Diagnosis, prevention and treatment of ulcerative colitis, and clinical subtypes thereof, using microbial UC pANCA antigens

The present invention relates to microbial UC pANCA antigens. The invention provides methods of diagnosing ulcerative colitis (UC) and methods of inducing tolerance in a pANCA-positive patient with UC using a histone H1-like antigen. The invention further provides methods of diagnosing UC and methods of inducing tolerance in a pANCA-positive patient with UC using a porin antigen. Methods of diagnosing UC and methods of inducing tolerance in a pANCA-positive patient with UC using a Bacteroides antigen also are provided.

BACKGROUND OF THE INVENTION 
1. Field of the Invention 
The invention relates generally to the fields of immunology and 
inflammatory bowel disease and more specifically to the diagnosis and 
treatment of a clinical subtype of ulcerative colitis. 
2. Background Information 
Inflammatory bowel disease (IBD) is the collective term used to describe 
two gastrointestinal disorders of unknown etiology: Crohn's disease (CD) 
and ulcerative colitis (UC). The course and prognosis of ulcerative 
colitis, which occurs world-wide and is reported to afflict as many as two 
million people, varies widely. Onset of ulcerative colitis is 
predominantly in young adulthood with diarrhea, abdominal pain, and fever 
the three most common presenting symptoms. The diarrhea may range from 
mild to severe and often is accompanied by bleeding. Anemia and weight 
loss are additional common signs of UC. Ten percent to fifteen percent of 
all patients with inflammatory bowel diseases such as UC will require 
surgery over a ten year period. In addition, patients with UC are at 
increased risk for the development of intestinal cancer. Reports of an 
increasing occurrence of psychological problems, including anxiety and 
depression, are perhaps not surprising symptoms of what is often a 
debilitating disease that strikes people in the prime of life. 
Unfortunately, the available therapies for ulcerative colitis are few, and 
both diagnosis and treatment have been hampered by a lack of knowledge 
regarding the etiology of the disease. What is clear, however, is that the 
pathogenesis of ulcerative colitis involves immune-mediated damage to the 
intestinal mucosa. Autoantibodies, specifically antibodies against 
cytoplasmic components of neutrophils (pANCA), have been reported in 
68-80% of patients with ulcerative colitis, further supporting a role for 
immune dysregulation in this disease. However, the antigens recognized by 
these pANCA autoantibodies, which would be useful in diagnosing and 
treating UC patients have, to date, escaped identification. 
In other inflammatory bowel diseases such as Crohn's disease, bacteria have 
been implicated in the initiation or progression of the disease. That 
microbes can play a role in Crohn's disease is supported, for example, by 
the efficacy of antibiotics and diet in mitigating disease in some Crohn's 
patients. However, until now a role for microbes or microbial antigens in 
the immune dysregulation producing UC has not been suspected. Such 
microbial antigens can be the original inducers of the disease-related 
immune response in UC and, as such, can contain displayed B-cell epitopes 
that react especially effectively with UC pANCA autoantibodies. As a 
consequence, these microbial antigens can increase the level of UC 
serodetection from its current level of 60-70% with the fixed neutrophil 
assay. Such microbial antigens also can bear a disease related T-cell 
epitope and, as likely original inducers of the disease-related immune 
response, can be particularly effective tolerogenic antigens for treating 
UC patients. 
Thus, there is a need for identification and isolation of UC pANCA target 
antigens, including antigens of microbial origin such as those expressed 
in colonic bacteria of UC patients. Such antigens would be useful for 
diagnosing and treating the large population of UC patients that have 
pANCA autoantibodies. The present invention satisfies this need by 
providing the histone H1 UC pANCA target antigen and additional UC pANCA 
microbial antigens. Related advantages are provided as well. 
SUMMARY OF THE INVENTION 
The present invention provides methods of diagnosing ulcerative colitis 
(UC) by obtaining a sample from a subject suspected of having inflammatory 
bowel disease; contacting the sample with a histone H1-like antigen, or 
pANCA-reactive fragment thereof, under conditions suitable to form a 
complex of histone H1-like antigen, or pANCA-reactive fragment thereof, 
and antibody to histone H1-like antigen; and detecting the presence or 
absence of the complex, where the presence of the complex indicates that 
the subject has ulcerative colitis. A histone H1-like antigen useful in 
these methods can be, for example, a protein immunoreactive with NANUC-2 
and having an amino acid sequence having at least 65% amino acid identity 
with SEQ ID NO: 27. 
The invention also provides methods of inducing tolerance in a 
pANCA-positive patient with UC by administering to the patient an 
effective dose of a histone-like H1 antigen, or tolerogenic fragment 
thereof. Such a histone H1-like antigen can be, for example, a protein 
immunoreactive with NANUC-2 and having an amino acid sequence having at 
least 65% amino acid identity with SEQ ID NO: 27. 
The present invention also provides a composition of histone H1-like 
antigen, or tolerogenic fragment thereof, combined with a tolerogizing 
molecule. In such a composition, a histone H1-like antigen can be, for 
example, a protein immunoreactive with NANUC-2 and having an amino acid 
sequence having at least 65% amino acid identity with SEQ ID NO: 27. 
In addition, the present invention provides methods of UC by obtaining a 
sample from a subject suspected of having inflammatory bowel disease; 
contacting the sample with a porin antigen, or pANCA-reactive fragment 
thereof, under conditions suitable to form a complex of porin antigen, or 
pANCA-reactive fragment thereof, and antibody to porin antigen; and 
detecting the presence or absence of the complex, where the presence of 
the complex indicates that the subject has ulcerative colitis. A porin 
antigen useful in these methods can be, for example, a protein 
immunoreactive with NANUC-2 and having at least 65% amino acid identity 
with SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 30. 
The invention also provides methods of inducing tolerance in a 
pANCA-positive patient with UC by administering to the patient an 
effective dose of a porin antigen, or tolerogenic fragment thereof. A 
porin antigen useful in these methods can be, for example, a protein 
immunoreactive with NANUC-2 and having at least 65% amino acid identity 
with SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 30. 
In addition, there is provided a porin antigen, or tolerogenic fragment 
thereof, combined with a tolerogizing molecule. In a composition of the 
invention, a porin antigen can be, for example, a protein immunoreactive 
with NANUC-2 and having at least 65% amino acid identity with SEQ ID NO: 
28, SEQ ID NO: 29 or SEQ ID NO: 30. 
The present invention further provides methods of diagnosing UC by 
obtaining a sample from a subject suspected of having inflammatory bowel 
disease; contacting the sample with a Bacteroides antigen, or 
pANCA-reactive fragment thereof, under conditions suitable to form a 
complex of Bacteroides antigen, or pANCA-reactive fragment thereof, and 
antibody to Bacteroides antigen; and detecting the presence or absence of 
the complex, where the presence of the complex indicates that the subject 
has ulcerative colitis. A Bacteroides antigen useful in these methods can 
be, for example, a Bacteroides cecae protein immunoreactive with NANUC-2 
and having a molecular weight of about 100 kDa by SDS-PAGE 
electrophoresis. 
The invention also provides methods of inducing tolerance in a 
pANCA-positive patient with UC by administering to the patient an 
effective dose of a Bacteroides antigen, or tolerogenic fragment thereof. 
Such a Bacteroides antigen useful in these methods can be, for example, A 
Bacteroides cecae protein immunoreactive with NANUC-2 and having a 
molecular weight of about 100 kDa by SDS-PAGE electrophoresis. 
Additionally, the invention provides a composition containing a Bacteroides 
antigen, or a tolerogenic fragment thereof, combined with a tolerogizing 
molecule. A Bacteroides cecae protein immunoreactive with NANUC-2 and 
having a molecular weight of about 100 kDa by SDS-PAGE electrophoresis is 
an example of a Bacteroides antigen useful in a composition of the 
invention. 
Further provided herein are methods for identifying an agent useful for 
treating UC. The methods involve obtaining a sample of enteric bacteria 
from a patient with UC; isolating from the sample a bacterial species that 
expresses a pANCA-reactive antigen; contacting the bacterial species with 
an agent; and assaying for the reduced growth or viability of the 
bacterial species, where the reduced growth or viability of the bacterial 
species indicates that the agent is an agent useful for treating UC. 
Enteric bacterial species useful in these methods can be, for example, 
from the genera of Mycobacteria, Escherichia or Bacteroides.

DETAILED DESCRIPTION OF THE INVENTION 
Perinuclear anti-neutrophil cytoplasmic antibodies (pANCA) are present in 
the sera of most patients with ulcerative colitis (UC), and are a familial 
trait associated with disease susceptibility and disease-associated MHC 
haplotypes. Although sera from pANCA-positive ulcerative colitis patients 
are known to react with a component of neutrophils, the antigen 
responsible for the UC pANCA reactivity has long eluded identification. 
The present invention is directed to the exciting discovery that the pANCA 
autoantibody present in the sera of most patients with UC reacts with 
histone H1. The present invention further is directed to the discovery 
that UC pANCA also reacts with antigens of microbial origin. In 
particular, disclosed herein are a pANCA-reactive histone H1-like antigen, 
porin antigen and 100 kDa antigen selectively expressed in Bacteroides, 
each of which is a microbial antigen useful in the diagnosis, prevention 
and treatment of ulcerative colitis. 
As disclosed herein, Western analysis demonstrates that a nuclear protein 
doublet of 32-33 kDa from neutrophils is specifically reactive with a 
representative UC pANCA monoclonal antibody, NANUC-2 (see FIG. 2). 
Purification and protein sequencing of the NANUC-2 reactive protein 
doublet identified the UC pANCA target antigen as histone H1. Specific 
binding of NANUC-2 to histone H1 was confirmed using purified human 
neutrophil histone H1 and purified calf thymus histone H1. Identification 
of histone H1 as a UC pANCA target antigen provides a valuable reagent for 
diagnosing the presence of pANCA in UC patients and for ameliorating the 
abnormal immune process involved in ulcerative colitis. Thus, the 
invention is directed to methods for diagnosing a pANCA-positive clinical 
subtype of UC and determining susceptibility to UC using histone H1. The 
invention also is directed to methods of treating UC by inducing tolerance 
in a pANCA-positive UC patient and preventing UC in a healthy individual 
by administering the recently identified UC pANCA target antigen, histone 
H1. 
The present invention provides methods of diagnosing UC by obtaining a 
sample from a subject suspected of having inflammatory bowel disease; 
contacting the sample with human histone H1, or pANCA-reactive fragment 
thereof, under conditions suitable to form a complex of human histone H1, 
or pANCA-reactive fragment thereof, and antibody to human histone H1; and 
detecting the presence or absence of the complex, where the presence of 
the complex indicates that the subject has ulcerative colitis. Human 
histone H1 useful in these methods can be, for example, histone H1 isoform 
H1s-2 or a pANCA-reactive fragment thereof such as SEQ ID NO: 7, SEQ ID 
NO: 13, SEQ ID NO: 14 or SEQ ID NO: 20. 
The present invention also provides methods of diagnosing a pANCA-positive 
clinical subtype of ulcerative colitis in a patient with UC. A 
pANCA-positive clinical subtype of UC can be diagnosed, for example, by 
obtaining a sample from a patient with UC; contacting the sample with 
human histone H1, or pANCA-reactive fragment thereof, under conditions 
suitable to form a complex of human histone H1, or pANCA-reactive fragment 
thereof, and antibody to human histone H1; and detecting the presence or 
absence of the complex, where the presence of the complex indicates that 
the patient has the pANCA-positive clinical subtype of UC. A 
pANCA-positive clinical subtype of UC also can be diagnosed by obtaining a 
sample from a patient with UC; contacting the sample with purified histone 
H1 isoform H1.sup.S -2, or pANCA-reactive fragment thereof, under 
conditions suitable to form a complex of histone H1 isoform H1.sup.S -2, 
or pANCA-reactive fragment thereof, and antibody to histone H1 isoform 
H1.sup.S -2; and detecting the presence or absence of the complex, where 
the presence of the complex indicates that the patient has the 
pANCA-positive clinical subtype of UC. 
The methods of the invention relate to diagnosing and treating UC, which is 
a disease of the large intestine characterized by chronic diarrhea with 
cramping abdominal pain, rectal bleeding, and loose discharges of blood, 
pus and mucus. The manifestations of this disease vary widely. A pattern 
of exacerbations and remissions typifies the clinical course of most UC 
patients (70%), although continuous symptoms without remission are present 
in some patients with UC. Local and systemic complications of UC include 
arthritis, eye inflammation such as uveitis, skin ulcers and liver 
disease. In addition, ulcerative colitis and especially long-standing, 
extensive disease is associated with an increased risk of colon carcinoma. 
Several pathologic features characterize UC in distinction to other 
inflammatory bowel diseases. Ulcerative colitis is a diffuse disease that 
usually extends from the most distal part of the rectum for a variable 
distance proximally. The term left-sided colitis describes an inflammation 
that involves the distal portion of the colon, extending as far as the 
splenic flexure. Sparing of the rectum or involvement of the right side 
(proximal portion) of the colon alone is unusual in ulcerative colitis. 
Furthermore, the inflammatory process of UC is limited to the colon and 
does not involve, for example, the small intestine, stomach or esophagus. 
In addition, ulcerative colitis is distinguished by a superficial 
inflammation of the mucosa that generally spares the deeper layers of the 
bowel wall. Crypt abscesses, in which degenerate intestinal crypts are 
filled with neutrophils, also are typical of the pathology of ulcerative 
colitis (Rubin and Farber, Pathology (Second Edition) Philadelphia: J. B. 
Lippincott Company (1994), which is incorporated herein by reference). 
As used herein, the term "ulcerative colitis" is synonymous with "UC" and 
means a disease having clinical features of left-sided colonic disease 
accompanied by a characteristic endoscopic or histopathologic feature of 
UC. Clinical features of left-sided colonic disease, as used herein, are 
rectal bleeding, urgency and tenesmus. The rectal bleeding may be 
accompanied by mucus discharge. Additional clinical features that may be 
present in UC include treatment with topical therapy and recommended or 
performed total or near-total colectomy. 
A characteristic endoscopic feature of UC, which when present with clinical 
features of left-sided colonic disease indicates ulcerative colitis, is 
inflammation that is more severe distally than proximally or continuous 
inflammation. Additional typical endoscopic features that may be present 
in UC include inflammation extending proximally from the rectum or shallow 
ulcerations or the lack of deep ulcerations. 
A characteristic histopathologic feature of UC, which when present with 
clinical features of left-sided colonic disease indicates ulcerative 
colitis, is homogeneous, continuous, predominantly superficial 
inflammation or a lack of "focality" within biopsy specimens. Additional 
typical histopathologic features that may be present in UC include the 
presence of crypt abscesses or a lack of granulomas. Characteristic 
clinical features of left-sided colonic disease and characteristic 
endoscopic and histopathologic features of ulcerative colitis are 
summarized in Table 1. 
As used herein, the term "subject suspected of having inflammatory bowel 
disease" means any animal capable of having ulcerative colitis, including 
a human, non-human primate, rabbit, rat or mouse, especially a human, and 
having one or more symptoms of ulcerative colitis or Crohn's disease as 
described hereinabove. 
As used herein, the term "patient with UC" means a patient having 
ulcerative colitis, as defined by the presence of clinical features of 
left-sided colonic disease accompanied by a characteristic endoscopic or 
histopathologic feature of UC as defined herein. 
The pathogenesis of ulcerative colitis, although poorly understood, 
ultimately involves immune-mediated tissue damage. Ulcerative colitis is 
associated with various immunologic abnormalities, many of which can be 
secondary to inflammation. Similar to autoimmune disorders such as 
diabetes mellitus and multiple sclerosis, ulcerative colitis can represent 
a process of immune dysfunction directed against intrinsic intestinal 
mucosa cells. However, ulcerative colitis occurs in a mucosal site 
interfacing with the intestinal lumen. Thus, a primary immune target also 
can be an extrinsic agent such as a chronic microbial colonist. In this 
case, the mucosal injury characteristic of UC is a consequence of 
inflammatory bystander damage to resident parenchymal cells. 
TABLE 1 
______________________________________ 
A. Clinical 1. Rectal bleeding possibly 
features of accompanied by mucus discharge 
left-sided 2. Urgency 
colonic disease 
3. Tenesmus 
4. Treatment with topical therapy 
5. Recommended or performed total 
or near-total colectomy 
B. Endoscopic 6. Inflammation that is more 
features of UC 
severe distally than proximally 
7. Continuous inflammation 
8. Inflammation extending 
proximally from the rectum 
9. Shallow ulcerations or lack of 
deep ulcerations 
C. 10. Homogeneous, continuous, 
Histopathologic 
predominantly superficial 
features of UC 
inflammation 
11. Lack of "focality" within 
biopsy specimens 
12. Crypt abscesses 
13. Lack of granulomas 
______________________________________ 
Host genetic factors can confer susceptibility or resistance to tissue 
damage elicited by a chronic local immune response. For example, IBD is 
associated with polymorphisms in MHC class II, ICAM-1 and TNF-.alpha. loci 
(Yang et al., J. Clin. Invest. 92:1080-1084 (1993)), and animal and 
clinical studies directly implicate TNF levels in disease. In the case of 
autoimmune diseases where the primary target is a self-antigen, host 
genetic factors can play a role in disease by controlling, for example, 
T-cell clonal abundance, peptide antigen presentation, and levels of 
cytokines modulating different effector responses. Host genetic diversity 
also can affect variable susceptibility to microbial organisms. Thus, 
pathogenesis of ulcerative colitis can result from a primary abnormality 
of the immune system, or from an initial injury by an infectious agent 
that is perpetuated through immune-mediated or other processes. 
Certain immune-mediated disorders, including systemic lupus erythematosis, 
primary biliary cirrhosis and autoimmune hepatitis, are closely associated 
with distinctive patterns of autoantibody production. In the case of 
ulcerative colitis, anti-neutrophil cytoplasmic antibodies that produce a 
perinuclear staining pattern (pANCA) are elevated in 68-80% of UC patients 
and less frequently in other disorders of the colon. Serum titers of ANCA 
are elevated regardless of clinical status and, thus, do not reflect 
disease activity. High levels of serum ANCA also persist in patients five 
years post-colectomy. Although pANCA is found only very rarely in healthy 
adults and children, healthy relatives of UC patients have an increased 
frequency of pANCA, indicating that pANCA may be an immunogenetic 
susceptibility marker. 
Serum antibodies to cytoplasmic components of a neutrophil (ANCA) can be 
detected, for example, using indirect immunofluorescence microscopy of 
alcohol-fixed neutrophils. ANCA activity has been divided into two broad 
categories: cytoplasmic neutrophil staining (cANCA) and perinuclear to 
nuclear staining or cytoplasmic staining with perinuclear highlighting 
(pANCA). As used herein, the term "perinuclear anti-neutrophil cytoplasmic 
antibody" is synonymous with "pANCA" and means an antibody that reacts 
specifically with a neutrophil to give perinuclear to nuclear staining or 
cytoplasmic staining with perinuclear highlighting. 
The term "clinical subtype of UC," as used herein, means a subgroup of 
patients having ulcerative colitis whose features of disease are more 
similar to each other than to other patients with ulcerative colitis. The 
term "pANCA-positive clinical subtype of UC" means that subgroup of UC 
patients having pANCA. 
Serum anti-neutrophil cytoplasmic antibodies previously have been used to 
characterize clinically distinct subsets of UC patients. For example, the 
presence of pANCA has been associated with treatment-resistant left-sided 
ulcerative colitis; aggressive UC (Vecchi et al., Digestion 55:34-39 
(1994)); the requirement for surgery early in the course of UC (Boerr et 
al., Gastroenterol. 108: A785 (1995)) or development of pouchitis 
following ileal pouch-anal anastomosis for UC (Sandborn et al., 
Gastroenterol. 104: A774 (1993); Patel et al., Br. J. Surg. 81:724-726 
(1994); Vecchi et al., Lancet 344:886-887 (1994); Sandborn et al., Am. J. 
Gastroenterol. 90:740-747 (1995)). Thus, the ability to identify a 
pANCA-positive clinical subtype of UC can be useful in predicting, for 
example, treatment-resistant UC; the progression of UC; the need for early 
surgery or the development of pouchitis. 
The present invention is directed to the surprising discovery that an 
antigen that reacts with pANCA of ulcerative colitis is histone H1. Thus, 
the UC pANCA target antigen is a member of the histone family, which are 
highly-conserved proteins characterized by basic residues that contact the 
negatively charged phosphate groups in DNA and organize the DNA of 
eukaryotes into chromatin. Histones H2A, H2B, H3 and H4 are the core 
histones that make up nucleosomes, while histone H1, which is associated 
with nucleosomes at a 1 to 1 ratio, is required for higher order chromatin 
structure. 
Histone H1 has a conserved central globular domain with extended, flexible 
N- and C-terminal domains. Sites of reversible chemical modification, such 
as phosphorylation and acetylation, occur in these extended N- and 
C-terminal regions and can regulate histone-DNA interactions (Bradbury et 
al., Bioessays 14: 9-16 (1992)). The histone H1 family has multiple 
isoforms including H1.sup.S -1, H1.sup.S -2, H1.sup.S -3 and H1-4, which 
are present in all normal somatic cells; the highly variable H1 isoform, 
which is associated with differentiated cell types; and the 
testis-specific isoform H1 t (Parseghian et al., Protein Sci. 3:575-587 
(1994), which is incorporated herein by reference). That functional 
differences can be associated with alternative histone H1 isoforms is 
supported by differences among the isoforms in the time of protein 
synthesis; turnover rate; amount and pattern of phosphorylation and 
ability to condense DNA in vitro. 
As used herein, the term "histone H1" means one or more proteins having at 
least about 80% amino acid identity with at least one amino acid sequence 
of human histone H1 isoform H1.sup.S -1 (SEQ ID NO: 1); H1.sup.S -2 (SEQ 
ID NO: 2); H1.sup.S -3 (SEQ ID NO: 3); H1.sup.S -4 (SEQ ID NO: 4); 
H1.sup.o (SEQ ID NO: 5); H1 t (SEQ ID NO: 6). Thus, the term histone H1 
encompasses, for example, one or more of the human histone H1 isoforms 
having an amino acid sequence shown in FIG. 1. 
The term histone H1 also encompasses one or more non-human histone H1 
isoforms having at least about 80% amino acid identity with at least one 
of the human histone H1 isoforms having an amino acid sequence shown in 
FIG. 1. For example, the term histone H1 encompasses, for example, a mouse 
or bovine H1.sup.S -1 isoform having an amino acid sequence described in 
Parseghian et al., supra, 1994, or a rabbit or bovine H1.sup.S -2 isoform 
having an amino acid sequence described in Parseghian et al., supra, 1994. 
Similarly, the term histone H1 encompasses, for example, a rabbit or rat 
H1.sup.S -3 isoform having an amino acid sequence described in Parseghian 
et al., supra, 1994, or a mouse, rat, rabbit or bovine H1.sup.S -4 isoform 
having an amino acid sequence described in Parseghian et al., supra, 1994. 
As disclosed herein, histone H1 useful in the invention can be obtained 
from a variety of species. For example, histone H1 that forms a complex 
with a representative UC monoclonal antibody (NANUC-2) and, thus, can form 
a complex with pANCA, can be purified from human neutrophil or calf thymus 
as described in Example I. 
As used herein, the term "human histone H1" means one or more proteins 
having at least one amino acid sequence of human histone H1 isoform 
H1.sup.S -1 (SEQ ID NO: 1); H1.sup.S -2 (SEQ ID NO: 2); H1.sup.S -3 (SEQ 
ID NO: 3); H1.sup.S -4 (SEQ ID NO: 4); H1.sup.o (SEQ ID NO: 5) or H1 t 
(SEQ ID NO: 6). 
As used herein, the term "histone H1 isoform H1.sup.S -3" is synonymous 
with "H1.sup.S -3" and means a protein having at least about 80% amino 
acid identity with the amino acid sequence of human histone isoform 
H1.sup.S -3 (SEQ ID NO: 3) shown in FIG. 1. For example, the term H1.sup.S 
-3 encompasses human histone H1 isoform H1.sup.S -3 having the amino acid 
sequence (SEQ ID NO: 3) shown in FIG. 1. The term H1.sup.S -3 also 
encompasses a non-human H1.sup.S -3 protein having at least about 80% 
amino acid identity with the amino acid sequence shown as SEQ ID NO: 3, 
such as a rabbit or rat H1.sup.S -3 isoform having an amino acid sequence 
described in Parseghian et al., supra, 1994. 
As used herein, the term "histone H1 isoform H1.sup.S -2" is synonymous 
with "H1.sup.S -2" and means a protein having at least about 80% amino 
acid identity with the amino acid sequence of human histone isoform 
H1.sup.S -2 (SEQ ID NO: 2) shown in FIG. 1. For example, the term H1s-2 
encompasses human histone H1 isoform H1.sup.S -2 having the amino acid 
sequence (SEQ ID NO: 2) shown in FIG. 1. The term H1.sup.S -2 also 
encompasses a non-human H1.sup.S -2 protein having at least about 80% 
amino acid identity with the amino acid sequence shown as SEQ ID NO: 2, 
such as a rat or bovine H1.sup.S -2 isoform having an amino acid sequence 
described in Parseghian et al., supra, 1994. 
As further disclosed herein, Western analysis demonstrates that an antigen 
of 30-32 kDa present in various species of Mycobacteria is specifically 
reactive with NANUC-2, a representative UC pANCA monoclonal antibody (see 
FIG. 7). Isolation and amino-terminal sequencing of the 30-32 kDa protein 
from M. avium paratuberculosis revealed that the amino-terminal sequence 
was nearly identical to the amino-terminal sequence of a predicted M. 
tuberculosis protein of 214 amino acids (SEQ ID NO: 27). This M. 
tuberculosis protein shares 48% sequence similarity with human histone H1 
isoform H1.5 (SEQ ID NO: 32) (see FIG. 8), indicating that the 214 amino 
acid M. tuberculosis protein is a histone H1-like antigen. 
Immunoreactivity with NANUC-2 confirmed that the 214 amino acid M. 
tuberculosis protein (SEQ ID NO: 27) is a UC pANCA antigen. 
Identification of a pANCA-reactive Mycobacterial histone H1-like antigen 
implicates Mycobacteria in the pathogenesis of UC and provides a valuable 
reagent for diagnosing or ameliorating UC. Based on this finding, the 
present invention provides methods for diagnosing UC or a pANCA-positive 
clinical subtype of UC as well as methods of determining susceptibility to 
UC. The present invention also provides methods of treating UC and methods 
of preventing UC in a healthy individual by administering the recently 
identified UC pANCA target antigen, a histone H1-like antigen. 
In particular, the present invention provides methods of diagnosing UC by 
obtaining a sample from a subject suspected of having inflammatory bowel 
disease; contacting the sample with a histone H1-like antigen, or 
pANCA-reactive fragment thereof, under conditions suitable to form a 
complex of the histone H1-like antigen, or pANCA-reactive fragment 
thereof, and antibody to the histone H1-like antigen; and detecting the 
presence or absence of the complex, where the presence of the complex 
indicates that the subject has ulcerative colitis. A histone H1-like 
antigen useful in these methods can be, for example, a protein 
immunoreactive with NANUC-2 and having at least 65% amino acid identity 
with SEQ ID NO: 27. 
The present invention also provides methods of diagnosing a pANCA-positive 
clinical subtype of ulcerative colitis in a patient with UC. A 
pANCA-positive clinical subtype of UC can be diagnosed, for example, by 
obtaining a sample from a patient with UC; contacting the sample with a 
histone H1-like antigen, or pANCA-reactive fragment thereof, under 
conditions suitable to form a complex of the histone H1-like antigen, or 
pANCA-reactive fragment thereof, and antibody to histone H1-like antigen; 
and detecting the presence or absence of the complex, where the presence 
of the complex indicates that the patient has the pANCA-positive clinical 
subtype of UC. 
As used herein, the term "histone H1-like antigen" means a pANCA-reactive 
protein having linear or conformational homology to histone H1. A histone 
H1-like antigen generally is characterized as having at least about 48% 
amino acid similarity with one or more of the following human histone H1 
isoforms: H1.sup.S -1 (SEQ ID NO: 1); H1.sup.S -2 (SEQ ID NO: 2); H1-3 
(SEQ ID NO: 3); H1.sup.S -4 (SEQ ID NO: 4); H1.sup.o (SEQ ID NO: 5); or H1 
t (SEQ ID NO: 6). 
The term "histone H1-like antigen" encompasses, for example, a microbial 
histone H1-like antigen, which is a histone H1-like antigen of microbial 
origin having a molecular weight of about 30-32 kDa on SDS-PAGE analysis. 
An example of a microbial histone H1-like antigen is a 30-32 kDa protein 
which is immunoreactive with NANUC-2 and is isolated from a Mycobacteria 
such as M. tuberculosis; M. bovis, and M. bovis BCG; M. smegmatis 1-2 c; 
M. avium; M. avium paratuberculosis and M. avium paratuberculosis "Linda" 
strain (see FIG. 7). A microbial histone H1-like antigen can be, for 
example, the M. tuberculosis histone H1-like protein (SEQ ID NO: 27). 
The term histone H1-like antigen encompasses a protein that has at least 
65% amino acid identity with the 214 amino acid M. tuberculosis histone 
H1-like antigen (SEQ ID NO: 27). In particular, a histone H1-like antigen 
can have an amino acid sequence having, for example, at least 70%, 80%, 
85%, 90% or 95% amino acid identity with SEQ ID NO: 27. 
A histone H1-like antigen can be isolated from a variety of eukaryotic and 
prokaryotic organisms, including bacteria such as Mycobacteria and others. 
A histone H1-like antigen can be isolated from a variety of species of 
Mycobacteria, including Mycobacterium tuberculosis, Mycobacterium bovis, 
Mycobacterium smegmatis 1-2 c, Mycobacterium avium and Mycobacterium avium 
paratuberculosis. Histone H1-like antigens isolated from a variety of 
Mycobacterial species are disclosed in Example V. 
The present invention also relates to a UC pANCA porin antigen expressed by 
enteric bacteria of UC patients. As disclosed in Example VI, Western 
analysis demonstrates that a 35 kDa protein isolated from colonic E. coli 
of UC patients is specifically reactive with the UC pANCA monoclonal 
antibody NANUC-2 (see FIG. 9). The larger and smaller of two 
pANCA-reactive E. coli proteins were isolated and each sequenced from the 
N-terminus, revealing identical N-terminal sequence (SEQ ID NO: 33). This 
amino-terminal sequence indicated that the two pANCA-reactive E. coli 
proteins were related to the outer membrane proteins F and C (OmpF and 
OmpC; see FIG. 10). As shown in FIG. 11, the porin antigen of the 
invention lacks detectable linear sequence homology with histone H1 but 
can have conformational sequence homology with one or more pANCA-reactive 
epitopes of histone H1. These results indicate that microbial antigens 
lacking detectable linear sequence homology to histone H1 can be expressed 
by enteric colonic bacteria in UC patients and can play a role in the 
immune dysregulation in UC. 
Isolation of the porin antigen disclosed herein provides a novel UC pANCA 
target antigen for diagnosing and treating ulcerative colitis. Based on 
this discovery, the invention provides methods for diagnosing UC or a 
pANCA-positive clinical subtype of UC and methods of determining 
susceptibility to UC using a porin antigen. The invention further provides 
methods of treating UC by inducing tolerance in a pANCA-positive UC 
patient and methods of preventing UC in a healthy individual by 
administering a porin antigen. 
In particular, the present invention provides a method of diagnosing UC by 
obtaining a sample from a subject suspected of having inflammatory bowel 
disease; contacting the sample with a porin antigen, or pANCA-reactive 
fragment thereof, under conditions suitable to form a complex of the porin 
antigen, or pANCA-reactive fragment thereof, and antibody to the porin 
antigen; and detecting the presence or absence of the complex, where the 
presence of the complex indicates that the subject has ulcerative colitis. 
A porin antigen useful in these methods can be, for example, a protein 
immunoreactive with NANUC-2 and having an amino acid sequence having at 
least 65% amino acid identity with SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID 
NO: 30. 
The present invention also provides methods of diagnosing a pANCA-positive 
clinical subtype of ulcerative colitis in a patient with UC. A 
pANCA-positive clinical subtype of UC can be diagnosed, for example, by 
obtaining a sample from a patient with UC; contacting the sample with a 
porin antigen, or pANCA-reactive fragment thereof, under conditions 
suitable to form a complex of the porin antigen, or pANCA-reactive 
fragment thereof, and antibody to porin antigen; and detecting the 
presence or absence of the complex, where the presence of the complex 
indicates that the patient has the pANCA-positive clinical subtype of UC. 
The porin antigens disclosed herein belong to a class of transmembrane 
proteins that are found in the outer membranes of bacteria, including 
gram-negative, enteric bacteria such as E. coli. The porins in the outer 
membrane of an E. coli cell provide channels for passage of disaccharides, 
phosphate and similar molecules. Porins can be trimers of identical 
subunits arranged to form a barrel-shaped structure with a pore at the 
center (Lodish et al., Molecular Cell Biology, Chapter 14 (1995), which is 
incorporated herein by reference). 
Two major porin proteins found in the outer membranes of bacteria such as 
E. coli are outer-membrane protein F ("OmpF") and outer-membrane protein C 
("OmpC"). These two porins are similar in structure and function, 
assembling as trimers in the outer membrane to form aqueous channels that 
allow the passive diffusion of small, hydrophilic molecules across the 
hydrophobic barrier. The diameters of the OmpF and OmpC pores differ with 
the pore of OmpF being 1.2 nm while the diameter of the OmpC pore is 1.1 
nm. This difference results in a faster rate of diffusion through the OmpF 
pores than through the OmpC pores. 
Porin expression can be influenced by environmental conditions, including 
osmolarity, temperature, growth phase and toxin concentration. For 
example, in the intestine, where both nutrient and toxic molecule 
concentrations are relatively high, OmpC, with a smaller pore diameter, is 
the predominant porin (Pratt et al., Mol. Micro., 20:911-917 (1996), which 
is incorporated herein by reference). 
As used herein, the term "porin antigen" means a pANCA-reactive protein 
that has linear or conformational homology to OmpF, OmpC or another E. 
coli porin. A porin antigen generally is a protein that, in nature, forms 
a trimeric structure in the outer membrane of bacteria that allows the 
passage of small molecules, or a precursor of such a protein. A porin 
antigen can be derived from a gram-negative bacterium, such as E. col, and 
can be, for example, OmpF or OmpC, or a homolog thereof. 
The term "porin antigen," as used herein, encompasses a protein that has at 
least 65% amino acid identity with one or more of the following proteins: 
SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 30. A porin antigen can have, 
for example, at least 70%, 80%, 85%, 90% or 95% amino acid identity with 
SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 30. 
The present invention also relates to a novel UC pANCA target antigen 
derived from Bacteroides. Bacteroides is a genus of gram-negative, 
anaerobic, nonspore-forming, rod-shaped bacteria. They are normal 
inhabitants of the intestinal tract, and may constitute the predominant 
bacteria of the normal human colon. Some species of Bacteroides are known 
to be pathogenic, causing serious abscesses and bacteriomas. 
As disclosed herein, an antigen of about 100 kDa isolated from extracts of 
Bacteroides cecae is specifically reactive with NANUC-2 (see FIG. 9B). 
This pANCA-reactive antigen is selectively expressed in Bacteroides and is 
not expressed in all bacteria, for example, in E. coli (see FIG. 9; 
compare lanes 2 and 3 of panel B with other lanes). Identification of a 
Bacteroides antigen as a UC pANCA target antigen provides an additional 
valuable reagent for diagnosing the presence of pANCA in UC patients and 
for treating the disease. The Bacteroides antigen disclosed herein can be 
used alone for diagnosis or treatment of UC, or can be used in combination 
with one or more other UC pANCA target antigens such as those disclosed 
herein. 
Thus, the present invention provides methods of diagnosing UC by obtaining 
a sample from a subject suspected of having inflammatory bowel disease; 
contacting the sample with a Bacteroides antigen, or pANCA-reactive 
fragment thereof, under conditions suitable to form a complex of the 
Bacteroides antigen, or pANCA-reactive fragment thereof, and antibody to 
the Bacteroides antigen; and detecting the presence or absence of the 
complex, where the presence of the complex indicates that the subject has 
ulcerative colitis. A Bacteroides antigen useful in these methods can be, 
for example, a Bacteroides cecae protein immunoreactive with NANUC-2 and 
having a molecular weight of about 100 kDa by SDS-PAGE electrophoresis. 
The present invention also provides methods of diagnosing a pANCA-positive 
clinical subtype of ulcerative colitis in a patient with UC. A 
pANCA-positive clinical subtype of UC can be diagnosed, for example, by 
obtaining a sample from a patient with UC; contacting the sample with a 
Bacteroides antigen, or pANCA-reactive fragment thereof, under conditions 
suitable to form a complex of the Bacteroides antigen, or pANCA-reactive 
fragment thereof, and antibody to Bacteroides antigen; and detecting the 
presence or absence of the complex, where the presence of the complex 
indicates that the patient has the pANCA-positive clinical subtype of UC. 
As used herein, the term "Bacteroides antigen" means a microbial 
pANCA-reactive protein of about 100 kDa that is selectively expressed, at 
least in part, in Bacteroides. A Bacteroides antigen can be a Bacteroides 
cecae antigen and can be isolated as described in Example VI. 
A sample useful in the methods of the invention can be obtained from any 
biological fluid having pANCA such as, for example, whole blood, plasma or 
other bodily fluid or tissue having pANCA, preferably serum. As used 
herein, the term "patient" means any animal capable of producing pANCA, 
including, for example, a human, non-human primate, rabbit, rat or mouse. 
A sample to be assayed according to the methods of the invention can be 
obtained from any such patient. 
As used herein, the term "complex" is synonymous with "immune complex" and 
means an aggregate of two or more molecules that results from specific 
binding between an antigen, such as a protein or peptide, and an antibody. 
For example, a complex can be formed by specific binding of histone H1 to 
an antibody against histone H1. 
As used herein, the term "antibody" means a population of immunoglobulin 
molecules, which can be polyclonal or monoclonal and of any isotype. As 
used herein, the term antibody encompasses an immunologically active 
fragment of an immunoglobulin molecule. Such an immunologically active 
fragment contains the heavy and light chain variable regions, which make 
up the portion of the antibody molecule that specifically binds an 
antigen. For example, an immunologically active fragment of an 
immunoglobulin molecule known in the art as Fab, Fab' or F(ab').sub.2 is 
included within the meaning of the term antibody. 
As used herein, the term "secondary antibody" means an antibody or 
combination of antibodies, which binds pANCA of UC. Preferably, a 
secondary antibody does not compete with histone H1 or another antigen of 
the invention for binding to pANCA. A secondary antibody can be an 
anti-pANCA antibody that binds any epitope of pANCA. A particularly useful 
secondary antibody is an anti-IgG antibody having specificity for the 
class determining portion of pANCA. A useful secondary antibody is 
specific for the species of the ANCA to be detected. For example, if human 
serum is the sample to be assayed, mouse anti-human IgG can be a useful 
secondary antibody. A combination of different antibodies, which can be 
useful in the methods of the invention, also is encompassed within the 
meaning of the term secondary antibody, provided that at least one 
antibody of the combination binds pANCA of UC. 
As used herein, the term "class determining portion," when used in 
reference to a secondary antibody, means the heavy chain constant-region 
sequence of an antibody that determines the isotype, such as IgA, IgD, 
IgE, IgG or IgM. Thus, a secondary antibody that has specificity for the 
class determining portion of an IgG molecule, for example, binds IgG in 
preference to other antibody isotypes. 
A secondary antibody useful in the invention can be obtained commercially 
or by techniques well known in the art. Such an antibody can be a 
polyclonal or, preferably, monoclonal antibody that binds pANCA. For 
example, IgG reactive polyclonal antibodies can be prepared using IgG or 
Fc fragments of IgG as an immunogen to stimulate the production of 
antibodies in the antisera of an animal such as a rabbit, goat, sheep or 
rodent, as described in Harlow and Lane, Antibodies: A Laboratory Manual 
New York: Cold Spring Harbor Laboratory (1988), which is incorporated 
herein by reference. 
A monoclonal antibody also is useful in the practice of the invention. As 
used herein, a monoclonal antibody refers to a population of antibody 
molecules that contain only one species of idiotope capable of binding a 
particular antigen epitope. Methods of producing a monoclonal antibody are 
well known (see, for example, Harlow and Lane, supra, 1988). An immunogen 
useful in generating a monoclonal antibody that binds pANCA can be, for 
example, human IgG or a Fc fragment of human IgG, pANCA or a Fab fragment 
of pANCA. A hybridoma that produces a useful monoclonal antibody can be 
identified by screening hybridoma supernatants for the presence of 
antibodies that bind pANCA (Harlow, supra, 1988). For example, hybridoma 
supernatants can be screened using neutrophil and pANCA-positive sera in a 
radioimmunoassay or enzyme-linked immunosorbent assay. In addition, a 
monoclonal antibody useful in the invention can be obtained from a number 
of commercial sources. 
The term "detectable secondary antibody" means a secondary antibody, as 
defined above, that can be detected or measured by analytical methods. 
Thus, the term secondary antibody includes an antibody labeled directly or 
indirectly with a detectable marker that can be detected or measured and 
used in a convenient assay such as an enzyme-linked immunosorbent assay, 
radioimmunoassay, radial immunodiffusion assay or Western blotting assay, 
for example. A secondary antibody can be labeled, for example, with an 
enzyme, radioisotope, fluorochrome or chemiluminescent marker. In 
addition, a secondary antibody can be rendered detectable using a 
biotin-avidin linkage such that a detectable marker is associated with the 
secondary antibody. Labeling of the secondary antibody, however, should 
not impair binding of the secondary antibody to pANCA of UC. If desired, a 
multiple antibody system can be used as the secondary antibody as 
discussed above. In such a system, at least one of the antibodies is 
capable of binding pANCA of UC and at least one of the antibodies can be 
readily detected or measured by analytical methods. 
A secondary antibody can be rendered detectable by labeling with an enzyme 
such as horseradish peroxidase (HRP), alkaline phosphatase (AP), 
.beta.-galactosidase or urease, for example. A horseradish-peroxidase 
detection system can be used, for example, with the chromogenic substrate 
tetramethylbenzidine (TMB), which yields a soluble product in the presence 
of hydrogen peroxide that is detectable by measuring absorbance at 450 nm. 
An alkaline phosphatase detection system can be used with the chromogenic 
substrate .rho.-nitrophenyl phosphate, for example, which yields a soluble 
product readily detectable by measuring absorbance at 405 nm. Similarly, a 
.beta.-galactosidase detection system can be used with the chromogenic 
substrate .omicron.-nitrophenyl-.beta.-D-galactopyranoside (ONPG), which 
yields a soluble product detectable by measuring absorbance at 410 nm, or 
a urease detection system can be used with a substrate such as 
urea-bromocresol purple (Sigma Immunochemicals, St. Louis, Mo.). A 
secondary antibody can be linked to an enzyme by methods well known in the 
art (Harlow and Lane, supra, 1988) or can be obtained from a number of 
commercial sources. For example, goat F(ab')2 anti-human IgG-alkaline 
phosphatase is a useful detectable secondary antibody that can be 
purchased from Jackson Immuno-Research (West Grove, Pa.). 
A secondary antibody also can be rendered detectable by labeling with a 
fluorochrome. Such a fluorochrome emits light of ultraviolet or visible 
wavelength after excitation by light or another energy source. DAPI, 
fluorescein, Hoechst 33258, R-phycocyanin, B-phycoerythrin, 
R-phycoerythrin, rhodamine, Texas red or lissamine, for example, is a 
fluorochrome that can be linked to a secondary antibody and used to detect 
the presence or absence of a complex. A particularly useful fluorochrome 
is fluorescein or rhodamine. Methods of conjugating and using these and 
other suitable fluorochromes are described, for example, in Van Vunakis 
and Langone, Methods in Enzymology, Volume 74, Part C (1991), which is 
incorporated herein by reference. A secondary antibody linked to a 
fluorochrome also can be obtained from commercial sources. For example, 
goat F(ab')2 anti-human IgG-FITC is available from Tago Immunologicals 
(Burlingame, Calif.). 
A pANCA titer also can be determined using a secondary antibody labeled 
with a chemiluminescent marker. Such a chemiluminescent secondary antibody 
is convenient for sensitive, non-radioactive detection of pANCA and can be 
obtained commercially from various sources such as Amersham Lifesciences, 
Inc. (Arlington Heights, Ill.). 
A secondary antibody further can be rendered detectable by labeling with a 
radioisotope. An iodine-125 labeled secondary antibody is a particularly 
useful detectable secondary antibody (see, for example, Harlow and Lane, 
supra, 1988). 
A signal from a detectable secondary antibody can be analyzed, for example, 
using a spectrophotometer to detect color from a chromogenic substrate; a 
fluorometer to detect fluorescence in the presence of light of a certain 
wavelength; or a radiation counter to detect radiation, such as a gamma 
counter for detection of iodine-125. For detection of an enzyme-linked 
secondary antibody, for example, a quantitative analysis of the amount of 
ANCA can be made using a spectrophotometer such as an EMAX Microplate 
Reader (Molecular Devices, Menlo Park, Calif.) in accordance with the 
manufacturer's instructions. If desired, the assays of the invention can 
be automated or performed robotically, and the signal from multiple 
samples can be detected simultaneously. 
The assays of the present invention can be forward, reverse or simultaneous 
as described in U.S. Pat. No. 4,376,110, issued Mar. 8, 1983, to David et 
al., which is incorporated herein by reference. In the forward assay, each 
reagent is sequentially contacted with histone H1 or another antigen of 
the invention. If desired, separation of bound from unbound reagent can be 
performed before the addition of the next reagent. In a reverse assay, all 
reagents are pre-mixed prior to contacting histone H1 or another antigen 
of the invention. A modified reverse assay is described in U.S. Pat. No. 
4,778,751 issued Oct. 18, 1988, to El Shami et al., which is incorporated 
herein by reference. In a simultaneous assay, all reagents are separately 
but contemporaneously contacted with histone H1 or another antigen of the 
invention. As used herein, reagent means any component useful to perform 
the assays of the present invention, for example, the sample, histone H1 
or another antigen of the invention, detectable secondary antibody, 
washing buffer or other solutions. 
Separation steps for the various assay formats described herein, including 
the removal of unbound secondary antibody from the complex, can be 
performed by methods known in the art (Harlow and Lane, supra, 1988). For 
example, washing with a suitable buffer can be followed by filtration, 
aspiration or magnetic separation. If histone H1, another antigen of the 
invention, or a pANCA-reactive fragment thereof is immobilized on a 
particulate support, such as on microparticles, the particulate material 
can be centrifuged, if desired, followed by removal of wash liquid. If 
histone H1, another antigen of the invention, or a pANCA-reactive fragment 
thereof is immobilized on a membrane, filter or well, a vacuum or liquid 
absorbing apparatus can by applied to the opposite side of the membrane, 
filter or well to draw the wash liquid away from the complex. 
The invention also provides methods of determining susceptibility to UC in 
an individual by obtaining a sample from the individual; contacting the 
sample with human histone H1, or pANCA-reactive fragment thereof, under 
conditions suitable to form a complex of human histone H1, or 
pANCA-reactive fragment thereof, and antibody to human histone H1; and 
detecting the presence or absence of the complex, where the presence of 
the complex indicates that the individual has increased susceptibility to 
UC. Susceptibility to UC in an individual also can be determined by 
obtaining a sample from the individual; contacting the sample with 
purified histone H1 isoform H1s-2, or pANCA-reactive fragment thereof, 
under conditions suitable to form a complex of purified histone H1 isoform 
H1.sup.S -2, or pANCA-reactive fragment thereof, and antibody to histone 
H1 isoform H1.sup.S -2; and detecting the presence or absence of the 
complex, where the presence of the complex indicates that the individual 
has increased susceptibility to UC. 
The term "individual," as used herein, means any animal capable of 
producing pANCA, including a human, non-human primate, rabbit, rat or 
mouse, provided that the animal does not have ulcerative colitis as 
defined by the clinical, endoscopic and histopathologic parameters 
disclosed herein. A sample to be assayed according to the methods of the 
invention can be obtained from any such individual. 
As used herein, the term "susceptibility to UC," when used in reference to 
an individual, means an inability to resist ulcerative colitis 
disease-causing factors. As used herein, the term "increased 
susceptibility to UC," as indicated by the presence of a complex of 
histone H1 and antibody to histone H1, means an increased inability to 
resist ulcerative colitis disease-causing factors, as compared with an 
individual from whom a sample is obtained that does not form a complex 
when contacted with histone H1, or pANCA-reactive fragment thereof. 
Similarly, increased susceptibility to UC that is indicated by the 
presence of a complex of a histone H1-like antigen, a porin antigen or a 
Bacteroides antigen, and antibody to one of these antigens, means an 
increased inability to resist ulcerative colitis disease-causing factors, 
as compared with an individual from whom a sample is obtained that does 
not form such a complex. Increased susceptibility to UC in an individual 
does not mean the individual will necessarily develop UC. However, 
increased susceptibility to UC in an individual is associated with an 
increased probability of having ulcerative colitis in the future. 
The term "pANCA-reactive fragment," as used in reference to histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen, means a 
peptide or polypeptide portion of the antigen that has pANCA-reactive 
activity as defined by the ability to form a complex with pANCA. Thus, the 
term "pANCA-reactive fragment of histone H1," as used herein, means a 
peptide or polypeptide that has an amino acid sequence having at least 80% 
identity to a portion of one of the amino acid sequences shown in FIG. 1 
and pANCA-reactive activity as defined by the ability to form a complex 
with pANCA. A pANCA-reactive fragment can have from about three amino 
acids to about 200 amino acids. Preferably, a pANCA-reactive fragment of 
one of the UC pANCA antigens disclosed herein has from about five to about 
fifty amino acids and most preferably from about eight to about twenty 
amino acids. 
Several pANCA-reactive fragments of histone H1 are disclosed herein. As set 
forth in Examples II and III, peptides SEQ ID NO: 13, SEQ ID NO: 14 and 
SEQ ID NO: are pANCA-reactive fragments of histone H1, identified by their 
reactivity with NANUC-1 and NANUC-2. Thus, pANCA-reactive fragments of 
histone H1 can include, for example, the amino acid sequence of SEQ ID NO: 
7, SEQ ID NO: 13, SEQ ID NO: 14 or SEQ ID NO: 20. A pANCA-reactive 
fragment of histone H1 can have, for example, the amino acid sequence 
Pro-Lys-Lys-Ala-Lys-Lys-Pro-Ala-Ala-Ala-Thr-Val-Thr-Lys-Lys (SEQ ID NO: 
20). 
As disclosed herein, a pANCA-reactive fragment of histone H1 can be, for 
example, SEQ ID NO: 34 (amino acids 160-174 of H1.5); SEQ ID NO: 35 (amino 
acids 170 to 184 of H1.5) or SEQ ID NO: 36 (amino acids 180-194 of H1.5). 
As also disclosed herein, a pANCA-reactive fragment of histone H1 can be 
SEQ ID NO: 37 (amino acids 172 to 184 of H1.5); SEQ ID NO: 38 (amino acids 
69 to 184 of H1.5); SEQ ID NO: 39 (amino acids 69 to 171 of H1.5); SEQ ID 
NO: 40 (amino acids 69 to 226 of H1.5); or SEQ ID NO: 41 (amino acids 172 
to 226 of H1.5), which were identified as pANCA-reactive fragments of 
histone H1 by their reactivity with NANUC-2 (see Example IV). Reactivity 
of pANCA antibody with these fragments indicates that a pANCA reactive 
fragment of histone H1 can have an epitope within or around amino acids 
172 to 184 of histone H1.5 (SEQ ID NO: 37). An additional UC pANCA epitope 
can be localized to amino acids 69 to 171 of histone H1.5, as shown by the 
reactivity of SEQ ID NO: 39 with NANUC-2. 
A pANCA-reactive fragment of an antigen disclosed herein can be identified 
by the ability to form a complex with pANCA. For example, a pANCA-reactive 
fragment of histone H1, a histone H1-like antigen, a porin antigen or a 
Bacteroides antigen can be identified by its ability to form a complex 
with pANCA when contacted with pANCA-positive UC sera. Assays for the 
formation of an antigen-pANCA complex using pANCA-positive sera are well 
known in the art. For example, an enzyme-linked immunosorbent assay 
(ELISA) as described in Saxon et al., J. Allergy Clin. Immunol. 86:202-210 
(1990), which is incorporated herein by reference, is particularly useful 
in identifying a pANCA-reactive fragment that forms a complex with pANCA. 
A pANCA-reactive fragment of histone H1, a histone H1-like antigen, a porin 
antigen or a Bacteroides antigen further can be identified by its ability 
to form a complex with a representative UC pANCA monoclonal antibody, such 
as NANUC-2. The sequences of the NANUC-2 heavy and light chains are 
provided herein, and assays for determining binding to NANUC-2 are 
described in Examples IA and IB. An ELISA assay, for example, is 
particularly useful in identifying a pANCA-reactive fragment. Example II 
describes identification of the pANCA-reactive fragments of histone H1 SEQ 
ID NO: 13 and SEQ ID NO: 14, and Example II describes identification of 
the pANCA-reactive fragment SEQ ID NO: 20 using ELISA analysis. One 
skilled in the art understands that a pANCA-reactive fragment of a histone 
H1-like antigen, a porin antigen or a Bacteroides antigen can be similarly 
identified. 
The histone H1, histone H1-like, porin and Bacteroides antigens of the 
invention also can be useful in treating UC. The present invention 
provides, for example, methods of inducing tolerance in a pANCA-positive 
patient with UC by administering an effective dose of histone H1, or 
tolerogenic fragment thereof, to the pANCA-positive patient with UC. A 
tolerogenic fragment of histone H1 useful in the methods of the invention 
can include, for example, the amino acid sequence of SEQ ID NO: 7, SEQ ID 
NO: 13, SEQ ID NO: 14 or SEQ ID NO: 20. A particularly useful tolerogenic 
fragment of histone H1 includes the amino acid sequence of SEQ ID NO: 20. 
A tolerogenic fragment of histone H1 can be, for example, a 15-mer having 
amino acid sequence 
Pro-Lys-Lys-Ala-Lys-Lys-Pro-Ala-Ala-Ala-Thr-Val-Thr-Lys-Lys (SEQ ID NO: 
20). 
The invention also provides methods of inducing tolerance in a 
pANCA-positive patient with UC by administering to the patient an 
effective dose of a histone-like H1 antigen, or tolerogenic fragment 
thereof. Such a histone H1-like antigen can be, for example, a protein 
immunoreactive with NANUC-2 and having an amino acid sequence having at 
least 65% amino acid identity with SEQ ID NO: 27. 
The invention also provides methods of inducing tolerance in a 
pANCA-positive patient with UC by administering to the patient an 
effective dose of a porin antigen, or tolerogenic fragment thereof. Such a 
porin antigen can be, for example, a protein immunoreactive with NANUC-2 
and having at least 65% amino acid identity with SEQ ID NO: 28, SEQ ID NO: 
29 or SEQ ID NO: 30. 
The invention also provides methods of inducing tolerance in a 
pANCA-positive patient with UC by administering to the patient an 
effective dose of a Bacteroides antigen, or tolerogenic fragment thereof. 
Such a Bacteroides antigen can be, for example, a Bacteroides cecae 
protein immunoreactive with NANUC-2 and having a molecular weight of about 
100 kDa by SDS-PAGE electrophoresis. 
The term "tolerogenic fragment," as used in reference to histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen, means a 
peptide or polypeptide portion of the antigen that has tolerogenic 
activity as defined by its ability either alone, or in combination with 
another molecule, to produce a decreased immunological response. For 
example, the term "tolerogenic fragment of histone H1," as used herein, 
means a peptide or polypeptide which has an amino acid sequence having at 
least 80% identity to a portion of one of the amino acid sequences shown 
in FIG. 1 and tolerogenic activity as defined by its ability either alone, 
or in combination with another molecule, to produce a decreased 
immunological response. A tolerogenic fragment of histone H1, a histone 
H1-like antigen, a porin antigen or a Bacteroides antigen has from about 
three amino acids to about 200 amino acids. Preferably, a tolerogenic 
fragment of histone H1, a histone H1-like antigen, a porin antigen or a 
Bacteroides antigen has from about five to about fifty amino acids and 
most preferably from about eight to about twenty amino acids. 
A particularly useful tolerogenic fragment of histone H1, a histone H1-like 
antigen, a porin antigen or a Bacteroides antigen can be a cryptic T-cell 
determinant that normally is not the target of T-cell recognition due to 
inefficient processing and antigen presentation (see, for example, Sercarz 
et al., Ann. Rev. Immunol. 11:729 (1993), which is incorporated herein by 
reference). Without wishing to be bound by the following, ulcerative 
colitis can be associated with an immune response to histone H1 in disease 
tissue due to expression of a normally cryptic histone H1 T-cell 
determinant in an immunogenic form in disease target tissues but not in 
other tissues. 
As disclosed herein, a variety of cell types have substantial amounts of 
NANUC-2 reactive histone H1, as assayed by Western analysis which involves 
denatured histone H1. In particular, all cell types assayed by Western 
analysis, including both hematopoietic and non-hematopoietic cells such as 
neutrophils, lymphocytes, Molt-4, HL60 promyelocytic leukemia and COS 
cells, have NANUC-2 reactive histone H1. However, as disclosed herein, 
only neutrophils and HL60 cells are reactive with NANUC-2 or UC sera when 
cells are methanol-fixed and assayed by an immunohistochemical analysis 
involving native protein. These results indicate that native, but not 
denatured, histone H1 can have different immunoaccessibility properties in 
neutrophilic and non-neutrophilic cell types. 
The cell-type specific immunoaccessibility of histone H1 is supported by 
polyclonal rabbit anti-histone H1 antisera directed against an N-terminal 
35 amino acid fragment of human histone H1 isoform H1.sup.S -2 (SEQ ID NO: 
7). 
The antiserum against SEQ ID NO: 7 recognizes all histone H1 isoforms and 
has nearly identical reactivity profiles as NANUC-2 using Western 
analysis. Furthermore, the antisera against SEQ ID NO: 7, like 
pANCA-positive sera from UC patients, stains methanol-fixed neutrophils in 
a perinuclear distribution but not non-neutrophilic cells such as 
eosinophils or lymphocytes. 
A tolerogenic fragment of histone H1, a histone H1-like antigen, a porin 
antigen or a Bacteroides antigen can be identified using a variety of 
assays, including in vitro assays such as T-cell proliferation or cytokine 
secretion assays and in vivo assays such as the induction of tolerance in 
murine models of ulcerative colitis. T-cell proliferation assays, for 
example, are well recognized in the art as predictive of tolerogenic 
activity (see, for example, Miyahara et al., Immunol. 86:110-115 (1995) or 
Lundin et al, J. Exp. Med. 178:187-196 (1993), each of which is 
incorporated herein by reference). A T-cell proliferation assay can be 
performed by culturing T-cells with irradiated antigen-presenting cells, 
such as normal spleen cells, in microtiter wells for 3 days with varying 
concentrations of a fragment of histone H1, a histone H1-like antigen, a 
porin antigen or a Bacteroides antigen to be assayed; adding .sup.3 
H-thymidine; and measuring incorporation of .sup.3 H-thymidine into DNA. 
In such an assay, a fragment of histone H1, a histone H1-like antigen, a 
porin antigen or a Bacteroides antigen can be tested for activity, for 
example, at concentrations of 20 .mu.g/ml and 40 .mu.g/ml. 
A tolerogenic fragment of histone H1, a histone H1-like antigen, a porin 
antigen or a Bacteroides antigen also can be identified using a T-cell 
cytokine secretion assay as is well known in the art. For example, T cells 
can be cultured with irradiated antigen-presenting cells in microtiter 
wells with varying concentrations of the fragment of interest and, after 
three days, the culture supernatants can be assayed for IL-2, IL-4 or 
IFN-.gamma. as described in Czerinsky et al., Immunol. Rev. 119:5-22 
(1991), which is incorporated herein by reference. 
Primary T-cells for use in a T-cell proliferation assay or cytokine 
secretion assay, for example, can be isolated from lamina propria or 
peripheral blood. In addition, a convenient source of T-cells for use in 
an in vitro assay for tolerogenic activity can be a T-cell line 
established from an ulcerative colitis patient, murine model of ulcerative 
colitis or a healthy animal immunized with histone H1. A preferred source 
of T-cells for use in identifying a tolerogenic fragment of histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen is an 
ulcerative colitis patient. 
A T-cell line can be established from a patient with UC, for example, by 
culturing T lymphocytes with about 1 .mu.g/ml histone H1, which is 
prepared, for example, from human bone marrow as described in Example I, 
in the presence of low concentrations of growth-supporting IL-2 (about 10 
.mu.g/ml). A T-cell line can be established by culturing T lymphocytes 
with antigen-presenting cells and feeding the cells on an alternating four 
to five day cycle with either IL-2 and histone H1 or IL-2 alone as 
described in Nanda et al., J. Exp. Med. 176:297-302 (1992), which is 
incorporated herein by reference. A cell line that develops into a 
reliably proliferating cell line dependent on the presence of histone H1 
is particularly useful in identifying tolerogenic fragments of histone H1. 
The establishment of T-cell lines from small intestinal mucosa is 
described, for example, in Lundin et al., supra, 1993. T cell lines 
dependent upon the presence of a histone H1-like antigen, a porin antigen 
or a Bacteroides antigen can be prepared similarly and used to identify 
tolerogenic fragments of a histone H1-like antigen, a porin antigen or a 
Bacteroides antigen, respectively. 
A tolerogenic fragment of histone H1, a histone H1-like antigen, a porin 
antigen or a Bacteroides antigen can also be identified by its ability to 
induce tolerance in vivo, as indicated by a decreased immunological 
response, which can be a decreased T-cell response, such as a decreased 
proliferative response or cytokine secretion response as described above, 
or a decreased antibody titer to the antigen. A neonatal or adult mouse 
can be tolerized with a fragment of histone H1, for example, and a T-cell 
response or anti-histone H1 antibody titer can be assayed after 
challenging by immunization. For example, a neonatal mouse can be 
tolerized within 48 hours of birth by intraperitoneal administration of 
about 100 .mu.g of a fragment of histone H1 emulsified with incomplete 
Freund's adjuvant and subsequently immunized with histone H1 at about 8 
weeks of age (see, for example, Miyahara, supra, 1995). An adult mouse can 
be tolerized intravenously with about 0.33 mg of a fragment of histone H1, 
administered daily for three days (total dose 1 mg), and immunized one 
week later with histone H1. A decreased T-cell response, such as decreased 
proliferation or cytokine secretion, which indicates tolerogenic activity, 
can be measured using T-cells harvested 10 days after immunization. In 
addition, a decreased anti-histone H1 antibody titer, which also indicates 
tolerogenic activity, can be assayed using blood harvested 4-8 weeks after 
immunization. Methods for assaying a T-cell response or anti-histone H1 
antibody titer are described above and are well known in the art. Neonatal 
or adult mice can be tolerized similarly with a histone H1-like antigen, a 
porin antigen, or a Bacteroides antigen and used to identify tolerogenic 
fragments of the histone H1-like antigen, the porin antigen or the 
Bacteroides antigen, respectively. 
A tolerogenic fragment of histone H1, a histone H1-like antigen, a porin 
antigen or a Bacteroides antigen also can be identified using a murine 
model of ulcerative colitis. Neonatal or adult mice having ulcerative 
colitis-like disease can be tolerized with a fragment of histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen as 
described above, and the T-cell response or anti-histone antibody titer 
assayed. A decreased T-cell response or decreased antibody titer to the 
antigen indicates a decreased immunological response and, thus, serves to 
identify a tolerogenic fragment of histone H1, the histone H1-like 
antigen, porin antigen or Bacteroides antigen. In addition, a tolerogenic 
fragment of histone H1, a histone H1-like antigen, a porin antigen or a 
Bacteroides antigen can be identified by the ability to reduce the 
frequency, time of onset or severity of colitis in a murine model of UC. 
Several well-accepted murine models of ulcerative colitis are useful in 
identifying a tolerogenic fragment of histone H1 or another UC pANCA 
antigen disclosed herein. For example, mice deficient in IL-2 as described 
in Sadlack et al., Cell 75:253-261 (1993), which is incorporated herein by 
reference, and mice deficient in IL-10 as described in Kuhn et al., Cell 
75:263-274 (1993), which is incorporated herein by reference, have 
ulcerative-colitis like disease and are useful in identifying a 
tolerogenic fragment of histone H1, a histone H1-like antigen, a porin 
antigen or a Bacteroides antigen. Furthermore, mice with mutations in T 
cell receptor (TCR) .alpha., TCR .beta., TCR .beta..times..delta., or the 
class II major histocompatiblility complex (MHC) as described in Mombaerts 
et al., Cell 75:275-282 (1993), which is incorporated herein by reference, 
develop inflammatory bowel disease that resembles ulcerative colitis and, 
thus, are useful in identifying a tolerogenic fragment of histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen. 
Similarly, a fragment can be assayed for tolerogenic activity in a SCID 
mouse reconstituted with CD45RB CD4+T-cells, which is a well-accepted 
model of human ulcerative colitis, as described in Powrie et al., Immunity 
1:553-562 (1994), which is incorporated herein by reference. Thus, a 
tolerogenic fragment of histone H1, a histone H1-like antigen, a porin 
antigen or a Bacteroides antigen can be readily identified by an in vitro 
or in vivo assay disclosed herein or by another assay well known in the 
art. 
A pANCA-reactive or tolerogenic fragment can be identified by screening, 
for example, fragments of the antigen produced by chemical or proteolytic 
cleavage. A fragment prepared from histone H1 purified from a target 
tissue such as intestinal mucosa can be particularly useful since such a 
fragment can have a post-translational modification that contributes to 
pANCA-reactive activity or tolerogenic activity. Methods for chemical and 
proteolytic cleavage and for purification of the resultant protein 
fragments are well known in the art (see, for example, Deutscher, Methods 
in Enzymology, Vol. 182, "Guide to Protein Purification," San Diego: 
Academic Press, Inc. (1990), which is incorporated herein by reference). 
For example, a chemical such as cyanogen bromide or a protease such as 
trypsin, chymotrypsin, V8 protease, endoproteinase Lys-C, endoproteinase 
Arg-C or endoproteinase Asp-N can be used to produce convenient fragments 
of histone H1, a histone H1-like antigen, a porin antigen or a Bacteroides 
antigen that can be screened for pANCA-reactive activity or tolerogenic 
activity using one of the assays disclosed herein. 
A pANCA-reactive or tolerogenic fragment of histone H1, a histone H1-like 
antigen, a porin antigen or a Bacteroides antigen also can be identified 
by screening a large collection, or library, of random peptides or 
peptides of interest for pANCA-reactive activity or tolerogenic activity. 
Peptide libraries include, for example, tagged chemical libraries 
comprising peptides and peptidomimetic molecules. Peptide libraries also 
comprise those generated by phage display technology. Phage display 
technology includes the expression of peptide molecules on the surface of 
phage as well as other methodologies by which a protein ligand is or can 
be associated with the nucleic acid which encodes it. Methods for 
production of phage display libraries, including vectors and methods of 
diversifying the population of peptides which are expressed, are well 
known in the art (see, for example, Smith and Scott, Methods Enzymol. 
217:228-257 (1993); Scott and Smith, Science 249:386-390 (1990); and Huse, 
WO 91/07141 and WO 91/07149, each of which is incorporated herein by 
reference). These or other well known methods can be used to produce a 
phage display library which can be screened, for example, with one of the 
disclosed assays for pANCA-reactive activity or tolerogenic activity. If 
desired, a population of peptides can be assayed for activity en masse. 
For example, to identify a pANCA-reactive fragment of histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen, a 
population of peptides can be assayed for the ability to form a complex 
with NANUC-2; the active population can be subdivided and the assay 
repeated in order to isolate a pANCA-reactive fragment from the 
population. 
In addition, a peptide library can be a panel of peptides spanning the 
entire sequence of an antigen of interest. For example, a panel of about 
75 individual 15-mer peptides spanning the sequence of human histone H1 
isoform H1.sup.S -2 (SEQ ID NO: 2) can be synthesized, each overlapping by 
three residue shifts using the Mimotope cleavable pin technology 
(Cambridge Research Biochemicals, Wilmington, Del. ), as described by 
Geysen et al., Science 235:1184 (1987), which is incorporated herein by 
reference. A panel of peptides spanning the sequence of any of the histone 
H1 isoforms such as those shown in FIG. 1 or another UC pANCA antigen 
disclosed herein can be generated similarly, and the panel screened for 
pANCA-reactive activity or tolerogenic activity using one of the assays 
described above (see, for example, Miyahara et al., supra, 1995, which is 
incorporated herein by reference). 
A library of peptides to be screened also can be made up of peptides of 
interest, such as a population of peptides related in amino acid sequence 
to SEQ ID NO: 7 or SEQ ID NO: 20 but having one or more amino acids that 
differ from SEQ ID NO: 7 or SEQ ID NO: 20. For identifying a tolerogenic 
fragment of histone H1, peptides of interest also can be peptides derived 
from a histone H1 sequence that have appropriate HLA-DR binding motifs as 
described, for example, in Sette et al., J. Immunol. 151:3163-3170 (1993), 
which is incorporated herein by reference. A particularly useful 
population of peptides is a population having a HLA-DR2 binding motif 
(Yang et al., supra, 1993). If desired, peptides of interest can be 
selected for HLA-DR binding activity as described in Sette et al., supra, 
1993, prior to screening for tolerogenic activity. 
As used herein, the term "fragment" means a peptide, polypeptide or 
compound containing naturally occurring amino acids, non-naturally 
occurring amino acids or chemically modified amino acids. A pANCA-reactive 
or tolerogenic fragment of histone H1, a histone H1-like antigen, a porin 
antigen or a Bacteroides antigen also can be a peptide mimetic, which is a 
non-amino acid chemical structure that mimics the structure of a peptide 
having an amino acid sequence, provided that the peptidomimetic retains 
pANCA-reactive activity or tolerogenic activity, as defined herein. Such a 
mimetic generally is characterized as exhibiting similar physical 
characteristics such as size, charge or hydrophobicity in the same spatial 
arrangement found in its peptide counterpart. A specific example of a 
peptide mimetic is a compound in which the amide bond between one or more 
of the amino acids is replaced, for example, by a carbon-carbon bond or 
other bond well known in the art (see, for example, Sawyer, Peptide Based 
Drug Design, ACS, Washington (1995), which is incorporated herein by 
reference). 
As used herein, the term "amino acid" refers to one of the twenty naturally 
occurring amino acids, including, unless stated otherwise, L-amino acids 
and D-amino acids. The term amino acid also refers to compounds such as 
chemically modified amino acids including amino acid analogs, naturally 
occurring amino acids that are not usually incorporated into proteins such 
as norleucine, and chemically synthesized compounds having properties 
known in the art to be characteristic of an amino acid, provided that the 
compound can be substituted within a peptide such that it retains 
pANCA-reactive activity or tolerogenic activity. Examples of amino acids 
and amino acids analogs are listed in Gross and Meienhofer, The Peptides: 
Analysis, Synthesis, Biology, Academic Press, Inc., New York (1983), which 
is incorporated herein by reference. An amino acid also can be an amino 
acid mimetic, which is a structure that exhibits substantially the same 
spatial arrangement of functional groups as an amino acid but does not 
necessarily have both the .alpha.-amino and .alpha.-carboxyl groups 
characteristic of an amino acid. 
A pANCA-reactive or tolerogenic fragment of histone H1, a histone H1-like 
antigen, a porin antigen or a Bacteroides antigen useful in the invention 
can be produced or synthesized using methods well known in the art. Such 
methods include recombinant DNA methods and chemical synthesis methods for 
production of a peptide. 
Recombinant methods of producing a peptide through expression of a nucleic 
acid sequence encoding the peptide in a suitable host cell are well known 
in the art and are described, for example, in Sambrook et al., Molecular 
Cloning: A Laboratory Manual, 2nd Ed, Vols 1 to 3, Cold Spring Harbor 
Laboratory Press, New York (1989), which is incorporated herein by 
reference. 
Nucleic acids encoding histone H1 are available to one skilled in the art 
as described in Eick et al., Eur. J. 
Cell. Biol. 49:110-115 (1989); Albig et al., Genomics 10:940-948 (1991); 
Carozzi et al., Science 224:1115-1117 (1984); La Bella et al., J. Biol. 
Chem. 263:2115-2118 (1988); Cole et al., Gene 89:265-269 (1990); Cheng et 
al., Proc. Natl. Acad. Sci. USA 86:7002-7006 (1989); Yan et al., J. Biol. 
Chem. 262:17118-17125 (1987); and Brown and Sitman, J. Biol. Chem. 
268:713-718 (1993), each of which is incorporated herein by reference. 
A pANCA-reactive or tolerogenic fragment of histone H1, a histone H1-like 
antigen, a porin antigen or a Bacteroides antigen useful in the invention 
also can be produced by chemical synthesis, for example, by the solid 
phase peptide synthesis method of Merrifield et al., J. Am. Chem. Soc. 
85:2149 (1964), which is incorporated herein by reference. Standard 
solution methods well known in the art also can be used to synthesize a 
pANCA-reactive or tolerogenic fragment useful in the invention (see, for 
example, Bodanszky, Principles of Peptide Synthesis, Springer-Verlag, 
Berlin (1984) and Bodanszky, Peptide Chemistry, Springer-Verlag, Berlin 
(1993), each of which is incorporated herein by reference). A newly 
synthesized peptide can be purified, for example, by high performance 
liquid chromatography (HPLC), and can be characterized using, for example, 
mass spectrometry or amino acid sequence analysis. 
It is understood that limited modifications can be made to histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen without 
destroying its biological function. Similarly, limited modifications can 
be made to a pANCA-reactive fragment of an antigen disclosed herein or a 
tolerogenic fragment of an antigen disclosed herein without destroying its 
pANCA-reactive activity or tolerogenic activity. A modification of an 
antigen disclosed herein that does not destroy pANCA-reactive activity or 
a modification of an antigen disclosed herein that does not destroy 
tolerogenic activity is within the definition of such antigen. Similarly, 
a modification of a pANCA-reactive fragment of an antigen disclosed herein 
that does not destroy its ability to form a complex with pANCA is within 
the definition of a pANCA-reactive fragment of such antigen. Furthermore, 
a modification of a tolerogenic fragment of an antigen disclosed herein 
that does not destroy its ability to produce a decreased immunological 
response is within the definition of a tolerogenic fragment of such 
antigen. A modification can be, for example, an addition, deletion, or 
substitution of amino acid residues; substitution of a compound that 
mimics amino acid structure or function; or addition of chemical moieties 
such as amino or acetyl groups. The activity of a modified antigen 
disclosed herein or a modified fragment of such antigen can be assayed, 
for example, using one of the assays for pANCA-reactive or tolerogenic 
activity disclosed herein. 
A particularly useful modification of an antigen disclosed herein or a 
pANCA-reactive or tolerogenic fragment of such antigen is a modification 
that confers, for example, increased stability. Incorporation of one or 
more D-amino acids is a modification useful in increasing stability of a 
protein or protein fragment. Similarly, deletion or substitution of lysine 
can increase stability by protecting against degradation. For example, 
such a substitution can increase stability and, thus, bioavailability of 
an antigen disclosed herein or a tolerogenic fragment of such antigen, 
provided that the substitution does not affect tolerogenic activity. 
As used herein, the term "effective dose" means the amount of histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen, or a 
tolerogenic fragment thereof, useful for inducing tolerance in a 
pANCA-positive patient with UC. For induction of oral tolerance, for 
example, multiple smaller oral doses can be administered or a large dose 
can be administered. Such doses can be extrapolated, for example, from the 
induction of tolerance in animal models (see, for example, Trentham et 
al., Science 261:1727-1730 (1993), which is incorporated herein by 
reference). 
The present invention also provides tolerogenic compositions that contain a 
UC pANCA antigen and are useful in inducing tolerance in a patient with 
UC. In particular, the invention provides a composition of histone H1, or 
fragment thereof, and a tolerogizing molecule. A composition of the 
invention can contain a fragment of histone H1 including the amino acid 
sequence of SEQ ID NO: 7, SEQ ID NO: 13, SEQ ID NO: 14 or SEQ ID NO: 20 
combined with a tolerogizing molecule. A composition of the invention also 
can contain a fragment of histone H1 having the amino acid sequence of SEQ 
ID NO: 20 combined with a tolerogizing molecule. 
The present invention also provides a composition of histone H1-like 
antigen, or tolerogenic fragment thereof, combined with a tolerogizing 
molecule. In such a composition, a histone H1-like antigen can be, for 
example, a protein having an amino acid sequence having at least 65% amino 
acid identity with SEQ ID NO: 27. 
In addition, there is provided a porin antigen, or tolerogenic fragment 
thereof, combined with a tolerogizing molecule. In a composition of the 
invention, a porin antigen can be, for example, a protein having at least 
65% amino acid identity with SEQ ID NO: 28, SEQ ID NO: 29 or SEQ ID NO: 
30. 
Also provided herein is a composition containing a Bacteroides antigen, or 
a tolerogenic fragment thereof, combined with a tolerogizing molecule. 
Such a Bacteroides antigen can be, for example, a Bacteroides cecae 
protein having a molecular weight of about 100 kDa by SDS-PAGE 
electrophoresis. 
Various molecules are known in the art to cause, promote or enhance 
tolerance. See, for example, U.S. Pat. No. 5,268,454, and citations 
therein, which are incorporated herein by reference. As used herein, the 
term "tolerogizing molecule" means a molecule, compound or polymer that 
causes, promotes or enhances tolerogenic activity when combined with 
histone H1, a histone H1-like antigen, a porin antigen or a Bacteroides 
antigen, or fragment thereof. A tolerogizing molecule can be, for example, 
conjugated to histone H1 or another UC pANCA antigen. Such tolerogizing 
molecules include, for example, polyethylene glycol and are well known in 
the art (see, for example, U.S. Pat. No. 5,268,454, supra). 
An effective dose of histone H1, a histone H1-like antigen, a porin 
antigen, or a Bacteroides antigen or a tolerogenic fragment thereof for 
inducing tolerance can be administered by methods well known in the art. 
Oral tolerance is well-recognized in the art as a method of treating 
autoimmune disease (see, for example, Weiner, Hospital Practice, pp. 53-58 
(Sep. 15, 1995), which is incorporated herein by reference). For example, 
orally administered autoantigens suppress several experimental autoimmune 
models in a disease- and antigen-specific fashion; the diseases include 
experimental autoimmune encephalomyelitis, uveitis, and myasthenia, 
collagen- and adjuvant-induced arthritis, and diabetes in the NOD mouse 
(see, for example, Weiner et al., Ann. Rev. Immunol. 12:809-837 (1994), 
which is incorporated herein by reference). Furthermore, clinical trials 
of oral tolerance have produced positive results in treating multiple 
sclerosis, rheumatoid arthritis and uveitis. In addition, parenteral 
administration of histone H1, another antigen of the invention, or a 
tolerogenic fragment thereof, can be used to induce tolerance. 
Subcutaneous injection, for example, can be used to deliver histone H1, a 
histone H1-like antigen, a porin antigen or a Bacteroides antigen, or a 
tolerogenic fragment thereof, to a pANCA-positive patient with UC 
(Johnson, Ann. Neurology 36(suppl.):S115-S117 (1994), which is 
incorporated herein by reference). 
The invention also provides methods of preventing UC in an individual by 
administering an effective dose of histone H1, a histone H1-like antigen, 
a porin antigen or a Bacteroides antigen, or a tolerogenic fragment 
thereof, to the individual. The methods of the invention are particularly 
useful for preventing UC in an individual having increased susceptibility 
to UC. Such methods can be particularly useful for preventing UC when an 
effective dose of the antigen or tolerogenic fragment is administered to a 
newborn individual. 
Prior to this time, a connection between specific enteric bacteria and UC 
has not been made although bacteria have been shown to play a role in the 
pathogenesis of other enteric diseases. For example, H. pylori has been 
implicated in the pathogenesis of peptic ulcer disease. Antibiotics 
against H. pylori have been shown to effectively treat this disease (see, 
for example, Sontag, Am. J. Gastroenterol. 92:1255-1261 (1997); and Pipkin 
et al., Helicobactor. 2:159-171 (1997), each of which is incorporated 
herein by reference). As disclosed herein, several colonic bacteria 
harbored in UC patients, including bacteria from the genera of 
Mycobacteria, Escherichia and Bacteroides, express antigens reactive with 
the pANCA autoantibody, which is present in the majority of patients with 
UC (see Examples V and VI). These results indicate that an agent directed 
against one or more of such pANCA-reactive bacteria can be useful in 
reducing the number of colonic bacteria, thereby diminishing the immune 
stimulus contributing to UC and ameliorating the symptoms of the disease. 
Thus, the invention provides a method of identifying an agent useful for 
treating UC by obtaining a sample of enteric bacteria from a patient with 
UC; isolating from the sample a bacterial species that expresses a 
pANCA-reactive antigen; contacting the bacterial species with an agent; 
and assaying for the reduced growth or viability of the bacterial species, 
where the reduced growth or viability of the bacterial species indicates 
that the agent is an agent useful for treating UC. The enteric bacterial 
species that expresses a pANCA-reactive antigen can be, for example, a 
member of the genera of Mycobacteria, Escherichia or Bacteroides. An 
enteric Mycobacteria that expresses a pANCA-reactive antigen can be, for 
example, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium 
smegmatis [1-2 c], Mycobacterium avium and Mycobacterium avium 
paratuberculosis. An enteric Escherichia that expresses a pANCA-reactive 
antigen can be, for example, Escherichia coli. An enteric Bacteroides that 
expresses a pANCA-reactive antigen can be, for example, Bacteroides cecae. 
One skilled in the art understands that the bacterial specieis which is 
contacted with an agent in the methods of the invention can be a single 
bacterial species or can be a mixture of two or more bacterial species 
that express a pANCA-reactive antigen. 
As used herein, the term "agent" means a biological or chemical compound 
such as a simple or complex organic molecule, a peptide, a protein, an 
antibody, a lipid or an oligonucleotide. 
As used herein, the term "agent useful for treating UC" means an agent that 
can reduce the viability or growth of a bacterial species that expresses a 
pANCA-reactive antigen. Thus, an agent useful for treating UC is an agent 
that functions as a bacteristat or bactericide against a bacterial species 
that expresses a pANCA-reactive antigen. An agent useful for treating UC 
can be a bacterial antibiotic, which is a molecule that is produced by a 
microorganism or a plant, or a close chemical derivative of such a 
molecule, that can reduce the growth or viability of a bacterial species 
that expresses a pANCA-reactive antigen. An agent useful for treating UC 
can function by a variety of mechanisms, for example, by inhibiting 
bacterial protein synthesis, inhibiting bacterial DNA synthesis, 
inhibiting the synthesis of a bacterial cell wall or inhibiting synthesis 
of an essential nutrient of a bacterial species that expresses a 
pANCA-reactive antigen. Such an agent can selectively reduce the viability 
or growth of a particular bacterial species that expresses a 
pANCA-reactive antigen. An agent useful for treating UC also can have 
activity in reducing the growth or viability of a broad spectrum of 
bacteria such as a genus of bacteria. One skilled in the art understands 
that, preferably, an agent useful for treating UC reduces the growth or 
viability of a bacterial specieis that expresses a pANCA-reactive antigen 
without significantly altering the growth or viability of mammalian cells, 
especially human cells. 
The following examples are intended to illustrate but not limit the present 
invention. 
EXAMPLE I 
Identification of the Ulcerative Colitis pANCA Target Antigen 
This example demonstrates that representative UC pANCA monoclonal 
antibodies bind histone H1 specifically. 
A. Histone H1 is an ulcerative colitis pANCA target antigen 
Representative UC pANCA monoclonal antibodies, designated NANUC-1 and 
NANUC-2, were isolated from a UC lamina propria lymphocyte phage display 
IgG library and use to screen human neutrophil. Western analysis 
demonstrated specific binding of NANUC-2 to a nuclear protein doublet of 
32-33 kDa. Purification by subcellular fractionation and preparative gel 
electrophoresis followed by protein microsequencing identified the NANUC-2 
reactive antigen as histone H1. 
Western analysis showed reactivity with lysine-rich calf thymus histone. In 
addition, histones purified from human neutrophil were fractionated into a 
perchloric acid insoluble fraction (containing core histones) and a 
perchloric acid soluble fraction (containing histone H1). As shown in FIG. 
2, NANUC-2 reacted with the perchloric acid soluble histone fraction, 
indicating that histone H1 is an ulcerative colitis pANCA target antigen. 
Purified core histones (H2A, H2B, H3 and H4) were minimally reactive with 
NANUC-2. In addition, purified human histone H1 isoforms H1.sup.3 -1, 
H1.sup.S -2, H1.sup.S -3, H1.sup.S -4 and H1.sup.o were analyzed by 
immunoblot analysis, and NANUC-2 was reactive with each of the isoforms 
including H1.sup.o. 
Histone H1 was purified according to the methods described in Prescott, 
Methods in Cell Biology, Vol XVI, "Chromatin and Chromosomal Protein 
Research" (New York, N.Y.: Academic Press (1977)), which is incorporated 
herein by reference, as follows. Purified bone marrow was obtained and red 
blood cell lysed prior to freezing. The bone marrow, which contained 
lymphocytes and granulocytes, was thawed rapidly and washed with 
phosphate-buffered saline (PBS). The cells were extracted with four cell 
volumes of 200 mM H.sub.2 SO.sub.4 /40 mM NaHSO.sub.3 in the presence of 
protease inhibitors, sonicated for 60 seconds on ice, and incubated on ice 
for one hour with occasional vortexing. Nuclei and cell debris were 
pelleted at 2500 rpm (Beckman JA-6) at 40.degree. C. for 20 minutes, the 
supernatant transferred to a new tube, and core histones (H2A, H2A, H3 and 
H4) precipitated at -20.degree. C. overnight by the addition of three to 
four volumes of 95% ethanol. The histone pellet was washed with 70% 
ethanol, dried and resuspended in 3 ml 40 mM NaHSO.sub.3 with protease 
inhibitors. 
Histone H1 was selectively extracted from core histones by addition of 70% 
perchloric acid (to a final concentration of 5%) followed by incubation on 
a rotating wheel at 4.degree. C. for 1 hour. Core histones were pelleted 
at 2500 rpm at 4.degree. C. for 20 minutes. Histone H1 was precipitated 
from the supernatant for 2 hours at -20.degree. C. with 10 ml of acidified 
acetone (10 ml acetone+77 .mu.l concentrated hydrochloric acid). Histone 
H1 was centrifuged as above, and the pellet washed with a solution of 3.5 
ml acetone/1 ml 1 M HCl to remove high-mobility group (HMG) proteins. The 
core histones and histone H1 pellets each were washed separately three 
times with 5 ml 95% ethanol and dried. Protein purity was established by 
polyacrylamide gel electrophoresis and Coomassie blue staining. 
Western analysis was performed as follows. Cells were lysed in 10 mM 
HEPES/1.5 mM MgCl.sub.2 /10 mM KCl pH 7.9 in the presence of protease 
inhibitors and sheared with a 20 G needle. Lysis was monitored by trypan 
blue exclusion. Nuclei were pelleted and resuspended in extraction buffer, 
and the cell fractions electrophoresed on a 12% polyacrylamide gel under 
non-reducing conditions. Proteins were transferred to nitrocellulose 
membranes, and the transfer verified by Ponceau S red staining (SIGMA, St. 
Louis, Mo.). Membranes were blocked with 5% milk in 0.1% Tween-20/PBS for 
1 hour. Primary and secondary antibody incubations were for 1 hour in 1% 
milk in 0.1% Tween-20/PBS. The primary antibodies, NANUC-1, NANUC-2, and 
anti-tetanus toxoid Fabs were used at a concentration of 0.1 to 1.0 
.mu.g/ml. The secondary antibody was goat anti-human Fab-alkaline 
phosphatase or goat anti-human kappa-biotin used at a dilution of 1 to 
1000 or 1 to 2000, respectively. Alkaline phosphatase labeled antibodies 
were detected with BCIP-NBT (SIGMA). Biotinylated antibodies were detected 
with SA-HRP (Amersham Lifesciences, Inc., Arlington Heights, Ill.) and 
enhanced chemiluminescence. 
B. Reactivity of NANUC-2 with histone H1 using ELISA analysis 
Microtiter plates coated with neutrophil, total histone or purified calf 
thymus histone H1 were used for ELISA analysis as described below. The 
reactivity of NANUC-1, NANUC-2 and negative control anti-tetanus toxoid 
antibody was tested against human PMN (neutrophil), total histone, calf 
thymus histone H1, or tetanus toxoid antigen. As shown in FIG. 3, the 
ELISA assays demonstrated that NANUC-1 and NANUC-2 react with human 
neutrophil. However, NANUC-2, but not NANUC-1 or anti-tetanus toxoid 
antibody, was reactive with total calf thymus histone (histone H1 and core 
histones) and calf thymus histone H1 (SIGMA). 
ELISA assays were performed as follows. For detection of total Fab 
immunoglobulin, microtiter plates (Costar 3069, Cambridge, Mass.) were 
coated overnight at 4.degree. C. with 500 ng/well antigen in bicarbonate 
pH 9.6 coating buffer. Wells were blocked with 0.25% BSA/PBS for 1 hour, 
incubated with rFabs diluted in 0.25% BSA/PBS for 1 hour, and washed five 
times with 0.5% Tween-20/PBS at room temperature. Plates were subsequently 
incubated with a 1 to 1000 dilution of alkaline phosphatase-labeled goat 
anti-human Fab (Pierce, Rockford, Ill.) for 1 hour; washed five times in 
0.5% Tween-20/PBS; washed three times with Tris-NaCl (50 mM Tris 150 mM 
NaCl pH 7.5); and developed with 5 mg/ml .rho.-nitrophenyl phosphate 
(SIGMA) in 10% diethanolamine/i mM MgCl.sub.2 pH 9.8. The absorbance of 
each sample was measured at 405 nm using a Biorad ELISA reader (Richmond, 
Calif.). Neutrophil samples were prepared as described in Saxon et al., 
supra, 1990; total calf thymus histone and calf thymus histone H1 were 
obtained from SIGMA. 
C. Reactivity of NANUC-2 with subcellular fractions 
Subcellular fractionation of human neutrophils demonstrated that NANUC-2 is 
almost exclusively reactive with a nuclear protein doublet of 32-33 kDa 
apparent molecular weight (see FIG. 4). The NANUC-2 reactive doublet was 
present in the nuclear fraction of neutrophils and represents histone H1 
subtypes H1.sup.S -1, H1.sup.S -2, H1.sup.S -3, H1.sup.S -4 and H1.sup.o 
as determined by apparent size on SDS-PAGE following Western blot 
detection. Additional lower molecular weight proteins, which have slight 
reactivity with NANUC-2, may represent the core histones or histone H1 
degradation products. NANUC-1 and the negative control anti-tetanus toxoid 
antibody were not reactive with any protein species on Western blots. 
In cell types other than neutrophils, histone H1 reactivity was detected in 
both whole cell lysate and nuclear fraction but not in the cytoplasmic 
fraction. In contrast, neutrophil nuclear fraction revealed a large amount 
of NANUC-2 reactive histone H1, but no reactivity was seen in whole cell 
lysate prepared from the same cells. The lack of reactivity in neutrophil 
whole cell lysate can be a result of very rapid degradation of histone H1 
by proteases found in neutrophilic granules but not in other cells such as 
Molt-4 cells (see FIG. 4). 
EXAMPLE II 
IDENTIFICATION OF pANCA-REACTIVE H1 FRAGMENTS 
This example demonstrates that particular fragments of histone H1 are 
reactive with the NANUC-2 antibody. 
To further characterize the pANCA-reactive histone H1 epitope, purified 
protein was subjected to chemical cleavage with N-N bromosuccinamide (NBS) 
and proteolysis with chymotryspin, and reactivity of the resulting 
fragments was analyzed by silver staining and immunoblotting. NBS cleavage 
of H1 resulted in two fragments: an N-terminal 73 amino acid fragment (SEQ 
ID NO: 12) and a C-terminal 147 amino acid fragment (SEQ ID NO: 13). 
Because of the extremely charged nature of these fragments, the apparent 
mobilities of the 73 and 147 amino acid fragments are 23 and 11 kD, 
respectively. 
Immunoblot analysis revealed that only the larger 147 amino acid fragment 
(SEQ ID NO: 13) was reactive with NANUC-2, indicating that a 
pANCA-reactive epitope lies within the carboxy-terminal 147 amino acids. 
Chymotrypsin digests the N-terminal portion of the 147 amino 
carboxy-terminal fragment, producing a fragment with an apparent molecular 
weight of 17 kD. Immunoblots of chymotrypsin-digested H1 revealed NANUC-2 
reactivity only with the carboxy-terminal fragment, thereby narrowing the 
pANCA-reactive epitope to the carboxy-terminal 113 amino acids (SEQ ID NO: 
14). As a control to show that the nonreactive N-terminal fragments were 
properly transferred, the same blots showed reactivity with a rabbit 
anti-H1-3 polyclonal specific for the N-terminal fragment (see Parseghian 
et al., Chromosoma 103:198 (1994) and Parseghian et al., Chrom. Res. 1:127 
(1993), each of which is incorporated herein by reference). 
H1 epitopes were mapped using N--N bromosuccinamide and chymotrypsin 
proteolysis with a procedure modified from Parseghian et al., supra, 1993; 
Sherod et al., J. Biol Chem. 12:3923 (1974) and Costa et al., Clin. Exp. 
Immunol. 63: 608 (1986), each of which is incorporated herein by 
reference. Briefly, in a 10 .mu.l reaction, 12 .mu.g of bone marrow 
histone H1 was cleaved with 0.85 .mu.g N--N bromosuccinamide (Sigma) in 
0.9 N acetic acid. The reaction was terminated at varying time points by 
transferring 2.5 .mu.L aliquots into 7.5 .mu.l stop buffer (0.125 M Tris 
Cl pH 7.6 with 10.7 .mu.g tyrosine (Sigma)). Chymotrypsin cleavage was 
performed in a 10 .mu.l reaction volume by incubating 6 .mu.g bone marrow 
histone H1 with 0.01 .mu.g chymotrypsin (Boehringer Mannheim, Ind., IN) in 
0.1 M Tris-Cl pH 8.0, 10 mM CaCl. Reactions were stopped at various time 
points by addition of 1 .mu.l 20 mM phenyl methyl sulfonyl fluoride (PMSF; 
Boehringer Mannheim), and 1.5 .mu.g of NBS and chymotryptic H1 fragments 
diluted in Laemli buffer were run on 13% acrylamide gels using a Biorad 
mini gel apparatus, transferred to nitrocellulose, and immunoblotted as 
described above. Gels were silver stained using a Biorad silver stain kit 
(Biorad, Richmond, Calif.). 
EXAMPLE III 
Identification of pANCA-Reactive Peptides Derived from Histone H1 
This example demonstrates that synthetic peptides spanning histone H1 can 
be assayed for NANUC-1 and NANUC-2 binding to identify pANCA-reactive 
peptides. 
Overlapping 15-mer peptides that spanned the C-terminal 109 amino acids of 
the human H1.sup.S -3 gene product with an N-terminal biotin were 
synthesized (P. Allen, Washington University, St. Louis). Each of the 
peptides overlapped adjacent peptide sequences by five amino acids except 
for peptide SEQ ID NO: 25. The eleven peptide sequences are shown in Table 
2. 
Peptides were tested for binding to 1.0, 3.0 and 10.0 .mu.g/ml NANUC-1, 
NANUC-2 and negative control anti-tetanus toxoid antibody P313 (anti-TT). 
As shown in FIG. 5, peptide SEQ ID NO: 20 was distinguished among the 11 
peptides assayed by significant binding to NANUC-1 and NANUC-2 (OD.sub.405 
of approximately 0.5; significant at 1.0 .mu.g/ml) compared to background 
levels observed with the rFab negative control anti-TT antibody, yielding 
an OD.sub.405 of less than 0.1. Neither of the two adjacent, overlapping 
peptides SEQ ID NO: 19 or SEQ ID NO: 21 showed significant binding to both 
NANUC antibodies. Peptide SEQ ID NO: 17 also reacted with NANUC-1 and 
NANUC-1; however, this binding was weaker (OD.sub.405 of approximately 
0.25 for both NANUC antibodies) than the reactivity seen with peptide SEQ 
ID NO: 20. 
TABLE 2 
______________________________________ 
Histone H1 peptide sequences 
SEQ ID NO: Amino acid sequence 
______________________________________ 
SEQ ID NO: 15 FKLNKKAASGEAKPK 
SEQ ID NO: 16 EAKPKVKKAGGTKPK 
SEQ ID NO: 17 GTKPKKPVGAAKKPK 
SEQ ID NO: 18 AKKPKKAAGGATPKK 
SEQ ID NO: 19 ATPKKSAKKTPKKAK 
SEQ ID NO: 20 PKKAKKPAAATVTKK 
SEQ ID NO: 21 TVTKKVAKSPKKAKV 
SEQ ID NO: 22 KKAKVAKPKKAAKSA 
SEQ ID NO: 23 AAKSAAKAVKPKAAK 
SEQ ID NO: 24 PKAAKPKVVKPKKAA 
SEQ ID NO: 25 KPKVVKPKKAAPKKK 
______________________________________ 
These data indicate that histone H1 peptide PKKAKKPAAATVTKK (SEQ ID NO: 20) 
is specifically reactive with two distinct UCPANCA monoclonal antibodies. 
Because adjacent peptides lack activity, the pANCA reactivity of peptide 
SEQ ID NO: 20 may depend on its unique internal linear amino acid sequence 
KPAAA (SEQ ID NO: 26) or may depend on the unique conformation of the 
peptide sequence SEQ ID NO: 20 in its entirety. 
The eleven H1 peptides SEQ ID NOS: 15 to 25 were assayed for reactivity 
with UC pANCA monoclonal antibodies NANUC-1 and NANUC-2 as follows. ELISA 
wells were coated with 50 .mu.l solution of the H1 peptide of interest (at 
a concentration of 250 .mu.g/ml) in carbonate buffer, pH 9.6, overnight at 
4.degree. C. Wells were blocked with phosphate buffered saline/0.5% 
Tween-20/500 .mu.g/ml bovine serum albumin (BSA; SIGMA) for 1 hour at room 
temperature. Wells were washed five times with 0.05% Tween-20 in PBS (wash 
buffer), then reacted with rFab antibody diluted in wash buffer at 
indicated concentrations for 2 hours at room temperature. Plates were 
washed five times, and immunocomplexes detected subsequently with 0. 05% 
alkaline phosphatase-conjugated goat anti-human Fab (Pierce) in wash 
buffer for 1 hour at room temperature. After washing, the samples were 
reacted with BCIP-NBT substrate (SIGMA). FIG. 5 shows the absorbance at 
405 nm (OD.sub.405) after normalization for background binding due to 
reactivity with secondary antibody alone. 
EXAMPLE IV 
Identification OF pANCA-Reactive Peptides Derived from Histone H1 
This example demonstrates that fragments of histone H1 isoform H1.5 bind 
NANUC-2, thus identifying these fragments as pANCA-reactive fragments of 
histone H1. 
Five recombinant fragments of human histone H1 isoform H1.5 (SEQ ID NO: 32) 
that spanned the C-terminal 158 amino acids of the H1.5 protein (amino 
acids 69 to 226 of SEQ ID NO: 32) with an N-terminal biotin were 
synthesized. The five fragments were as follows: SEQ ID NO: 37 (amino 
acids 172 to 184 of H1.5); SEQ ID NO: 38 (amino acids 69 to 184 of H1.5); 
SEQ ID NO: 39 (amino acids 69 to 171 of H1.5; SEQ ID NO: 40 (amino acids 
69 to 226 of H1.5); and SEQ ID NO: 41 (amino acids 172 to 226 of H1.5). 
Each of these five fragments bound selectively to NANUC-2 but did not bind 
to a control anti-tetanus toxoid antibody. The binding of SEQ ID NOS: 37, 
38, 40 and 41 to NANUC-2 indicates the presence of a pANCA-reactive 
epitope of histone H1 that is in the region of amino acids 172 to 184 of 
histone H1.5. This region of histone isoform H1.5 is highly conserved 
among varying species and isoforms of histone H1 and is present, for 
example, in histone H1.sup.S -3. The binding of SEQ ID NO: 39 to NANUC-2 
indicates the presence of an additional pANCA-reactive epitope of histone 
H1 isoform H1.5 outside amino acids 172 to 184, within amino acids 69 to 
171 of H1.5. In sum, these results demonstrate that histone H1 contains at 
least two distinct pANCA-reactive epitopes. 
EXAMPLE V 
Identification of Ulcerative Colitis pANCA Histone H1-Like Target Antigens 
This example demonstrates that histone H1-like antigens present in a 
variety of Mycobacterial species are reactive with the NANUC-2 antibody. 
A. A mycobacterial histone H1-like antigen is a pANCA reactive protein 
BLAST analysis was used to search the microbial databases for linear 
peptide homologues of the C-terminal random coil domain of human histone 
H1 isoform H1.5 (SEQ ID NO: 32). This analysis revealed homologous 
sequences reported in the M. tuberculosis genome database as anonymous 
open reading frames (ORFs). 
In view of these homologous M. tuberculosis ORFs, seven Mycobacterial 
strains from five Mycobacterial species were obtained from the American 
Type Culture Collection and from St. Mary's Hospital Medical School 
(London, UK). The Mycobacteria were grown using the media and growth 
conditions shown in FIG. 6. Whole cell extracts were prepared and analyzed 
by Western analysis using the NANUC-2 antibody essentially as described in 
Example I. As shown in FIG. 7, the NANUC-2 antibody detected a single 
30-32 kDa protein, with a slightly varying size in each of the 
Mycobacterial species. 
The pANCA-reactive 30-32 kDa protein from M. avium paratuberculosis was 
isolated by SDS-PAGE electrophoresis and PVDF membrane transfer. As shown 
in FIG. 8, the sequence of the first 18 amino acids of the N-terminal 
fragment (SEQ ID NO: 31) obtained by peptide sequencing was nearly 
identical to the amino-terminal sequence of a predicted protein of 214 
amino acids from the M. tuberculosis genome (SEQ ID NO: 27). The two amino 
acid differences in the N-terminal 18 amino acid sequence can reflect 
sequencing artifacts or sequence polymorphisms between M. avium 
paratuberculosis and M. tuberculosis. Alignment of the entire 214 amino 
acid M. tuberculosis protein (SEQ ID NO: 27) with human histone H1 isoform 
H1.5 (SEQ ID NO: 32) revealed 48% sequence similarity. 
A nucleic acid encoding the M. tuberculosis 214 amino acid histone H1-like 
protein (SEQ ID NO: 27) was cloned into an expression vector, and the 
expressed product analyzed. Immunoreactivity with NANUC-2 confirmed that 
this protein is a pANCA-reactive antigen. These results demonstrate that a 
histone H1-like antigen, such as Mycobacterial histone H1-like antigen of 
30-32 kDa, can be a UC pANCA target antigen. 
B. A Mycobacterial histone H1-like antigen is differentially reactive with 
normal and pANCA-positive UC patient sera 
Samples of human sera are taken from patients diagnosed with UC and from 
control normal individuals. Each UC sample is assayed against human PMN 
(neutrophil) for the presence of UC pANCA. pANCA-positive UC sera and 
normal sera are then assayed for reactivity against the M. tuberculosis 
214 amino acid histone H1-like antigen (SEQ ID NO: 27). The results show 
that a significantly greater percentage of UC pANCA-positive samples are 
reactive with the histone H1-like antigen as compared to the percentage of 
normal samples that react. These results demonstrate that a histone 
H1-like microbial protein can be a UC pANCA antigen useful in the 
diagnosis of ulcerative colitis. 
EXAMPLE VI 
Identification of Ulcerative Colitis pANCA Porin Target Antigens 
This example demonstrates that porin and Bacteroides antigens expressed by 
enteric bacteria from UC patients are reactive with the NANUC-2 antibody. 
A. Enteric E. coli from UC patients express a pANCA-reactive antigen P The 
disease-specific immune response exemplified by UC pANCA can be elicited 
by cross-reactive proteins of particular enteric bacteria. To isolate 
these bacteria, colonic biopsy specimens were obtained from three patients 
diagnosed with UC. The specimens were minced, and the colonic bacteria 
cultured using varying oxygen availability and culture media. After 
harvesting bacteria from the cultures, bacterial extracts were tested by 
Western analysis with the NANUC-2 antibody essentially as described above. 
Cross-reactive proteins were only identified in the anaerobic cultures. The 
NANUC-2-reactive cultures were plated, and single colonies isolated and 
individually screened for UC pANCA antigen expression by Western analysis. 
Seven positive clones were isolated and identified by 16S rRNA sequencing 
essentially as described in Wilson and Blitchington, Applied and Environ. 
Microbiol. 62:2273-2278 (1996). 
In particular, five clones were identified by 16S rRNA-typing as members of 
the E. coli species (P1Bc5, P1Bc9, P2c2, P2c5 and P2Lc2). As shown in FIG. 
9, each of the five types of E. coli expressed a pANCA-reactive protein of 
about 35 kDa. These pANCA-reactive proteins could be divided into larger 
and smaller types, which were isolated by SDS-PAGE electrophoresis and 
PVDF membrane transfer. N-terminal amino acid sequencing of the larger and 
smaller pANCA-reactive proteins revealed an identical 19-mer peptide (SEQ 
ID NO: 33). 
BLAST analysis revealed that this 19 amino acid sequence (SEQ ID NO: 33) is 
shared by a set of three closely related putative ORFs of the porin 
outer-membrane protein family (SEQ ID NOS: 28, 29 and 30; see FIG. 10). 
Shown in FIG. 11 is the CLUSTAL and BEST-FIT alignment of one such porin 
antigen (SEQ ID NO: 28) with histone H1.5 (SEQ ID NO: 32). This alignment 
reveals that porin antigens lack detectable linear sequence homology with 
histone H1.5 (SEQ ID NO: 32). B. A porin antigen expressed in E. coli is 
differentially reactive with normal and UC pANCA-positive patient sera 
Samples of human sera are taken from patients diagnosed with UC and from 
control normal individuals. Each UC sample is assayed against human PMN 
(neutrophil) for the presence of UC pANCA. pANCA-positive UC sera and 
normal sera are then assayed for reactivity against the E. coli porin 
antigens described above (SEQ ID NOS: 28, 29 and 30). The results show 
that a significantly greater percentage of UC pANCA-positive samples are 
reactive with the porin antigen as compared to the percentage of normal 
samples that react. These results demonstrate that a porin antigen, such 
as one of the E. coli porin antigens described above (SEQ ID NOS: 28, 29 
and 30), can be a UC pANCA antigen useful in the diagnosis of ulcerative 
colitis. 
C. Enteric Bacteroides from UC patients express a UC pANCA-reactive antigen 
Two clones were identified by 16S rRNA-typing as described above as members 
of the Bacteroides cecae family (P2Lc3 and P2Lc5). As shown in FIG. 9B, 
these family members expressed a pANCA-reactive protein of about 100 kDa. 
Western analysis showed that the pANCA-reactive 100 kDa Bacteroides 
antigen was selectively expressed in Bacteroides but not expressed, for 
example, in E. coli. 
D. An antigen expressed in Bacteroides is differentially reactive with 
normal and UC pANCA-positive patient 
Samples of human sera are taken from patients diagnosed with UC and from 
control normal patients. Each UC sample is assayed against human PMN 
(neutrophil) for the presence of UC pANCA. pANCA-positive UC sera and 
normal sera are then assayed for reactivity against a protein of about 100 
kDa that is isolated from Bacteroides cecae using SDS-PAGE electrophoresis 
and PVDF membrane transfer. The results show that a significantly greater 
percentage of UC pANCA-positive samples are reactive with the Bacteroides 
antigen as compared to the percentage of normal samples that react. These 
results demonstrate that a Bacteroides antigen, such as the 100 kDa 
antigen isolated from Bacteroides cecae, can be a UC pANCA antigen useful 
in the diagnosis of ulcerative colitis. 
All journal article, reference and patent citations provided above, in 
parentheses or otherwise, whether previously stated or not, are 
incorporated herein by reference in their entirety. 
Although the invention has been described with reference to the examples 
above, it should be understood that various modifications can be made 
without departing from the spirit of the invention. Accordingly, the 
invention is limited only by the following claims. 
__________________________________________________________________________ 
# SEQUENCE LISTING 
- (1) GENERAL INFORMATION: 
- (iii) NUMBER OF SEQUENCES: 41 
- (2) INFORMATION FOR SEQ ID NO:1: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 212 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ix) FEATURE: 
(A) NAME/KEY: Peptide 
(B) LOCATION: 1..212 
#/note= "product = Human Histone 
H1-S-1" 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: 
- Ser Glu Thr Ala Pro Ala Ala Pro Ala Ala Al - #a Pro Pro Ala Glu Lys 
# 15 
- Ala Pro Val Lys Lys Lys Ala Ala Lys Lys Al - #a Gly Gly Thr Pro Arg 
# 30 
- Lys Ala Ser Gly Pro Pro Val Ser Glu Leu Il - #e Thr Lys Ala Val Ala 
# 45 
- Ala Ser Lys Glu Arg Ser Gly Val Ser Leu Al - #a Ala Leu Lys Lys Ala 
# 60 
- Leu Ala Ala Ala Gly Tyr Asp Val Glu Lys As - #n Asn Ser Arg Ile Lys 
#80 
- Leu Gly Leu Lys Ser Leu Val Ser Lys Gly Th - #r Leu Val Gln Thr Lys 
# 95 
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# 125 
- Lys Pro Val Gly Ala Ala Lys Lys Pro Lys Ly - #s Ala Ala Gly Gly Ala 
# 140 
- Thr Pro Lys Lys Ser Ala Lys Lys Thr Pro Ly - #s Lys Ala Lys Lys Pro 
145 1 - #50 1 - #55 1 - 
#60 
- Ala Ala Ala Thr Val Thr Lys Lys Val Ala Ly - #s Ser Pro Lys Lys Ala 
# 175 
- Lys Val Ala Lys Pro Lys Lys Ala Ala Lys Se - #r Ala Ala Lys Ala Val 
# 190 
- Lys Pro Lys Ala Ala Lys Pro Lys Val Val Ly - #s Pro Lys Lys Ala Ala 
# 205 
- Pro Lys Lys Lys 
210 
- (2) INFORMATION FOR SEQ ID NO:2: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 220 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ix) FEATURE: 
(A) NAME/KEY: Peptide 
(B) LOCATION: 1..220 
#/note= "product = Human Histone 
H1-S-2" 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: 
- Ser Glu Thr Ala Pro Leu Ala Pro Thr Ile Pr - #o Ala Pro Ala Glu Lys 
# 15 
- Thr Pro Val Lys Lys Lys Ala Lys Lys Ala Gl - #y Ala Thr Ala Gly Lys 
# 30 
- Arg Lys Ala Ser Gly Pro Pro Val Ser Glu Le - #u Ile Thr Lys Ala Val 
# 45 
- Ala Ala Ser Lys Glu Arg Ser Gly Val Ser Le - #u Ala Ala Leu Lys Lys 
# 60 
- Ala Leu Ala Ala Ala Gly Tyr Asp Val Glu Ly - #s Asn Asn Ser Arg Ile 
#80 
- Lys Leu Gly Leu Lys Ser Leu Val Ser Lys Gl - #y Thr Leu Val Gln Thr 
# 95 
- Lys Gly Thr Gly Ala Ser Gly Ser Phe Lys Le - #u Asn Lys Lys Ala Ala 
# 110 
- Ser Gly Glu Gly Lys Pro Lys Ala Lys Lys Al - #a Gly Ala Ala Lys Pro 
# 125 
- Arg Lys Pro Ala Gly Ala Ala Lys Lys Pro Ly - #s Lys Val Ala Gly Ala 
# 140 
- Ala Thr Pro Lys Lys Ser Ile Lys Lys Thr Pr - #o Lys Lys Val Lys Lys 
145 1 - #50 1 - #55 1 - 
#60 
- Pro Ala Thr Ala Ala Gly Thr Lys Lys Val Al - #a Lys Ser Ala Lys Lys 
# 175 
- Val Lys Thr Pro Gln Pro Lys Lys Ala Ala Ly - #s Ser Pro Ala Lys Ala 
# 190 
- Lys Ala Pro Lys Pro Lys Ala Ala Lys Pro Ly - #s Ser Gly Lys Pro Lys 
# 205 
- Val Thr Lys Ala Lys Lys Ala Ala Pro Lys Ly - #s Lys 
# 220 
- (2) INFORMATION FOR SEQ ID NO:3: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 222 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ix) FEATURE: 
(A) NAME/KEY: Peptide 
(B) LOCATION: 1..222 
#/note= "product = Human Histone 
H1-S-3" 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: 
- Ser Glu Thr Ala Pro Ala Glu Thr Ala Thr Pr - #o Ala Pro Val Glu Lys 
# 15 
- Ser Pro Ala Lys Lys Lys Ala Thr Lys Lys Al - #a Ala Gly Ala Gly Ala 
# 30 
- Ala Lys Arg Lys Ala Thr Gly Pro Pro Val Se - #r Glu Leu Ile Thr Lys 
# 45 
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- Ala Ala Ser Gly Glu Ala Lys Pro Lys Ala Ly - #s Lys Ala Gly Ala Ala 
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# 140 
- Ala Gly Ala Lys Lys Ala Val Lys Lys Thr Pr - #o Lys Lys Ala Lys Lys 
145 1 - #50 1 - #55 1 - 
#60 
- Pro Ala Ala Ala Gly Val Lys Lys Val Ala Ly - #s Ser Pro Lys Lys Ala 
# 175 
- Lys Ala Ala Ala Lys Pro Lys Lys Ala Thr Ly - #s Ser Pro Ala Lys Pro 
# 190 
- Lys Ala Val Lys Pro Lys Ala Ala Lys Pro Ly - #s Ala Ala Lys Pro Lys 
# 205 
- Ala Ala Lys Pro Lys Ala Lys Lys Ala Ala Al - #a Lys Lys Lys 
# 220 
- (2) INFORMATION FOR SEQ ID NO:4: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 218 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ix) FEATURE: 
(A) NAME/KEY: Peptide 
(B) LOCATION: 1..218 
#/note= "product = Human Histone 
H1-S-4" 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: 
- Ser Glu Thr Ala Pro Ala Ala Pro Ala Ala Pr - #o Ala Pro Ala Glu Lys 
# 15 
- Thr Pro Val Lys Lys Lys Ala Arg Lys Ser Al - #a Gly Ala Ala Lys Arg 
# 30 
- Lys Ala Ser Gly Pro Pro Val Ser Glu Leu Il - #e Thr Lys Ala Val Ala 
# 45 
- Ala Ser Lys Glu Arg Ser Gly Val Ser Leu Al - #a Ala Leu Lys Lys Ala 
# 60 
- Leu Ala Ala Ala Gly Tyr Asp Val Glu Lys As - #n Asn Ser Arg Ile Lys 
#80 
- Leu Gly Leu Lys Ser Leu Val Ser Lys Gly Th - #r Leu Val Gln Thr Lys 
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- Gly Thr Gly Ala Ser Gly Ser Phe Lys Leu As - #n Lys Lys Ala Ala Ser 
# 110 
- Gly Glu Ala Lys Pro Lys Ala Lys Lys Ala Gl - #y Ala Ala Lys Ala Lys 
# 125 
- Lys Pro Ala Gly Ala Ala Lys Lys Pro Lys Ly - #s Ala Thr Gly Ala Ala 
# 140 
- Thr Pro Lys Lys Ser Ala Lys Lys Thr Pro Ly - #s Lys Ala Lys Lys Pro 
145 1 - #50 1 - #55 1 - 
#60 
- Ala Ala Ala Ala Gly Ala Lys Lys Ala Lys Se - #r Pro Lys Lys Ala Lys 
# 175 
- Ala Ala Lys Pro Lys Lys Ala Pro Lys Ser Pr - #o Ala Lys Ala Lys Ala 
# 190 
- Val Lys Pro Lys Ala Ala Lys Pro Lys Thr Al - #a Lys Pro Lys Ala Ala 
# 205 
- Lys Pro Lys Lys Ala Ala Ala Lys Lys Lys 
# 215 
- (2) INFORMATION FOR SEQ ID NO:5: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 193 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ix) FEATURE: 
(A) NAME/KEY: Peptide 
(B) LOCATION: 1..193 
#/note= "product = Human Histone 
H1-o" 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: 
- Thr Glu Asn Ser Thr Ser Ala Pro Ala Ala Ly - #s Pro Lys Arg Ala Lys 
# 15 
- Ala Ser Lys Lys Ser Thr Asp His Pro Lys Ty - #r Ser Asp Met Ile Val 
# 30 
- Ala Ala Ile Gln Ala Glu Lys Asn Arg Ala Gl - #y Ser Ser Arg Gln Ser 
# 45 
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# 60 
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#80 
- Lys Gln Thr Lys Gly Val Gly Ala Ser Gly Se - #r Phe Arg Leu Ala Lys 
# 95 
- Ser Asp Glu Pro Lys Lys Ser Val Ala Phe Ly - #s Lys Thr Lys Lys Glu 
# 110 
- Ile Lys Lys Val Ala Thr Pro Lys Lys Ala Se - #r Lys Pro Lys Lys Ala 
# 125 
- Ala Ser Lys Ala Pro Thr Lys Lys Pro Lys Al - #a Thr Pro Val Lys Lys 
# 140 
- Ala Lys Lys Lys Leu Ala Ala Thr Pro Lys Ly - #s Ala Lys Lys Pro Lys 
145 1 - #50 1 - #55 1 - 
#60 
- Thr Val Lys Ala Lys Pro Val Lys Ala Ser Ly - #s Pro Lys Lys Ala Lys 
# 175 
- Pro Val Lys Pro Lys Ala Lys Ser Ser Ala Ly - #s Arg Ala Gly Lys Lys 
# 190 
- Lys 
- (2) INFORMATION FOR SEQ ID NO:6: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 206 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ix) FEATURE: 
(A) NAME/KEY: Peptide 
(B) LOCATION: 1..206 
#/note= "product = Human Histone 
H1t" 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:6: 
- Ser Glu Thr Val Pro Ala Ala Ser Ala Ser Al - #a Gly Val Ala Ala Met 
# 15 
- Glu Lys Leu Pro Thr Lys Lys Arg Gly Arg Ly - #s Pro Ala Gly Leu Ile 
# 30 
- Ser Ala Ser Arg Lys Val Pro Asn Leu Ser Va - #l Ser Lys Leu Ile Thr 
# 45 
- Glu Ala Leu Ser Val Ser Gln Glu Arg Val Gl - #y Met Ser Leu Val Ala 
# 60 
- Leu Lys Lys Ala Leu Ala Ala Ala Gly Tyr As - #p Val Glu Lys Asn Asn 
#80 
- Ser Arg Ile Lys Leu Ser Leu Lys Ser Leu Va - #l Asn Lys Gly Ile Leu 
# 95 
- Val Gln Thr Arg Gly Thr Gly Ala Ser Gly Se - #r Phe Lys Leu Ser Lys 
# 110 
- Lys Val Ile Pro Lys Ser Thr Arg Ser Lys Al - #a Lys Lys Ser Val Ser 
# 125 
- Ala Lys Thr Lys Lys Leu Val Leu Ser Arg As - #p Ser Lys Ser Pro Lys 
# 140 
- Thr Ala Lys Thr Asn Lys Arg Ala Lys Lys Pr - #o Arg Ala Thr Thr Pro 
145 1 - #50 1 - #55 1 - 
#60 
- Lys Thr Val Arg Ser Gly Arg Lys Ala Lys Gl - #y Ala Lys Gly Lys Gln 
# 175 
- Lys Gln Lys Ser Pro Val Lys Ala Arg Ala Se - #r Lys Ser Lys Leu Thr 
# 190 
- Gln His His Glu Val Asn Val Arg Lys Ala Th - #r Ser Lys Lys 
# 205 
- (2) INFORMATION FOR SEQ ID NO:7: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 35 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7: 
- Ser Glu Thr Ala Pro Ala Glu Thr Ala Thr Pr - #o Ala Pro Val Glu Lys 
# 15 
- Ser Pro Ala Lys Lys Lys Ala Thr Lys Lys Al - #a Ala Gly Ala Gly Ala 
# 30 
- Ala Lys Arg 
35 
- (2) INFORMATION FOR SEQ ID NO:8: 
- (i) SEQUENCE CHARACTERISTICS: 
#pairs (A) LENGTH: 699 base 
(B) TYPE: nucleic acid 
(C) STRANDEDNESS: double 
(D) TOPOLOGY: linear 
- (ix) FEATURE: 
(A) NAME/KEY: CDS 
(B) LOCATION: 1..699 
- (ix) FEATURE: 
(A) NAME/KEY: misc.sub.-- - #feature 
(B) LOCATION: 1..699 
#/note= "product = NANUC-2 heavy 
chain" 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8: 
- GCC CAG GTG AAA CTG CTC GAG CAG TCT GGG GG - #A GGC GTG GTC CAG CCT 
48 
Ala Gln Val Lys Leu Leu Glu Gln Ser Gly Gl - #y Gly Val Val Gln Pro 
# 15 
- GGG AAG TCC CTG AGA CTC TCC TGT GCA GCC TC - #T GGA TTC ACC TTC AGG 
96 
Gly Lys Ser Leu Arg Leu Ser Cys Ala Ala Se - #r Gly Phe Thr Phe Arg 
# 30 
- AAC TAT GGC ATG CAC TGG GTC CGG CAG GCT CC - #A GGC AAG GGG CTG GAG 
144 
Asn Tyr Gly Met His Trp Val Arg Gln Ala Pr - #o Gly Lys Gly Leu Glu 
# 45 
- TGG GTG GCA GGT ATT TCC TCT GAT GGA AGA AA - #A AAA AAG TAT GTA GAC 
192 
Trp Val Ala Gly Ile Ser Ser Asp Gly Arg Ly - #s Lys Lys Tyr Val Asp 
# 60 
- TCC GTG AAG GGC CGA TTC ACC ATC TCC AGA GA - #C AAG TCC AAG AAC ACG 
240 
Ser Val Lys Gly Arg Phe Thr Ile Ser Arg As - #p Lys Ser Lys Asn Thr 
# 80 
- CTG TAT CTG CAA ATG AAC AGC CTC AGA GCT GA - #G GAC ACG GCT GTG TAT 
288 
Leu Tyr Leu Gln Met Asn Ser Leu Arg Ala Gl - #u Asp Thr Ala Val Tyr 
# 95 
- TAC TGT GCG AAA TTG TCC CGC GCG GGT GGT TT - #T GAC ATC TGG GGC CAA 
336 
Tyr Cys Ala Lys Leu Ser Arg Ala Gly Gly Ph - #e Asp Ile Trp Gly Gln 
# 110 
- GGG ACA ATG GTC ACC GTC TCT TCA GCC TCC AC - #C AAG GGC CCA TCG GTC 
384 
Gly Thr Met Val Thr Val Ser Ser Ala Ser Th - #r Lys Gly Pro Ser Val 
# 125 
- TTT CCC CTG GCA CCC TCC TCC AAG AGC ACC TC - #T GGG GGC ACA GCG GCC 
432 
Phe Pro Leu Ala Pro Ser Ser Lys Ser Thr Se - #r Gly Gly Thr Ala Ala 
# 140 
- CTG GGC TGC CTG GTC AAG GAC TAC TTC CCC GA - #A CCG GTG ACG GTG TCG 
480 
Leu Gly Cys Leu Val Lys Asp Tyr Phe Pro Gl - #u Pro Val Thr Val Ser 
145 1 - #50 1 - #55 1 - 
#60 
- TGG AAC TCA GGC GCC CTG ACC AGC GGC GTG CA - #C ACC TTC CCG GCT GTC 
528 
Trp Asn Ser Gly Ala Leu Thr Ser Gly Val Hi - #s Thr Phe Pro Ala Val 
# 175 
- CTA CAG TCC TCA GGA CTC TAC TCC CTC AGC AG - #C GTG GTG ACC GTG CCC 
576 
Leu Gln Ser Ser Gly Leu Tyr Ser Leu Ser Se - #r Val Val Thr Val Pro 
# 190 
- TCC AGC AGC TTG GGC ACC CAG ACC TAC ATC TG - #C AAC GTG AAT CAC AAG 
624 
Ser Ser Ser Leu Gly Thr Gln Thr Tyr Ile Cy - #s Asn Val Asn His Lys 
# 205 
- CCC AGC AAC ACC AAG GTG GAC AAG AAA GCA GA - #G CCC AAA TCT TGT GAC 
672 
Pro Ser Asn Thr Lys Val Asp Lys Lys Ala Gl - #u Pro Lys Ser Cys Asp 
# 220 
# 699 AC CAC CAC CAC CAC 
Lys Thr Ser His His His His His His 
225 2 - #30 
- (2) INFORMATION FOR SEQ ID NO:9: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 233 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: protein 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9: 
- Ala Gln Val Lys Leu Leu Glu Gln Ser Gly Gl - #y Gly Val Val Gln Pro 
# 15 
- Gly Lys Ser Leu Arg Leu Ser Cys Ala Ala Se - #r Gly Phe Thr Phe Arg 
# 30 
- Asn Tyr Gly Met His Trp Val Arg Gln Ala Pr - #o Gly Lys Gly Leu Glu 
# 45 
- Trp Val Ala Gly Ile Ser Ser Asp Gly Arg Ly - #s Lys Lys Tyr Val Asp 
# 60 
- Ser Val Lys Gly Arg Phe Thr Ile Ser Arg As - #p Lys Ser Lys Asn Thr 
# 80 
- Leu Tyr Leu Gln Met Asn Ser Leu Arg Ala Gl - #u Asp Thr Ala Val Tyr 
# 95 
- Tyr Cys Ala Lys Leu Ser Arg Ala Gly Gly Ph - #e Asp Ile Trp Gly Gln 
# 110 
- Gly Thr Met Val Thr Val Ser Ser Ala Ser Th - #r Lys Gly Pro Ser Val 
# 125 
- Phe Pro Leu Ala Pro Ser Ser Lys Ser Thr Se - #r Gly Gly Thr Ala Ala 
# 140 
- Leu Gly Cys Leu Val Lys Asp Tyr Phe Pro Gl - #u Pro Val Thr Val Ser 
145 1 - #50 1 - #55 1 - 
#60 
- Trp Asn Ser Gly Ala Leu Thr Ser Gly Val Hi - #s Thr Phe Pro Ala Val 
# 175 
- Leu Gln Ser Ser Gly Leu Tyr Ser Leu Ser Se - #r Val Val Thr Val Pro 
# 190 
- Ser Ser Ser Leu Gly Thr Gln Thr Tyr Ile Cy - #s Asn Val Asn His Lys 
# 205 
- Pro Ser Asn Thr Lys Val Asp Lys Lys Ala Gl - #u Pro Lys Ser Cys Asp 
# 220 
- Lys Thr Ser His His His His His His 
225 2 - #30 
- (2) INFORMATION FOR SEQ ID NO:10: 
- (i) SEQUENCE CHARACTERISTICS: 
#pairs (A) LENGTH: 642 base 
(B) TYPE: nucleic acid 
(C) STRANDEDNESS: double 
(D) TOPOLOGY: linear 
- (ix) FEATURE: 
(A) NAME/KEY: CDS 
(B) LOCATION: 1..642 
- (ix) FEATURE: 
(A) NAME/KEY: misc.sub.-- - #feature 
(B) LOCATION: 1..642 
#/note= "product = NANUC-2 light 
chain" 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10: 
- GCC GAG CTC ACG CAG TCT CCA GGC ACC CTG TC - #T TTG TTT CCA GGG GAA 
48 
Ala Glu Leu Thr Gln Ser Pro Gly Thr Leu Se - #r Leu Phe Pro Gly Glu 
# 15 
- AGA GCC ACT CTC TCC TGC AGG GCC AGT CAG AG - #A ATT AGC ACC AGT TTC 
96 
Arg Ala Thr Leu Ser Cys Arg Ala Ser Gln Ar - #g Ile Ser Thr Ser Phe 
# 30 
- TTA GCC TGG TAC CAG CAG AAG CCT GGC CAG TC - #T CCC AGG CTC CTC ATC 
144 
Leu Ala Trp Tyr Gln Gln Lys Pro Gly Gln Se - #r Pro Arg Leu Leu Ile 
# 45 
- TTT GAT GCA TCC ACC AGG GCC CCT GGC ATC CC - #T GAC AGG TTC AGT GCC 
192 
Phe Asp Ala Ser Thr Arg Ala Pro Gly Ile Pr - #o Asp Arg Phe Ser Ala 
# 60 
- AGT TGG TCT GGG ACA GAC TTC ACT CTC ACC AT - #C AGC AGA CTG GAG CCT 
240 
Ser Trp Ser Gly Thr Asp Phe Thr Leu Thr Il - #e Ser Arg Leu Glu Pro 
# 80 
- GAA GAT TTT GCA GTC TAT TAC TGT CAA CAT TA - #T GGT GGG TCT CCC TGG 
288 
Glu Asp Phe Ala Val Tyr Tyr Cys Gln His Ty - #r Gly Gly Ser Pro Trp 
# 95 
- ACG TTC GGC CAA GGG ACC AAG GTG GAA ATC AA - #G CGA ACT GTG GCT GCA 
336 
Thr Phe Gly Gln Gly Thr Lys Val Glu Ile Ly - #s Arg Thr Val Ala Ala 
# 110 
- CCA TCT GTC TTC ATC TTC CCG CCA TCT GAT GA - #G CAG TTG AAA TCT GGA 
384 
Pro Ser Val Phe Ile Phe Pro Pro Ser Asp Gl - #u Gln Leu Lys Ser Gly 
# 125 
- ACT GCC TCT GTT GTG TGC CTG CTG AAT AAC TT - #C TAT CCC AGA GAG GCC 
432 
Thr Ala Ser Val Val Cys Leu Leu Asn Asn Ph - #e Tyr Pro Arg Glu Ala 
# 140 
- AAA GTA CAG TGG AAG GTG GAT AAC GCC CTC CA - #A TCG GGT AAC TCC CAG 
480 
Lys Val Gln Trp Lys Val Asp Asn Ala Leu Gl - #n Ser Gly Asn Ser Gln 
145 1 - #50 1 - #55 1 - 
#60 
- GAG AGT GTC ACA GAG CAG GAC AGC AAG GAC AG - #C ACC TAC AGC CTC AGC 
528 
Glu Ser Val Thr Glu Gln Asp Ser Lys Asp Se - #r Thr Tyr Ser Leu Ser 
# 175 
- AGC ACC CTG ACG CTG AGC AAA GCA GAC TAC GA - #G AAA CAC AAA GTC TAC 
576 
Ser Thr Leu Thr Leu Ser Lys Ala Asp Tyr Gl - #u Lys His Lys Val Tyr 
# 190 
- GCC TGC GAA GTC ACC CAT CAG GGC CTG AGC TC - #G CCC GTC ACA AAG AGC 
624 
Ala Cys Glu Val Thr His Gln Gly Leu Ser Se - #r Pro Val Thr Lys Ser 
# 205 
# 642 AG TGT 
Phe Asn Arg Gly Glu Cys 
210 
- (2) INFORMATION FOR SEQ ID NO:11: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 214 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: protein 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11: 
- Ala Glu Leu Thr Gln Ser Pro Gly Thr Leu Se - #r Leu Phe Pro Gly Glu 
# 15 
- Arg Ala Thr Leu Ser Cys Arg Ala Ser Gln Ar - #g Ile Ser Thr Ser Phe 
# 30 
- Leu Ala Trp Tyr Gln Gln Lys Pro Gly Gln Se - #r Pro Arg Leu Leu Ile 
# 45 
- Phe Asp Ala Ser Thr Arg Ala Pro Gly Ile Pr - #o Asp Arg Phe Ser Ala 
# 60 
- Ser Trp Ser Gly Thr Asp Phe Thr Leu Thr Il - #e Ser Arg Leu Glu Pro 
# 80 
- Glu Asp Phe Ala Val Tyr Tyr Cys Gln His Ty - #r Gly Gly Ser Pro Trp 
# 95 
- Thr Phe Gly Gln Gly Thr Lys Val Glu Ile Ly - #s Arg Thr Val Ala Ala 
# 110 
- Pro Ser Val Phe Ile Phe Pro Pro Ser Asp Gl - #u Gln Leu Lys Ser Gly 
# 125 
- Thr Ala Ser Val Val Cys Leu Leu Asn Asn Ph - #e Tyr Pro Arg Glu Ala 
# 140 
- Lys Val Gln Trp Lys Val Asp Asn Ala Leu Gl - #n Ser Gly Asn Ser Gln 
145 1 - #50 1 - #55 1 - 
#60 
- Glu Ser Val Thr Glu Gln Asp Ser Lys Asp Se - #r Thr Tyr Ser Leu Ser 
# 175 
- Ser Thr Leu Thr Leu Ser Lys Ala Asp Tyr Gl - #u Lys His Lys Val Tyr 
# 190 
- Ala Cys Glu Val Thr His Gln Gly Leu Ser Se - #r Pro Val Thr Lys Ser 
# 205 
- Phe Asn Arg Gly Glu Cys 
210 
- (2) INFORMATION FOR SEQ ID NO:12: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 73 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12: 
- Ser Glu Thr Ala Pro Leu Ala Pro Thr Ile Pr - #o Ala Pro Ala Glu Lys 
# 15 
- Thr Pro Val Lys Lys Lys Ala Lys Lys Ala Gl - #y Ala Thr Ala Gly Lys 
# 30 
- Arg Lys Ala Ser Gly Pro Pro Val Ser Glu Le - #u Ile Thr Lys Ala Val 
# 45 
- Ala Ala Ser Lys Glu Arg Ser Gly Val Ser Le - #u Ala Ala Leu Lys Lys 
# 60 
- Ala Leu Ala Ala Ala Gly Tyr Asp Val 
#70 
- (2) INFORMATION FOR SEQ ID NO:13: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 147 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13: 
- Glu Lys Asn Asn Ser Arg Ile Lys Leu Gly Le - #u Lys Ser Leu Val Ser 
# 15 
- Lys Gly Thr Leu Val Gln Thr Lys Gly Thr Gl - #y Ala Ser Gly Ser Phe 
# 30 
- Lys Leu Asn Lys Lys Ala Ala Ser Gly Glu Gl - #y Lys Pro Lys Ala Lys 
# 45 
- Lys Ala Gly Ala Ala Lys Pro Arg Lys Pro Al - #a Gly Ala Ala Lys Lys 
# 60 
- Pro Lys Lys Val Ala Gly Ala Ala Thr Pro Ly - #s Lys Ser Ile Lys Lys 
#80 
- Thr Pro Lys Lys Val Lys Lys Pro Ala Thr Al - #a Ala Gly Thr Lys Lys 
# 95 
- Val Ala Lys Ser Ala Lys Lys Val Lys Thr Pr - #o Gln Pro Lys Lys Ala 
# 110 
- Ala Lys Ser Pro Ala Lys Ala Lys Ala Pro Ly - #s Pro Lys Ala Ala Lys 
# 125 
- Pro Lys Ser Gly Lys Pro Lys Val Thr Lys Al - #a Lys Lys Ala Ala Pro 
# 140 
- Lys Lys Lys 
145 
- (2) INFORMATION FOR SEQ ID NO:14: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 113 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: 
- Asn Lys Lys Ala Ala Ser Gly Glu Gly Lys Pr - #o Lys Ala Lys Lys Ala 
# 15 
- Gly Ala Ala Lys Pro Arg Lys Pro Ala Gly Al - #a Ala Lys Lys Pro Lys 
# 30 
- Lys Val Ala Gly Ala Ala Thr Pro Lys Lys Se - #r Ile Lys Lys Thr Pro 
# 45 
- Lys Lys Val Lys Lys Pro Ala Thr Ala Ala Gl - #y Thr Lys Lys Val Ala 
# 60 
- Lys Ser Ala Lys Lys Val Lys Thr Pro Gln Pr - #o Lys Lys Ala Ala Lys 
#80 
- Ser Pro Ala Lys Ala Lys Ala Pro Lys Pro Ly - #s Ala Ala Lys Pro Lys 
# 95 
- Ser Gly Lys Pro Lys Val Thr Lys Ala Lys Ly - #s Ala Ala Pro Lys Lys 
# 110 
- Lys 
- (2) INFORMATION FOR SEQ ID NO:15: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15: 
- Phe Lys Leu Asn Lys Lys Ala Ala Ser Gly Gl - #u Ala Lys Pro Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:16: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:16: 
- Glu Ala Lys Pro Lys Val Lys Lys Ala Gly Gl - #y Thr Lys Pro Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:17: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17: 
- Gly Thr Lys Pro Lys Lys Pro Val Gly Ala Al - #a Lys Lys Pro Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:18: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18: 
- Ala Lys Lys Pro Lys Lys Ala Ala Gly Gly Al - #a Thr Pro Lys Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:19: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19: 
- Ala Thr Pro Lys Lys Ser Ala Lys Lys Thr Pr - #o Lys Lys Ala Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:20: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:20: 
- Pro Lys Lys Ala Lys Lys Pro Ala Ala Ala Th - #r Val Thr Lys Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:21: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:21: 
- Thr Val Thr Lys Lys Val Ala Lys Ser Pro Ly - #s Lys Ala Lys Val 
# 15 
- (2) INFORMATION FOR SEQ ID NO:22: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:22: 
- Lys Lys Ala Lys Val Ala Lys Pro Lys Lys Al - #a Ala Lys Ser Ala 
# 15 
- (2) INFORMATION FOR SEQ ID NO:23: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:23: 
- Ala Ala Lys Ser Ala Ala Lys Ala Val Lys Pr - #o Lys Ala Ala Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:24: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24: 
- Pro Lys Ala Ala Lys Pro Lys Val Val Lys Pr - #o Lys Lys Ala Ala 
# 15 
- (2) INFORMATION FOR SEQ ID NO:25: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:25: 
- Lys Pro Lys Val Val Lys Pro Lys Lys Ala Al - #a Pro Lys Lys Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:26: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 5 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:26: 
- Lys Pro Ala Ala Ala 
1 5 
- (2) INFORMATION FOR SEQ ID NO:27: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 214 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:27: 
- Met Asn Lys Ala Glu Leu Ile Asp Val Leu Th - #r Gln Lys Leu Gly Ser 
# 15 
- Asp Arg Arg Gln Ala Thr Ala Ala Val Glu As - #n Val Val Asp Thr Ile 
# 30 
- Val Arg Ala Val His Lys Gly Asp Ser Val Th - #r Ile Thr Gly Phe Gly 
# 45 
- Val Phe Glu Gln Arg Arg Arg Ala Ala Arg Va - #l Ala Arg Asn Pro Arg 
# 60 
- Thr Gly Glu Thr Val Lys Val Lys Pro Thr Se - #r Val Pro Ala Phe Arg 
#80 
- Pro Gly Ala Gln Phe Lys Ala Val Val Ser Gl - #y Ala Gln Arg Leu Pro 
# 95 
- Ala Glu Gly Pro Ala Val Lys Arg Gly Val Gl - #y Ala Ser Ala Ala Lys 
# 110 
- Lys Val Ala Lys Lys Ala Pro Ala Lys Lys Al - #a Thr Lys Ala Ala Lys 
# 125 
- Lys Ala Ala Thr Lys Ala Pro Ala Arg Lys Al - #a Ala Thr Lys Ala Pro 
# 140 
- Ala Lys Lys Ala Ala Thr Lys Ala Pro Ala Ly - #s Lys Ala Val Lys Ala 
145 1 - #50 1 - #55 1 - 
#60 
- Thr Lys Ser Pro Ala Lys Lys Val Thr Lys Al - #a Val Lys Lys Thr Ala 
# 175 
- Val Lys Ala Ser Val Arg Lys Ala Ala Thr Ly - #s Ala Pro Ala Lys Lys 
# 190 
- Ala Ala Ala Lys Arg Pro Ala Thr Lys Ala Pr - #o Ala Lys Lys Ala Thr 
# 205 
- Ala Arg Arg Gly Arg Lys 
210 
- (2) INFORMATION FOR SEQ ID NO:28: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 323 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:28: 
- Met Lys Ser Lys Val Leu Ala Leu Leu Ile Pr - #o Ala Leu Leu Ala Ala 
# 15 
- Gly Ala Ala His Ala Ala Glu Val Tyr Asn Ly - #s Asp Gly Asn Lys Leu 
# 30 
- Asp Leu Tyr Gly Lys Val Asp Gly Leu His Ty - #r Phe Ser Asp Asn Ser 
# 45 
- Ala Lys Asp Gly Asp Gln Ser Tyr Ala Arg Le - #u Gly Phe Lys Gly Glu 
# 60 
- Thr Gln Ile Asn Asp Gln Leu Thr Gly Tyr Gl - #y Gln Trp Glu Tyr Asn 
#80 
- Ile Gln Ala Asn Asn Thr Glu Ser Ser Lys As - #n Gln Ser Trp Thr Arg 
# 95 
- Leu Ala Phe Ala Gly Leu Lys Phe Ala Asp Ty - #r Gly Ser Phe Asp Tyr 
# 110 
- Gly Arg Asn Tyr Gly Val Met Tyr Asp Ile Gl - #u Gly Trp Thr Asp Met 
# 125 
- Leu Pro Glu Phe Gly Gly Asp Ser Tyr Thr As - #n Ala Asp Asn Phe Met 
# 140 
- Thr Gly Arg Ala Asn Gly Val Ala Thr Tyr Ar - #g Asn Thr Asp Phe Phe 
145 1 - #50 1 - #55 1 - 
#60 
- Gly Leu Val Asn Gly Leu Asn Phe Ala Val Gl - #n Tyr Gln Gly Asn Asn 
# 175 
- Glu Gly Ala Ser Asn Gly Gln Glu Gly Thr As - #n Asn Gly Arg Asp Val 
# 190 
- Arg His Glu Asn Gly Asp Gly Trp Gly Leu Se - #r Thr Thr Tyr Asp Leu 
# 205 
- Gly Met Gly Phe Ser Ala Gly Ala Ala Tyr Th - #r Ser Ser Asp Arg Thr 
# 220 
- Asn Asp Gln Val Asn His Thr Ala Ala Gly Gl - #y Asp Lys Ala Asp Ala 
225 2 - #30 2 - #35 2 - 
#40 
- Trp Thr Ala Gly Leu Lys Tyr Asp Ala Asn As - #n Ile Tyr Leu Ala Thr 
# 255 
- Met Tyr Ser Glu Thr Arg Asn Met Thr Pro Ph - #e Gly Asp Ser Asp Tyr 
# 270 
- Ala Val Ala Asn Lys Thr Gln Asn Phe Glu Va - #l Thr Ala Gly Tyr Gln 
# 285 
- Phe Asp Phe Gly Leu Arg Pro Ala Val Ser Ph - #e Leu Met Ser Lys Gly 
# 300 
- Arg Asp Leu His Ala Ala Gly Gly Ala Asp As - #n Pro Ala Gly Val Asp 
305 3 - #10 3 - #15 3 - 
#20 
- Asp Lys Asp 
- (2) INFORMATION FOR SEQ ID NO:29: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 377 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:29: 
- Met Lys Ser Lys Val Leu Ala Leu Leu Ile Pr - #o Ala Leu Leu Ala Ala 
# 15 
- Gly Ala Ala His Ala Ala Glu Val Tyr Asn Ly - #s Asp Gly Asn Lys Leu 
# 30 
- Asp Leu Tyr Gly Lys Val Asp Gly Leu His Ty - #r Phe Ser Asp Asn Ser 
# 45 
- Ala Lys Asp Gly Asp Gln Ser Tyr Ala Arg Le - #u Gly Phe Lys Gly Glu 
# 60 
- Thr Gln Ile Asn Asp Gln Leu Thr Gly Tyr Gl - #n Gln Trp Glu Tyr Asn 
#80 
- Ile Gln Ala Asn Asn Thr Glu Ser Ser Lys As - #n Gln Ser Trp Thr Arg 
# 95 
- Leu Ala Phe Ala Gly Leu Lys Phe Ala Asp Ty - #r Gly Ser Phe Asp Tyr 
# 110 
- Gly Arg Asn Tyr Gly Val Met Tyr Asp Ile Gl - #u Gly Trp Thr Asp Met 
# 125 
- Leu Pro Glu Phe Gly Gly Asp Ser Tyr Thr As - #n Ala Asp Asn Phe Met 
# 140 
- Thr Gly Arg Ala Asn Gly Val Ala Thr Tyr Ar - #g Asn Thr Asp Phe Phe 
145 1 - #50 1 - #55 1 - 
#60 
- Gly Leu Val Asn Gly Leu Asn Phe Ala Val Gl - #n Tyr Gln Gly Asn Asn 
# 175 
- Glu Gly Ala Ser Asn Gly Gln Glu Gly Thr As - #n Asn Gly Arg Asp Val 
# 190 
- Arg His Glu Asn Gly Asp Gly Trp Gly Leu Se - #r Thr Thr Tyr Asp Leu 
# 205 
- Gly Met Gly Phe Ser Ala Gly Ala Ala Tyr Th - #r Ser Ser Asp Arg Thr 
# 220 
- Asn Asp Gln Val Asn His Thr Ala Ala Gly Gl - #y Asp Lys Ala Asp Ala 
225 2 - #30 2 - #35 2 - 
#40 
- Trp Thr Ala Gly Leu Lys Tyr Asp Ala Asn As - #n Ile Tyr Leu Ala Thr 
# 255 
- Met Tyr Ser Glu Thr Arg Asn Met Thr Pro Ph - #e Gly Asp Ser Asp Tyr 
# 270 
- Ala Val Ala Asn Lys Thr Gln Asn Phe Glu Va - #l Thr Ala Gln Tyr Gln 
# 285 
- Phe Asp Phe Gly Leu Arg Pro Ala Val Ser Ph - #e Leu Met Ser Lys Gly 
# 300 
- Arg Asp Leu His Ala Ala Gly Gly Ala Asp As - #n Pro Ala Gly Val Asp 
305 3 - #10 3 - #15 3 - 
#20 
- Asp Lys Asp Leu Val Lys Tyr Ala Asp Ile Gl - #y Ala Thr Tyr Tyr Phe 
# 335 
- Asn Lys Asn Met Ser Thr Tyr Val Asp Tyr Ly - #s Ile Asn Leu Ile Asp 
# 350 
- Glu Asp Asp Ser Phe Tyr Ala Ala Asn Gly Il - #e Ser Thr Asp Asp Ile 
# 365 
- Val Ala Leu Gly Leu Val Tyr Gln Phe 
# 375 
- (2) INFORMATION FOR SEQ ID NO:30: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 367 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:30: 
- Met Lys Val Lys Val Leu Ser Leu Leu Val Pr - #o Ala Leu Leu Val Ala 
# 15 
- Gly Ala Ala Asn Ala Ala Glu Val Tyr Asn Ly - #s Asp Gly Asn Lys Leu 
# 30 
- Asp Leu Tyr Gly Lys Val Asp Gly Leu His Ty - #r Phe Ser Asp Asn Lys 
# 45 
- Asp Val Asp Gly Asp Gln Thr Tyr Met Arg Le - #u Gly Phe Lys Gly Glu 
# 60 
- Thr Gln Val Thr Asp Gln Leu Thr Gly Tyr Gl - #y Gln Trp Glu Tyr Gln 
#80 
- Ile Gln Gly Asn Ser Ala Glu Asn Glu Asn As - #n Ser Trp Thr Arg Val 
# 95 
- Ala Phe Ala Gly Leu Lys Phe Gln Asp Val Gl - #y Ser Phe Asp Tyr Gly 
# 110 
- Arg Asn Tyr Gly Val Val Tyr Asp Val Thr Se - #r Trp Thr Asp Val Leu 
# 125 
- Pro Glu Phe Gly Gly Asp Thr Tyr Gly Ser As - #p Asn Phe Met Gln Gln 
# 140 
- Arg Gly Asn Gly Phe Ala Thr Tyr Arg Asn Th - #r Asp Phe Phe Gly Leu 
145 1 - #50 1 - #55 1 - 
#60 
- Val Asp Gly Leu Asn Phe Ala Val Gln Tyr Gl - #n Gly Lys Asn Gly Asn 
# 175 
- Pro Ser Gly Glu Gly Phe Thr Ser Gly Val Th - #r Asn Asn Gly Arg Asp 
# 190 
- Ala Leu Arg Gln Asn Gly Asp Gly Val Gly Gl - #y Ser Ile Thr Tyr Asp 
# 205 
- Tyr Glu Gly Phe Gly Ile Gly Gly Ala Ile Se - #r Ser Ser Lys Arg Thr 
# 220 
- Asp Ala Gln Asn Thr Ala Ala Tyr Ile Gly As - #n Gly Asp Arg Ala Glu 
225 2 - #30 2 - #35 2 - 
#40 
- Thr Tyr Thr Gly Gly Leu Lys Tyr Asp Ala As - #n Asn Ile Tyr Leu Ala 
# 255 
- Ala Gln Tyr Thr Gln Thr Tyr Asn Ala Thr Ar - #g Val Gly Ser Leu Gly 
# 270 
- Trp Ala Asn Lys Ala Gln Asn Phe Glu Ala Va - #l Ala Gln Tyr Gln Phe 
# 285 
- Asp Phe Gly Leu Arg Pro Ser Leu Ala Tyr Le - #u Gln Ser Lys Gly Lys 
# 300 
- Asn Leu Gly Arg Gly Tyr Asp Asp Glu Asp Il - #e Leu Lys Tyr Val Asp 
305 3 - #10 3 - #15 3 - 
#20 
- Val Gly Ala Thr Tyr Tyr Phe Asn Lys Asn Me - #t Ser Thr Tyr Val Asp 
# 335 
- Tyr Lys Ile Asn Leu Leu Asp Asp Asn Gln Ph - #e Thr Arg Asp Ala Gly 
# 350 
- Ile Asn Thr Asp Asn Ile Val Ala Leu Gly Le - #u Val Tyr Gln Phe 
# 365 
- (2) INFORMATION FOR SEQ ID NO:31: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 27 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:31: 
- Met Asn Lys Ala Glu Leu Ile Asp Val Leu Th - #r Thr Lys Met Xaa Ser 
# 15 
- Asp Arg Arg Gln Xaa Thr Ala Xaa Val Glu As - #p 
# 25 
- (2) INFORMATION FOR SEQ ID NO:32: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 226 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:32: 
- Met Ser Glu Thr Ala Pro Ala Glu Thr Ala Th - #r Pro Ala Pro Val Glu 
# 15 
- Lys Ser Pro Ala Lys Lys Lys Ala Thr Lys Ly - #s Ala Ala Gly Ala Gly 
# 30 
- Ala Ala Lys Arg Lys Ala Thr Gly Pro Pro Va - #l Ser Glu Leu Ile Thr 
# 45 
- Lys Ala Val Ala Ala Ser Lys Glu Arg Asn Gl - #y Leu Ser Leu Ala Ala 
# 60 
- Leu Lys Lys Ala Leu Ala Ala Gly Gly Tyr As - #p Val Glu Lys Asn Asn 
#80 
- Ser Arg Ile Lys Leu Gly Leu Lys Ser Leu Va - #l Ser Lys Gly Thr Leu 
# 95 
- Val Gln Thr Lys Gly Thr Gly Ala Ser Gly Se - #r Phe Lys Leu Asn Lys 
# 110 
- Lys Ala Ala Ser Gly Glu Ala Lys Pro Lys Al - #a Lys Lys Ala Gly Ala 
# 125 
- Ala Lys Ala Lys Lys Pro Ala Gly Ala Thr Pr - #o Lys Lys Ala Lys Lys 
# 140 
- Ala Ala Gly Ala Lys Lys Ala Val Lys Lys Th - #r Pro Lys Lys Ala Lys 
145 1 - #50 1 - #55 1 - 
#60 
- Lys Pro Ala Ala Ala Gly Val Lys Lys Val Al - #a Lys Ser Pro Lys Lys 
# 175 
- Ala Lys Ala Ala Ala Lys Pro Lys Lys Ala Th - #r Lys Ser Pro Ala Lys 
# 190 
- Pro Lys Ala Val Lys Pro Lys Ala Ala Lys Pr - #o Lys Ala Ala Lys Pro 
# 205 
- Lys Ala Ala Lys Pro Lys Ala Ala Lys Ala Ly - #s Lys Ala Ala Ala Lys 
# 220 
- Lys Lys 
225 
- (2) INFORMATION FOR SEQ ID NO:33: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 19 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:33: 
- Ala Glu Val Tyr Asn Lys Asp Gly Asn Lys Le - #u Asp Leu Tyr Gly Lys 
# 15 
- Val Asp Gly 
- (2) INFORMATION FOR SEQ ID NO:34: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:34: 
- Lys Lys Pro Ala Ala Ala Gly Val Lys Lys Va - #l Ala Lys Ser Pro 
# 15 
- (2) INFORMATION FOR SEQ ID NO:35: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:35: 
- Val Ala Lys Ser Pro Lys Lys Ala Lys Ala Al - #a Ala Lys Pro Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:36: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 15 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:36: 
- Ala Ala Lys Pro Lys Lys Ala Thr Lys Ser Pr - #o Ala Lys Pro Lys 
# 15 
- (2) INFORMATION FOR SEQ ID NO:37: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 13 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:37: 
- Lys Ser Pro Lys Lys Ala Lys Ala Ala Ala Ly - #s Pro Lys 
# 10 
- (2) INFORMATION FOR SEQ ID NO:38: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 116 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:38: 
- Leu Ala Ala Gly Gly Tyr Asp Val Glu Lys As - #n Asn Ser Arg Ile Lys 
# 15 
- Leu Gly Leu Lys Ser Leu Val Ser Lys Gly Th - #r Leu Val Gln Thr Lys 
# 30 
- Gly Thr Gly Ala Ser Gly Ser Phe Lys Leu As - #n Lys Lys Ala Ala Ser 
# 45 
- Gly Glu Ala Lys Pro Lys Ala Lys Lys Ala Gl - #y Ala Ala Lys Ala Lys 
# 60 
- Lys Pro Ala Gly Ala Thr Pro Lys Lys Ala Ly - #s Lys Ala Ala Gly Ala 
#80 
- Lys Lys Ala Val Lys Lys Thr Pro Lys Lys Al - #a Lys Lys Pro Ala Ala 
# 95 
- Ala Gly Val Lys Lys Val Ala Lys Ser Pro Ly - #s Lys Ala Lys Ala Ala 
# 110 
- Ala Lys Pro Lys 
115 
- (2) INFORMATION FOR SEQ ID NO:39: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 103 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:39: 
- Leu Ala Ala Gly Gly Tyr Asp Val Glu Lys As - #n Asn Ser Arg Ile Lys 
# 15 
- Leu Gly Leu Lys Ser Leu Val Ser Lys Gly Th - #r Leu Val Gln Thr Lys 
# 30 
- Gly Thr Gly Ala Ser Gly Ser Phe Lys Leu As - #n Lys Lys Ala Ala Ser 
# 45 
- Gly Glu Ala Lys Pro Lys Ala Lys Lys Ala Gl - #y Ala Ala Lys Ala Lys 
# 60 
- Lys Pro Ala Gly Ala Thr Pro Lys Lys Ala Ly - #s Lys Ala Ala Gly Ala 
#80 
- Lys Lys Ala Val Lys Lys Thr Pro Lys Lys Al - #a Lys Lys Pro Ala Ala 
# 95 
- Ala Gly Val Lys Lys Val Ala 
100 
- (2) INFORMATION FOR SEQ ID NO:40: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 158 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:40: 
- Leu Ala Ala Gly Gly Tyr Asp Val Glu Lys As - #n Asn Ser Arg Ile Lys 
# 15 
- Leu Gly Leu Lys Ser Leu Val Ser Lys Gly Th - #r Leu Val Gln Thr Lys 
# 30 
- Gly Thr Gly Ala Ser Gly Ser Phe Lys Leu As - #n Lys Lys Ala Ala Ser 
# 45 
- Gly Glu Ala Lys Pro Lys Ala Lys Lys Ala Gl - #y Ala Ala Lys Ala Lys 
# 60 
- Lys Pro Ala Gly Ala Thr Pro Lys Lys Ala Ly - #s Lys Ala Ala Gly Ala 
#80 
- Lys Lys Ala Val Lys Lys Thr Pro Lys Lys Al - #a Lys Lys Pro Ala Ala 
# 95 
- Ala Gly Val Lys Lys Val Ala Lys Ser Pro Ly - #s Lys Ala Lys Ala Ala 
# 110 
- Ala Lys Pro Lys Lys Ala Thr Lys Ser Pro Al - #a Lys Pro Lys Ala Val 
# 125 
- Lys Pro Lys Ala Ala Lys Pro Lys Ala Ala Ly - #s Pro Lys Ala Ala Lys 
# 140 
- Pro Lys Ala Ala Lys Ala Lys Lys Ala Ala Al - #a Lys Lys Lys 
145 1 - #50 1 - #55 
- (2) INFORMATION FOR SEQ ID NO:41: 
- (i) SEQUENCE CHARACTERISTICS: 
#acids (A) LENGTH: 55 amino 
(B) TYPE: amino acid 
(D) TOPOLOGY: linear 
- (ii) MOLECULE TYPE: peptide 
- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:41: 
- Lys Ser Pro Lys Lys Ala Lys Ala Ala Ala Ly - #s Pro Lys Lys Ala Thr 
# 15 
- Lys Ser Pro Ala Lys Pro Lys Ala Val Lys Pr - #o Lys Ala Ala Lys Pro 
# 30 
- Lys Ala Ala Lys Pro Lys Ala Ala Lys Pro Ly - #s Ala Ala Lys Ala Lys 
# 45 
- Lys Ala Ala Ala Lys Lys Lys 
# 55 
__________________________________________________________________________