow expression of the coding sequence in a
prokaryotic or mammalian cell.
34. A polynucleotide according to any one of claims 31 to 33 which
is a vector or which is in the form of a vector.
35. A cell comprising a polynucleotide as defined in any one of
claims 31 to 34 or which has been transformed with such a
polynucleotide.
36. A cell according to claim 35 which is a prokaryotic cell or a
mammalian cell.
37. A mammal that expresses a T cell receptor as defined in claim
1.
38. A method of diagnosing coeliac disease, or susceptibility to
coeliac disease, in an individual comprising: (a) contacting a
sample from the host with at least one agent selected from: i) a
peptide comprising at least one epitope comprising a sequence
selected from the group consisting of: SEQ ID NOS: 1-1927, and
equivalents thereof; and ii) an analogue of (i) which is capable of
being recognised by a T cell receptor that recognises (i) and which
is not more than 50 amino acids in length; and (b) determining in
vitro whether T cells in the sample recognise the agent;
recognition by the T cells indicating that the individual has, or
is susceptible to, coeliac disease.
39. Use of an agent as defined in claim 38 for the preparation of a
diagnostic means for use in a method of diagnosing coeliac disease,
or susceptibility to coeliac disease, in an individual, said method
comprising determining whether T cells of the individual recognise
the agent, recognition by the T cells indicating that the
individual has, or is susceptible to, coeliac disease.
40. A method or use according to claim 38 or 39 wherein the agent
is an analogue (iii) which comprises (i) or (ii) bound to (a) an
HLA molecule, or (b) a fragment of an HLA molecule capable of
binding (i) or (ii).
41. A method or use according to claim 40 wherein the HLA molecule
or fragment is in a complex comprising four HLA molecules or
fragments of HLA molecules.
42. Use according to any one of claims 39-41 wherein the method
comprises administering the agent to the skin of an individual and
detecting the presence of inflammation at the site of
administration, the detection of inflammation indicating that the T
cells of the individual recognise the agent.
43. A method according to claim 39, 41 or 42 wherein the sample is
blood sample.
44. A method according to claim 38, 40, 41 or 43 wherein the T
cells are not restimulated in antigen specific manner in vitro
before the said determining.
45. A method or use according to any one claims 38-44 in which the
recognition of the agent by the T cells is determined by detecting
the secretion of a cytokine from the T cells.
46. A method or use according to claim 45 in which the cytokine is
IFN-.gamma..
47. A method or use according to claim 45 or claim 46 in which the
cytokine is detected by allowing the cytokine to bind to an
immobilised antibody specific to the cytokine and then detecting
the presence of the antibody/cytokine complex.
48. A method or use according to any one of claims 38 to 44 wherein
said determining is done by measuring whether the agent binds the T
cell receptor.
49. A method for identifying an analogue as defined in a claim 38,
40 or 41 comprising determining whether a candidate substance is
recognised by a T cell receptor that recognises an epitope
comprising sequence as defined in claim 38, recognition of the
substance indicating that the substance is an analogue.
50. A method of diagnosing coeliac disease, or susceptibility to
coeliac disease, in an individual comprising determining the
presence of an antibody that binds to an epitope of an epitope
comprising sequence as defined in claim 38 in a sample from the
individual, the presence of the antibody indicating that the
individual has, or is susceptible to, coeliac disease.
51. A method of determining whether a composition is capable of
causing coeliac disease comprising determining whether a protein
capable of being modified by a transglutaminase to an oligopeptide
sequence as defined in claim 38 is present in the composition, the
presence of the protein indicating that the composition is capable
of causing coeliac disease.
52. A method according to claim 51 wherein the said determining is
done by contacting the composition with an antibody specific for
the sequence which is capable of being modified to the i
oligopeptide sequence, binding of the antibody to a protein in the
composition indicating the composition is capable of causing
coeliac disease.
53. A method of identifying an antagonist of a T cell, which T cell
recognises an agent as defined in claim 1, comprising contacting a
candidate substance with the T cell and detecting whether the
substance causes a decrease in the ability of the T cell to undergo
an antigen specific response, the detecting of any such decrease in
said ability indicating that the substance is an antagonist.
54. A kit for carrying out a method or use according to any one of
claims 38 to 48 comprising an agent as defined in claim 38, 40 or
41 and a means to detect the recognition of the peptide by the T
cell.
55. A kit according to claim 54 wherein the means to detect
recognition comprises an antibody to IFN-.gamma..
56. A kit according to claim 55 wherein the antibody is immobilised
on a solid support and optionally the kit also comprises a means to
detect the antibody/IFN-.gamma. complex.
57. Use of an agent or antagonist as defined in claim 56 or a wild
type sequence as defined in claim 30 to produce an antibody
specific to the agent, antagonist or wild type sequence.
58. Use of a mutation in an epitope of a gluten protein, which
epitope is as defined in claim 38, to decrease the ability of the
gluten protein to cause coeliac disease.
59. A method of identifying a product which is therapeutic for
coeliac disease comprising administering a candidate substance to a
mammal as defined in claim 37 which has, or which is susceptible
to, coeliac disease and determining whether substance prevents or
treats coeliac disease in the mammal, the prevention or treatment
of coeliac disease indicating that the substance is a therapeutic
product.
60. A therapeutic product as identified in the method of claim 59
for use in a method of preventing or treating coeliac disease.
61. A method of diagnosing coeliac disease, or susceptibility to
coeliac disease in an individual comprising administering an agent
as defined in claim 38 and determining in vivo whether T cells in
the individual recognise the agent, recognition of the agent
indicating that the individual has or is susceptible to coeliac
disease.
62. A cell according to claim 35 which is a cell of a graminaceous
monocotyledonous species.
63. A cell according to claim 62 which is a cell of wheat, maize,
oats, rye, rice, barley, triticale, sorghum, or sugar cane.
64. A process for the production of a protein encoded by a coding
sequence as defined in claim 31 which process comprises: (a)
cultivating a cell according to any one of claim 35, 36, 62 or 63
under conditions that allow the expression of the protein; and
optionally (b) recovering the expressed protein.
65. A method of obtaining a transgenic plant cell comprising: (a)
transforming a plant cell with a vector according to claim 34 to
give a transgenic plant cell.
66. A method of obtaining a first-generation transgenic plant
comprising: (a) regenerating a transgenic plant cell transformed
with a vector according to claim 34 to give a transgenic plant.
67. A method of obtaining a transgenic plant seed comprising: (a)
obtaining a transgenic seed from a transgenic plant obtainable by
step (b) of claim 66.
68. A method of obtaining a transgenic progeny plant comprising
obtaining a second-generation transgenic progeny plant from a
first-generation transgenic plant obtainable by a method according
to claim 66, and optionally obtaining transgenic plants of one or
more further generations from the second-generation progeny plant
thus obtained.
69. A method according to claim 68 comprising: (a) obtaining a
transgenic seed from a first-generation transgenic plant obtainable
by the method according to claim 67, then obtaining a
second-generation transgenic progeny plant from the transgenic
seed; and/or (b) propagating clonally a first-generation transgenic
plant obtainable by the method according to claim 66 to give a
second-generation progeny plant; and/or (c) crossing a
first-generation transgenic plant obtainable by a method according
to claim 66 with another plant to give a second-generation progeny
plant; and optionally (d) obtaining transgenic progeny plants of
one or more further generations from the second-generation progeny
plant thus obtained.
70. A transgenic plant cell, plant, plant seed or progeny plant
obtainable by a method according to any one of claims 65 to 69.
71. A transgenic plant or plant seed comprising plant cells
according to claim 62 or 63.
72. A transgenic plant cell callus comprising plant cells according
to claim 62 or 63 obtainable from a transgenic plant cell,
first-generation plant, plant seed or progeny as defined in any one
of claims 62, 63, or 65 to 69.
73. A plant or callus according to any one of claims claim 70 to 72
which is of a species as defined in claim 62 or 63.
74. A method of obtaining a crop product comprising harvesting a
crop product from a plant according to any one of claims 70 to 73
and optionally further processing the harvested product.
75. A method according to claim 74 wherein the plant is a wheat
plant and the harvested crop product is grain; optionally further
processed into flour or another grain product.
76. A crop product obtainable by a method according to claim 74 or
75.
77. A food that comprises a protein as defined in any claim 25 or
30.
78. A food according to claim 77 in which a protein as defined in
claim 25 or 30 is used instead of wild-type gluten.
Description
[0001] The invention relates to epitopes useful in the diagnosis
and therapy of coeliac disease, including diagnostics,
therapeutics, kits, and methods of using the foregoing.
[0002] Coeliac disease is caused by an immune mediated
hypersensitivity to dietary gluten. Gluten proteins in wheat, rye,
barley and in some cases oats are toxic in coeliac disease. Gluten
is composed of alpha/beta, gamma and omega gliadins, and low and
high molecular weight (LMW and HMW) glutenins in wheat, hordeins in
barley, secalins in rye and avenins in oats. Hordeins and secalins
are homologous to gamma and omega gliadins and low and high
molecular weight glutenins in wheat. Avenins are phylogenetically
more distant than hordeins and secalins from wheat gluten.
[0003] The goal of research in coeliac disease has been to define
the toxic components of gluten by defining the peptides that
stimulate gluten-specific T-cells. Precise definition of gluten
epitopes permits development of new diagnostics, therapeutics,
tests for gluten contamination in food and non-toxic grains that
retain the cooking/baking qualities of traditional gluten. Many of
these applications require a comprehensive understanding of all
rather than the most common toxic peptides in gluten.
[0004] Genes encoding HLA-DQ2 and/or HLA-DQ8 are present in over
99% of individuals with coeliac disease compared to approximately
35% of the general Caucasian population. Gluten-derived peptides
(epitopes) bound to HLA-DQ2 or HLA-DQ8 stimulate specific T-cells.
HLA-DQ2 and DQ8-restricted epitopes include a "core" 9 amino acid
sequence that directly interacts with the peptide binding groove of
HLA-DQ2 or DQ8 and with cognate T-cell receptors. In general,
libraries of overlapping peptides (usually 15 to 20mers) containing
all unique 10 or 12mer peptides in an antigen have been used to map
HLA class II-restricted T-cells epitopes.
[0005] A series of gluten peptides are known to activate gluten
specific T-cells in coeliac disease. Previous studies have
identified gluten peptides from selected gluten proteins or gluten
digests. T-cell clones and lines isolated from intestinal biopsies
have been used to screen these gluten components.
[0006] Modification of gluten by the enzyme, tissue
transglutaminase (tTG) present in intestinal tissue, substantially
increases gluten's stimulatory capacity on gluten specific T-cells.
Most of the known epitopes for gluten-specific T-cells correspond
to tTG-deamidated gluten peptides. Transglutaminase mediates
deamidation of specific glutamine residues (to glutamate) in
gluten. Glutamine-containing sequences susceptible to deamidation
by tTG generally conform to a motif: QXPX or QXX (FYMILVW) (see
Vader W. et al 2002 J. Exp. Med. 195:643-649, PCT WO 03/066079, and
Fleckenstein B. 2002. J Biol Chem 277:34109-16). The motif for
peptides that bind to HLA-DQ2 and that are susceptible to
deamidation by tTG has been used to predict certain gluten epitopes
(Vader et al J Exp Med 2002 J. Exp. Med. 195:643-649, PCT WO
03/066079).
[0007] However, other groups have identified epitopes for
gluten-specific intestinal T-cell clones and lines using panels of
eleven recombinant alpha/beta (11) and five gamma gliadins
(Arentz-Hansen H. 2000. J. Exp. Med. 191:603-612, Arentz-Hansen H.
2002. Gastroenterology 123:803-809, PCT WO 02/083722), and lysates
of purified gluten proteins (Sjostrom H. et al 1998. Scand. J.
Immunol. 48,111-115; van de Wal, Y. et al 1998J. Immunol.
161(4):1585-1588; van de Wal, Y. et al 1999. Eur. J. Immunol.
29:3133-3139; Vader W. et al 2002. Gastroenterology
122:1729-1737.).
[0008] Our work has exploited the observation that gluten challenge
in vivo induces HLA-DQ2 restricted CD4+ gluten-specific T-cells in
peripheral blood expressing a gut-homing integrin (alpha4beta7).
This technique allowed the mapping of the dominant epitope in
A-gliadin (57-73 QE65) (Anderson, R P et al 2000. Nat. Med.
6:337-342, WO 01/25793). A-gliadin 57-73 QE65 corresponds to two
overlapping epitopes identified using intestinal T-cell clones
(Arentz-Hansen H. et al 2000. J. Exp. Med. 191:603-612,
Arentz-Hansen H. et al 2002. Gastroenterology 123:803-809). The
advantage of in vivo gluten challenge to induce gluten specific
T-cells is that any food can be consumed and the resulting T-cells
induced in blood (quantified in peripheral blood using a simple
overnight interferon gamma ELISPOT assay) will have been stimulated
in vivo by endogenously presented epitopes, rather than primed in
vitro by a synthetic or purified antigen. Overnight assays of fresh
polyclonal peripheral blood T-cells also avoid the potential for
artefacts associated with the lengthy purification of T-cell
clones.
[0009] Interestingly, T-cell clones and lines specific for several
gamma-gliadin epitopes (Arentz-Hansen H. 2002. Gastroenterology
123:803-809, PCT WO 02/083722) cross-react with the originally
defined A-gliadin epitope 57-73 QE65.
[0010] Although there is substantial homology within the alpha/beta
gliadins, earlier work (see WO 03/104273) has shown that the
dominant epitope recognized in HLA-DQ2-associated coeliac disease,
"A-gliadin 57-73 QE65", is encoded by a minority of the alpha/beta
gliadins present in Genbank.
SUMMARY OF THE INVENTION
[0011] The current study set out to develop a method that would
allow mapping of all T-cell epitopes in gluten. Consumption of
wheat bread (200 g daily for 3 days) or oats (100 g daily for 3
days) was used to induce gluten or avenin-specific T-cells in
peripheral blood (collected 6 days after beginning the challenge).
Peripheral blood mononuclear cells (PBMC) were assessed in
overnight interferon gamma ELISPOT assays using a library of gluten
and avenin peptides including all unique 12mer sequences included
in every Genbank entry for wheat gluten and/or oat avenins. This
goal was achieved by establishing an algorithm to design peptides
spanning all potential epitopes in gluten proteins in Genbank (2922
20mers included all 14 964 unique 9mers--potential T-cell
epitopes), adapting the interferon-gamma ELISPOT assay to a high
throughput assay capable of screening over 1000 peptides with a
single individual's blood and developing bioinformatics tools to
analyse and interpret the data generated.
[0012] A series of 41 "superfamilies" of wheat gluten peptides were
identified as putative T-cell epitopes. Superfamilies shared motifs
in which a limited level of redundancy was allowed. Many of the
most potent families include known T-cell epitopes including the
previously described dominant epitope, A-gliadin 57-73.
[0013] Through comprehensive mapping of gluten epitopes using PBMC
after gluten challenge, the inventors have found a series of novel
gliadin, LMW and HMW glutenin, and avenin epitopes for coeliac
disease associated with HLA-DQ2 and HLA-DQ8. Novel epitopes were
identified for HLA-DQ2 and HLA-DQ8-associated coeliac disease.
HLA-DQ2 and HLA-DQ8 associated coeliac disease are genetically and
functionally distinct in terms of the range of T-cell epitopes that
are recognized. In addition, three peptides present in avenin
proteins of oats also activated peripheral blood mononuclear cells
(PBMC) following oats challenge in HLA-DQ2+ coeliac subjects, the
first time oats epitopes have been defined. Identification of
avenin peptides recognized by T-cells following oats challenge in
vivo provides a molecular basis for the observed occasional relapse
of coeliacs following oat exposure (Lundin K E A et al. 2003 Gut
52:1649-52) and may provide a basis for a predictive diagnostic or
genetic de-toxification of oats.
[0014] The data presented here will provide a comprehensive basis
for definition of both common "dominant" and occasional "weak"
T-cell epitopes in coeliac disease. This information is the
platform for functional applications such as diagnostics, food
tests, immunotherapeutics and prophylactics, and for design of
non-toxic gluten proteins useful in modified grains.
[0015] In particular, through comprehensive mapping of gluten T
cell epitopes, the inventors have found epitopes bioactive in
coeliac disease in HLA-DQ2+ patients in wheat gliadins and
glutenins, having similar core sequences (e.g., SEQ ID NOS: 1-199)
and similar extended sequences (e.g., SEQ ID NOS: 200-1554,
1555-1655, 1656-1671, and 1830-1903). The inventors have also found
epitopes bioactive in coeliac disease in HLA-DQ2+ patients in: oat
avenins having similar core sequences (e.g., SEQ ID NOS: 1684-1695)
and similar extended sequences (e.g., SEQ ID NO: 1672-1683,
1696-1698, and 1764-1768); rye secalins (SEQ ID NOS: 1769-1786);
and barley hordeins (SEQ ID NOS: 1787-1829). Additionally, epitopes
bioactive in coeliac disease in HLA-DQ8+ patients have been
identified in wheat gliadins having similar core sequences (e.g.,
SEQ ID NOS: 1699-1721) and similar extended sequences (e.g., SEQ ID
NOS: 1722-1763 and 1908-1927). This comprehensive mapping thus
provides dominant epitopes recognized by T cells in coeliac
patients. Thus, the methods of the invention described herein may
be performed using any of these identified epitopes, and analogues
and equivalents thereof. That is, the agents of the invention
include these epitopes. Additionally, combinations of epitopes,
i.e., "combitopes" or single peptides comprising two or more
epitiopes, have been shown to induce equivalent responses as the
individual epitopes, indicating that several epitopes may be
utilized for therapeutic, diagnostic, and other uses of the
invention. Such combitopes may be in the form of, e.g., SEQ ID NO:
1906. Preferably, the agents of the invention include one or more
of the epitopes having the sequences listed recited in SEQ ID NOS:
1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671,
1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903,
1906, and 1908-1927 and analogues and equivalents thereof as
defined herein.
[0016] Preferred agents that are bioactive in coeliac disease in
HLA-DQ8+ patients possess a glutamine in a sequence that suggests
susceptibility to deamidation separated by seven residues from a
second glutamine also susceptible to deamidation (e.g., as found in
QGS FQPSQQ) wherein the deamidated sequences are high affinity
binders for HLA-DQ8 following deamidation by tTG (The binding motif
for HLA-DQ8 favours glutamate at positions 1 and 9.) In a less
preferred embodiment, the agent possesses glutamine residues
susceptible to deamidation but not separated by seven residues from
a second glutamine susceptible to tTG-mediated deamidation.
[0017] The invention thus provides a method of diagnosing coeliac
disease, or susceptibility to coeliac disease, in an individual,
comprising the steps of: (a) contacting a sample from the host with
an agent selected from (i) the epitope comprising an amino acid
sequence selected from SEQ ID NOS: 1-1927, preferably selected from
SEQ ID NOS: 1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655,
1656-1671, 1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829,
1895-1903, 1906, and 1908-1927, or an equivalent sequence from a
naturally occurring gluten protein, (ii) an analogue of (i) which
is capable of being recognised by a T cell receptor that recognises
(i), which in the case of a peptide analogue is not more than 50
amino acids in length, or (iii) a product comprising two or more
agents as defined in (i) or (ii); and (b) determining in vitro
whether T cells in the sample recognise the agent, with recognition
by the T cells indicating that the individual has, or is
susceptible to, coeliac disease.
[0018] The term "gluten protein" encompasses alpha/beta, gamma and
omega gliadins, and low and high molecular weight (LMW and HMW)
glutenins in wheat, hordeins in barley, secalins in rye, and
avenins in oats. The invention is particularly concerned with
gliadins and avenins.
[0019] The invention also provides use of the agent for the
preparation of a diagnostic means for use in a method of diagnosing
coeliac disease, or susceptibility to coeliac disease, in an
individual, said method comprising determining whether T cells of
the individual recognise the agent, recognition by the T cells
indicating that the individual has, or is susceptible to, coeliac
disease.
[0020] The finding of epitopes which are modified by
transglutaminase also allows diagnosis of coeliac disease based on
determining whether other types of immune response to these
epitopes are present. Thus the invention also provides a method of
diagnosing coeliac disease, or susceptibility to coeliac disease,
in an individual comprising determining the presence of an antibody
that binds to the epitope in a sample from the individual, the
presence of the antibody indicating that the individual has, or is
susceptible to, coeliac disease.
[0021] The invention provides a method of determining whether a
composition is capable of causing coeliac disease comprising
determining whether a protein capable of being modified by a
transglutaminase to an oligopeptide sequence as defined above is
present in the composition, the presence of the protein indicating
that the composition is capable of causing coeliac disease.
[0022] The invention also provides a mutant gluten protein whose
wild-type sequence can be modified by a transglutaminase to a
sequence that comprises an epitope comprising sequence as defined
above, but which mutant gluten protein has been modified in such a
way that it does not contain sequence which can be modified by a
transglutaminase to a sequence that comprises such an epitope
comprising sequence; or a fragment of such a mutant gluten protein
which is at least 7 amino acids long (e.g., at least 7, 8, 9, 10,
11, 12, 13, 14 or 15 amino acids long) and which comprises sequence
which has been modified in said way.
[0023] The invention also provides a protein that comprises a
sequence which is able to bind to a T cell receptor, which T cell
receptor recognises the agent, and which sequence is able to cause
antagonism of a T cell that carries such a T cell receptor.
[0024] Additionally the invention provides a food that comprises
the proteins defined above.
[0025] The invention additionally provides the agent, optionally in
association with a carrier, for use in a method of treating or
preventing coeliac disease by tolerising T cells which recognise
the agent. Also provided is an antagonist of a T cell which has a T
cell receptor that recognises (i), optionally in association with a
carrier, for use in a method of treating or preventing coeliac
disease by antagonising such T cells. Additionally provided is the
agent or an analogue that binds an antibody (that binds the agent)
for use in a method of treating or preventing coeliac disease in an
individual by tolerising the individual to prevent the production
of such an antibody.
[0026] The invention also provides methods of preventing or
treating coeliac disease comprising administering to an individual
at least one agent selected from: a) a peptide comprising at least
one epitope comprising a sequence selected from the group
consisting of SEQ ID NOs: 1-1927, preferably from the group
consisting of SEQ ID NOS: 1578-1579, 1582-1583, 1587-1593,
1600-1620, 1623-1655, 1656-1671, 1672-1698, 1699-1763, 1764-1768,
1769-1786, 1787-1829, 1895-1903, 1906, and 1908-1927, and
equivalents thereof; and b) an analogue of a) which is capable of
being recognised by a T cell receptor that recognises the peptide
of a) and which is not more than 50 amino acids in length. In some
embodiments, the agent is HLA-DQ2-restricted, HLA-DQ8-restricted or
one agent is HLA-DQ2-restricted and a second agent is
HLA-DQ8-restricted. In some embodiments, the agent comprises a
wheat epitope, an oat epitope, a rye epitope, a barley epitope or
any combination thereof either as a single agent or as multiple
agents.
[0027] The present invention also provides methods of preventing or
treating coeliac disease comprising administering to an individual
a pharmaceutical composition comprising an agent as described above
and pharmaceutically acceptable carrier or diluent.
[0028] The present invention also provides methods of preventing or
treating coeliac disease comprising administering to an individual
a pharmaceutical composition comprising an antagonist of a T cell
which has a T cell receptor as defined above, and a
pharmaceutically acceptable carrier or diluent.
[0029] The present invention also provides methods of preventing or
treating coeliac disease comprising administering to an individual
a composition for tolerising an individual to a gluten protein to
suppress the production of a T cell or antibody response to an
agent as defined above, which composition comprises an agent as
defined above.
[0030] The present invention also provides methods of preventing or
treating coeliac disease by 1) diagnosing coeliac disease in an
individual by either: a) contacting a sample from the host with at
least one agent selected from: i) a peptide comprising at least one
epitope comprising a sequence selected from the group consisting
of: SEQ ID NOS: 1-1927, preferably selected from the group
consisting of SEQ ID NOS: 1578-1579, 1582-1583, 1587-1593,
1600-1620, 1623-1655, 1656-1671, 1672-1698, 1699-1763, 1764-1768,
1769-1786, 1787-1829, 1895-1903, 1906, and 1908-1927, and
equivalents thereof; and ii) an analogue of i) which is capable of
being recognised by a T cell receptor that recognises i) and which
is not more than 50 amino acids in length; and determining in vitro
whether T cells in the sample recognise the agent; recognition by
the T cells indicating that the individual has, or is susceptible
to, coeliac disease; or b) administering an agent as defined above
and determining in vivo whether T cells in the individual recognise
the agent, recognition of the agent indicating that the individual
has or is susceptible to coeliac disease; and 2) administering to
an individual diagnosed as having, or being susceptible to, coeliac
disease a therapeutic agent for preventing or treating coeliac
disease.
[0031] The present invention also provides agents as defined above,
optionally in association with a carrier, for use in a method of
treating or preventing coeliac disease by tolerising T cells which
recognise the agent.
[0032] The present invention also provides antagonists of a T cell
which has a T cell receptor as defined above, optionally in
association with a carrier, for use in a method of treating or
preventing coeliac disease by antagonising such T cells.
[0033] The present invention also provides proteins that comprises
a sequence which is able to bind to a T cell receptor, which T cell
receptor recognises an agent as defined above, and which sequence
is able to cause antagonism of a T cell that carries such a T cell
receptor.
[0034] The present invention also provides pharmaceutical
compositions comprising an agent or antagonist as defined and a
pharmaceutically acceptable carrier or diluent.
[0035] The present invention also provides compositions for
tolerising an individual to a gluten protein to suppress the
production of a T cell or antibody response to an agent as defined
above, which composition comprises an agent as defined above.
[0036] The present invention also provides compositions for
antagonising a T cell response to an agent as defined above, which
composition comprises an antagonist as defined above.
[0037] The present invention also provides mutant gluten proteins
whose wild-type sequence can be modified by a transglutaminase to a
sequence which is an agent as defined above, which mutant gluten
protein comprises a mutation which prevents its modification by a
transglutaminase to a sequence which is an agent as defined above;
or a fragment of such a mutant gluten protein which is at least 7
amino acids long (e.g., at least 7, 8, 9, 10, 11, 12, 13, 14 or 15
amino acids long) and which comprises the mutation.
[0038] The present invention also provides polynucleotides that
comprise a coding sequence that encodes a protein or fragment as
defined above.
[0039] The present invention also provides cells comprising a
polynucleotide as defined above or which have been transformed with
such a polynucleotide.
[0040] The present invention also provides mammals that expresses a
T cell receptor as defined above.
[0041] The present invention also provides methods of diagnosing
coeliac disease, or susceptibility to coeliac disease, in an
individual comprising: a) contacting a sample from the host with at
least one agent selected from i) a peptide comprising at least one
epitope comprising a sequence selected from the group consisting
of: SEQ ID NOS: 1-1927, preferably selected from the group
consisting of SEQ ID NOS: SEQ ID NOS: 1578-1579, 1582-1583,
1587-1593, 1600-1620, 1623-1655, 1656-1671, 1672-1698, 1699-1763,
1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906, and 1908-1927,
and equivalents thereof; and ii) an analogue of i) which is capable
of being recognised by a T cell receptor that recognises i) and
which is not more than 50 amino acids in length; and b) determining
in vitro whether T cells in the sample recognise the agent;
recognition by the T cells indicating that the individual has, or
is susceptible to, coeliac disease.
[0042] The present invention also provides methods of determining
whether a composition is capable of causing coeliac disease
comprising determining whether a protein capable of being modified
by a transglutaminase to an oligopeptide sequence is present in the
composition, the presence of the protein indicating that the
composition is capable of causing coeliac disease.
[0043] The present invention also provides methods of identifying
an antagonist of a T cell, which T cell recognises an agent as
defined above, comprising contacting a candidate substance with the
T cell and detecting whether the substance causes a decrease in the
ability of the T cell to undergo an antigen specific response, the
detecting of any such decrease in said ability indicating that the
substance is an antagonist.
[0044] The present invention also provides kits for carrying out
any of the methods described above comprising an agent as defined
above and a means to detect the recognition of the peptide by the T
cell.
[0045] The present invention also provides methods of identifying a
product which is therapeutic for coeliac disease comprising
administering a candidate substance to a mammal as defined above
which has, or which is susceptible to, coeliac disease and
determining whether substance prevents or treats coeliac disease in
the mammal, the prevention or treatment of coeliac disease
indicating that the substance is a therapeutic product.
[0046] The present invention also provides processes for the
production of a protein encoded by a coding sequence as defined
above which process comprises: a) cultivating a cell described
above under conditions that allow the expression of the protein;
and optionally b) recovering the expressed protein.
[0047] The present invention also provides methods of obtaining a
transgenic plant cell comprising transforming a plant cell with a
vector as described above to give a transgenic plant cell.
[0048] The present invention also provides methods of obtaining a
first-generation transgenic plant comprising regenerating a
transgenic plant cell transformed with a vector as described above
to give a transgenic plant.
[0049] The present invention also provides methods of obtaining a
transgenic plant seed comprising obtaining a transgenic seed from a
transgenic plant obtainable as described above.
[0050] The present invention also provides methods of obtaining a
transgenic progeny plant comprising obtaining a second-generation
transgenic progeny plant from a first-generation transgenic plant
obtainable by a method as described above, and optionally obtaining
transgenic plants of one or more further generations from the
second-generation progeny plant thus obtained.
[0051] The present invention also provides transgenic plant cells,
plants, plant seeds or progeny plants obtainable by any of the
methods described above.
[0052] The present invention also provides transgenic plants or
plant seeds comprising plant cells as described above.
[0053] The present invention also provides transgenic plant cell
calluses comprising plant cells as described above obtainable from
a transgenic plant cell, first-generation plant, plant seed or
progeny as defined above.
[0054] The present invention also provides methods of obtaining a
crop product comprising harvesting a crop product from a plant
according to any method described above and optionally further
processing the harvested product.
[0055] The present invention also provides food that comprises a
protein as defined above.
BRIEF DESCRIPTION OF THE DRAWINGS
[0056] FIG. 1 (FIG. 1) shows a method to generate all possible
peptide epitopes from a group of proteins.
[0057] FIG. 2A and FIG. 2B show Genbank accession numbers for
gluten gene products present in the Genbank database on 16, Jun.
2003 (see FIG. 2A and FIG. 2B).
[0058] FIG. 3A (FIG. 3A) shows an expectation maximization (EM)
algorithm to analyze data from ELISpot.
[0059] FIG. 3B (FIG. 3B) shows a test on a dataset of patients with
coeliac disease.
[0060] FIG. 4 (FIG. 4) shows an iterative procedure to find minimal
set of responsive epitopes.
[0061] FIG. 5A, FIG. 5B, FIG. 5C, FIG. 5D, FIG. 5E, FIG. 5F, FIG.
5G, FIG. 5H, FIG. 5I, FIG. 5J, FIG. 5K, FIG. 5L, FIG. 5M, FIG. 5N,
FIG. 5O, FIG. 5P, FIG. 5Q, FIG. 5R, FIG. 5S, FIG. 5T, FIG. 5U, FIG.
5W, FIG. 5V, FIG. 5X, FIG. 5Y, FIG. 5Z, and FIG. 5AA show gliadin
and glutenin sequences (SEQ ID NOS: 1-1554). In the "consensus"
column, letters in lower case use the standard one letter amino
acid code, but letters in upper case have a different meaning: E=[e
or q], F=[f or y or w], I=[i or l or v], S=[s or t], R[r or k or
h]. The "sequence" column uses the standard one letter amino acid
code.
[0062] FIG. 6A, FIG. 6B, FIG. 6C, and FIG. 6D show gluten peptides
that stimulate gamma interferon in PBMC collected 6 days after
gluten challenge in HLA-DQ2+ coeliac disease volunteers (SEQ ID
NOS: 1555-1655). The indicated 9mers are common to 200 groups of
bioactive "structurally" related 20mer peptides. The gluten
sequences are ranked according to the bioactivity.times.proportion
of subjects responding.
[0063] FIG. 7 (FIG. 7) shows the results of a wheat challenge
experiment (SEQ ID NOS: 1656-1671). These peptides gave high
quality responses (indicated `Y`) in ten subjects (A-J) after wheat
challenge.
[0064] FIG. 8 (FIG. 8) shows Avenin peptides (+/-deamidation by
tTG) that stimulate interferon-.gamma. in PBMC collected 6 days
after gluten challenge in HLA-DQ2+ coeliac disease volunteers (SEQ
ID NOS: 1672-1698). Those marked with a * are optimal unique 20mers
inducing IFN-.gamma. after oats challenge.
[0065] FIG. 9 (FIG. 9) shows the most potent 40 20mers (SEQ ID NOS:
1699-1763) in two HLA-DQ8 (not HLA-DQ2) subjects grouped according
to shared core sequences. The core sequence of group 6 (QGSFQPSQQ)
corresponds to the alpha-gliadin epitope described by van de Wal et
al (J. Immunol. 1998, 161(4):1585-1588). The maximum response in
Subject A was 271 SFC (medium alone, no peptide response: 4 SFC),
and in B it was 26 SFC (medium alone, no peptide response: 1
SFC).
[0066] FIG. 10 (FIG. 10) shows the amino acid sequence of A-gliadin
(SEQ ID NO: 1928) based on amino acid sequencing.
DETAILED DESCRIPTION OF THE INVENTION
[0067] The term "coeliac disease" encompasses a spectrum of
conditions caused by varying degrees of gluten sensitivity,
including a severe form characterised by a flat small intestinal
mucosa (hyperplastic villous atrophy) and other forms characterised
by milder symptoms.
[0068] The individual mentioned above (in the context of diagnosis
or therapy) is human. They may have coeliac disease (symptomatic or
asymptomatic) or be suspected of having it. They may be on a gluten
free diet. They may be in an acute phase response (for example they
may have coeliac disease, but have only ingested gluten in the last
24 hours before which they had been on a gluten free diet for 14 to
28 days).
[0069] The individual may be susceptible to coeliac disease, such
as a genetic susceptibility (determined for example by the
individual having relatives with coeliac disease or possessing
genes which cause predisposition to coeliac disease).
The Agent
[0070] The agent is typically a peptide, for example of length 7 to
50 amino acids, such as 10 to 40, 12 to 35 or 15 to 30 amino acids
in length.
[0071] The agent may be the peptide represented by any of SEQ ID
NOS: 1-1927 or an epitope comprising sequence that comprises any of
SEQ ID NOS: 1-1927 which is an isolated oligopeptide derived from a
gluten protein; or an equivalent of these sequences from a
naturally occurring gluten protein. In a further set of embodiments
of the invention, the agent is any peptide epitope of an oat gluten
(e.g. any T cell epitope of an avenin).
[0072] Preferably, the agent is the peptide represented by any of
SEQ ID NOS: 1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655,
1656-1671, 1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829,
1895-1903, 1906, and 1908-1927 or an epitope comprising sequence
that comprises any of SEQ ID NOS: 1578-1579, 1582-1583, 1587-1593,
1600-1620, 1623-1655, 1656-1671, 1672-1698, 1699-1763, 1764-1768,
1769-1786, 1787-1829, 1895-1903, 1906, and 1908-1927 which is an
isolated oligopeptide derived from a gluten protein; or an
equivalent of these sequences from a naturally occurring gluten
protein.
[0073] Thus the epitope may be a derivative of a naturally
occurring gluten protein, particularly from a wheat or oat gluten.
Such a derivative is typically a fragment of the gluten protein, or
a mutated derivative of the whole protein or fragment. Therefore
the epitope of the invention does not include the naturally
occurring whole gluten protein, and does not include other whole
naturally occurring gluten proteins.
[0074] Typically such fragments will be at least 7 amino acids in
length (e.g., at least 7, 8, 9, 10, 11, 12, 13, 14 or 15 amino
acids in length).
[0075] Typically such fragments will be recognised by T cells to at
least the same extent that the agents from which they are derived
are recognised in any of the assays described herein using samples
from coeliac disease patients.
[0076] The agent may be the peptide represented by any of SEQ ID
NOS: 1-1927, preferably the peptide represented by any of SEQ ID
NOS: 1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655,
1656-1671, 1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829,
1895-1903, 1906, and 1908-1927 or a protein comprising a sequence
corresponding to any of SEQ ID NOS: 1-1927, preferably comprising a
sequence corresponding to any of from SEQ ID NOS: 1578-1579,
1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671, 1672-1698,
1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903, 1906, and
1908-1927 (such as fragments of a gluten protein comprising any of
SEQ ID NOS: 1-1927 and preferably any of from SEQ ID NOS:
1578-1579, 1582-1583, 1587-1593, 1600-1620, 1623-1655, 1656-1671,
1672-1698, 1699-1763, 1764-1768, 1769-1786, 1787-1829, 1895-1903,
1906, and 1908-1927, for example after the gluten protein has been
treated with transglutaminase). Bioactive fragments of such
sequences are also agents of the invention. Typically such
fragments will be at least 7 amino acids in length (e.g., at least
7, 8, 9, 10, 11, 12, 13, 14 or 15 amino acids in length). Sequences
equivalent to any of SEQ ID NOS: 1-1927 or analogues of these
sequences are also agents of the invention.
[0077] In the case where the epitope comprises a sequence
equivalent to the above epitopes (including fragments) from another
gluten protein (e.g. any of the gluten proteins mentioned herein or
any gluten proteins which cause coeliac disease), such equivalent
sequences will correspond to a fragment of a gluten protein
typically treated (partially or fully) with transglutaminase. Such
equivalent peptides can be determined by aligning the sequences of
other gluten proteins with the gluten protein from which the
original epitope derives (for example using any of the programs
mentioned herein). Transglutaminase is commercially available (e.g.
Sigma T-5398).
[0078] The agent which is an analogue is capable of being
recognised by a TCR which recognises (i). Therefore generally when
the analogue is added to T cells in the presence of (i), typically
also in the presence of an antigen presenting cell (APC) (such as
any of the APCs mentioned herein), the analogue inhibits the
recognition of (i), i.e. the analogue is able to compete with (i)
in such a system.
[0079] The analogue may be one which is capable of binding the TCR
which recognises (i). Such binding can be tested by standard
techniques. Such TCRs can be isolated from T cells which have been
shown to recognise (i) (e.g. using the method of the invention).
Demonstration of the binding of the analogue to the TCRs can then
shown by determining whether the TCRs inhibit the binding of the
analogue to a substance that binds the analogue, e.g. an antibody
to the analogue. Typically the analogue is bound to a class II MHC
molecule (e.g. HLA-DQ2) in such an inhibition of binding assay.
[0080] Typically the analogue inhibits the binding of (i) to a TCR.
In this case the amount of (i) which can bind the TCR in the
presence of the analogue is decreased. This is because the analogue
is able to bind the TCR and therefore competes with (i) for binding
to the TCR.
[0081] T cells for use in the above binding experiments can be
isolated from patients with coeliac disease, for example with the
aid of the method of the invention. Other binding characteristics
of the analogue may also be the same as (i), and thus typically the
analogue binds to the same MHC class II molecule to which the
peptide binds (HLA-DQ2 or -DQ8). The analogue typically binds to
antibodies specific for (i), and thus inhibits binding of (i) to
such antibodies.
[0082] The analogue is typically a peptide. It may have homology
with (i), typically at least 70% homology, preferably at least 80,
90%, 95%, 97% or 99% homology with (i), for example over a region
of at least 7, 8, 9, 10, 11, 12, 13, 14, 15 or more (such as the
entire length of the analogue and/or (i), or across the region
which contacts the TCR or binds the MHC molecule) contiguous amino
acids. Methods of measuring protein homology are well known in the
art and it will be understood by those of skill in the art that in
the present context, homology is calculated on the basis of amino
acid identity (sometimes referred to as "hard homology").
[0083] For example the UWGCG Package provides the BESTFIT program
which can be used to calculate homology (for example used on its
default settings) (Devereux et al (1984) Nucleic Acids Research 12,
p 387-395). The PILEUP and BLAST algorithms can be used to
calculate homology or align sequences (typically on their default
settings), for example as described in Altschul S. F. (1993) J Mol
Evol 36:290-300; Altschul, S, F et al (1990) J Mol Biol
215:403-10.
[0084] Software for performing BLAST analyses is publicly available
through the National Center for Biotechnology Information on the
world wide web through the Internet at, for example,
"www.ncbi.nlm.nih.gov/". This algorithm involves first identifying
high scoring sequence pair (HSPs) by identifying short words of
length W in the query sequence that either match or satisfy some
positive-valued threshold score T when aligned with a word of the
same length in a database sequence. T is referred to as the
neighbourhood word score threshold (Altschul et al, supra). These
initial neighbourhood word hits act as seeds for initiating
searches to find HSPs containing them. The word hits are extended
in both directions along each sequence for as far as the cumulative
alignment score can be increased. Extensions for the word hits in
each direction are halted when: the cumulative alignment score
falls off by the quantity X from its maximum achieved value; the
cumulative score goes to zero or below, due to the accumulation of
one or more negative-scoring residue alignments; or the end of
either sequence is reached. The BLAST algorithm parameters W, T and
X determine the sensitivity and speed of the alignment. The BLAST
program uses as defaults a word length (W) of 11, the BLOSUM62
scoring matrix (see Henikoff and Henikoff (1992) Proc. Natl. Acad.
Sci. USA 89: 10915-10919) alignments (B) of 50, expectation (E) of
10, M=5, N=4, and a comparison of both strands.
[0085] The BLAST algorithm performs a statistical analysis of the
similarity between two sequences; see e.g., Karlin and Altschul
(1993) Proc. Natl. Acad. Sci. USA 90: 5873-5787. One measure of
similarity provided by the BLAST algorithm is the smallest sum
probability (P(N)), which provides an indication of the probability
by which a match between two nucleotide or amino acid sequences
would occur by chance. For example, a sequence is considered
similar to another sequence if the smallest sum probability in
comparison of the first sequence to the second sequence is less
than about 1, preferably less than about 0.1, more preferably less
than about 0.01, and most preferably less than about 0.001.
[0086] The homologous peptide analogues typically differ from (i)
by 1, 2, 3, 4, 5, 6, 7, 8 or more mutations (which may be
substitutions, deletions or insertions). These mutations may be
measured across any of the regions mentioned above in relation to
calculating homology. The substitutions are preferably
`conservative`. These are defined according to the following Table
Amino acids in the same block in the second column and preferably
in the same line in the third column may be substituted for each
other:
TABLE-US-00001 ALIPHATIC Non-polar G A P I L V Polar - uncharged C
S T M N Q Polar - charged D E K R AROMATIC H F W Y
[0087] Typically the amino acids in the analogue at the equivalent
positions to amino acids in (i) that contribute to binding the MHC
molecule or are responsible for the recognition by the TCR, are the
same or are conserved.
[0088] Typically the analogue peptide comprises one or more
modifications, which may be natural post-translation modifications
or artificial modifications. The modification may provide a
chemical moiety (typically by substitution of a hydrogen, e.g. of a
C--H bond), such as an amino, acetyl, hydroxy or halogen (e.g.
fluorine) group or carbohydrate group. Typically the modification
is present on the N or C terminus.
[0089] The analogue may comprise one or more non-natural amino
acids, for example amino acids with a side chain different from
natural amino acids. Generally, the non-natural amino acid will
have an N terminus and/or a C terminus. The non-natural amino acid
may be an L- or a D-amino acid.
[0090] The analogue typically has a shape, size, flexibility or
electronic configuration that is substantially similar to (i). It
is typically a derivative of (i). In one embodiment the analogue is
a fusion protein comprising the sequence of any of SEQ ID NOS:
1-1927 and non-gluten sequence. Preferably, the analogue according
to this embodiment is a fusion protein comprising the sequence of
any of SEQ ID NOs: 1578-1579, 1582-1583, 1587-1593, 1600-1620,
1623-1655, 1656-1671, 1672-1698, 1699-1763, 1764-1768, 1769-1786,
1787-1829, 1895-1903, 1906, and 1908-1927 and non-gluten
sequence
[0091] In one embodiment the analogue is or mimics (i) bound to a
MHC class II molecule. 2, 3, 4 or more of such complexes may be
associated or bound to each other, for example using a
biotin/streptavidin based system, in which typically 2, 3 or 4
biotin labelled MHC molecules bind to a streptavidin moiety. This
analogue typically inhibits the binding of the (i)/MHC Class II
complex to a TCR or antibody which is specific for the complex.
[0092] The analogue is typically an antibody or a fragment of an
antibody, such as a Fab or F(ab').sub.2 fragment. The analogue may
be immobilised on a solid support, particularly an analogue that
mimics peptide bound to a MHC molecule.
[0093] The analogue is typically designed by computational means
and then synthesised using methods known in the art. Alternatively
the analogue can be selected from a library of compounds. The
library may be a combinatorial library or a display library, such
as a phage display library. The library of compounds may be
expressed in the display library in the form of being bound to a
MHC class II molecule, such as HLA-DQ2 or -DQ8. Analogues are
generally selected from the library based on their ability to mimic
the binding characteristics (i). Thus they may be selected based on
ability to bind a TCR or antibody which recognises (i).
[0094] Typically analogues will be recognised by T cells to at
least the same extent as any of the agents (i), for example at
least to the same extent as the equivalent epitope is recognised in
any of the assays described herein, typically using T cells from
coeliac disease patients. Analogues may be recognised to these
extents in vivo and thus may be able to induce coeliac disease
symptoms to at least the same extent as any of the agents mentioned
herein (e.g. in a human patient or animal model).
[0095] Analogues may be identified in a method comprising
determining whether a candidate substance is recognised by a T cell
receptor that recognises an epitope of the invention, recognition
of the substance indicating that the substance is an analogue. Such
TCRs may be any of the TCRs mentioned herein, and may be present on
T cells. Any suitable assay mentioned herein can be used to
identify the analogue. In one embodiment this method is carried out
in vivo. As mentioned above preferred analogues are recognised to
at least the same extent as the equivalent epitope, and so the
method may be used to identify analogues which are recognised to
this extent.
[0096] In one embodiment the method comprises determining whether a
candidate substance is able to inhibit the recognition of an
epitope of the invention, inhibition of recognition indicating that
the substance is an analogue.
[0097] The agent may be a product comprising at least 2, 5, 10 or
20 agents as defined by (i) or (ii). Typically the composition
comprises epitopes of the invention (or equivalent analogues) from
different gluten proteins, such as any of the species or variety of
or types of gluten protein mentioned herein. Preferred compositions
comprise at least one epitope of the invention, or equivalent
analogue, from all of the glutens present in any of the species or
variety mentioned herein, or from 2, 3, 4 or more of the species
mentioned herein (such as from the panel of species consisting of
wheat, rye, barley, oats and triticale). Thus, the agent may be
monovalent or multivalent.
[0098] According to certain embodiments of the invention, the agent
does not have or is not based on a sequence disclosed in WO
02/083722 and/or WO 01/25793 and/or WO03/104273 and/or recited in
any of SEQ ID NOS: 1555-1577, 1580-1581, 1584-1586, 1594-1599,
1621-1622 and/or is not an agent derived from A-gliadin, the
sequence of which is given in FIG. 10.
[0099] Within SEQ ID NOs: 1-1927, a preferred subset is SEQ ID NOs:
1-1763. Within SEQ ID NOs: 1764-1927, preferred subsets are: (a)
oat sequences 1764-1768, (b) rye sequences 1769-1786, (c) barley
sequences 1787-1829, (d) wheat sequences 1895-1903, (e) wheat DQ8
sequences 1908-1927, and (f) combitope sequence 1906. Other
preferred subsets are: (a) 1764-1768, (b) 1769-1773, (c) 1774-1786,
(d) 1787-1792, (e) 1793-1829, (f) 1830-1894, (g) 1895-1903, (h)
1830-1903, (i) 1904-1906, (j) 1908-1916, (k) 1917-1927, and (l)
1908-1913, 1915-1923 and 1925-1927.
[0100] Within SEQ ID NOs: 1578-1579, 1582-1583, 1587-1593,
1600-1620, 1623-1655, 1656-1671, 1672-1698, 1699-1763, &
1764-1927, particularly preferred wheat epitopes are SEQ ID NOs:
1656-1671, 1830-1903, and 1907-1927.
[0101] Within SEQ ID NOs: 1830-1894 (Table 1), some sequences have
N-terminal and C-terminal glycines. The invention extends to these
sequences omitting the C-terminal glycine and/or the N-terminal
glycine. Preferably, both the C-terminal glycine and the N-terminal
glycine are omitted.
Diagnosis
[0102] As mentioned above the method of diagnosis of the invention
may be based on the detection of T cells that bind the agent or on
the detection of antibodies that recognise the agent.
[0103] The T cells that recognise the agent in the method (which
includes the use mentioned above) are generally T cells that have
been pre-sensitised in vivo to one or more gluten proteins. As
mentioned above such antigen-experienced T cells have been found to
be present in the peripheral blood.
[0104] In the method the T cells can be contacted with the agent in
vitro or in vivo, and determining whether the T cells recognise the
agent can be performed in vitro or in vivo. Thus the invention
provides the agent for use in a method of diagnosis practiced on
the human body. Different agents are provided for simultaneous,
separate or sequential use in such a method.
[0105] The in vitro method is typically carried out in aqueous
solution into which the agent is added. The solution will also
comprise the T cells (and in certain embodiments the APCs discussed
below). The term `contacting` as used herein includes adding the
particular substance to the solution.
[0106] Determination of whether the T cells recognise the agent is
generally accomplished by detecting a change in the state of the T
cells in the presence of the agent or determining whether the T
cells bind the agent. The change in state is generally caused by
antigen specific functional activity of the T cell after the TCR
binds the agent. The change of state may be measured inside (e.g.
change in intracellular expression of proteins) or outside (e.g.
detection of secreted substances) the T cells.
[0107] The change in state of the T cell may be the start of or
increase in secretion of a substance from the T cell, such as a
cytokine, especially IFN-.gamma., IL-2 or TNF-.alpha..
Determination of IFN-.gamma. secretion is particularly preferred.
The substance can typically be detected by allowing it to bind to a
specific binding agent and then measuring the presence of the
specific binding agent/substance complex. The specific binding
agent is typically an antibody, such as polyclonal or monoclonal
antibodies. Antibodies to cytokines are commercially available, or
can be made using standard techniques.
[0108] Typically the specific binding agent is immobilised on a
solid support. After the substance is allowed to bind the solid
support can optionally be washed to remove material which is not
specifically bound to the agent. The agent/substance complex may be
detected by using a second binding agent that will bind the
complex. Typically the second agent binds the substance at a site
which is different from the site which binds the first agent. The
second agent is preferably an antibody and is labelled directly or
indirectly by a detectable label.
[0109] Thus the second agent may be detected by a third agent that
is typically labelled directly or indirectly by a detectable label.
For example the second agent may comprise a biotin moiety, allowing
detection by a third agent which comprises a streptavidin moiety
and typically alkaline phosphatase as a detectable label.
[0110] In one embodiment the detection system which is used is the
ex-vivo ELISPOT assay described in WO 98/23960. In that assay
IFN-.gamma. secreted from the T cell is bound by a first
IFN-.gamma. specific antibody that is immobilised on a solid
support. The bound IFN-.gamma. is then detected using a second
IFN-.gamma. specific antibody which is labelled with a detectable
label. Such a labelled antibody can be obtained from MABTECH
(Stockholm, Sweden). Other detectable labels which can be used are
discussed below.
[0111] The change in state of the T cell that can be measured may
be the increase in the uptake of substances by the T cell, such as
the uptake of thymidine. The change in state may be an increase in
the size of the T cells, or proliferation of the T cells, or a
change in cell surface markers on the T cell.
[0112] In one embodiment the change of state is detected by
measuring the change in the intracellular expression of proteins,
for example the increase in intracellular expression of any of the
cytokines mentioned above. Such intracellular changes may be
detected by contacting the inside of the T cell with a moiety that
binds the expressed proteins in a specific manner and which allows
sorting of the T cells by flow cytometry.
[0113] In one embodiment when binding the TCR the agent is bound to
an MHC class II molecule (typically HLA-DQ2 or -DQ8), which is
typically present on the surface of an antigen presenting cell
(APC). However as mentioned herein other agents can bind a TCR
without the need to also bind an MHC molecule.
[0114] Generally the T cells which are contacted in the method are
taken from the individual in a blood sample, although other types
of samples which contain T cells can be used. The sample may be
added directly to the assay or may be processed first. Typically
the processing may comprise diluting of the sample, for example
with water or buffer. Typically the sample is diluted from 1.5 to
100 fold, for example 2 to 50 or 5 to 10 fold.
[0115] The processing may comprise separation of components of the
sample. Typically mononuclear cells (MCs) are separated from the
samples. The MCs will comprise the T cells and APCs. Thus in the
method the APCs present in the separated MCs can present the
peptide to the T cells. In another embodiment only T cells, such as
only CD4 T cells, can be purified from the sample. PBMCs, MCs and T
cells can be separated from the sample using techniques known in
the art, such as those described in Lalvani et al (1997) J. Exp.
Med. 186, p 859-865.
[0116] In one embodiment, the T cells used in the assay are in the
form of unprocessed or diluted samples, or are freshly isolated T
cells (such as in the form of freshly isolated MCs or PBMCs) which
are used directly ex vivo, i.e. they are not cultured before being
used in the method. Thus the T cells have not been restimulated in
an antigen specific manner in vitro. However the T cells can be
cultured before use, for example in the presence of one or more of
the agents, and generally also exogenous growth promoting
cytokines. During culturing the agent(s) are typically present on
the surface of APCs, such as the APC used in the method.
Pre-culturing of the T cells may lead to an increase in the
sensitivity of the method. Thus the T cells can be converted into
cell lines, such as short term cell lines (for example as described
in Ota et al (1990) Nature 346, p 183-187).
[0117] The APC that is typically present in the method may be from
the same individual as the T cell or from a different host. The APC
may be a naturally occurring APC or an artificial APC. The APC is a
cell that is capable of presenting the peptide to a T cell. It is
typically a B cell, dendritic cell or macrophage. It is typically
separated from the same sample as the T cell and is typically
co-purified with the T cell. Thus the APC may be present in MCs or
PBMCs. The APC is typically a freshly isolated ex vivo cell or a
cultured cell. It may be in the form of a cell line, such as a
short term or immortalised cell line. The APC may express empty MHC
class II molecules on its surface.
[0118] In the method one or more (different) agents may be used.
Typically the T cells derived from the sample can be placed into an
assay with all the agents which it is intended to test or the T
cells can be divided and placed into separate assays each of which
contain one or more of the agents.
[0119] The invention also provides the agents such as two or more
of any of the agents mentioned herein (e.g. the combinations of
agents which are present in the composition agent discussed above)
for simultaneous separate or sequential use (eg. for in vivo
use).
[0120] In one embodiment agent per se is added directly to an assay
comprising T cells and APCs. As discussed above the T cells and
APCs in such an assay could be in the form of MCs. When agents that
can be recognised by the T cell without the need for presentation
by APCs are used then APCs are not required. Analogues which mimic
the original (i) bound to a MHC molecule are an example of such an
agent.
[0121] In one embodiment the agent is provided to the APC in the
absence of the T cell. The APC is then provided to the T cell,
typically after being allowed to present the agent on its surface.
The peptide may have been taken up inside the APC and presented, or
simply be taken up onto the surface without entering inside the
APC.
[0122] The duration for which the agent is contacted with the T
cells will vary depending on the method used for determining
recognition of the peptide. Typically 10.sup.5 to 10.sup.7,
preferably 5.times.10.sup.5 to 10.sup.6 PBMCs are added to each
assay. In the case where agent is added directly to the assay its
concentration is from 10.sup.1 to 10.sup.3 m/ml, preferably 0.5 to
50 m/ml or 1 to 10 m/ml.
[0123] Typically the length of time for which the T cells are
incubated with the agent is from 4 to 24 hours, preferably 6 to 16
hours. When using ex vivo PBMCs it has been found that
0.3.times.10.sup.6 PBMCs can be incubated in 10 m/ml of peptide for
12 hours at 37.degree. C.
[0124] The determination of the recognition of the agent by the T
cells may be done by measuring the binding of the agent to the T
cells (this can be carried out using any suitable binding assay
format discussed herein). Typically T cells which bind the agent
can be sorted based on this binding, for example using a FACS
machine. The presence of T cells that recognise the agent will be
deemed to occur if the frequency of cells sorted using the agent is
above a "control" value. The frequency of antigen-experienced T
cells is generally 1 in 10.sup.6 to 1 in 10.sup.3, and therefore
whether or not the sorted cells are antigen-experienced T cells can
be determined.
[0125] The determination of the recognition of the agent by the T
cells may be measured in vivo. Typically the agent is administered
to the host and then a response which indicates recognition of the
agent may be measured. The agent is typically administered
intradermally or epidermally. The agent is typically administered
by contacting with the outside of the skin, and may be retained at
the site with the aid of a plaster or dressing. Alternatively the
agent may be administered by needle, such as by injection, but can
also be administered by other methods such as ballistics (e.g. the
ballistics techniques which have been used to deliver nucleic
acids). EP-A-0693119 describes techniques that can typically be
used to administer the agent. Typically from 0.001 to 1000 .mu.g,
for example from 0.01 to 100 .mu.g or 0.1 to 10 .mu.g of agent is
administered.
[0126] In one embodiment a product can be administered which is
capable of providing the agent in vivo. Thus a polynucleotide
capable of expressing the agent can be administered, typically in
any of the ways described above for the administration of the
agent. The polynucleotide typically has any of the characteristics
of the polynucleotide provided by the invention which is discussed
below. The agent is expressed from the polynucleotide in vivo.
Typically from 0.001 to 1000 .mu.g, for example from 0.01 to 100
.mu.g or 0.1 to 10 .mu.g of polynucleotide is administered.
[0127] Recognition of the agent administered to the skin is
typically indicated by the occurrence of inflammation (e.g.
induration, erythema or oedema) at the site of administration. This
is generally measured by visual examination of the site.
[0128] The method of diagnosis based on the detection of an
antibody that binds the agent is typically carried out by
contacting a sample from the individual (such as any of the samples
mentioned here, optionally processed in any manner mentioned
herein) with the agent and determining whether an antibody in the
sample binds the agent, such a binding indicating that the
individual has, or is susceptible to coeliac disease. Any suitable
format of binding assay may be used, such as any such format
mentioned herein.
Therapy
[0129] The identification of the immunodominant epitope and other
epitopes described herein allows therapeutic products to be made
which target the T cells which recognise this epitope (such T cells
being ones which participate in the immune response against gluten
proteins). These findings also allow the prevention or treatment of
coeliac disease by suppressing (by tolerisation) an antibody or T
cell response to the epitope(s).
[0130] Certain agents of the invention bind the TCR that recognises
the epitope of the invention (as measured using any of the binding
assays discussed above) and cause tolerisation of the T cell that
carries the TCR. Such agents, optionally in association with a
carrier, can therefore be used to prevent or treat coeliac
disease.
[0131] Generally tolerisation can be caused by the same peptides
which can (after being recognised by the TCR) cause antigen
specific functional activity of the T cell (such as any such
activity mentioned herein, e.g. secretion of cytokines). Such
agents cause tolerisation when they are presented to the immune
system in a `tolerising` context.
[0132] Tolerisation leads to a decrease in the recognition of a T
cell or antibody epitope by the immune system. In the case of a T
cell epitope this can be caused by the deletion or anergising of T
cells that recognise the epitope. Thus T cell activity (for example
as measured in suitable assays mentioned herein) in response to the
epitope is decreased. Tolerisation of an antibody response means
that a decreased amount of specific antibody to the epitope is
produced when the epitope is administered.
[0133] Methods of presenting antigens to the immune system in such
a context are known and are described for example in Yoshida et al.
Clin. Immunol. Immunopathol. 82, 207-215 (1997), Thurau et al.
Clin. Exp. Immunol. 109, 370-6 (1997), and Weiner et al. Res.
Immunol. 148, 528-33 (1997). In particular certain routes of
administration can cause tolerisation, such as oral, nasal or
intraperitoneal. Tolerisation may also be accomplished via
dendritic cells and tetramers presenting peptide. Particular
products which cause tolerisation may be administered (e.g. in a
composition that also comprises the agent) to the individual. Such
products include cytokines, such as cytokines that favour a Th2
response (e.g. IL-4, TGF-.beta. or IL-10). Products or agent may be
administered at a dose that causes tolerisation.
[0134] The invention provides a protein that comprises a sequence
able to act as an antagonist of the T cell (which T cell recognises
the agent). Such proteins and such antagonists can also be used to
prevent or treat coeliac disease. The antagonist will cause a
decrease in the T cell response. In one embodiment, the antagonist
binds the TCR of the T cell (generally in the form of a complex
with HLA-DQ2 or -DQ8) but instead of causing normal functional
activation causing an abnormal signal to be passed through the TCR
intracellular signalling cascade, which causes the T cell to have
decreased function activity (e.g. in response to recognition of an
epitope, typically as measured by any suitable assay mentioned
herein).
[0135] In one embodiment the antagonist competes with epitope to
bind a component of MHC processing and presentation pathway, such
as an MHC molecule (typically HLA-DQ2 or -DQ8). Thus the antagonist
may bind HLA-DQ2 or -DQ8 (and thus be a peptide presented by this
MHC molecule) or a homologue thereof.
[0136] Methods of causing antagonism are known in the art. In one
embodiment the antagonist is a homologue of the epitopes mentioned
above and may have any of the sequence, binding or other properties
of the agent (particularly analogues). The antagonists typically
differ from any of the above epitopes (which are capable of causing
a normal antigen specific function in the T cell) by 1, 2, 3, 4 or
more mutations (each of which may be a substitution, insertion or
deletion). Such antagonists are termed "altered peptide ligands" or
"APL" in the art. The mutations are typically at the amino acid
positions that contact the TCR.
[0137] For example, the antagonist may differ from the epitope by a
substitution within the sequence that is equivalent to the sequence
represented by amino acids 64 to 67 of A-gliadin (the sequence of
A-gliadin is given in FIG. 10). Thus preferably the antagonist has
a substitution at the equivalent of position 64, 65 or 67.
Preferably the substitution is 64W, 67W, 67M or 65T.
[0138] Since the T cell immune response to the epitope of the
invention in an individual is polyclonal, more than one antagonist
may need to be administered to cause antagonism of T cells of the
response which have different TCRs. Therefore the antagonists may
be administered in a composition which comprises at least 2, 4, 6
or more different antagonists, which each antagonise different T
cells.
[0139] The invention also provides a method of identifying an
antagonist of a T cell (which recognises the agent), comprising
contacting a candidate substance with the T cell and detecting
whether the substance causes a decrease in the ability of the T
cell to undergo an antigen specific response (e.g. using any
suitable assay mentioned herein), the detecting of any such
decrease in said ability indicating that the substance is an
antagonist.
[0140] In one embodiment, the antagonists (including combinations
of antagonists to a particular epitope) or tolerising (T cell and
antibody tolerising) agents are present in a composition comprising
at least 2, 4, 6 or more antagonists or agents which antagonise or
tolerise to different epitopes of the invention, for example to the
combinations of epitopes discussed above in relation to the agents
which are a product comprising more than one substance.
Testing Whether a Composition is Capable of Causing Coeliac
Disease
[0141] As mentioned above the invention provides a method of
determining whether a composition is capable of causing coeliac
disease comprising detecting the presence of a protein sequence
which is capable of being modified by a transglutaminase to as
sequence comprising the agent or epitope of the invention (such
transglutaminase activity may be a human intestinal
transglutaminase activity). Typically this is performed by using a
binding assay in which a moiety which binds to the sequence in a
specific manner is contacted with the composition and the formation
of sequence/moiety complex is detected and used to ascertain the
presence of the agent. Such a moiety may be any suitable substance
(or type of substance) mentioned herein, and is typically a
specific antibody. Any suitable format of binding assay can be used
(such as those mentioned herein).
[0142] In one embodiment, the composition is contacted with at
least 2, 5, 10 or more antibodies which are specific for epitopes
of the invention from different gluten proteins, for example a
panel of antibodies capable of recognising the combinations of
epitopes discussed above in relation to agents of the invention
which are a product comprising more than one substance.
[0143] The composition typically comprises material from a plant
that expresses a gluten protein which is capable of causing coeliac
disease (for example any of the gluten proteins or plants mentioned
herein). Such material may be a plant part, such as a harvested
product (e.g. seed). The material may be processed products of the
plant material (e.g. any such product mentioned herein), such as a
flour or food that comprises the gluten protein. The processing of
food material and testing in suitable binding assays is routine,
for example as mentioned in Kricka L J, J. Biolumin Chemilumin 13,
189-93 (1998).
Binding Assays
[0144] The determination of binding between any two substances
mentioned herein may be done by measuring a characteristic of
either or both substances that changes upon binding, such as a
spectroscopic change.
[0145] The binding assay format may be a `band shift` system. This
involves determining whether the presence of one substance (such as
a candidate substance) advances or retards the progress of the
other substance during gel electrophoresis.
[0146] The format may be a competitive binding method which
determines whether the one substance is able to inhibit the binding
of the other substance to an agent which is known to bind the other
substance, such as a specific antibody.
Mutant Gluten Proteins
[0147] The invention provides a gluten protein in which an epitope
sequence of the invention, or sequence which can be modified by a
transglutaminase to provide such a sequence has been mutated so
that it no longer causes, or is recognised by, a T cell response
that recognises the epitope. In this context the term recognition
refers to the TCR binding the epitope in such a way that normal
(not antagonistic) antigen-specific functional activity of the T
cell occurs.
[0148] Methods of identifying equivalent epitopes in other gluten
proteins are discussed above. The wild type of the mutated gluten
protein is one which causes coeliac disease. Such a mutated gluten
protein may have homology with the wild type of the mutated gluten
protein, for example to the degree mentioned above (in relation to
the analogue) across all of its sequence or across 15, 30, 60, 100
or 200 contiguous amino acids of its sequence. The sequences of
other natural gluten proteins are known in the art.
[0149] The mutated gluten protein will not cause coeliac disease or
will cause decreased symptoms of coeliac disease. Typically the
mutation decreases the ability of the epitope to induce a T cell
response. The mutated epitope may have a decreased binding to
HLA-DQ2 or -DQ8, a decreased ability to be presented by an APC or a
decreased ability to bind to or to be recognised (i.e. cause
antigen-specific functional activity) by T cells that recognise the
agent. The mutated gluten protein or epitope will therefore show no
or reduced recognition in any of the assays mentioned herein in
relation to the diagnostic aspects of the invention.
[0150] The mutation may be one or more deletions, additions or
substitutions of length 1 to 3, 4 to 6, 6 to 10, 11 to 15 or more
in the epitope, for example across any of SEQ ID NOS: 1-1927; or
across equivalents thereof. Preferably the mutant gluten protein
has at least one mutation in the sequence of any of SEQ ID NO:
1-1927. A preferred mutation is at the position equivalent to
position 65 in A-gliadin (see FIG. 10). Preferably, a naturally
occurring glutamine is substituted to histidine, tyrosine,
tryptophan, lysine, proline, or arginine.
[0151] The invention thus also provides use of a mutation (such any
of the mutations in any of the sequences discussed herein) in an
epitope of a gluten protein, which epitope is an epitope of the
invention, to decrease the ability of the gluten protein to cause
coeliac disease.
[0152] In one embodiment the mutated sequence is able to act as an
antagonist. Thus the invention provides a protein that comprises a
sequence which is able to bind to a T cell receptor, which T cell
receptor recognises an agent of the invention, and which sequence
is able to cause antagonism of a T cell that carries such a T cell
receptor.
[0153] The invention also provides proteins which are fragments of
the above mutant gluten proteins, which are at least 7 amino acids
long (e.g. at least 8, 9, 10, 11, 12, 13, 14, 15, 30, 60, 100, 150,
200, or 250 amino acids long) and which comprise the mutations
discussed above which decrease the ability of the gluten protein to
be recognised. Any of the mutant proteins (including fragments)
mentioned herein may also be present in the form of fusion
proteins, for example with other gluten proteins or with non-gluten
proteins.
[0154] The equivalent wild type protein to the mutated gluten
protein is typically from a graminaceous monocotyledon, such as a
plant of a genus selected from Triticum, Secale, Hordeum, Triticale
or Avena, (e.g. wheat, rye, barley, oats or triticale). For
example, the protein may be an a, .alpha..beta., .beta., .gamma. or
.omega. gliadin or an avenin.
Kits
[0155] The invention also provides a kit for carrying out the
method comprising one or more agents and optionally a means to
detect the recognition of the agent by the T cell. Typically the
different agents are provided for simultaneous, separate or
sequential use. Typically the means to detect recognition allows or
aids detection based on the techniques discussed above.
[0156] Thus the means may allow detection of a substance secreted
by the T cells after recognition. The kit may thus additionally
include a specific binding moiety for the substance, such as an
antibody. The moiety is typically specific for IFN-.gamma.. The
moiety is typically immobilised on a solid support. This means that
after binding the moiety the substance will remain in the vicinity
of the T cell which secreted it. Thus "spots" of substance/moiety
complex are formed on the support, each spot representing a T cell
which is secreting the substance. Quantifying the spots, and
typically comparing against a control, allows determination of
recognition of the agent.
[0157] The kit may also comprise a means to detect the
substance/moiety complex. A detectable change may occur in the
moiety itself after binding the substance, such as a colour change.
Alternatively a second moiety directly or indirectly labelled for
detection may be allowed to bind the substance/moiety complex to
allow the determination of the spots. As discussed above the second
moiety may be specific for the substance, but binds a different
site on the substance than the first moiety.
[0158] The immobilised support may be a plate with wells, such as a
microtitre plate. Each assay can therefore be carried out in a
separate well in the plate.
[0159] The kit may additionally comprise medium for the T cells,
detection moieties or washing buffers to be used in the detection
steps. The kit may additionally comprise reagents suitable for the
separation from the sample, such as the separation of PBMCs or T
cells from the sample. The kit may be designed to allow detection
of the T cells directly in the sample without requiring any
separation of the components of the sample.
[0160] The kit may comprise an instrument which allows
administration of the agent, such as intradermal or epidermal
administration. Typically such an instrument comprises plaster,
dressing or one or more needles. The instrument may allow ballistic
delivery of the agent. The agent in the kit may be in the form of a
pharmaceutical composition.
[0161] The kit may also comprise controls, such as positive or
negative controls. The positive control may allow the detection
system to be tested. Thus the positive control typically mimics
recognition of the agent in any of the above methods. Typically in
the kits designed to determine recognition in vitro the positive
control is a cytokine. In the kit designed to detect in vivo
recognition of the agent the positive control may be antigen to
which most individuals should response.
[0162] The kit may also comprise a means to take a sample
containing T cells from the host, such as a blood sample. The kit
may comprise a means to separate mononuclear cells or T cells from
a sample from the host.
Polynucleotides, Cells, Transgenic Mammals and Antibodies
[0163] The invention also provides a polynucleotide which is
capable of expression to provide the agent or mutant gluten
proteins. Typically the polynucleotide is DNA or RNA, and is single
or double stranded. The polynucleotide will preferably comprise at
least 50 bases or base pairs, for example 50 to 100, 100 to 500,
500 to 1000 or 1000 to 2000 or more bases or base pairs. The
polynucleotide therefore comprises a sequence which encodes the
sequence of any of SEQ ID NO: 1-1927 or any of the other agents
mentioned herein. To the 5' and 3' of this coding sequence the
polynucleotide of the invention has sequence or codons which are
different from the sequence or codons 5' and 3' to these sequences
in the corresponding gluten protein gene.
[0164] 5' and/or 3' to the sequence encoding the peptide the
polynucleotide has coding or non-coding sequence. Sequence 5'
and/or 3' to the coding sequence may comprise sequences which aid
expression, such as transcription and/or translation, of the
sequence encoding the agent. The polynucleotide may be capable of
expressing the agent prokaryotic or eukaryotic cell. In one
embodiment the polynucleotide is capable of expressing the agent in
a mammalian cell, such as a human, primate or rodent (e.g. mouse or
rat) cell.
[0165] A polynucleotide of the invention may hybridise selectively
to a polynucleotide that encodes a gluten protein from which the
agent is derived at a level significantly above background.
Selective hybridisation is typically achieved using conditions of
medium to high stringency (for example 0.03M sodium chloride and
0.03M sodium citrate at from about 50.degree. C. to about
60.degree. C.). However, such hybridisation may be carried out
under any suitable conditions known in the art (see Sambrook et al
(1989), Molecular Cloning: A Laboratory Manual). For example, if
high stringency is required, suitable conditions include
0.2.times.SSC at 60.degree. C. If lower stringency is required,
suitable conditions include 2.times.SSC at 60.degree. C.
[0166] Agents or proteins of the invention may be encoded by the
polynucleotides described herein.
[0167] The polynucleotide may form or be incorporated into a
replicable vector. Such a vector is able to replicate in a suitable
cell. The vector may be an expression vector. In such a vector the
polynucleotide of the invention is operably linked to a control
sequence which is capable of providing for the expression of the
polynucleotide. The vector may contain a selectable marker, such as
the ampicillin resistance gene.
[0168] The polynucleotide or vector may be present in a cell. Such
a cell may have been transformed by the polynucleotide or vector.
The cell may express the agent. The cell will be chosen to be
compatible with the said vector and may for example be a
prokaryotic (bacterial), yeast, insect or mammalian cell. The
polynucleotide or vector may be introduced into host cells using
conventional techniques including calcium phosphate precipitation,
DEAE-dextran transfection, or electroporation.
[0169] The invention provides processes for the production of the
proteins of the invention by recombinant means. This may comprise
(a) cultivating a transformed cell as defined above under
conditions that allow the expression of the protein; and preferably
(b) recovering the expressed polypeptide. Optionally, the
polypeptide may be isolated and/or purified, by techniques known in
the art.
[0170] The invention also provides TCRs which recognise (or bind)
the agent, or fragments thereof which are capable of such
recognition (or binding). These can be present in the any form
mentioned herein (e.g. purity) discussed herein in relation to the
protein of the invention. The invention also provides T cells which
express such TCRs which can be present in any form (e.g. purity)
discussed herein for the cells of the invention.
[0171] The invention also provides monoclonal or polyclonal
antibodies which specifically recognise the agents (such as any of
the epitopes of the invention) and which recognise the mutant
gluten proteins (and typically which do not recognise the
equivalent wild-type gluten proteins) of the invention, and methods
of making such antibodies. Antibodies of the invention bind
specifically to these substances of the invention.
[0172] For the purposes of this invention, the term "antibody"
includes antibody fragments such as Fv, F(ab) and F(ab').sub.2
fragments, as well as single-chain antibodies.
[0173] A method for producing a polyclonal antibody comprises
immunising a suitable host animal, for example an experimental
animal, with the immunogen and isolating immunoglobulins from the
serum. The animal may therefore be inoculated with the immunogen,
blood subsequently removed from the animal and the IgG fraction
purified. A method for producing a monoclonal antibody comprises
immortalising cells which produce the desired antibody. Hybridoma
cells may be produced by fusing spleen cells from an inoculated
experimental animal with tumour cells (Kohler and Milstein (1975)
Nature 256, 495-497).
[0174] An immortalized cell producing the desired antibody may be
selected by a conventional procedure. The hybridomas may be grown
in culture or injected intraperitoneally for formation of ascites
fluid or into the blood stream of an allogenic host or
immunocompromised host. Human antibody may be prepared by in vitro
immunisation of human lymphocytes, followed by transformation of
the lymphocytes with Epstein-Barr virus.
[0175] For the production of both monoclonal and polyclonal
antibodies, the experimental animal is suitably a goat, rabbit, rat
or mouse. If desired, the immunogen may be administered as a
conjugate in which the immunogen is coupled, for example via a side
chain of one of the amino acid residues, to a suitable carrier. The
carrier molecule is typically a physiologically acceptable carrier.
The antibody obtained may be isolated and, if desired,
purified.
[0176] The polynucleotide, agent, protein or antibody of the
invention, may carry a detectable label. Detectable labels which
allow detection of the secreted substance by visual inspection,
optionally with the aid of an optical magnifying means, are
preferred. Such a system is typically based on an enzyme label
which causes colour change in a substrate, for example alkaline
phosphatase causing a colour change in a substrate. Such substrates
are commercially available, e.g. from BioRad. Other suitable labels
include other enzymes such as peroxidase, or protein labels, such
as biotin; or radioisotopes, such as .sup.32P or .sup.35S. The
above labels may be detected using known techniques.
[0177] Polynucleotides, agents, proteins, antibodies or cells of
the invention may be in substantially purified form. They may be in
substantially isolated form, in which case they will generally
comprise at least 80% e.g. at least 90, 95, 97 or 99% of the
polynucleotide, peptide, antibody, cells or dry mass in the
preparation. The polynucleotide, agent, protein or antibody is
typically substantially free of other cellular components. The
polynucleotide, agent, protein or antibody may be used in such a
substantially isolated, purified or free form in the method or be
present in such forms in the kit.
[0178] The invention also provides a transgenic non-human mammal
which expresses a TCR of the invention. This may be any of the
mammals discussed herein (e.g. in relation to the production of the
antibody). Preferably the mammal has, or is susceptible, to coeliac
disease. The mammal may also express HLA-DQ2 or -DQ8 or HLA-DR3-DQ2
and/or may be given a diet comprising a gluten protein which causes
coeliac disease (e.g. any of the gluten proteins mentioned herein).
Thus the mammal may act as an animal model for coeliac disease.
[0179] The invention also provides a method of identifying a
product which is therapeutic for coeliac disease comprising
administering a candidate substance to a mammal of the invention
which has, or which is susceptible to, coeliac disease and
determining whether substance prevents or treats coeliac disease in
the mammal, the prevention or treatment of coeliac disease
indicating that the substance is a therapeutic product. Such a
product may be used to treat or prevent coeliac disease.
[0180] The invention provides therapeutic (including prophylactic)
agents or diagnostic substances (the agents, proteins and
polynucleotides of the invention). These substances are formulated
for clinical administration by mixing them with a pharmaceutically
acceptable carrier or diluent. For example they can be formulated
for topical, parenteral, intravenous, intramuscular, subcutaneous,
intraocular, intradermal, epidermal or transdermal administration.
The substances may be mixed with any vehicle which is
pharmaceutically acceptable and appropriate for the desired route
of administration. The pharmaceutically carrier or diluent for
injection may be, for example, a sterile or isotonic solution such
as Water for Injection or physiological saline, or a carrier
particle for ballistic delivery.
[0181] The dose of the substances may be adjusted according to
various parameters, especially according to the agent used; the
age, weight and condition of the patient to be treated; the mode of
administration used; the severity of the condition to be treated;
and the required clinical regimen. As a guide, the amount of
substance administered by injection is suitably from 0.01 mg/kg to
30 mg/kg, preferably from 0.1 mg/kg to 10 mg/kg.
[0182] The routes of administration and dosages described are
intended only as a guide since a skilled practitioner will be able
to determine readily the optimum route of administration and dosage
for any particular patient and condition.
[0183] The substances of the invention may thus be used in a method
of treatment of the human or animal body, or in a diagnostic method
practised on the human body. In particular they may be used in a
method of treating or preventing coeliac disease. The invention
also provide the agents for use in a method of manufacture of a
medicament for treating or preventing coeliac disease. Thus the
invention provides a method of preventing or treating coeliac
disease comprising administering to a human in need thereof a
substance of the invention (typically a non-toxic effective amount
thereof).
[0184] The agent of the invention can be made using standard
synthetic chemistry techniques, such as by use of an automated
synthesizer. The agent may be made from a longer polypeptide e.g. a
fusion protein, which polypeptide typically comprises the sequence
of the peptide. The peptide may be derived from the polypeptide by
for example hydrolysing the polypeptide, such as using a protease;
or by physically breaking the polypeptide. The polynucleotide of
the invention can be made using standard techniques, such as by
using a synthesiser.
Plant Cells and Plants that Express Mutant Gluten Proteins or
Express Proteins Comprising Sequences which can Act as
Antagonists
[0185] The cell of the invention may be a plant cell, such as a
cell of a graminaceous monocotyledonous species. The species may be
one whose wild-type form expresses gluten proteins, such as any of
the gluten proteins mentioned herein. Such a gluten protein may
cause coeliac disease in humans. The cell may be of wheat, maize,
oats, rye, rice, barley, triticale, sorghum, or sugar cane.
Typically the cell is of the Triticum genus, such as aestivum,
spelta, polonicum or monococcum.
[0186] The plant cell of the invention is typically one which does
not express one or more wild-type gluten proteins (such as any of
the gluten proteins mentioned herein which may cause coeliac
disease), or one which does not express one or more gluten proteins
comprising a sequence that can be recognised by a T cell that
recognises the agent. Thus if the wild-type plant cell did express
such a gluten protein then it may be engineered to prevent or
reduce the expression of such a gluten protein or to change the
amino acid sequence of the gluten protein so that it no longer
causes coeliac disease (typically by no longer expressing the
epitope of the invention).
[0187] This can be done for example by introducing mutations into
1, 2, 3 or more or all of such gluten protein genes in the cell,
for example into coding or non-coding (e.g. promoter regions). Such
mutations can be any of the type or length of mutations discussed
herein (e.g., in relation to homologous proteins). The mutations
can be introduced in a directed manner (e.g., using site directed
mutagenesis or homologous recombination techniques) or in a random
manner (e.g. using a mutagen, and then typically selecting for
mutagenised cells which no longer express the gluten protein (or a
gluten protein sequence which causes coeliac disease)).
[0188] In the case of plants or plant cells that express a protein
that comprises a sequence able to act as an antagonist such a plant
or plant cell may express a wild-type gluten protein (e.g. one
which causes coeliac disease). Preferably though the presence of
the antagonist sequence will cause reduced coeliac disease symptoms
(such as no symptoms) in an individual who ingests a food
comprising protein from the plant or plant cell.
[0189] The polynucleotide which is present in (or which was
transformed into) the plant cell will generally comprise promoter
capable of expressing the mutant gluten protein the plant cell.
Depending on the pattern of expression desired, the promoter may be
constitutive, tissue- or stage-specific; and/or inducible. For
example, strong constitutive expression in plants can be obtained
with the CAMV 35S, Rubisco ssu, or histone promoters. Also,
tissue-specific or stage-specific promoters may be used to target
expression of protein of the invention to particular tissues in a
transgenic plant or to particular stages in its development. Thus,
for example seed-specific, root-specific, leaf-specific,
flower-specific etc promoters may be used. Seed-specific promoters
include those described by Dalta et al (Biotechnology Ann. Rev.
(1997), 3, pp. 269-296). Particular examples of seed-specific
promoters are napin promoters (EP-A-0 255, 378), phaseolin
promoters, glutenine promoters, helianthenine promoters
(WO92/17580), albumin promoters (WO98/45460), oleosin promoters
(WO98/45461) and ATS1 and ATS3 promoters (WO99/20775).
[0190] The cell may be in any form. For example, it may be an
isolated cell, e.g. a protoplast, or it may be part of a plant
tissue, e.g. a callus, or a tissue excised from a plant, or it may
be part of a whole plant. The cell may be of any type (e.g. of any
type of plant part). For example, an undifferentiated cell, such as
a callus cell; or a differentiated cell, such as a cell of a type
found in embryos, pollen, roots, shoots or leaves. Plant parts
include roots; shoots; leaves; and parts involved in reproduction,
such as pollen, ova, stamens, anthers, petals, sepals and other
flower parts.
[0191] The invention provides a method of obtaining a transgenic
plant cell comprising transforming a plant cell with a
polynucleotide or vector of the invention to give a transgenic
plant cell. Any suitable transformation method may be used (in the
case of wheat the techniques disclosed in Vasil V et al,
Biotechnology 10, 667-674 (1992) may be used). Preferred
transformation techniques include electroporation of plant
protoplasts and particle bombardment. Transformation may thus give
rise to a chimeric tissue or plant in which some cells are
transgenic and some are not.
[0192] The cell of the invention or thus obtained cell may be
regenerated into a transgenic plant by techniques known in the art.
These may involve the use of plant growth substances such as
auxins, giberellins and/or cytokinins to stimulate the growth
and/or division of the transgenic cell. Similarly, techniques such
as somatic embryogenesis and meristem culture may be used.
Regeneration techniques are well known in the art and examples can
be found in, e.g. U.S. Pat. No. 4,459,355, U.S. Pat. No. 4,536,475,
U.S. Pat. No. 5,464,763, U.S. Pat. No. 5,177,010, U.S. Pat. No.
5,187,073, EP 267,159, EP 604, 662, EP 672, 752, U.S. Pat. No.
4,945,050, U.S. Pat. No. 5,036,006, U.S. Pat. No. 5,100,792, U.S.
Pat. No. 5,371,014, U.S. Pat. No. 5,478,744, U.S. Pat. No.
5,179,022, U.S. Pat. No. 5,565,346, U.S. Pat. No. 5,484,956, U.S.
Pat. No. 5,508,468, U.S. Pat. No. 5,538,877, U.S. Pat. No.
5,554,798, U.S. Pat. No. 5,489,520, U.S. Pat. No. 5,510,318, U.S.
Pat. No. 5,204,253, U.S. Pat. No. 5,405,765, EP 442,174, EP
486,233, EP 486,234, EP 539,563, EP 674,725, WO91/02071 and WO
95/06128.
[0193] In many such techniques, one step is the formation of a
callus, i.e. a plant tissue comprising expanding and/or dividing
cells. Such calli are a further aspect of the invention as are
other types of plant cell cultures and plant parts. Thus, for
example, the invention provides transgenic plant tissues and parts,
including embryos, meristems, seeds, shoots, roots, stems, leaves
and flower parts. These may be chimeric in the sense that some of
their cells are cells of the invention and some are not. Transgenic
plant parts and tissues, plants and seeds of the invention may be
of any of the plant species mentioned herein.
[0194] Regeneration procedures will typically involve the selection
of transformed cells by means of marker genes.
[0195] The regeneration step gives rise to a first generation
transgenic plant. The invention also provides methods of obtaining
transgenic plants of further generations from this first generation
plant. These are known as progeny transgenic plants. Progeny plants
of second, third, fourth, fifth, sixth and further generations may
be obtained from the first generation transgenic plant by any means
known in the art.
[0196] Thus, the invention provides a method of obtaining a
transgenic progeny plant comprising obtaining a second-generation
transgenic progeny plant from a first-generation transgenic plant
of the invention, and optionally obtaining transgenic plants of one
or more further generations from the second-generation progeny
plant thus obtained.
[0197] Progeny plants may be produced from their predecessors of
earlier generations by any known technique. In particular, progeny
plants may be produced by: (a) obtaining a transgenic seed from a
transgenic plant of the invention belonging to a previous
generation, then obtaining a transgenic progeny plant of the
invention belonging to a new generation by growing up the
transgenic seed; and/or (b) propagating clonally a transgenic plant
of the invention belonging to a previous generation to give a
transgenic progeny plant of the invention belonging to a new
generation; and/or (c) crossing a first-generation transgenic plant
of the invention belonging to a previous generation with another
compatible plant to give a transgenic progeny plant of the
invention belonging to a new generation; and optionally (d)
obtaining transgenic progeny plants of one or more further
generations from the progeny plant thus obtained.
[0198] These techniques may be used in any combination. For
example, clonal propagation and sexual propagation may be used at
different points in a process that gives rise to a transgenic plant
suitable for cultivation. In particular, repetitive back-crossing
with a plant taxon with agronomically desirable characteristics may
be undertaken. Further steps of removing cells from a plant and
regenerating new plants therefrom may also be carried out.
[0199] Also, further desirable characteristics may be introduced by
transforming the cells, plant tissues, plants or seeds, at any
suitable stage in the above process, to introduce desirable coding
sequences other than the polynucleotides of the invention. This may
be carried out by the techniques described herein for the
introduction of polynucleotides of the invention.
[0200] For example, further transgenes may be selected from those
coding for other herbicide resistance traits, e.g. tolerance to:
Glyphosate (e.g. using an EPSP synthase gene (e.g. EP-A-0,293,358)
or a glyphosate oxidoreductase (WO 92/00377) gene); or tolerance to
fosametin; a dihalobenzonitrile; glufosinate, e.g. using a
phosphinothrycin acetyl transferase (PAT) or glutamine synthase
gene (cf. EP-A-0,242,236); asulam, e.g. using a dihydropteroate
synthase gene (EP-A-0,369,367); or a sulphonylurea, e.g. using an
ALS gene); diphenyl ethers such as acifluorfen or oxyfluorfen, e.g.
using a protoporphyrogen oxidase gene); an oxadiazole such as
oxadiazon; a cyclic imide such as chlorophthalim; a phenyl pyrazole
such as TNP, or a phenopylate or carbamate analogue thereof.
[0201] Similarly, genes for beneficial properties other than
herbicide tolerance may be introduced. For example, genes for
insect resistance may be introduced, notably genes encoding
Bacillus thuringiensis (Bt) toxins. Likewise, genes for disease
resistance may be introduced, e.g. as in WO91/02701 or
WO95/06128.
[0202] Typically, a protein of the invention is expressed in a
plant of the invention. Depending on the promoter used, this
expression may be constitutive or inducible. Similarly, it may be
tissue- or stage-specific, i.e. directed towards a particular plant
tissue (such as any of the tissues mentioned herein) or stage in
plant development.
[0203] The invention also provides methods of obtaining crop
products by harvesting, and optionally processing further,
transgenic plants of the invention. By crop product is meant any
useful product obtainable from a crop plant.
Products that Contain Mutant Gluten Proteins or Proteins that
Comprise Sequence Capable of Acting as an Antagonist
[0204] The invention provides a product that comprises the mutant
gluten proteins or protein that comprises sequence capable of
acting as an antagonist. This is typically derived from or comprise
plant parts from plants mentioned herein which express such
proteins. Such a product may be obtainable directly by harvesting
or indirectly, by harvesting and further processing the plant of
the invention. Directly obtainable products include grains.
Alternatively, such a product may be obtainable indirectly, by
harvesting and further processing. Examples of products obtainable
by further processing are flour or distilled alcoholic beverages;
food products made from directly obtained or further processed
material, e.g. baked products (e.g. bread) made from flour.
Typically such food products, which are ingestible and digestible
(i.e. non-toxic and of nutrient value) by human individuals.
[0205] In the case of food products that comprise the protein which
comprises an antagonist sequence the food product may also comprise
the wild-type gluten protein, but preferably the antagonist is able
to cause a reduction (e.g. completely) in the coeliac disease
symptoms after such food is ingested.
Deamidation
[0206] Where a sequence described herein includes a Gln residue,
the invention also provides that sequence where the Gln residue has
been deamidated to a Glu residue. One or more (e.g., 1, 2, 3, 4, 5,
etc.) Gln residue(s) per sequence may be deamidated, but when there
is more than one Gln residue, not all of them must be deamidated.
Preferably, the Gln residues that are deamidated are those
susceptible to deamidation by transglutaminase.
[0207] Examples where Gln may be deamidated are given in the
sequence listing. For example, residue 4 of SEQ ID NO:1 can be a
Gln residue or a Glu residue, residue 6 of SEQ ID NO:2 can be a Gln
residue or a Glu residue, residues 4 and 7 of SEQ ID NO:6 can each
independently be Gln or Glu residues, etc. The Gln residues that
are susceptible to deamidation, and their deamidated Glu
counterparts, are referred to as "Glx" residues.
[0208] Where the agent includes more than one Glx residue, these
may be arranged in any configuration. For example, the Glx residues
may be consecutive residues, and/or may be separated by one or more
(e.g., 1, 2, 3, 4, 5, 6, 7, 8, etc.) other residues. As mentioned
above, for HLA-DQ8 epitopes, the agent preferably comprises a Glx
residue that is separated by seven residues from another Glx
residue.
[0209] Preferred agents of the invention are deamidated agents,
i.e., the agent comprises the one or more Glx residues in the Glu
form. This can be achieved in various ways, e.g., by including Glu
residues during production, or by converting Gln residues to Glu by
deamidation. Conversion of Gln to Glu can be achieved by treating
an agent that contains Gln residues that are susceptible to
deamidation with a deamidating agent. The one or more Gln residues
are preferably deamidated to Glu by transglutaminase, for example
as described in the examples.
[0210] The skilled person will be able to determine which
particular Gln residues in the agent are susceptible to deamidation
and thus which residues should be Glu residues arising from
deamidation of a Gln residue. For example, Gln-containing sequences
susceptible to deamidation by transglutaminase generally conform to
a motif: e.g., QXPX, QXPF (Y), QXX (FYMILVW), QXPF, QXX (FY), PQ
(QL) P (FY) P. For example, the sequence PQ (QL) P (FY) P
facilitates deamidation of the underlined Q at position 2 by
transglutaminase.
[0211] In particular, agents comprising the deamidated versions of
SEQ ID NOs: 1-1927 are preferred (where such sequences are not
already deamidated). Most preferably, the agents of the invention
comprise the transglutaminase-deamidated versions of SEQ ID NOs:
1-1927 (again, where not already deamidated). Analogues and
equivalents of these agents, as defined herein, are also
encompassed within the scope of the invention.
Examples
[0212] The invention is illustrated by the following nonlimiting
Examples:
Initial Gliadin Epitope Screening Library
[0213] In initial experiments involving 29 HLA-DQ2+ individuals
with coeliac disease on long-term gluten free diet,
interferon-gamma ELISPOT assays were used to screen a previous
Pepset (described in WO 03/104273, which is incorporated herein by
reference) initially as pools of peptides and then in 15 subjects
as individual peptides with and without deamidation by tTG. This
Pepset library consisted of 652 20mer gliadin peptides spanning all
unique 12mers contained within all Genbank entries described as
wheat gliadins found in September 2001. This Pepset library was
designed "manually" from gene-derived protein sequences aligned
using ClustalW software (MegAlign) arranged into phylogenetic
groupings.
[0214] Approximately 0.6 micromole of each of 652 of the 20mers was
provided. Two marker 20mer peptides were included in each set of 96
(VLQQHNIAHGSSQVLQESTY--peptide 161, and IKDFHVYFRESRDALWKGPG) and
were characterized by reverse phase-HPLC and amino acid sequence
analysis. Average purities of these marker peptides were 19% and
50%, respectively. Peptides were initially dissolved in
acetonitrile (10%) and Hepes 100 mM to 10 mg/ml. The final
concentration of individual peptides incubated with PBMC for the
IFN.gamma. ELISpot assays was 20 mcg/ml. These peptides were
deamidated by incubation with guinea pig tissue tTG (Sigma T5398)
in the ratio 100:32 mcg/ml for two hours at 37.degree. C. Peptides
solutions were stored at -20.degree. C. and freshly thawed prior to
use. These studies were conducted in Oxford, UK. ELIspot assays
were performed as described for those conducted in Melbourne,
Australia (all other studies described herein). "Oxford" data
regarding subject responses to individual peptides was pooled with
"Melbourne" data for subsequent "minimal" epitope analysis in the
"EM algorithm" (see below).
Second Round Gliadin Epitope Screening Library
[0215] A second round gliadin epitope library was designed
according the bioactive sequences identified from the initial
gliadin epitope screening library of 652 20mers. Gliadin 20mers
with mean bioactivity equivalent to >5% of the most potent
gliadin 20mer (91: PQPFPPQLPYPQPQLPYPQP) in 15 HLA-DQ2+ subjects
assessed with all 652 deamidated 20mers were defined. Since earlier
studies (see WO 03/104273) indicated that deamidated pools of this
Pepset were more potent than without deamidation, glutamine
residues within bioactive 20mers potentially deamidated by tTG were
identified according to the motif QXPX, QXZ (FYWILVM) where x is
any amino acid except proline, and P is proline, Z is any amino
acid, and FYWILVM represent hydrophobic amino acids (consistent
with the motifs for tTG-mediated deamidation published by Vader W.
et al J Exp Med 2002 J. Exp. Med. 195:643-649, PCT WO 03/066079,
and Fleckenstein B. 2002. J Biol Chem 277:34109-16).
[0216] 12mer peptides were then identified in which each potential
deamidation site could be in position 4, 6 or 7 in the 9mer located
within HLA-DQ2 binding groove (HLA-DQ2 anchors at these positions
show a preference for glutamate). Candidate 12mer core epitope
sequences were then flanked with glycine followed by the N-terminal
residue present in the parent gliadin polypeptide and at the
C-terminal by the C-terminal residue present in the parent gliadin
polypeptide followed by glycine (i.e. GXXXXXXXQXXXXXXG).
[0217] Peptides were synthesised with glutamine or glutamate in
position 9. Peptides (100 mcg/ml) (+/-deamidation by tTG) were then
assessed in interferon gamma ELISPOT assays using PBMC from 15
HLA-DQ2+ coeliac volunteers after gluten challenge. Results of
these assays were analysed according to the EM algorithm (see
below). In addition, the most potent distinct peptides were
synthesised and purified to >80% (Mimotopes) and assessed in
interferon gamma ELISPOT assays using PBMC from 15 HLA-DQ2+ coeliac
volunteers after wheat gluten challenge.
Complete Gluten Epitope Screening Library
[0218] To make practical the design of a substantially larger
peptide library spanning all wheat gliadin and glutenin, rye,
barley, and oat gluten-like proteins (prolamines), and to confirm
data from the previous gliadin peptide library, an iterative
algorithm was developed to automate design of a minimal set of
20mers including all unique 12mers (excluding signal peptide
sequences) in gluten proteins. The ScanSet algorithm is shown in
FIG. 1.
[0219] The method tests for all possible peptide epitopes from a
group of proteins whether they are potential antigens in a range of
patients. T-cell epitopes range in size between 9 and 15 AA. To
test all possible 12mers in a set of proteins, becomes quickly
unfeasible because of the high numbers.
[0220] Here we use the fact that, for example, a 20mer peptide can
cover up to 9 different 12mers. We therefore developed a
combinatorial approach to cover all possible 12mers represented in
a family of proteins.
[0221] 20 amino acid (20mer) long peptides are generated that are
tested as antigens, and that cover all 12mer peptide sequences that
exist in the group of proteins. We define the length of peptides to
generate as L (e.g. 20) and the length of the epitopes we want to
cover as S. We developed a computer program that generates all
uniquely occurring Lmers from a set of proteins. Further, we
generate all uniquely occurring Smers from this set of proteins.
Next we select a set of N Lmers that contains all sequences of
Lmers. FIG. 1 outlines how this algorithm works.
[0222] On 16 Jun. 2003, Genbank contained accession numbers for 53
alpha/beta, 53 gamma and 2 omega gliadins, and 77 LMW and 55 HMW
glutenins from T. aestivum, 59 hordeins, 14 secalins, and 20
avenins (see FIG. 2A and FIG. 2B). In total, ScanSet identified
18117 unique 12mers contained in the 225 gluten gene products.
[0223] All unique gluten 12mers could be subsumed in 2922 20mers.
These 20mers were synthesised in a Pepset peptide library
(Mimotopes Inc., Melbourne, Australia). Pepset peptides were
synthesized in batches of 96 (Mimotopes Inc., Melbourne Australia).
Approximately 0.7 to 1.3 micromole of each of 2922 20mers was
provided. Two marker 20mer peptides were included in each set of 96
(one representative peptide from the 94 other peptides on each
particular plate, and IKDFHVYFRESRDALWKGPG) and were characterized
by reverse phase-HPLC and mass spectroscopy. Average purities of
these marker peptides were 36% (range: 5-68%) and 64%
(range:55-71%), respectively.
[0224] Peptides were initially dissolved in aqueous acetonitrile
(50%). Peptides in aqueous acetontrile were transferred to sterile
96-well plates and diluted in sterile PBS with 1 mM calcium (250
mcg/ml) and then incubated with tTG (25 mcg/ml) (Sigma T5398) for 6
h 37.degree. C. and then stored frozen (-20.degree. C.) until
use.
[0225] Subjects all had biopsy-proven coeliac disease and had
followed a strict gluten free diet for at least 6 months. All
subjects possessed HLA-DQB01*02 (HLA-DQ2) alone (n=100) or
HLA-DQA1*03 and HLA-DQB1*0302 (HLA-DQ8) alone (n=5). In all cases,
tTG-IgA was assessed before gluten challenge and was in the normal
range (30% of initial volunteers were found to have elevated
tTG-IgA and were excluded since chronic gluten exposure is
associated with failure to induce peripheral blood gluten-specific
T-cells by short-term gluten challenge). Volunteers consumed
Baker's Delight "white bread block loaf" (200 g daily for three
days) or Uncle Toby's oats (100 g daily for three days). All but
three subjects completed the three day challenge (one withdrew
after first mouthful of bread, and the other two vomited after
initial two slices of bread. Data from the latter two were included
in subsequent analysis). Blood (300 ml) was drawn six days after
commencing gluten challenge. Gluten peptide-specific IFN.gamma.
ELISpot responses have not been found in our previous studies, and
so "pre-challenge" blood was not assessed in this set of
experiments (Anderson, R P et al 2000. Nat. Med. 6:337-342, WO
01/25793, WO 03/104273).
[0226] IFN.gamma. ELISpot assays (Mabtech, Sweden) were performed
in 96-well plates (MAIP S-45, Millipore) in which each well
contained 25 mcl of peptide solution and 100 mcl of PBMC
(2-8.times.10.sup.5/well) in RPMI containing 10% heat inactivated
human AB serum. After development and drying, IFN.gamma. ELISpot
plates were assessed using the MAIP automated ELISpot plate
counter. Data was then analysed according to a novel algorithm
(Expectation Maximization: EM) to define and quantify
interferon-gamma responses to 9mer sequences contained within the
peptide library (see FIG. 3 and below). 9mer peptides were then
rationalised according to an algorithm that assumes redundancy in
T-cell recognition, the "IterativeCluster" algorithm (see FIG. 4
and below), by allowing groups of amino acids with similar chemical
properties at any one position in the 9mer, or for glutamate to
replace glutamine at any position (assuming deamidation may have
occurred).
[0227] Since there were data sets from only two HLA-DQ8+
individuals who were not also HLA-DQ2+, and these were utilizing
only the 721 wheat gliadin 20mers from the "Complete gluten epitope
screening library", bioactive peptides were identified by taking
the average rank of peptide-specific IFN.gamma. ELISPOT responses
in the two subjects. For prediction of likely HLA-DQ8-restricted
gliadin epitopes, it was assumed that a glutamine residue
susceptible to tTG-mediated deamidation occupied either position 1
or 9 in potential 9mer core regions of epitopes, consistent with
the HLA-DQ8 binding motif and the findings of van de Wal et al (van
de Wal, Y. et al 1998. J Immunol. 161(4):1585-1588).
Expectation Maximization (EM) Algorithm to Analyze Data from
ELISpot:
[0228] FIG. 3 shows an algorithm to analyze data coming from an
assay using the ELISpot. T-cell responses to different peptides are
measured in 96 well plates using T-cell assays. Assays are
performed on many patients using many different peptide antigens.
The result of the T-cell assays can be summarized in a table where
the rows represent peptides and the columns patients and the
individual measurements (counts) are in the table (e.g., see FIG.
3B). The purpose of the EM algorithm is to differentiate between
response and non response of a patient to a peptide and to estimate
a mean rate of response and a proportion of people responding for
each peptide.
[0229] Responses are measured for a number of different patients (i
will be used to indicate the patient) and for many different
peptides (j will be used to indicate the peptide). Each measurement
(yij) represents a count of T-cells from patient i responding to
peptide j. In order to estimate, whether a measurement for a
certain peptide in a patient can be called a response or whether it
is more likely to be coming from a background distribution, we
propose a model for an incomplete data problem, with yij being the
observed count of spots and zij an unobserved indicator, whether
person i responds to peptide j.
[0230] The observed number of counts yij are modelled to come from
independent Poisson distributions: poisson(ai, .lamda.), if patient
i is responding to peptide j, i.e. zij=1, and poisson(ai,
.lamda.0), if patient i is not responding to peptide j, i.e. zij=0.
[0231] Complete data: yij (observed counts), zij (response
indicator, not observed). [0232] Parameters: .theta.=(ai, .lamda.j,
.lamda.0, pj) [0233] ai: Patients overall responsiveness. [0234]
.lamda.j: Peptide induced rate of response. [0235] .lamda.0:
Background rate of response. [0236] pj: Proportion of people
responding to peptide j.
EM Algorithm:
[0236] [0237] Set variables initially to random values [0238]
E-step: compute likelihood [0239] M-step: maximize likelihood
function [0240] Iterate E- and M-step
Iterative Procedure to Find Minimal Set of Responsive Epitopes
[0241] A program to compute a minimal set of peptides for use in a
vaccine based on the T-cell responses estimated in the EM algorithm
was developed. We measured T-Cell responses to Lmers from a group
of proteins. The peptides were generated to cover all possible
Smers. We estimated the following parameters for the response by an
EM algorithm: rate of response, number of people responding,
proportion of people responding. The proportion of people
responding multiplied with the estimated rate of response is used
as a criterion to define epitopes which are good antigens. Many of
the measured Lmers contain the same Smer epitopes. In order to find
the epitopes (Smers) which can explain all the responses in Lmers
we select the Smer which is contained in Lmers that in the mean
have the highest responses. Then we remove all Lmers that contain
this Smer from our measurements. Next we select the Smer with the
highest responses in the remaining Lmers. We iterate this procedure
until no Smers with responses higher than a specified cutoff exist.
We use several iterations with different cutoffs. This process is
sketched in FIG. 4. The such defined list of clustered Lmers can be
used as a basis to define the optimal epitopes and select peptides
that function as good antigens.
HLA-DQ2 Epitopes in Wheat Gluten
[0242] HLA-DQ2 epitopes in wheat gliadins and glutenins were
identified using PBMC collected on day 6 after commencing gluten
challenge in a total of 76 HLA-DQ2+ individuals in gamma-interferon
ELISPOT assays (Initial gliadin epitope library: n=15, Second round
gliadin epitope screening library: n=15, Complete gluten epitope
screening library: n=46). All data relating to individual peptide
responses in coeliac subjects was pooled and analysed by the EM
algorithm.
[0243] A series of 9mer sequences were identified and ordered
according to the intensity of gamma-interferon responses and the
proportion of individuals responding (see FIG. 5A, FIG. 5B, FIG.
5C, FIG. 5D, FIG. 5E, FIG. 5F, FIG. 5G, FIG. 5H, FIG. 5I, FIG. 5J,
FIG. 5K, FIG. 5L, FIG. 5M, FIG. 5N, FIG. 5O, FIG. 5P, FIG. 5Q, FIG.
5R, FIG. 5S, FIG. 5T, FIG. 5U, FIG. 5W, FIG. 5V, FIG. 5X, FIG. 5Y,
FIG. 5Z, and FIG. 5AA). Many of the sequences identified could be
grouped in "superfamilies" allowing for several different amino
acids with similar chemical properties to be present at any one
position in the putative epitope (see FIG. 6A, FIG. 6B, FIG. 6C,
and FIG. 6D). For example, in "Sequence 1" of FIG. 6A (SEQ ID NO:
1555) P (QR) P (QE) LP (FY) PQ, glutamine (Q) or arginine (R) are
both accepted at position 2 except that Q generates a substantially
more bioactive epitope.
[0244] By reviewing the 110 most "active" 9mer sequences identified
by the EM algorithm, the "list" of 9mer motifs could be condensed
to 41 9mers, many of which overlapped (for example "Sequence 1" and
"2" (SEQ ID NOS: 1555 and 1558 respectively) overlap by 7 residues
and are both present in A-gliadin 57-73 QE65). In selected cases,
high-grade peptides were synthesised and confirmed the bioactivity
of peptides identified by the EM algorithm (see FIG. 7).
HLA-DQ2 Epitopes in Oats Avenins
[0245] Avenin peptides were assessed after challenge with oats
(n=30 subjects) or after wheat bread (n=8) in HLA-DQ2+ coeliac
subjects. ELISPOT responses were found for the peptides found in
FIG. 8. One of the reactive avenin peptides was homologous to a
sequence in wheat gluten (SEQ ID NO: 1590).
Oats (Avenin) High Quality Peptide Studies
[0246] High grade avenin peptides were assessed 3 days after
completing oats challenge with pure wheat-free oats, 100 g/d for 3
days ("day 6" PBMC interferon gamma ELISPOT responses). These
peptides were designed upon peptides previously defined using the
screening grade ("first round") avenin peptide library and on
potential deamidation sites. There were 25 peptides (as 16mers)
with purity verified by HPLC as >80%, and sequences confirmed by
mass spectroscopy.
[0247] Interferon gamma ELISPOT responses to the high grade avenin
peptides following deamidation by tTG were compared in 18 subjects
with DQ2+ coeliac disease.
[0248] The dominant (>70% maximal response) peptides after oats
challenge included: EQQFGQNIFSGFSVQL (SEQ ID NO: 1764) (11/18
subjects), QLRCPAIHSVVQAIIL (SEQ ID NO: 1765) (4/18 subjects), and
QYQPYPEQEQPILQQQ (SEQ ID NO: 1766) (3/18 subjects). 2/18 subjects
did not have avenin specific responses (defined by SFU (spot
forming units)>3.times.blank) and 6/18 subjects mean maximal SFU
were less than 10. Two additional peptides elicited positive
responses: QIPEQLRCPAIHSVVQ (SEQ ID NO: 1767) (3/18 subjects) and
EQYQPEQQPFMQPL (SEQ ID NO: 1768) (>40% maximal peptide response
in 5/18 subjects). The panel of 25 peptides included several
peptides similar to peptide 1490 (SEQYQPYPEQQEPFVQ) reported in
Arentz-Hansen, PLoS Medicine (October 2004, vol. 1, issue 1
(84-92), however, that peptide induced a strong positive response
in only one subject, and far weaker response in 5 subjects.
[0249] Interferon gamma ELISPOT responses to high grade avenin
peptides were absent prior to gluten challenge, and were blocked by
pre-treatment of PBMC with anti-HLA DQ but not anti-HLA DR
antibody.
Rye and Barley Screening Peptide Libraries
[0250] Secalin and hordein 20mer first round peptide libraries were
assessed 3 days after completing rye (bread, 100 g/d for 3 days) or
barley (boiled, 100 g/d for 3 days) challenge ("day 6" PBMC
interferon gamma ELISPOT responses). Although iterative analysis
using 2nd and 3rd round peptide libraries to define epitopes has
not yet been performed, the 20mers pre-treated with tTG found to
induce "potent" responses shared substantial structural similarity
to the bioactive peptides identified after wheat challenge.
However, the dominant peptide sequences after rye or barley
challenge did not include peptides with the PQPQLPY sequence found
to be dominant after wheat challenge. The dominant (>70% maximal
response) 20mer after rye challenge was usually
PQQLFPLPQQPFPQPQQPFP (SEQ ID NO: 1769) (8/14 subjects), or
occasionally QPFPQPQQPTPIQPQQPFPQ (SEQ ID NO: 1770) (4/14),
QQPQQLFPQTQQSSPQQPQQ (SEQ ID NO: 1771) (1/14), PQTQQPQQPFPQPQQPQQLF
(SEQ ID NO: 1772) (1/14) and/or QEQREGVQILLPQSHQQLVG (SEQ ID NO:
1773) (1/14). Additional peptides noted for greater than 40%
maximal response in at least 1 subject include:
TABLE-US-00002 (SEQ ID NO: 1774) FPQQPQQPFPQPQQQLPLQP (3/14, 2 >
70%) (SEQ ID NO: 1775) PQQPFPQQPEQIIPQQPQQP (5/14, 3 > 70%) (SEQ
ID NO: 1776) QQLPLQPQQPFPQPQQPIPQ (6/14, 2 > 70%) (SEQ ID NO:
1777) QQPQQPFPLQPQQPVPQQPQ (3/14, 1 > 70%) (SEQ ID NO: 1778)
SIPQPQQPFPQPQQPFPQSQ (4/14, 1 > 70%) (SEQ ID NO: 1779)
QTQQSIPQPQQPFPQPQQPF (3/14, 1 > 70%) (SEQ ID NO: 1780)
NMQVGPSGQVEWPQQQPLPQ (2/14, 1 > 70%) (SEQ ID NO: 1781)
VGPSGQVSWPQQQPLPQPQQ (2/14, 2 > 70%) (SEQ ID NO: 1782)
QQPFLLQPQQPFSQPQQPFL (1/14, 1 > 70%) (SEQ ID NO: 1783)
FPLQPQQPFPQQPEQIISQQ (5/14, 1 > 70%) (SEQ ID NO: 1784)
PQQPQRPFAQQPEQIISQQP (3/14, 1 > 70%) (SEQ ID NO: 1785)
SPQQPQLPFPQPQQPFVVVV (4/14, 1 > 70%) (SEQ ID NO: 1786)
QQPSIQLSLQQQLNPCKNVL (1/14, 1 > 70%)
[0251] Typically, the dominant peptides after barley challenge
included one of six peptide motifs, or were one of eight other
individual 20mers "dominant" in only one of 17 subjects after
barley challenge. The six motifs identified:
TABLE-US-00003 (SEQ ID NO: 1787) QQPIPQQPQPY (SEQ ID NO: 1788)
PFPQPQQPFPW (SEQ ID NO: 1789) LQPQQPFPQ (SEQ ID NO: 1790) PQPQOASPL
(SEQ ID NO: 1791) IIPQQPQQPF (SEQ ID NO: 1792) YPEQPQQPF
[0252] The barley hordein peptides showing at least 40% maximal
peptide response in at least one subject include the following,
wherein an asterisk indicates the eight individual peptides showing
maximal response in a single individual:
TABLE-US-00004 (SEQ ID NO: 1793) QQQPFPQQPIPQQPQPYPQQ (8/17, 2 >
70%) (SEQ ID NO: 1794) QQPQPFSQQPIPQQPQPYPQ (9/17, 8 > 70%) (SEQ
ID NO: 1795) PQQPVPQQPQPYPQQPQPFP (5/17, 1 > 70%) (SEQ ID NO:
1796) PQPFPQQPIPQQPQPYPQQP (6/17, 2 > 70%) (SEQ ID NO: 1797)
YPQQPQPFPQQPIPQQPQPY (6/17. 2 > 70%) (SEQ ID NO: 1798)
QPQPYPQQPQPYPQQPFQPQ (7/17, 2 > 70%) (SEQ ID NO: 1799)
QPQQPQPFPQQPVPQQPQPY (5/17, 2 > 70%) (SEQ ID NO: 1800)
PQPYPQQPQPFPQQPPFCQQ (1/17, 1 > 70%)* (SEQ ID NO: 1801)
QPFPQPQQPFPWQPQQPFPQ (10/17,2 > 70%) (SEQ ID NO: 1802)
PFPQQPQQPFPQPQQPFRQQ (6/17, 3 > 70%) (SEQ ID NO: 1803)
WQPQQPFPQPQQPFPLQPQQ (9/17, 5 > 70%)* (SEQ ID NO: 1804)
PWQPQQPFPQPQEPIPQQPQ (1/17. 1 > 70%) (SEQ ID NO: 1805)
QQPFPQPQQPIPYQPQQPFN (5/17, 1 > 70%) (SEQ ID NO: 1806)
PQQPQQPFPQPQQPFSWQPQ (6/17, 2 > 70%)* (SEQ ID NO: 1807)
QPQQPFPQPQQPIPYQPQQP (4/17, 1 > 70%)* (SEQ ID NO: 1808)
QSQQQFPQPQQPFPQQPQQP (1/17, 0 > 70%) (SEQ ID NO: 1809)
PFPQPQQPFSWQPQQPFLQP (1/17, 0 > 70%) (SEQ ID NO: 1810)
FPQPQEPFPQQPQQPFPLQP (1/17, 0 > 70%) (SEQ ID NO: 1811)
PFPQPQQPFPWQPQQPFPQP (6/17, 0 > 70%) (SEQ ID NO: 1812)
FPQYQIPTPLQPQQPFPQQP (2/17, 1 > 70%) (SEQ ID NO: 1813)
FPLQPQQPFPQQPQQPFPQQ (1/17, 0 > 70%) (SEQ ID NO: 1814)
QQPFPLQPQQPFPQPQPFPQ (1/17, 0 > 70%) (SEQ ID NO: 1815)
SPLQPQQPFPQGSEQIIPQQ (1/17, 0 > 70%) (SEQ ID NO: 1816)
PQQASPLQPQPQQASPLQPQ (1/17, 1 > 70%) (SEQ ID NO: 1817)
PQQPPFWPQQPFPQQPPFGL (1/17, 1 > 70%)* (SEQ ID NO: 1818)
PVLSQQQPCTQDQTPLLQEQ (1/17, 1 > 70%) (SEQ ID NO: 1819)
RQLPKYIIPQQPQQPFLLQP (1/17, 1 > 70%) (SEQ ID NO: 1820)
QGSEQIIPQQPQQPFPLQPH (7/17, 3 > 70%)* (SEQ ID NO: 1821)
PQGSEQIIPQQPFPLQPQPF (2/17, 1 > 70%) (SEQ ID NO: 1822)
QPFPTPQQFFPYLPQQTFPP (4/17, 1 > 70%) (SEQ ID NO: 1823)
PFPQPPQQKYPEQPQQPFPW (1/17, 1 > 70%) (SEQ ID NO: 1824)
QKYPEQPQQPFPWQQPTIQL (1/17, 1 > 70%) (SEQ ID NO: 1825)
FQQPQQSYPVQPQQPFPQPQ (3/17, 1 > 70%) (SEQ ID NO: 1826)
QIPYVHPSILQQLNPCKVFL (1/17, 1 > 70%) (SEQ ID NO: 1827)
LAAQLPAMCRLEGGGGLLAS (1/17, 1 > 70%) (SEQ ID NO: 1828)
PYLPEELSPQYQIPTPLQPQ (1/17, 1 > 70%)* (SEQ ID NO: 1829)
VSPHPGQQTTVSPHQGQQTT (1/17, 1 > 70%)*
Second and Third Round Wheat Glutenin and Gliadin Peptide
Libraries
[0253] The second round wheat gliadin and glutenin library was
designed upon the sequences of 20mer wheat gliadin and glutenin
peptides that induced at least 5% of the response (interferon gamma
ELISPOT) stimulated by the most active transglutaminase (tTG)
pre-treated (enzymatically deamidated) 20mer peptide in any
subject. All 2nd round 16mer peptides were assessed in at least 18
subjects. The 2nd round library generated from the "Oxford" gliadin
20mer library had been assessed in ten subjects--this data was
merged with data generated from the 18 subjects used to assess the
new 2nd round (expanded) gliadin/glutenin library. Hence,
individual 16mer peptides pre-treated with transglutaminase were
assessed in either 18 (novel gliadin/glutenin sequences based on
"Melbourne" 20mer library) or 28 subjects (gliadin sequences based
on "Oxford" 20mer library). All 16mers identified for the second
round Oxford library also fulfilled the selection criteria for the
Melbourne second round library.
[0254] The second round peptide library data was analysed according
to the "dominance" of peptide responses in the interferon gamma
ELISPOT in individual subjects i.e. the percent response of an
individual's PBMC to a specific peptide normalized against that
individual's maximal peptide-induced response. Sequences of
peptides that stimulated at least 40% of the maximal
peptide-specific response in at least one subject are shown in
Table 1 below. The dataset supports the consistency and "dominance"
of peptides conforming to the sequences identified using the first
round 20mer peptide library using the Expectation Maximization (EM)
algorithm described above.
TABLE-US-00005 TABLE 1 Peptides confirmed in Second Round Library
as at least 40% as active as the peptide with maximal activity in
any one subject: Ranked according to potency of peptide family SEQ
ID Peptide NO: >70% 40-70% 10-40% <10% G-QLPYPQPQLPYPQP-G
1830 18/28 4/28 3/28 3/28 G-LQPFPQPQLPYPQP-G 1831 14/28 8/28 Nil
6/28 G-LQPFPQPQLPFPQP-G 1832 4/28 8/28 5/28 10/28
G-LQPFPQPQLPYLQP-G 1833 1/28 1/28 12/28 14/28 G-LQPFPQPQLPYSQP-G
1834 2/28 3/28 12/28 11/28 G-LQPFPQPQLSYSQP-G 1835 Nil 1/28 2/28
25/28 G-QQPFPQPQQPFPWQ-G 1837 9/28 8/28 5/28 6/28
G-QQPFPQPQQPIPVQ-G 1838 8/28 5/28 7/28 8/28 G-QQPFPQPQQPFSQQ-G 1839
4/28 7/28 8/28 9/28 G-QQPFPQPQQPFCQQ-G 1840 2/28 2/28 13/28 11/28
G-GLERPWQQQPLPPQ-G 1841 2/18 1/18 Nil 15/18 G-QTFPHQPQQAFPQP-G 1842
1/28 2/28 Nil 25/28 LQQQCSPVAMPQRLAR 1843 1/28 1/28 11/28 15/28
QGQQGYYPISPQQSGQ 1844 1/18 1/18 1/18 15/18 PGQGQSGYYPTSPQQS 1845
1/18 1/18 Nil 16/18 QGQPGYYPTSPQQIGQ 1846 1/18 1/18 1/18 15/18
GQGQSGYYPTSPQQSG 1847 1/18 Nil 2/18 15/18 QQGYYPTSPQQSGQGQ 1848 Nil
1/18 Nil 17/18 QGQQGYYPTSPQQPPQ 1849 Nil 1/18 Nil Nil
QQGYYPISPQQLGQGQ 1850 Nil 1/18 Nil Nil YVPPDCSTINVPYANI 1851 1/18
1/18 1/18 15/18 IIMQQEQQEQRQGVQI 1852 1/28 Nil 8/28 19/28
VAHAIIMHQQQQQQQE 1853 Nil 1/28 2/28 25/28 G-QPIPQQPQQPFPLQ-G 1854
1/28 Nil 5/28 G-FPQLQQPQQPFPQQ-G 1855 1/28 Nil 1/28 26/28
G-FPQTQQPQQPFPQQ-G 1856 Nil 1/28 2/28 25/28 G-QPLSQQPQQTFPQQ-G 1857
Nil 1/28 Nil 27/28 G-QQPQQQPQQPFPQQ-G 1858 Nil 1/28 5/28 22/28
G-FPQPQQPQQPFPQQ-G 1859 Nil 1/28 3/28 25/28 G-FPQPQQPQQSFPQQ-G 1860
Nil 1/28 1/28 26/28 G-QPQQTFPQQPQLPF-G 1861 1/18 Nil 2/18 15/18
G-MQVDPSGQVQWPQQ-G 1862 1/18 Nil Nil 17/18 G-IQVDPSGQVQWPQQ-G 1863
1/18 Nil Nil 17/18 G-MQADPSGQVQWPQQ-G 1864 1/18 Nil Nil 17/18
G-MQVDPSSQVQWPQQ-G 1865 1/18 Nil Nil 17/18 G-QQEQQILQQILQQQ-G 1866
1/18 Nil Nil 17/18 VPLYRTTTSVPFGVGT 1867 Nil Nil Nil 17/18
LQTLPSMCNVYIPPYC 1868 Nil Nil Nil 17/18 LALQTLPAMCNVYIPP 1869 Nil
Nil Nil 17/18 DAIRAIIYSIVLQEQQ 1870 Nil Nil Nil 17/18
G-QQQFSQPQQQFPQP-G 1871 Nil 5/28 7/28 16/28 G-FFPQPQQQFPQPQQ-G 1872
Nil 1/28 10/28 17/28 G-FPQQPQQQFPQPQQ-G 1873 Nil 1/28 Nil 27/28
G-QQPFPQPQQQFPQP-G 1874 Nil 1/28 12/28 15/28 G-QPQPFLPQLPYPQP-G
1875 Nil 4/28 9/28 15/28 G-QQPFPQPQQQLPQP-G 1876 Nil 3/28 6/28
19/28 G-LPFPQQPQQPLPQP-G 1877 Nil 2/18 4/18 12/18
G-QQAFPQPQQTFPHQ-G 1878 Nil 3/28 8/28 17/28 G-QQPFTQPQQPTPIQ-G 1879
Nil 1/28 4/28 23/28 G-QQIFPQPQQTFPHQ-G 1880 Nil 1/28 10/28 17/28
G-QQQFIQPQQPFPQQ-G 1881 Nil 2/28 11/28 15/28 G-QPFPLQPQQPFPQQ-G
1882 Nil 2/28 7/28 19/28 G-QPFPWQPQQPFPQQ-G 1883 Nil 2/28 8/28
18/28 G-QPTPIQPQQPFPQQ-G 1884 Nil 2/28 5/28 21/28
G-QVSFQQPQQQYPSP-G 1885 Nil 2/28 4/28 22/28 G-FFQQPQQQYPSSQQ-G 1886
Nil 1/28 1/28 26/28 G-GKSQVLQQSTYQLL-G 1887 Nil 2/18 1/18 15/18
GQVVNNHGQTVFNDIG 1888 Nil 1/18 4/18 G-QPQLPFPQQPQQQF-G 1889 Nil
1/28 2/28 25/28 G-QPFPQPQQAQLPFP-G 1890 Nil 1/28 2/28 25/28
G-HQQPGQRQQGYYPT-G 1891 Nil 1/18 1/18 16/18 G-HQQFPQQQIPVVQP-G 1892
Nil 1/18 1/18 16/18 LEAVTSIALRTLPTMC 1893 Nil 1/18 1/18
G-QQPQFSQQQQIPVI-G 1894 Nil 1/28 Nil 17/18
[0255] The third round peptide library consisted of 74 peptides
based upon structurally distinct sequences in the second round
library found to induce at least 10% of the maximal response to any
peptide in any subject. These peptides corresponded to wild-type
(non-deamidated) sequences virtually identical to those used in the
second round library. The distinct feature of this library was that
it consisted of peptides with purity verified by HPLC as >80%,
and with sequences confirmed by mass spectroscopy.
[0256] Interferon gamma ELSIPOT responses to the 3rd round library
peptides following deamidation by tTG were compared in 14 subjects.
Once again, sequences including the PQPQLPY motif were "dominant"
in 9/14 subjects. However PFPQPQQPFPW (SEQ ID NO: 1895) stimulated
>70% of maximal response in 1/14 subjects, PFPQQPQQPFPQ (SEQ ID
NO: 1896) in 1/14, PQPFLPQLPYPQP (SEQ ID NO: 1897) in 1/14,
QPFPQPQQPQQP (SEQ ID NO: 1898) in 4/14 (including 3 subjects in
whom PQPQLPY peptides were not potent epitopes) SGQGVSQSQQQSQQQ
(SEQ ID NO: 1899) in 2/14 (including one in which PQPQLPY peptides
were not potent), QYEVIRSLVLRTLPNM (SEQ ID NO: 1900) and
GLARSQMLQQSICHVG (SEQ ID NO: 1901) each in one (the same) subject
in whom PQPQLPY peptides were not potent epitopes, RTTTSVPFGVGTGVGA
(SEQ ID NO: 1902) in 1/14 subjects and AIHTVIHSIIMQQEQQ (SEQ ID NO:
1903) in 1/14 subjects.
[0257] Many of the sequences tested in third round were
structurally related and individual subject's responses were
present or absent according to the "relatedness" of certain
sequences, suggesting redundancy of peptides recognized by gluten
specific T cells induced by in vivo gluten challenge.
[0258] Interferon gamma ELISPOT responses to 3rd round peptides
were absent before gluten challenge, and were blocked by
pre-treatment of PBMC with anti-HLA DQ but not HLA DR antibody.
Combitopes
[0259] The issue of epitope redundancy and the potential utility in
diagnostics and therapeutics of peptides designed to combine
"unique" dominant epitopes was addressed by comparing interferon
gamma ELISPOT responses after wheat (n=16 HLA DQ2 coeliac disease
subjects), rye (n=17) or barley (n=13) challenge to the sequences:
QLQPFPQPELPYPQPQL (SEQ ID NO: 1904) ("P04724E"), QPEQPFPQPEQPFPWQP
(SEQ ID NO: 1905) ("626fEE"), and
QLQPFPQPELPYPQPFPQQPEQPFPQPEQPFPWQP (SEQ ID NO: 1906)
("Combitope"). After rye and barley challenge the sum of the median
ELISPOT responses (spot forming units) to P04724E and 626fEE were
almost identical (99%, and 102%, respectively) to the response to a
similar (optimal) concentration of the Combitope. However, after
wheat challenge (n=16 subjects), median P04724E response was 89% of
that to Combitope, and median 626fEE responses was 70% of the
response to Combitope. These findings would be consistent with
substantial redundancy of these related epitope sequences, P04724E
and 626fEE, after wheat challenge but not after rye or barley, and
that combining dominant epitope sequences within longer peptides
does not reduce their biological availability. Hence, combitopes
derived from selected potent epitopes may be efficient delivery
devices for T cell epitope-based therapeutics and diagnostics in
coeliac disease.
Epitopes in Wheat Gluten Associated with HLA-DQ8+Coeliac
Disease
[0260] Epitopes in wheat gliadins were identified using PBMC after
gluten challenge in two individuals, one HLA-DQ8 homozygous, and
one HLA-DQ8 heterozygote. Induced T-cell responses in other HLA-DQ8
(not DQ2) coeliac individuals responded weakly to gluten challenge
and their data did not allow detailed analysis.
[0261] Deamidated 20mers including the core sequence: QGSFQPSQQ
(SEQ ID NO: 1907), corresponding to the known HLA-DQ8-restricted
alpha-gliadin epitope (in which Q1 and Q9 are deamidated by tTG for
optimal activity), induced moderately strong peptide responses.
However, a series of "core" peptides were associated with more
potent responses in 20mers derived from gamma and omega gliadins
(see FIG. 9). The most potent peptides possessed glutamine in a
sequence that would suggest susceptibility to deamidation separated
by seven residues from a second glutamine also susceptible to
deamidation (as found in QGSFQPSQQ (SEQ ID NO: 1907)) suggesting
that these deamidated sequences would become high affinity binders
for HLA-DQ8 following deamidation by tTG. (The binding motif for
HLA-DQ8 favours glutamate at positions 1 and 9.) A further group of
20mers possessed glutamine residues susceptible to deamidation but
not separated by seven residues from a second glutamine susceptible
to tTG-mediated deamidation.
HLA DQ8 Coeliac Disease Gliadin and Glutenin Epitopes
[0262] Five subjects with coeliac disease that possess HLA DQ2 and
HLA DQ8 alleles underwent wheat gluten challenge. PBMC from two
subjects initially challenged were used to screen the first round
"Melbourne" wheat gliadin 20mer library. The 20mer sequences
identified using PBMC from these two HLA DQ8 CD subjects were
dissected further by screening, in five HLA DQ8+DQ2-CD subjects
including the two original subjects, a second round library based
on reactive 20mers in the 1.sup.st round library. The 2.sup.nd
round library consisted of screening grade overlapping 16mers, and
13mers predicted to correspond to tTG-mediated deamidation products
of epitopes with the potential for deamidation of glutamine at
position 1 and/or position 9 (consistent with the HLA DQ8 peptide
binding motif). In addition, the 1400 glutenin (HMW and LMW)
tTG-pretreated 20mers in the "Melbourne" wheat gluten library were
also screened in these five subjects.
[0263] The most potent and consistently dominant gliadin 16mers
were the related sequences VYIPPYCTIAPFGIFG (SEQ ID NO: 1908) (3/5
subjects >70% response to maximal gliadin 16mer) and
AMCNVYIPPYCAMAPF (SEQ ID NO: 1908) also dominant in 3/5 subjects
(4/5 subjects produced dominant responses to one or both of these
peptides). In addition, a series of peptides derived from
previously identified bioactive 20mers whose responses in the
ELISPOT were enhanced or permissive to specific glutamine residues
being deamidated were identified: (QE) QPTPIQP (QE) (SEQ ID NO:
1909), (QE) QPFPLQP (QE) (SEQ ID NO: 1910), (QE) QPIPVQP (QE) (SEQ
ID NO: 1911), (QE) QPQQPFP (QE) (SEQ ID NO: 1912), (QE) QP (4E)
LPFP (QE) (SEQ ID NO: 1913), (QE) GSFQPSQ (QE) (SEQ ID NO: 1914)
(previously published HLA DQ8 epitope, van der Wal 1998), (QE) LPFP
(QE) QP (QE) (SEQ ID NO: 1915), and (QE) QPFP (QE) QP (QE) (SEQ ID
NO: 1916).
[0264] Screening the glutenin 20mer library identified a further
series of sequences that were dominant in at least one of the five
subjects. Dominant 20mer peptides shared the motifs or had the
sequences: PQQQQQQLVQQQ (SEQ ID NO: 1917), QGIFLQPH (LQ) I (AS)
QLEV (SEQ ID NO: 1918), QPGQGQQG (HY) Y (SEQ ID NO: 1919),
QSRYEAIRAII (FY) S (SEQ ID NO: 1920), RTTTSVPFD (SEQ ID NO: 1921),
QPPFWRQQP (SEQ ID NO: 1922), Q (PS) (PS) (FI) (PS) QQQQ (SEQ ID NO:
1923), (QPLR) GYYPTSPQ (SEQ ID NO: 1924) (previously identified HLA
DQ8 epitope, van der Wal 2001), QGSYYPGQASPQ (SEQ ID NO: 1925),
GYYPTSSLQPEQGQQGYYPT (SEQ ID NO: 1926), and QGQQLAQGQQGQQPAQVQQG
(SEQ ID NO: 1927). Glutenin peptides were assessed after
pre-treatment with transglutaminase. Hence, the requirement for
deamidation for these epitopes is not known.
[0265] A comprehensive library of "uncharacterised" screening grade
peptides including all unique 12mer sequences encoded by genes
present in Genbank defined as (bread making) wheat (Triticum
aestivum), rye, barley, or oats gluten, gliadin, glutenin, secalin,
hordein, or avenin have been assessed using T cells from HLA
DQ2+(and in some cases HLA DQ8+) coeliac disease volunteers six
days after commencing in vivo gluten challenge. A relatively
consistent pattern of epitope hierarchy has been identified in HLA
DQ2 coeliac disease that is similar to but not identical after
consumption of other grains toxic in coeliac disease. Peptides with
the sequence PQPQLPY are dominant after wheat challenge in at least
two thirds of HLA DQ2+ coeliac disease, but other epitopes are
occasionally dominant while PQLPY peptides are essentially inactive
in fewer than one in six HLA DQ2+ subjects with coeliac disease.
The contribution of rare dominant epitopes will be better assessed
after screening large numbers (e.g. >30) subjects (in progress).
Epitope hierarchy after rye and barley consumption is similar to
that after wheat with the exception that deamidated peptides
similar to the gliadin/hordein/secalin sequences PQPQQPFP or
PFPQQPQQP are usually dominant rather than PQPQLPY (a sequence
unique to wheat alpha-gliadins). Combitopes that comprise serial
and partially overlapping gluten epitopes are as active or more
active than single epitopes alone and offer a means of efficiently
delivering multiple gluten epitopes for T cell recognition. Such
combitopes are therefore useful in design and delivery of peptide
therapies in coeliac disease that target multiple unique T cell
epitopes.
REFERENCES
[0266] 1. Molberg O, et al. Nature Med. 4, 713-717 (1998). [0267]
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H, Van der Wal Y, Kooy Y M C, Lundin K E A, Koning F, Roepstorff P,
Sollid L M, McAdam S N. The intestinal T cell response to
alpha-gliadin in adult celiac disease is focused on a single
deamidated glutamine targeted by tissue transglutaminase. J Exp
Med. 2000; 191:603-12. [0277] 12. Vader L W, de Ru A, van der Wal,
Kooy Y M C, Benckhuijsen W, Mearin M L, Drijfhout J W, van Veelen
P, Koning F. Specificity of tissue transglutaminase explains cereal
toxicity in celiac disease. J Exp Med 2002; 195:643-649. [0278] 13.
van der Wal Y, Kooy Y, van Veelan P, Pena S, Mearin L, Papadopoulos
G, Koning F. Selective deamidation by tissue transglutaminase
strongly enhances gliadin-specific T cell reactivity. J Immunol.
1998; 161:1585-8. [0279] 14. van der Wal Y, Kooy Y, van Veelan P,
Pena S, Mearin L, Molberg O, Lundin K E A, Sollid L, Mutis T,
Benckhuijsen W E, Drijfhout J W, Koning F. Proc Natl Acad Sci USA
1998; 95:10050-10054. [0280] 15. Vader W, Kooy Y, Van Veelen P et
al. The gluten response in children with celiac disease is directed
toward multiple gliadin and glutenin peptides. Gastroenterology
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[0282] Each of the PCT publications, U.S. patents, other patents,
journal references, and any other publications cited or referred to
herein is incorporated herein by reference in their entirety.
Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20170296651A9).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20170296651A9).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References