Stimulation of Hypoxia Inducible Factor -lalpha (FflF-lα) for the treatment of Clostridium Difficile Associated Disease (CDAD), for Intestinal Motility and for Detecting Infection

Field

[0001] The present application relates to methods and compositions for treating Clostridium difficile - associated disease (CDAD) by administering an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels.

5 Background

[0002] Clostridium difficile is an anaerobic spore forming gram-positive bacillus that is the leading cause of nosocomial infectious diarrhea [1-3]. Although C. c//7f/c//e-associated disease (CDAD) can be mild, recent outbreaks of more virulent strains have been associated with significant pathology (e.g.,0 pseuomembraneous colitis; PMC) and mortality [4-6]. C. difficile produces an enterotoxin, toxin A (TcdA; MW, 308 kDa), and a cytotoxin, toxin B (TxB; MW, 270 kDa). Both TcdA and TcdB are glucosyltransferases that irreversibly inactivate the Ras superfamily of small GTPases [7]. The toxins can modulate numerous physiological signaling pathways in a variety of cell populations.5 Changes in the actin cytoskeleton and disruption of tight junction and perijunctional ring formation in epithelial cells [8, 9] are thought to be involved in the increased intestinal permeability seen in CDAD. Furthermore, C. difficile toxins can induce inflammatory events that are associated with CDAD. To date most of these studies have focused on TcdA and some of the responses0 identified include increases in cytokine and chemokine production [10, 11], neutrophil infiltration [12-14], adhesion molecule expression [15], activation of submucosal neurons [16], production of reactive oxygen intermediates [17], mast cell activation [18, 19], substance P production [20], and apoptosis [21 , 22]. 5 [0003] The hypoxia-inducible factor (HIF-1) is a transcriptional complex known for its contribution to the maintenance of oxygen and energy homoeostasis [23, 24]. In its active form, HIF-1 is a heterodimeric complex composed of HIF-1α and HIF-1 β subunits. The HIF-1α subunit is ubiquitously and constitutively expressed, but in normoxic conditions the protein is subject0 to hydroxylation by prolyl hydroxylases which trigger binding of von Hippel

Lindau protein to HIF-1α and targeting of HIF-1α to the proteasome for degradation (for review, see [23]). HIF-1α binds to hypoxia responsive elements (HREs) present in promoter or enhancer regions to promote gene expression. Furthermore, HIF-1α has been found to have regulatory actions in a wide variety of cellular processes involved in immune reactions [25, 26]. HIF-1α can increase the transcription of genes (e.g., VEGF, EPO, eNOS, iNOS, COX-2, and HO-1) that are involved in wound repair, inflammation, cellular permeability, and apoptosis.

[0004] Inflammatory mediators including IL-1 β, IFN-γ, NO and TNF-α can induce HIF-1α gene expression, even in normoxic conditions [26]. In rat intestinal epithelial cells, IL-1 β, TNF-α and IFN-γ stabilize the HIF-1 heterodimer (protecting the α subunit from proteolysis) and induce HIF-1 α gene expression [27, 28]. IL-1 β can also increase HIF-1 levels by inhibiting the pVHL-dependent degradation of HIF-1 α [29]. While it is known that C. difficile toxins can induce inflammatory events that are associated with CDAD

[30], the specific role of HIF-1 has not been studied in CDAD.

Summary

[0005] The present inventors have determined that hypoxia-inducible factor 1α (HIF-1 α) is induced by Clostridium difficile toxins. The inventors have shown that HIF-1 α activation has a protective effect in CDAD. The inventors have also shown that HIF-1α activation increases ileal smooth muscle contraction.

[0006] Intestinal epithelial cells (IECs) in which HIF-1 α had been

'knocked-down' with siRNA technology exhibited impaired wound repair capabilities, increased susceptibility to C. difficile toxin-mediated changes in transepithelial potential difference, and decreased cellular viability upon exposure to toxin. The inventors have further established that murine IEC lines deficient in intestinal HIF-1 α protein are more susceptible to C. difficile toxin-induced injury. HIF-1α knock-out mice develop more severe C. difficile toxin-induced injury and inflammation as evidenced by more marked ileal dilation, fluid secretion, histological changes, and higher tissue

myeloperoxidase levels. The inventors also studied the impact of HIF-1α on smooth muscle contractility in the HIF-1α knock-out mice. The results show that HIF-1α signaling can influence smooth muscle Ca ²⁺ sensitization via Rho- associated kinase (ROK) signaling during challenge with C. difficile toxin. [0007] Accordingly, the present application provides a method of treating C. difficile associated disease (CDAD) comprising administering an effective amount of an agent that increases hypoxia-inducible factor 1α (HIF- 1α) levels, to an animal in need thereof. The present application also provides a use of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels for treating C. difficile associated disease (CDAD) in an animal in need thereof. Also provided is use of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels in the preparation of a medicament for treating C. difficile associated disease (CDAD) in an animal in need thereof. Further provided is an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels for use in treating C. difficile associated disease (CDAD) in an animal in need thereof.

[0008] The present application also provides a method of increasing intestinal motility comprising administering an effective amount of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels, to an animal in need thereof. The present application also provides a use of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels for increasing intestinal motility in an animal in need thereof. Also provided is use of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels in the preparation of a medicament for increasing intestinal motility in an animal in need thereof. Further provided is an agent that increases hypoxia-inducible factor 1α (HIF- 1α) levels for use in increasing intestinal motility in an animal in need thereof.

[0009] The present application also includes screening assays for identifying agents that can induce HIF-1α comprising the steps of:

(a) incubating a test compound with a cell that can express HIF-1α; and

(b) determining the effect of the compound on HIF-1α expression levels or activity and comparing with a control wherein a change in HIF-1α activity or expression as compared to the control indicates that the test compound can induce HIF-1α. [0010] The present application further includes a pharmaceutical composition comprising an effective amount of an agent that increases HIF-1α levels. The pharmaceutical compositions can further comprise a suitable diluent or carrier.

[0011] The present application further provides a method for detecting C. difficile infection in a patient comprising:

(a) providing a sample from the patient;

(b) detecting the level of HIF-1α in the sample; and

(c) comparing the level of HIF-1α in the sample to a control sample, wherein increased levels of HIF-1α as compared to the control indicates that the patient has a C. difficile infection.

[0012] Other features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples while indicating preferred embodiments of the disclosure are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description.

Brief description of the drawings

[0013] The application will now be described in relation to the drawings in which:

[0014] Figure 1. HIF-1α mRNA levels are increased following treatment of human epithelial (Caco-2) cells under normoxic conditions with C. difficile crude toxin. Total RNA was isolated, and the expression of HIF-1α and β2- microglobin (internal control) was determined by semi-quantitative RT-PCR.

(A) ₁ Caco-2 cells were exposed to crude toxin (100 μg/mL) for 4 and 24h. (B), Caco-2 cells were exposed to crude toxin (0.1 μg/mL) or C0CI2 (100 μM) for 1 , 2, or 4h. PBS was added to the cells as a control. (C), SYBR Green-based quantitative real-time RT-PCR was used to quantify HIF-1α gene expression following treatment of Caco-2 cells for 4 h with increasing amounts of C. difficile crude toxin.

[0015] Figure 2. HIF-1α protein expression is increased in Caco-2 cells following treatment with crude C. difficile toxin. HIF-1α protein levels were assessed following 4 h treatment of Caco-2 cells with C. difficile crude toxin (100 μg/mL) or C0CI ₂ (100 μM). Nuclear extracts (50 μg total protein) were analyzed for HIF-1α protein levels by Western blotting.

[0016] Figure 3. C. difficile toxin exposure promotes HIF-1α dependent promoter binding activity in human colonic epithelial (Caco-2) cells. DNA binding of HIF-1α to the EPO hypoxia response element (HRE) was assessed by electrophoretic mobility shift assay (EMSA). Nuclear extracts were prepared from Caco-2 cells that had been exposed to C. difficile crude toxin (100 μg/mL), or CoCI ₂ (100 μM). In some cases, "supershifts" (SS) were generated during EMSA with addition of 2 μL mouse anti-HIF-1α monoclonal antibody to the DNA binding reactions. [0017] Figure 4. C. difficile toxin exposure promotes HIF-1α transcriptional activity in human colonic epithelial (Caco-2) cells. Caco-2 cells were transiently co-transfected with firefly luciferase reporter (pGL3-Luc- 3*HRE) and Renilla luciferase control (pRL-SV40) plasmids. Cells were incubated for 4, 18, or 24 h under normoxic conditions withiO μg/mL C. difficile crude toxin or 100 μM CoCI ₂ . The tranfection efficiency was corrected by normalizing firefly luciferase activity to the Renilla luciferase activity. Control cells were transfected with empty pGL3 vector and treated for 24 h with C. difficile crude toxin or CoCI ₂ . All values (mean ± S. E. M., n=4) are expressed as fold-induction relative to the controls that were arbitrarily defined as 1.

[0018] Figure 5. HIF-1α expression and HIF-1α DNA binding activities are induced by individual C. difficile toxins TcdA and TcdB. Caco-2 cells were treated with crude filtrate isolated from either TcdA+/TcdB- or TcdA-/TcdB+ C. difficile cultures. TcdA and TcdB toxins were also purified from C. difficile strain 04-CT-01-2007. CoCI ₂ (100 μM) and C. difficile crude toxin (TcdA+/TcdB+; 100 μg/mL) treatments are included for comparison. (A), Nuclear extracts (50 μg total protein) were analyzed for HIF-1α protein levels by Western blotting. (B), HIF-1α binding to the W18 oligonucleotide containing the EPO hypoxia response element (HRE) was assessed by electrophoretic mobility shift assay (EMSA). (C), SDS-PAGE gel showing purity of TcdA (Lane 1) and TcdB (Lane 2) isolated from C. difficile 04-CT-01-2007 crude toxin (Lane 3).

[0019] Figure 6. C. d/Yf/c/ ^' /e-associated colitis is associated with increased HIF-1α expression. To investigate whether HIF-1α expression is altered in human disease, colonic tissue biopsies and sections from patients undergoing colonic resection for CDAD were obtained. Tissue sections were stained for HIF-1α using a mouse anti-HIF-1α monoclonal antibody (NB100- 105), an anti-mouse HRP-coupled secondary antibody and diaminobenzidine substrate. Immunolocalization of HIF-1α was determined in human colonic tissue obtained from patients with C. d/7frc/7e-associated colitis (biopsy or surgical resection; a minimum of 5 per group were assessed). As shown in figure 6 there was minimal HIF-1α staining in normal tissues (figure 6a: A-B). Intense HIF-1α staining was noted in the mucosa, submucosa, and muscularis (Figure 6a-C) with discrete staining identified in inflammatory cells (Figure 6a-E, F), epithelial cells (Figure 6a-D), endothelial cells (Figure 6a-E, F), as well as smooth muscle cells of the muscularis mucosa (C, between arrows), the initimal vasculature (Figure 6a-E- F) and the muscularis (Figure 6a-E). Figure 6b: Marked HIF-1α staining was noted in sections obtained from patients undergoing biopsy or colonic resection for ischemic colitis (Figure 6b- G, H) and ulcerative colitis (Figure 6b-l, J). Similar staining patterns were noted in biopsy tissue and colonic resection tissue. Standard

immunohistochemical controls were negative (e.g. omission of mouse anti- HIF-1α antibody). As shown in figure 6c, the increase in HIF-1α protein was accompanied by an increase in HIF-1α mRNA expression in tissues derived from patients with C. c//7f/c/7e-associated colitis compared to normal controls. [0020] Figure 7. The contractile responses of ileal smooth muscle from

HIF-1α ^("A) mice are also enhanced with short-term exposure to C. difficile toxin. (A) The contractile responses to high extracellular K ⁺ solution (118 mM K ⁺ ) and carbachol (10 μM) were examined in circular smooth muscle isolated from ileal loops of HIF-Ia^ mice. Ileal loops were treated with PBS or C. diff crude toxin for 4 h. (B) Cumulative results are representative of 4 independent experiments. Error bars indicate S. E. M with statistical significance (*) determined by Student's t-test.

[0021] Figure 8. ROK contribution to carbachol-induced smooth muscle contraction is suppressed in C. difficile toxin-treated ileal loops from HIF-1α(-/-) mice. Murine ileal loops were generated, smooth muscle contraction was monitored, and ROK contribution was defined. (A) The contractile responses to carbachol (10 μM) were recorded from smooth muscle isolated from ileal loops of HIF-1α ^("λ) mice after 4 h C. diff toxin exposure. (B) Cumulative results of ROK contribution to contraction are representative of 3 independent experiments. *- significantly different from control (medium injected) HIF-1α ^("A) mice (Student's t-test, p < 0.05). ^** - significantly different from wild-type (WT) C. d/7f-treated mice (ANOVA with post-hoc SNK analysis, p < 0.05).

[0022] Figure 9. Caco-2 cells deficient in HIF-1α are more susceptible to C. diff toxin-induced injury. (A) HIF-1α protein levels in Caco-2 cells stably transfected with HIF-1α siRNA (Caco-2 HIF-1α-/-) were not affected by C. diff. crude toxin or CoCb. Decreased HIF-1α expression in Caco-2 HIF-1α-/- cells display increased susceptibility to C. diff. toxin, as assessed by transepithelial electrical resistance (B), and decreased viability (C), as measured by MTT assay (Caco-2 HIF-1α -/- = broken line; WT Caco-2 = solid line). All values (mean ± S.E.M., n=4). * denotes p<0.05

[0023] Figure 10. C. diff. toxin increases HIF-1α expression and induces inflammation in an in vivo model of CDAD. (A) HIF-1α mRNA levels from ileum isolated from control animals (no surgery), mice treated with control media and treated with 100 μg of C. diff. crude toxin as measured with semi-quantitative PCR (* denotes p<0.05 compared to control and culture media, n=5). (B) HIF-1α protein levels in tissue isolated from mice treated with control media or treated with 100 μg of C. diff. crude toxin. (* denotes p<0.05 compared to culture media, n=4). (C) Tissue inflammation as assessed by myeloperoxidase levels from ileum isolated from control animals (no surgery), mice treated with control media and treated with 100 μg of C. diff. crude toxin (* denotes p<0.05 compared to control and culture media, ** denotes p<0.05 culture media, n=9). (D) Real-time PCR data from RNA isolated from toxin-treated ileal loops. VEGFa - vascular endothelial growth factor-a; MDR-1 - multidrug resistance gene-1 ; ITF - intestinal trefoil factor; CD73 - ecto-5'-nucleotidase; TNF - tumor necrosis factor; CXCL1 - murine KC. Data is expressed as fold-change from control (i.e. media-treated ileal loops) where a fold-change of 1 is equal to the expression in the control group. Dashed line indicates control values. * denotes p<0.05 compared to control, n=3. [0024] Figure 11. Target deletion of HIF-1α in intestinal epithelium

(HIF-1α -/-) renders animals more susceptible to C. diff. toxin-induced inflammation. (A) Toxin-induced increases in serum nitric oxide (NO) levels are significantly greater in HIF-1α -/- as compared to wild-type 129 mice. (B) Tissue inflammation as assessed by myeloperoxidase levels from ileum isolated from wild-type I29 and HIF-1α (-/-) mice treated with 100 μg of C. diff. crude toxin. (C) Hematoxylin and eosin stained ileal sections from HIF-1α (ep-/-) (top row) and wild-type I29 (bottom row) mice treated with 100 μg of C. diff. crude toxin. ^* denotes p<0.05 compared to wild-type I29, n=6.

[0025] Figure 12. Animals pretreated with DMOG (dimethyloxaloylglycine; 8 mg/day for 2 days prior to surgery) to stabilize HIF-

1α through inhibition of prolyl-4-hydroxylases display significantly less C. diff.

toxin-induced inflammation and tissue damage. (A-F) Representative sections of ileum stained with eosin and hematoxylin from mice treated with culture media (A-B), C. diff. toxin (C-D), treated with DMOG prior to C. diff. toxin (E-F). (G) Tissue inflammation as assessed by myeloperoxidase levels from ileum isolated from wild-type 129 mice treated with culture media, C. diff. toxin and treatment with DMOG and toxin. Control bar indicates levels measured in animals not undergoing surgery. * denotes p<0.05 compared to control and culture media, ψ denotes p<0.05 compared to C. diff. toxin, n=6- 8. (H) Histological analysis of ileal sections derived from mice treated with culture media, C. diff. toxin or DMOG followed by C. diff. toxin. Arch. Sc. - Architectural Score; Infl. Sc. - Inflammation Score; Epith. Dam. - Epithelial Damage; Neu. Sc. - Neutrophil Score. * denotes p<0.05 compared to culture media; # denotes p<0.05 compared to C. diff. toxin; n=8-12.

[0026] Figure 13. Treatment with DMOG prior to C. diff. toxin is associated with elevated levels of factors associated with intestinal barrier function and protection factors (A) and reduced levels of inflammatory mediators (B) as measured with real-time PCR. Data is expressed as fold- change from toxin (i.e. C. diff. toxin-treated ileal loops) where a fold-change of 1 is equal to the expression in the toxin group. VEGFa - vascular endothelial growth factor-a; ITF - intestinal trefoil factor; CD73 - ecto-5'-nucleotidase; TNF - tumor necrosis factor; CXCL1 - murine KC Dashed line indicates control values. ^* denotes p<0.05 compared to toxin, n=3

Detailed description I. Methods of Treatment and Uses

[0027] Clostridium c//7f/c/Ve-associated disease (CDAD) is a severe medical condition that has both increasing incidence and mortality rates. C. difficile toxins can affect numerous physiological events, including epithelial permeability, apoptosis, cytokine and chemokine production. HIF (hypoxia- inducible factor) is a transcriptional regulator that plays a central role in the cellular response to hypoxia, inflammation, and energy homeostasis. The

present inventors determined that HIF-1α is activated in intestinal epithelial cells by exposure to C. difficile toxin. The inventors detected potent activation of HIF-1α signaling by C. difficile toxin under normal oxygen concentrations. Enhanced HIF-1α mRNA and protein expression were exhibited in Caco-2 cells following exposure to both crude and purified (TcdA and TcdB) toxins. Treatment with C. difficile crude toxin induced HIF-1α DNA binding activity in nuclear extracts as determined by gel-shift analysis. The accumulation of HIF- 1α protein in Caco-2 cells following exposure to C. difficile toxin was correlated with transcriptional activation of HIF-1α as measured by luciferase reporter assay. To further investigate whether HIF-1α expression is altered in human disease, the inventors examined colonic tissue sections from patients undergoing colonic resection for PMC. Up-regulation of HIF-1α expression was noted in biopsy samples as well as in colonic resection specimens in PMC and generally correlated with disease activity. [0028] The present application provides a method of treating C. difficile associated disease (CDAD) comprising administering and effective amount of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels, to an animal in need thereof. The present application also provides a use of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels for treating C. difficile associated disease (CDAD) in an animal in need thereof. Also provided is use of an agent that increases hypoxia-inducible factor 1α (HIF- 1α) levels in the preparation of a medicament for treating C. difficile associated disease (CDAD) in an animal in need thereof. Further provided is an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels for use in treating C. difficile associated disease (CDAD) in an animal in need thereof.

[0029] The inventors have also shown that exposure of intestinal epithelium to C. difficile toxins stimulated HIF-1α levels and increased the contraction of illeal smooth muscle.

[0030] Alterations in gastrointestinal motility with resultant changes in transit can contribute to abdominal pain, intestinal cramping and diarrhea.

Furthermore, defects in smooth muscle function are associated with the

development of toxic megacolon. This condition is characterized by marked dilation of the distal colon and can occur with severe ulcerative colitis, in Hirschsprung's disease, and in some forms of infectious colitis (i.e. CDAD). Coordinated regulation of contraction is a key property of gastrointestinal smooth muscle, which when functioning normally, contributes to general health and wellness, but when dysfunctional is associated with morbidity and mortality. Thus, motility disorders that arise in the context of inflammation or immune activation are clinically important as they can lead to systemic disease. [0031] Motility dysfunction is a classic clinical feature of CDAD. In early stages of CDAD, patients complain of abdominal cramping, urgency and diarrhea suggesting increased motility. In more severe cases there can be a phase of decreased motility with abdominal distension and colonic dilation that can progress on to toxic megacolon. This decreased motility can lead to increased C. difficile bacterial load and toxin levels resulting in more severe mucosal injury.

[0032] The present application also provides a method of increasing intestinal motility comprising administering an effective amount of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels to an animal in need thereof. The present application also provides a use of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels for increasing intestinal motility in an animal in need thereof. Also provided is use of an agent that increases hypoxia-inducible factor 1α (HIF-1α) levels in the preparation of a medicament for increasing intestinal motility in an animal in need thereof. Further provided is an agent that increases hypoxia-inducible factor 1α (HIF- 1α) levels for use in increasing intestinal motility in an animal in need thereof.

[0033] Increasing intestinal motility can reduce the C. difficile bacterial load and toxin levels and therefore reduce the intestinal injury. Increasing intestinal motility can also be useful in treating toxic megacolon, Hirschsprung disease, intestinal pseudo-obstruction, post-surgical motility dysfunction and irritable bowel syndrome.

[0034] The agent that increases HIF-1α levels can be any agent that can activate and/or induce expression of endogenous HIF-1α or an agent that mimics the activity of HIF-1α or an agent that prevents the degradation of HIF- 1α. The agent can also be exogenous HIF-1α protein or a nucleic acid encoding HIF-1α.

[0035] In one embodiment, the agent that increases HIF-1α levels is an agent that can activate endogenous HIF-1α. Such agents include, but are not limited to, bacterial toxins, proteins, nucleic acids molecules, small molecules, peptides mimetics and any agent identified according to the screening assays described herein.

[0036] In one embodiment, the agent that activates endogenous HIF-

1α is a bacterial toxin, preferably a toxin from Clostridium difficile. Most preferably, the C. difficile toxin is TcdA or TcdB.

[0037] In another embodiment, the agent that activates endogenous HIF-1α is selected from the group consisting of cobalt, nickel, manganese, iron chelators (e.g. desferrioxamine), proteasome inhibitors (e.g. MG132), viral oncogenes (e.g human T-cell leukaemia virus type 1 , Hepatitis B virus X protein, Kaposi's sarcoma herpes virus G-protein-coupled receptor & Epstein-

Barr virus latent membrane protein 1), agents that block factors inhibiting HIF-1 (FIH-1 & α-HIF), insulin, cytokines, growth factors, protein kinases

(PI3K/Akt/mTOR), HIF-1 promoter transactivators (Sp1 and NF-κβ), and inhibitors of prolyl hydroxylation.

[0038] Prolyl hydroxylases regulate the oxygen-dependent degradation of HIF-1 α. Examples of inhibitors of prolyl hydroxylation include, without limitation, 2-oxoacid molecules and derivatives thereof and 2-oxoglutarate analogs, such as N-oxalylglycine (NOG) or dimethyloxalylglycine (DMOG). For example, see WO2005/094236 and Wamecke et al. (2003 FASEB J. 17, 1186-1188), both of which are incorporated herein by reference. Accordingly, in one embodiment, the agent is an inhibitor of prolyl hydroxylase. In another embodiment, the inhibitor is dimethyloxalyl glycine or a derivative or analog thereof.

[0039] Hypoxia, or low oxygen conditions (e.g. <1% oxygen) can also be used to induce HIF-1α levels.

[0040] In another embodiment, the agent that increases HIF-1α levels is an HIF-1α protein or a nucleic acid encoding HIF-1α protein or variants thereof. The HIF-1α protein may be obtained from known sources or prepared using recombinant DNA techniques. The protein may have any of the known-published sequences for HIF-1α including Rat, NM_024359; Mouse, NM_010431 ; Human, BC012527.2, BT009776, CH471061.1. The nucleic acid may have any of the known-published sequences for the HIF-1α gene including human, NM_001530 (gi: 194473733) variant 1 , NM_18054 (gi: 194473734) variant 2; mouse, NM_010431 (gi:7363432); rat, NM_024359 (gi: 13242249).

[0041] The term "variant" as used herein includes modifications, substitutions, additions, derivatives, analogs, fragments or chemical equivalents of the HIF-1α amino acid sequences disclosed herein that perform substantially the same function in substantially the same way. For instance, the variants of the HIF-1α would have the same function of being able to induce expression of VEGF, EPO, iNOS, eNOS, COX-2 and/or HO-1.

[0042] Variants also include peptides with amino acid sequences that are substantially or essentially identical to the amino acid sequences of HIF- 1α.

[0043] The term "substantially identical" or "essentially identical" as used herein means an amino acid sequence that, when optimally aligned, for example using the methods described herein, share at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity with a second amino acid sequence.

[0044] The term "sequence identity" as used herein refers to the percentage of sequence identity between two polypeptide and/or nucleotide sequences.

[0045] To determine the percent identity of two amino acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues at corresponding amino acid positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=number of identical overlapping positions/total number of positions.times.100%). In one embodiment, the two sequences are the same length. The determination of percent identity between two sequences can also be accomplished using a mathematical algorithm. A preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. U.S.A. 87:2264-2268, modified as in Karlin and Altschul, 1993, Proc. Natl. Acad. Sci. U.S.A. 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al., 1990, J. MoI. Biol. 215:403. BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g., for score=100, wordlength=12 to obtain nucleotide sequences homologous to a nucleic acid molecule of the present application. BLAST protein searches can be performed with the XBLAST program parameters set, e.g., to score-50, wordlength=3 to obtain amino acid sequences homologous to a protein molecule of the present disclosure. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., 1997, Nucleic Acids Res. 25:3389- 3402. Alternatively, PSI-BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., of XBLAST and NBLAST) can be used (see, e.g., the NCBI website). Another preferred, non-limiting example of a

mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4:11-17. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted. [0046] The percentage of identity between two polypeptide sequences, the amino acid sequences of such two sequences are aligned, for example using the Clustal W algorithm (Thompson, JD, Higgins DG, Gibson TJ, 1994, Nucleic Acids Res. 22(22): 4673-4680.), together with BLOSUM 62 scoring matrix (Henikoff S. and Henikoff J. G., 1992, Proc. Natl. Acad. Sci. USA 89: 10915-10919.) and a gap opening penalty of 10 and gap extension penalty of 0.1 , so that the highest order match is obtained between two sequences wherein at least 50% of the total length of one of the sequences is involved in the alignment.

[0047] Other methods that may be used to align sequences are the alignment method of Needleman and Wunsch (Needleman and Wunsch. J.

MoI. Biol., 1970, 48:443), as revised by Smith and Waterman (Smith and

Waterman. Adv. Appl. Math. 1981 , 2:482) so that the highest order match is obtained between the two sequences and the number of identical amino acids is determined between the two sequences. Other methods to calculate the percentage identity between two amino acid sequences are generally art recognized and include, for example, those described by Carillo and Lipton

(Carillo and Lipton SIAM J. Applied Math. 1988, 48:1073) and those described in Computational Molecular Biology (Computational Molecular

Biology, Lesk, e.d. Oxford University Press, New York, 1988, Biocomputing: Informatics and Genomics Projects). Generally, computer programs will be employed for such calculations.

[0048] The HIF-1α protein may also be modified to contain amino acid substitutions, insertions and/or deletions that do not alter the properties of the protein. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. Conserved amino acid substitutions involve replacing one or more amino acids of the HIF-1α amino acid sequence with amino acids of similar charge, size, and/or hydrophobicity characteristics. When only conserved substitutions are made the resulting analog should be functionally equivalent to the HIF-1α protein. Non-conserved substitutions involve replacing one or more amino acids of the HIF-1α amino acid sequence with one or more amino acids which possess dissimilar charge, size, and/or hydrophobicity characteristics.

[0049] Variants of the HIF-1α amino acid sequences of the present application also include additions and deletions to the amino acid sequences disclosed herein.

[0050] The HIF-1α protein may be modified to make it more therapeutically effective or suitable. For example, the HIF-1α protein may be cyclized as cyclization allows a peptide to assume a more favourable conformation. Cyclization of the HIF-1α peptides may be achieved using techniques known in the art. In particular, disulphide bonds may be formed between two appropriately spaced components having free sulfhydryl groups. The bonds may be formed between side chains of amino acids, non-amino acid components or a combination of the two. In addition, the HIF-1α protein or peptides of the present application may be converted into pharmaceutical salts by reacting with inorganic acids including hydrochloric acid, sulphuric acid, hydrobromic acid, phosphoric acid, etc., or organic acids including formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, succinic acid, malic acid, tartaric acid, citric acid, benzoic acid, salicylic acid, benzenesulphonic acid, and tolunesulphonic acids.

[0051] Peptide mimetics of HIF-1α may also be used as an agent that increases HIF-1α levels. Such peptides may include competitive inhibitors, enhancers, and the like. All of these peptides as well as molecules substantially homologous, complementary or otherwise functionally or structurally equivalent to these peptides may be used for purposes of the present application.

[0052] "Peptide mimetics" are structures which serve as substitutes for peptides in interactions between molecules (See Morgan et al. (1989), Ann. Reports Med. Chem. 24:243-252 for a review). Peptide mimetics include synthetic structures which may or may not contain amino acids and/or peptide bonds but retain the structural and functional features of a peptide, or enhancer or inhibitor of the application. Peptide mimetics also include peptoids, oligopeptoids (Simon et al. (1972) Proc. Natl. Acad. Sci. USA 89:9367); and peptide libraries containing peptides of a designed length representing all possible sequences of amino acids corresponding to a peptide of the application.

[0053] Peptide mimetics may be designed based on information obtained by systematic replacement of L-amino acids by D-amino acids, replacement of side chains with groups having different electronic properties, and by systematic replacement of peptide bonds with amide bond replacements. Local conformational constraints can also be introduced to determine conformational requirements for activity of a candidate peptide mimetic. The mimetics may include isosteric amide bonds, or D-amino acids to stabilize or promote reverse turn conformations and to help stabilize the molecule. Cyclic amino acid analogues may be used to constrain amino acid residues to particular conformational states. The mimetics can also include mimics of inhibitor peptide secondary structures. These structures can model the 3-dimensional orientation of amino acid residues into the known secondary conformations of proteins. Peptoids may also be used which are oligomers of N-substituted amino acids and can be used as motifs for the generation of chemically diverse libraries of novel molecules.

[0054] Variant HIF-1α peptides and peptide activators of the present application also include derivatives thereof. The term "derivative" refers to a peptide having one or more residues chemically derivatized by reaction of a functional side group. Such derivatized molecules include for example, those molecules in which free amino groups have been derivatized to form amine hydrochlorides, p-toluene sulfonyl groups, carbobenzoxy groups, t- butyloxycarbonyl groups, chloroacetyl groups or formyl groups. Free carboxyl groups may be derivatized to form salts, methyl and ethyl esters or other types of esters or hydrazides. Free hydroxyl groups may be derivatized to form O-acyl or O-alkyl derivatives. The imidazole nitrogen of histidine may be derivatized to form N-im-benzylhistidine. Also included as derivatives are those peptides which contain one or more naturally occurring amino acid derivatives of the twenty standard amino acids. For examples: 4- hydroxyproline may be substituted for proline; 5-hydroxylysine may be substituted for lysine; 3-methylhistidine may be substituted for histidine; homoserine may be substituted for serine; and ornithine may be substituted for lysine. A derivative of a polypeptide also optionally includes polypeptides comprising forms of amino acids that are oxidized.

[0055] Variant HIF-1α peptides and peptide activators of the present application also include fragments thereof. The term "fragment" as used herein means a portion of a polypeptide that contains, preferably, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more of the entire length of the reference polypeptide.

[0056] Administration of an "effective amount" of an agent that increases the HIF-1α levels is defined as an amount effective, at dosages and for periods of time necessary to achieve the desired result. The effective amount of the agent may vary according to factors such as the disease state, age, sex, and weight of the animal. Dosage regimen may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation.

[0057] The term "animal" as used herein includes all members of the animal kingdom including humans.

H. Screening Assays

[0058] The present application also includes screening assays for identifying agents that activate HIF-1α and that are useful in treating CDAD and/or increasing intestinal motility.

[0059] Accordingly, the present application also includes screening assays for identifying agents that can induce HIF-1α comprising the steps of:

(a) incubating a test compound with a cell that can express

H I F- 1α; and

(b) determining the effect of the compound on HIF-1α expression levels or activity and comparing with a control wherein a change in HIF-1α activity or expression as compared to the control indicates that the test compound can induce HIF-1α.

[0060] In above screening assay, the test compound can be any compound which one wishes to test including, but not limited to, bacterial toxins, proteins, peptides, nucleic acids (including RNA, DNA, antisense oligonucleotide, peptide nucleic acids), carbohydrates, organic compounds, small molecules, natural products, library extracts, bodily fluids and other samples that one wishes to test for activating HIF-1α.

[0061] The cell used in the screening assay can be any cell that expresses HIF-1α or a cell that has been transfected with HIF-1α. Types of cells that may be used include, but are not limited to, Caco-2, COS-7 or 293 cell lines. In a specific embodiment, the cells also express a HIF-1α -sensitive reporter gene that drives the expression of a detectable product such as luciferase or green fluorescent protein which can be detected on a fluorometric plate reader. A potentially useful HIF-1α activator would be expected to increase luciferase activity or the fluorescent signal measured.

[0062] The screening methods of the application include high- throughput screening applications. For example, a high-throughput screening assay may be used which comprises any of the methods according to the application wherein aliquots of cells transfected with HIF-1α are exposed to a plurality of test compounds within different wells of a multi-well plate. Further, a high-throughput screening assay according to the application involves aliquots of transfected cells which are exposed to a plurality of candidate factors in a miniaturized assay system of any kind. Another embodiment of a high-throughput screening assay could involve exposing a transfected cell population simultaneously to a plurality of test compounds.

[0063] The method of the application may be "miniaturized" in an assay system through any acceptable method of miniaturization, including but not limited to multi-well plates, such as 24, 48, 96 or 384-wells per plate, microchips or slides. The assay may be reduced in size to be conducted on a micro-chip support, advantageously involving smaller amounts of reagent and other materials. Any miniaturization of the process which is conducive to high-throughput screening is within the scope of the application.

[0064] The application extends to any compounds or modulators of

HIF-1α identified using the screening method of the application that are useful in treating CDAD.

III. Pharmaceutical Compositions

[0065] The present application includes pharmaceutical compositions containing one or more agents that activate HIF-1α. Accordingly, the present application provides a pharmaceutical composition comprising an effective amount of an agent that activates or increases HIF-1α levels in admixture with a suitable diluent or carrier.

[0066] In one embodiment, the present application provides a pharmaceutical composition for use in treating CDAD and/or increasing intestinal motility comprising an effective amount of a C. difficile toxin, preferably TcdA or TcdB, in admixture with a suitable diluent or carrier.

[0067] In another embodiment, the present application provides a pharmaceutical composition for use in treating CDAD and/or increasing intestinal motility comprising an effect amount of an inhibitor of prolyl hydroxylase, preferably.dimethyloxalyl glycine or a derivative or analog thereof, in admixture with a suitable diluent of carrier.

[0068] The application also includes a pharmaceutical composition comprising a modulator of HIF-1α identified using the screening method of the application in admixture with a suitable diluent or carrier. The application further includes a method of preparing a pharmaceutical composition for use in treating CDAD comprising mixing a modulator of HIF-1α identified according to the screening assay of the application with a suitable diluent or carrier.

[0069] Such pharmaceutical compositions can be for intralesional, intravenous, topical, rectal, parenteral, local, inhalant or subcutaneous, intradermal, intramuscular, intrathecal, transperitoneal, oral, and intracerebral use. The composition can be in liquid, solid or semisolid form, for example pills, tablets, creams, gelatin capsules, capsules, suppositories, soft gelatin capsules, gels, membranes, tubelets, solutions or suspensions. The HIF-1α activator is preferably injected in a saline solution either intravenously, intraperitoneal^ or subcutaneously.

[0070] The pharmaceutical compositions of the application can be intended for administration to humans or animals. Dosages to be administered depend on individual needs, on the desired effect and on the chosen route of administration. [0071] The pharmaceutical compositions can be prepared by per se known methods for the preparation of pharmaceutically acceptable compositions which can be administered to patients, and such that an effective quantity of the active substance is combined in a mixture with a pharmaceutically acceptable vehicle. Suitable vehicles are described, for example, in Remington's Pharmaceutical Sciences (Remington's

Pharmaceutical Sciences, Mack Publishing Company, Easton, Pa., USA 1985).

[0072] On this basis, the pharmaceutical compositions include, albeit not exclusively, the active compound or substance in association with one or more pharmaceutically acceptable vehicles or diluents, and contained in buffered solutions with a suitable pH and iso-osmotic with the physiological fluids. The pharmaceutical compositions may additionally contain other immune modulatory agents.

[0073] The composition may be in the form of a pharmaceutically acceptable salt which includes, without limitation, those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylarnino ethanol, histidine, procaine, etc [0074] The compositions of the application may be used alone or in combination with other known agents useful for treating or preventing CDAD.

IV. Diagnosis Assays

[0075] As previously mentioned, the inventors have shown that HIF-1α is markedly increased in patients with a C. difficile infection and CDAD. Hence, HIF-1α is a useful maker for detecting C. difficile infection and/or CDAD.

[0076] In an embodiment, a method is provided for detecting C. difficile infection in a patient comprising:

(a) providing a sample from the patient; (b) detecting the level of HIF-1α in the sample; and

(c) comparing the level of HIF-1α in the sample to a control sample, wherein increased levels of HIF-1α as compared to the control indicates that the patient has a C. difficile infection.

[0077] The phrase "detecting the level of HIF-1α" includes the detection of the levels of the HIF-1α protein as well as detection of the levels of nucleic acid molecules encoding the HIF-1α protein. Methods for detecting proteins and nucleic acids are discussed in greater detail below. [0078] The term "sample from a patient" as used herein means any sample containing cells that one wishes to test including, but not limited to, colonic tissue faeces, intestinal tissue, bowel, epithelial cells, inflammatory cells of the lamina propria and submucosa, and endothelial cells of the microvasculature. In a preferred embodiment, the sample is colonic tissue. [0079] The "patient" can be any mammal, preferably human, suspected of having a C. difficile infection and/or CDAD.

[0080] The term "control sample" includes any sample that can be used to establish a base or normal level, and may include tissue samples taken from healthy persons or samples mimicking physiological fluid. Examples of control samples include normal colonic tissues.

[0081] A variety of methods can be employed for the above described diagnostic methods. Such methods may rely, for example, on the detection of nucleic acid molecules encoding HIF-1α, and fragments thereof, or the detection of the HIF-1α protein using, for example, antibodies directed against HIF-1α, including peptide fragments. Each of these is described below.

(a) Methods for Detecting Nucleic Acid Molecules

[0082] In one embodiment, the methods of the application involve the detection of nucleic acid molecules encoding HIF-1α. Those skilled in the art can construct nucleotide probes for use in the detection of nucleic acid sequences encoding HIF-1α in samples. Suitable probes include nucleic acid molecules based on nucleic acid sequences encoding at least 5 sequential amino acids from regions of HIF-1α, preferably they comprise 15 to 30 nucleotides. A nucleotide probe may be labeled with a detectable substance such as a radioactive label which provides for an adequate signal and has sufficient half-life such as 32P, 3H, 14C or the like. Other detectable

substances which may be used include antigens that are recognized by a specific labeled antibody, fluorescent compounds, enzymes, antibodies specific for a labeled antigen, and luminescent compounds. An appropriate label may be selected having regard to the rate of hybridization and binding of the probe to the nucleotide to be detected and the amount of nucleotide available for hybridization. Labeled probes may be hybridized to nucleic acids on solid supports such as nitrocellulose filters or nylon membranes as generally described in Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual (2nd ed.). The nucleic acid probes may be used to detect genes, preferably in human cells, that encode HIF-1α.

[0083] The probe may be used in hybridization techniques to detect genes that encode HIF-1α proteins. The technique generally involves contacting and incubating nucleic acids (e.g. recombinant DNA molecules, cloned genes) obtained from a sample from a patient or other cellular source with a probe under conditions favorable for the specific annealing of the probes to complementary sequences in the nucleic acids. After incubation, the non-annealed nucleic acids are removed, and the presence of nucleic acids that have hybridized to the probe if any are detected.

[0084] The detection of nucleic acid molecules may involve the amplification of specific gene sequences using an amplification method such as polymerase chain reaction (PCR), followed by the analysis of the amplified molecules using techniques known to those skilled in the art. Suitable primers are described in Example 1 although others can be routinely designed by one of skill in the art. [0085] Hybridization and amplification techniques described herein may be used to assay qualitative and quantitative aspects of expression of genes encoding HIF-1α. For example, RNA may be isolated from a cell type or tissue known to express a gene encoding HIF-1α, and tested utilizing the hybridization (e.g. standard Northern analyses) or PCR techniques referred to herein.

[0086] The primers and probes may be used in the above described methods in situ i.e. directly on tissue sections (fixed and/or frozen) of patient tissue obtained from biopsies or resections.

[0087] Accordingly, the present application provides a method of detecting C. difficile infection in a patient comprising:

(a) providing a sample from the patient;

(b) extracting nucleic acid molecules comprising the HIF-1α gene or portion thereof from the sample;

(c) amplifying the extracted nucleic acid molecules using the polymerase chain reaction;

(d) determining the presence of nucleic acid molecules encoding HIF-1α; and

(e) comparing the level of HIF-1α in the sample to a control sample, wherein increased levels of HIF-1α as compared to the control indicates that the patient has a C. difficile infection.

(b) Methods for Detecting HIF-1 Proteins

[0088] In another embodiment, the methods of the application involve the detection of the HIF-1 α protein. In one embodiment, the HIF-1 α protein is detected using antibodies that specifically bind to HIF-1 α. [0089] Antibodies to HIF-1 α may be prepared using techniques known in the art. For example, by using a peptide of HIF-1 α, polyclonal antisera or monoclonal antibodies can be made using standard methods. A mammal, (e.g., a mouse, hamster, or rabbit) can be immunized with an immunogenic form of the peptide which elicits an antibody response in the mammal. Techniques for conferring immunogenicity on a peptide include conjugation to carriers or other techniques well known in the art. For example, the protein or peptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassay procedures can be used with

the immunogen as antigen to assess the levels of antibodies. Following immunization, antisera can be obtained and, if desired, polyclonal antibodies isolated from the sera.

[0090] To produce monoclonal antibodies, antibody producing cells (lymphocytes) can be harvested from an immunized animal and fused with myeloma cells by standard somatic cell fusion procedures thus immortalizing these cells and yielding hybridoma cells. Such techniques are well known in the art, (e.g., the hybridoma technique originally developed by Kohler and Milstein (Nature 256, 495-497 (1975)) as well as other techniques such as the human B-cell hybridoma technique (Kozbor et al., Immunol. Today 4, 72 (1983)), the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al. Monoclonal Antibodies in Cancer Therapy (1985) Allen R. Bliss, Inc., pages 77-96), and screening of combinatorial antibody libraries (Huse et al., Science 246, 1275 (1989)). Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with the peptide and the monoclonal antibodies can be isolated.

[0091] The term "antibody" as used herein is intended to include fragments thereof which also specifically react with an HIF-1α or fragments thereof. Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above. For example, F(ab')2 fragments can be generated by treating antibody with pepsin. The resulting F(ab')2 fragment can be treated to reduce disulfide bridges to produce Fab ¹ fragments.

[0092] Chimeric antibody derivatives, i.e., antibody molecules that combine a non-human animal variable region and a human constant region are also contemplated within the scope of the application. Chimeric antibody molecules can include, for example, the antigen binding domain from an antibody of a mouse, rat, or other species, with human constant regions.

Conventional methods may be used to make chimeric antibodies containing the immunoglobulin variable region which recognizes the gene product of HIF-

1α antigens of the application (See, for example, Morrison et al., Proc. Natl.

Acad. Sci. U.S.A. 81 ,6851 (1985); Takeda et al., Nature 314, 452 (1985), Cabilly et al., U.S. Patent No. 4,816,567; Boss et al., U.S. Patent No. 4,816,397; Tanaguchi et al., European Patent Publication EP171496; European Patent Publication 0173494, United Kingdom patent GB 2177096B). It is expected that chimeric antibodies would be less immunogenic in a human subject than the corresponding non-chimeric antibody.

[0093] Monoclonal or chimeric antibodies specifically reactive with a protein of the application as described herein can be further humanized by producing human constant region chimeras, in which parts of the variable regions, particularly the conserved framework regions of the antigen-binding domain, are of human origin and only the hypervariable regions are of non- human origin. Such immunoglobulin molecules may be made by techniques known in the art, (e.g., Teng et al., Proc. Natl. Acad. Sci. U.S.A., 80, 7308- 7312 (1983); Kozbor et al., Immunology Today, 4, 7279 (1983); Olsson et al., Meth. Enzymol., 92, 3-16 (1982)), and PCT Publication WO92/06193 or EP 0239400). Humanized antibodies can also be commercially produced (Scotgen Limited, 2 Holly Road, Twickenham, Middlesex, Great Britain.)

[0094] Specific antibodies, or antibody fragments, such as, but not limited to, single-chain Fv monoclonal antibodies reactive against HIF-1α may also be generated by screening expression libraries encoding immunoglobulin genes, or portions thereof, expressed in bacteria with peptides produced from the nucleic acid molecules of HIF-1α. For example, complete Fab fragments, VH regions and FV regions can be expressed in bacteria using phage expression libraries (See for example Ward et al., Nature 341 , 544-546: (1989); Huse et al., Science 246, 1275-1281 (1989); and McCafferty et al. Nature 348, 552-554 (1990)). Alternatively, a SCID-hu mouse, for example the model developed by Genpharm, can be used to produce antibodies or fragments thereof. [0095] Antibodies specifically reactive with HIF-1α, or derivatives, such as enzyme conjugates or labeled derivatives, may be used to detect HIF-1α in

various samples (e.g. biological materials). They may be used as diagnostic or prognostic reagents and they may be used to detect abnormalities in the level of protein expression, or abnormalities in the structure, and/or temporal, tissue, cellular, or subcellular location of an HIF-1α. In vitro immunoassays may also be used to assess or monitor the efficacy of particular therapies. The antibodies of the application may also be used in vitro to determine the level of expression of a gene encoding HIF-1α in cells genetically engineered to produce an HIF-1α protein.

[0096] The antibodies may be used in any known immunoassays which rely on the binding interaction between an antigenic determinant of HIF-1α and the antibodies. Examples of such assays are radioimmunoassays, enzyme immunoassays (e.g. ELISA), immunofluorescence, immunoprecipitation, latex agglutination, hemagglutination, and histochemical tests. The antibodies may be used to detect and quantify HIF-1α in a sample in order to determine its role in C. difficile infection and CDAD.

[0097] In particular, the antibodies of the application may be used in immuno-histochemical analyses, for example, at the cellular and subcellular level, to detect an HIF-1α protein, to localize it to particular cells and tissues, and to specific subcellular locations, and to quantitate the level of expression. [0098] Cytochemical techniques known in the art for localizing antigens using light and electron microscopy may be used to detect HIF-1α. Generally, an antibody of the application may be labeled with a detectable substance and an HIF-1α protein may be localized in tissues and cells based upon the presence of the detectable substance. Examples of detectable substances include, but are not limited to, the following: radioisotopes (e.g., 3 H, 14C, 35S, 1251, 1311), fluorescent labels (e.g., FITC, rhodamine, lanthanide phosphors), luminescent labels such as luminol; enzymatic labels (e.g., horseradish peroxidase, beta-galactosidase, luciferase, alkaline phosphatase, acetylcholinesterase), biotinyl groups (which can be detected by marked avidin e.g., streptavidin containing a fluorescent marker or enzymatic activity that can be detected by optical or calorimetric methods), predetermined

polypeptide epitopes recognized by a secondary reporter (e.g., leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). In some embodiments, labels are attached via spacer arms of various lengths to reduce potential steric hindrance. Antibodies may also be coupled to electron dense substances, such as ferritin or colloidal gold, which are readily visualised by electron microscopy.

[0099] The antibody or sample may be immobilized on a carrier or solid support which is capable of immobilizing cells, antibodies etc. For example, the carrier or support may be nitrocellulose, or glass, polyacrylamides, gabbros, and magnetite. The support material may have any possible configuration including spherical (e.g. bead), cylindrical (e.g. inside surface of a test tube or well, or the external surface of a rod), or flat (e.g. sheet, test strip). Indirect methods may also be employed in which the primary antigen- antibody reaction is amplified by the introduction of a second antibody, having specificity for the antibody reactive against HIF-1α protein. By way of example, if the antibody having specificity against HIF-1α protein is a rabbit IgG antibody, the second antibody may be goat anti-rabbit gamma-globulin labeled with a detectable substance as described herein.

[00100] Where a radioactive label is used as a detectable substance, HIF-1α may be localized by autoradiography. The results of autoradiography may be quantitated by determining the density of particles in the autoradiographs by various optical methods, or by counting the grains.

[00101] Accordingly, in another embodiment the present application provides a method for detecting C. difficile infection in a patient comprising: (a) providing a sample from the patient;

(b) contacting the sample with an antibody that binds to HIF- 1α;

(c) detecting the level of HIF-1α in the sample; and

(d) comparing the level of HIF-1α in the sample to a control sample, wherein increased levels of HIF-1α as compared to the control indicates that the patient has a C. difficile infection.

[00102] The methods of the application described herein may also be performed using microarrays, such as oligonucleotide arrays, cDNA arrays, genomic DNA arrays, or tissue arrays. Preferably the arrays are tissue microarrays.

[00103] The following non-limiting examples are illustrative of the present application: EXAMPLES Example 1 Materials and Methods

[00104] C. difficile toxin — Clostridium difficile strains TcdA+/TcdB+ (producing both TcdA and TcdB toxins), TcdA+/TcdB-, and TcdA-/TcdB+ were kindly supplied by Dr. Tom Louie (University of Calgary). C. difficile cultures were grown in brain-heart infusion under anaerobic conditions. After centrifugation, and the toxin-containing supernatant was removed, filtered, and used as a source of crude toxin. TcdA and TcdB were purified as previously described [33] from the crude culture filtrate of TcdA+/TcdB+ (04- CT-01-2007).

[00105] Cell culture — Caco-2 cells were obtained from American Type Culture Collections (Manassas, VA) and grown in Dulbecco's Minimum Essential Medium Eagle supplemented with L-glutamine (2 mM), sodium pyruvate (1 mM), non-essential amino acids (0.1 mM), 5% FBS, penicillin (200 U/mL), streptomycin (200 μg/mL) in a humidified incubator at 37°C and 5% CO ₂ . Caco-2 cells were passaged using a trypsin (0.25%), EDTA (0.03%) solution and culture dishes were re-seeded following a 1 :4 dilution.

[00106] Assessment of mRNA expression: RNA Isolation, semiquantitative RT-PCR, and real-time RT-PCR analysis — Caco-2 cells were

collected in Trizol and rapidly frozen on dry ice; the cells were later thawed and dispersed with a PT10/35 sonicating polytron homogenizer. Total RNA was extracted with an RNeasy minikit (Qiagen Inc) according to the manufacturer's instructions. The total RNA was reverse transcribed by means of random hexamer priming with p(dN) ₆ (Roche Diagnostics Inc) with Superscript Il reverse transcriptase (Invitrogen). The resulting cDNAs were subjected to PCR amplification with primers specific for HIF-1α and β2- microglobin. Primers were designed from sequences obtained from GenBank: β2-microglobin forward primer, S'-TCCAAAGATTCAGGTTTACTCA-S' (SEQ ID NO:1); reverse primer, δ'-ATATTAAAAAGCAAGCAAGCAG-S' (SEQ ID NO:2); HIF-1α forward primer, δ'-GTCGGACAGCCTCACCAAACAGAGC-S' (SEQ ID NO:3); and reverse primer, 5'-GTTAACTTGATCCAAAGCTCTGAG- 3' (SEQ ID NO:4). The polymerase chain reaction (PCR) was carried out with 2 μl_ of the reverse transcription (RT) reaction product. 1.5 mM MgC^, 0.2 mM mixed nucleotide triphosphates, and 0.5 μM HIF-1α forward and reverse primer in PCR buffer (Invitrogen). DNA Taq polymerase was added as a hot- start. The mixture was then cycled on an Eppendorf Mastercycler as follows: 95 ⁰ C for 30 s, at 64 ⁰ C for 30 s, and 72 ⁰ C for 30 s. The β2-microglobin primers were added to the same tubes for the last 25 cycles followed by a final extension period at 72 ⁰ C for 5 min. The number of cycles was optimized for each product: 29 cycles for HIF-1α and 25 cycles for β2-microglobin. PCR products were separated by 1.0% agarose gel electrophoresis and stained with ethidium bromide. The RT-PCR products were 488 bp for HIF-1α and 365 bp for β2-microglobin. [00107] To quantitate changes in gene expression an ABI 7500 real-time PCR thermocycler was used to survey HIF-1α mRNA levels. All RNA samples were reversed transcribed to cDNA using MMLV reverse transcriptase with gene-specific primers. HIF-1α specific real time primers for a 176 bp product, δ'-GGACAAGTCACCACAGGA-S' (SEQ ID NO:5) and 5'- GGAGAAAATCAAGTCGTG-3' (SEQ ID NO:6) annealing in exon 12, were reproduced as previously described [34]. The reaction was incubated for 30 minutes at 42°C in a thermocycler. The cDNA samples were then incubated

at 95 ⁰ C for 10 min in the thermocycler to inactivate the reverse transcriptase and activate AmpliTaq DNA polymerase. Additionally, the RT-PCR mix contained TaqMan universal PCR master mix and AmpliTaq DNA polymerase, AmpErase UNG, dNTPs with dUTP, the mixture of gene-specific primers and TaqMan probes for the specific gene products, and RNase-free water. Amplification plots were examined with the accompanying Sequence Detection Software to determine the threshold cycle (Cj). In all reactions endogenous control (β2-microglobin) was amplified, and the Cj was determined. [00108] Preparation of Nuclear Protein Extracts — Caco-2 cells were harvested in ice-cold phosphate-buffered saline after exposure to C0CI2 or C. difficile toxins. The cell suspension was centrifuged, and the resulting pellet was homogenized in ice-cold lysis buffer (10 mM HEPES pH 7.2, 10 mM KCI, 1.5 mM MgCI ₂ , 1 mM dithiothreitol, 2 mM Na ₃ VO ₄ , 5 mM NaF, 0.1 % (v/v) NP- 40 with 1 mM phenylmethyl sulfonyl fluoride (PMSF) and CompleteTM protease inhibitor cocktail). The samples were centrifuged for 15 min at 3,000 rpm at 4 ⁰ C. The supernatants (cytosolic extracts) were discarded, and the resulting pellet (nuclear fraction) was resuspended in buffer B (20 mM HEPES, 1.5 mM MgCI ₂ , 420 mM NaCI, 1 mM dithiothreitol, 2 mM Na ₃ VO ₄ , 5 mM NaF, 25% glycerol, 1 mM PMSF and Complete™ protease inhibitor cocktail). The suspension was mixed vigorously with tips and incubated on ice for 30 min. The samples were centrifuged for 10 min at 14,000 rpm at 4 ⁰ C, and the supernatants (nuclear extracts) were stored at -80°C.

[00109] Western Blot Analysis — Western immunoblots were performed on nuclear extracts of Caco-2 cells or homogenates of tissue biopsies.

Proteins were denatured by boiling in Laemmli SDS-polyacrylamide gel electrophoresis (SDS-PAGE) sample buffer for 5 min, separated on 8% SDS-

PAGE mini-gels (50 μg protein/lane), and then transferred onto polyvinylidine diflouride (PVDF) membrane. The membrane was incubated for 1 h in blocking buffer (Tris-buffered saline (TBS) containing 0.05% Tween 20 and

5% non-fat skim milk powder) at room temperature. Next, the membrane was

incubated for 16 h at 4 °C with mouse anti-HIF-1α monoclonal antibody (NB100-105, Novus Biological Inc., Littleton, CO). After several TBS/0.05% Tween 20 washes, the membrane was incubated with anti-mouse HRP- coupled secondary antibody for 1 h at room temperature. Protein signals were detected with a chemiluminescence detection system (Pierce Biotechnology, Rockford, IL). Image analysis was performed with a Storm860 Imaging densitometer with ImageQuant analysis software.

[00110] Electrophoretic mobility shift assay (EMSA) — EMSA was performed according to the method of Semenza and Wang [35] with the EPO gene-derived W18 oligonucleotide sequence δ'-GCCCTACGTGCTGTCTCA- 3' (SEQ ID NO:7) containing a HIF-binding site. Sense and antisense oligonucleotides were incubated in annealing buffer and then labeled with [γ~ ³² P]ATP by T4 polynucleotide kinase. Unincorporated nucleotides were removed with a G50 Sephadex desalting column. Nuclear protein was added to binding buffer (50 mM Hepes pH 7.2, 5 mM EDTA, 300 mM KCI, 10% (v/v) glycerol, 5 mM dithiothreitol) containing 1.5 μg poly(dl-dC) (Sigma, St. Louis, MO). The mixture was kept on ice for 30 min before addition of 10 ⁴ cpm of W18 oligonucleotide probe for an additional hour of incubation. In some cases, supershift-EMSAs were completed by inclusion of 2 μL of anti-HIF-1α antibody. Samples were run on 4% non-denaturing polyacrylamide gels at 250 V for 3 h in 0.5X TBE buffer (Tris-borate-EDTA) at 4 ⁰ C. Afterwards, the gels were dried and exposed to a phosphorimaging plate.

[00111] Luciferase Assays — The Dual Luciferase Reporter Assay System (Promega) was used to monitor HIF-1α reporter gene activation by C. difficile toxin. Caco-2 cells were cultured in 24 well plates (Costar, Corning Inc., NY) and transiently transfected with pGL3-Luc-3*HRE construct along with Renilla luciferase plasmid (pRL-SV40) using a 3:1 ratio of Lipofectamine 2000:DNA in OptiMEM medium (Invitrogen). After treatment with CoCI ₂ (100 μM) or C. difficile crude toxin (10 μg/mL) in 0.5% oxygen for 4 or 24 hours, cell lysates were obtained by scraping cells into lysis buffer. Firefly and Renilla luciferase activity was determined with a microplate luminometer.

Firefly activity was normalised to Renilla activity to compensate for differences in transfection efficiency. Statistical analysis was performed using a student's t-test, a p value < 0.05 was considered statistically significant.

[00112] Human studies — Colonic tissue sections were obtained from patients undergoing colonic resection for C. c//7f/c//e-associated disease.

Tissue was fixed in 10% formalin and embedded in paraffin. In addition, colonic biopsies were obtained from patients undergoing colonoscopy for diagnostic purposes. Two biopsies per patient were removed, immediately rinsed with sterile saline solution, and placed in oxygenated PBS for transport to the laboratory. All studies involving human tissue were approved by the

Conjoint Health Research Ethics Board at the University of Calgary, Calgary,

AB, Canada.

[00113] Human HIF-1α (immunohistochemistry — Deparaffinized colonic sections were placed in Target Unmasking Fluid (Cedarlane) to expose masked epitopes. Slides were washed in 0.1 M Tris/0.005% BSA. Serial sections were probed for 48 h at 4 ⁰ C with HIF-1α antibody (mouse monoclonal, NB100-105, Novus Biologicals Inc.), diluted 1 :25 in 0.1 M Tris/0.005% BSA/10% NGS. After three washes in 0.1 M Tris/0.005% BSA, anti-rabbit HRP (1 :25 dilution; GE Bioscience, Baie D'Urfe, PQ) was added to the slides for 2 h at room temperature. To visualize immunoreactivity in the sections, a diaminobenzidine substrate kit (Vector Laboratories, Burlingame, CA) was used. Finally, slides were counterstained with Mayer's haematoxylin (Sigma) and graded for staining intensity by a blinded observer.

Results [00114] Effects of C. difficile toxin exposure on HIF-1α mRNA— The HIF-1α mRNA content of Caco-2 cells was analyzed by RT-PCR immediately following exposure to C. difficile crude toxin. RT-PCR results for amplification HIF-1α and β2-microglobin transcripts are shown in Figure 1A. The relative abundance of HIF-1α mRNA was dramatically increased with respect to β2- microglobin mRNA following 4 and 24 h exposure with 100 μg/mL C. difficile crude toxin, suggesting that C. difficile toxin regulates HIF-1α mRNA

transcription. Exposure of Caco-2 cells to physiologically relevant levels of C. difficile crude toxin (0.1 μg/mL) also resulted in time dependent increases in HIF-1α mRNA levels (Figure 1 B). Real-time RT-PCR was used to accurately characterize the concentration dependency of C. difficile toxin on HIF-1α mRNA levels. As presented in Figure 1C, HIF-1α mRNA levels rose in a concentration-dependent manner with application of C. difficile toxin to Caco-2 cells. Treatment with 0.1 μg/mL crude toxin for 4 h resulted in a 3.7 ± 0.45- fold increase in HIF-1α mRNA. Increasing toxin concentrations during the exposure resulted in a plateau of the response with a maximum HIF-1α mRNA induction of 5.4 ± 0.25 -fold increase over control levels when 50 μg/mL of crude toxin was applied to the cells.

[00115] Effects of C. difficile toxin exposure on HIF-Ia protein expression — HIF-1α protein was detected in Caco-2 cells at 120 kDa by Western blot (Figure 2A). A faint band was present in the nuclear extracts isolated from control Caco-2 cells. Normoxic stabilization of HIF-1α has been reported previously and has been correlated with cell culture confluency [36]. Given the nature of epithelial growth displaying high cell-to-cell contact, this normoxic level of HIF-1α is considered to be representative of normal epithelial cell cultures. As expected, HIF-1α protein was significantly increased (2.0 ± 0.7-fold) following treatment with C0CI ₂ , as a positive control for HIF-1α-mediated activation [35]. The amount of HIF-1α protein was also increased following treatment with C. difficile crude toxin. The increase in HIF- 1α protein expression by crude toxin (1.9 ± 0.5 -fold) was similar to that induced by CoCI ₂ . [00116] These results demonstrate that stimulation of HIF-1α protein levels by C. difficile toxins can occur under aerobic conditions.

[00117] Effects of C. difficile toxin exposure on the DNA-binding activities of HIF-1α — To determine whether the accumulation of HIF-1α protein in Caco-2 cells following exposure to C. difficile toxins was correlated with an activation of functional HIF-1α transcription factor complex, the HIF-1α specific DNA-binding activity was assessed by EMSA (Figure 3).

Constitutively expressed DNA-binding activity was present in all conditions. However, treatment with C. difficile crude toxin or C0CI2 induced HIF-1α DNA binding activity in nuclear extracts as determined by gel-shift analysis. Supershift assays, in which nuclear extracts from C. difficile crude toxin- and CoCb-treated Caco-2 cells were incubated with a monoclonal antibody to HIF- 1α prior to the mobility shift assay, confirmed the specificity of the interaction between HIF-1α and the HRE sequence in the W18 oligonucleotide.

[00118] In addition, the inventors examined whether C. difficile toxins could enhance HIF-1α transcriptional activity in vivo. A HIF-1α-dependent reporter construct was prepared which contained three HRE sites in the pGL3-Luc vector. The luciferase construct was co-transfected into Caco-2 cells with the Renilla luciferase plasmid under the control of the SV40 promoter. Firefly luciferase activity was normalized to Renilla luciferase activity to account for variation in transfection efficiency. Significant increases in luciferase activity, 15.5 ± 6.8-fold, 21.2 ± 2.1 and 63.3 ± 6.2-fold, were observed when the pGL3-Luc-3(HRE promoter construct was exposed to C. difficile toxin for 4, 18, and 24 hours, respectively (Figure 4). Treatment with C0CI ₂ induced similar responses. No elevation in luciferase activity was detected in cells transfected with the control pGL3 DNA. Therefore, the accumulation of HIF-1α subunit induced by C. difficile toxin can be correlated with the activation of the transcription factor HIF-1α.

[00119] HIF-Ia expression and HIF-1α DNA binding activities are induced by C. difficile toxins TcdA and TcdB — To test if HIF-1α protein levels were affected equally by application of individual C. difficile toxins, the inventors examined HIF-1α expression in Caco-2 cells following 24 h exposure to crude filtrate isolated from TcdA+/TcdB- and TcdA-/TcdB+ cultures. Exposure to either the TcdA+/TcdB- or the TcdA-/TcdB+ filtrate caused marked increases in HIF-1α protein levels (Figure 5A). As an alternative approach, TcdA was separated from TcdB by anion-exchange chromatography and then further purified using immobilized-thyroglobulin

affinity chromatrography [33]. Exposure of Caco-2 cells with purified TcdA or TcdB toxin produced similar increases in HIF-1α protein expression.

[00120] Individual toxin effects on HIF-1α specific DNA-binding activity were assessed by EMSA (Figure 5B). Treatment with TcdA toxin (i.e., TcdA+/TcdB- culture filtrate) or TcdB toxin (Le.,TcdA-/TcdB+ filtrate) could induce HIF-1α DNA binding activity in nuclear extracts as determined by

EMSA gel-shift analysis. TcdB elicited a more intense HIF-1α gel shift than that of TcdA, both for the purified TcdB toxin and the TcdA-/TcdB+ filtrate.

These results suggest that the TcdB toxin may generate a more robust HIF- 1α response in colonic epithelial cells although downstream HIF-1α signaling molecules remain to be examined.

[00121] HIF-Ia expression following C. difficile toxin exposure in CDAD — To further investigate whether HIF-1α expression is altered in human disease, the inventors obtained colonic tissue sections from patients undergoing colonic resection for CDAD. As shown in Figure 6, there was minimal HIF-1α staining in normal tissues. In patients with PMC, there was a marked increase in HIF-1α in the epithelial cells, inflammatory cells of the lamina propria and submucosa as well as in endothelial cells of the microvasculature. HIF-1α expression was also noted in smooth muscle cells surrounding vessels as well as in the muscularis mucosa and muscularis propria. Upregulation of HIF-1α expression was noted in biopsy samples as well as in colonic resection specimens in PMC and generally appeared to correlate with disease activity. Tissue was also obtained for comparison purposes from patients with active ischaemic colitis and ulcerative colitis. In agreement with other reports [31], increased HIF-1α staining was observed in epithelial cells.

[00122] Knock-down of HIF-Ia augments C. difficile toxin-induced loss of barrier function. Stable transfections of Caco-2 cell with HIF-1α siRNA construct reduced C0CI2- and C. cliff, toxin-induced up-regulation of HIF-1α compared to cells transfected with empty vector control cells (figure 9A). Treating stable HIF-1α knockdown Caco-2 monolayers with 10 μg/mL C. diff.

toxin for 24 h led to a significantly greater drop in transepithelial resistance to 37.5+/-8% of the non-treated monolayers (figure 9B) and decreased viability as measured by MTT assay to 75 +/- 5% of non-treated controls (figure 9C).

[00123] HIF-Ia expression following C. difficile toxin exposure in vivo. Injection of C. difficile toxin in ileal loops ( 100 μg for 4 h) in wild-type I29 mice led to significant increase in HIF-1α mRNA (figure 10A) and protein levels

(figure 10B). C.diff toxin also induces significant inflammation as measured by myeloperoxidase levels from isolated ileum (figure 10C). This was also associated with an increase in HIF-regulated gene products VEGFs and ITF and inflammatory markers TNF and murine KC (CXCL1) (figure 10D).

[00124] C. d iff toxin exposure in mice with targeted deletion of HIF- 1α in the intestinal epithelium. Injection of C. difficile toxin into ileal loops (100 μg for 4 h) from HIF (ep-/-) mice led to significantly greater MPO (figure 11A), serum nitric oxide values (figure 11 B) and tissue damage (figure 11C) as compared to levels observed in wild-type animals treated with toxin.

[00125] C. diff. toxin exposure following pretreatment with HIF-I α stabilizer DMOG (dimethyloxaloylglycine). Injection of C. difficile toxin into ileal loops (100 μg for 4 h) in wild-type I29 mice led to a significant increase in MPO (figure 12G) as compared to levels observed in animals treated with the vehicle control (i.e. matched volume of culture media) and those not operated on (control). Pretreatment with DMOG (dimethyloxaloylglycine; 8 mg/day for 2 days prior to surgery) to stablilize HIF-1α, through inhibition of prolyl-4- hydroxylases, significantly attenuated toxin-induced inflammation as measured by MPO (figure 12G). The attenuation in inflammation was associated with a significant reduction in tissue damage as assessed through histology. As mentioned previously, ileum exposed to C. diff toxin displayed significant structural damage including a loss of villus structure and overall muscosal architecture (figure 12 C ₁ D) as compared to the media treated animals (figure 12 A ₁ B). Pretreatment with DMOG significantly reduced toxin- induced damage (figure 12 E, F). A quantitative assessment of the histological

and immunological changes was performed and indicated that pretreatment significantly reduced scoring at each index (figure 12H).

[00126] Gene expression in mice treated with DMOG prior to C. diff toxin exposure. To further examine the protective effects of DMOG pretreatment expression of factors reported to be protective in models of intestinal inflammation were examined. Following toxin exposure RNA was isolated from ileum of mice exposed to C. diff. toxin that were pretreated with DMOG or vehicle for the previous two-days. DMOG treatment followed by toxin exposure led to a significant increase in the mRNA levels for VEGFa, intestinal trefoil factor and CD73 when compared to mice treated with vehicle control and subsequently exposed to toxin (figure 13A). Since DMOG was shown to reduce the overall inflammation in ileum exposed to C. diff. toxin the levels of TNF and CXCL1/murine KC, the analogue of human IL-8 were also examined. Transcripts for both TNF and CXCL1/murine KC were significantly reduced in the ileum of mice pretreated with DMOG when compared to mice treated with vehicle (figure 13B).

Discussion

[00127] CDAD/PMC is characterized by acute mucosal inflammation with an infiltration of neutrophils, epithelial cell destruction, and increased production of proinflammatory mediators [3]. HIF-1α is known to be a critical mediator of intestinal protection during the hypoxia and inflammation that accompanies mucosal insult. Yet, the role of HIF-1α has not been examined in CDAD/PMC. In this study, the inventors identified a previously uncharacterized molecular link between C. difficile toxins and the HIF-1α signaling pathway. The inventors determined that HIF-1α signaling in intestinal epithelial cells could be activated by C. difficile toxins under aerobic conditions. This activation by C. difficile toxins was shown to involve enhanced HIF-1α mRNA and protein levels, HIF-1α DNA binding and transcriptional activity. The activation of HIF-1α signaling was demonstrated to have important functional consequences for epithelial cell survival. The C. difficile toxin-dependent induction of HIF-1α in epithelial cells represents a

novel protective mechanism that may guard the intestinal tract during exposure to pathogenic luminal bacteria and toxins during episodes of CDAD.

[00128] The finding that HIF-1α could be induced in intestinal epithelial cells by C. difficile toxin is consistent with reports of the importance of HIF-1α in pathophysiological conditions involving mucosal inflammation and damage. HIF-1α is known to induce the transcription of several genes for proteins that act on the intestinal tract in a protective capacity, including vascular endothelial growth factor (VEGF) [37], heme oxygenase-1 (HO-1) [38], erythropoietin (EPO) [39], endothelial nitric oxide synthase (eNOS) [40], and inducible nitric oxide synthase (iNOS) [41]. Several inflammatory mediators are known to induce HIF-1α accumulation in normoxia and can further stabilize HIF-1α levels in hypoxia [26]. In rat small intestinal epithelial cells, IL- 1 β [42], TNF-α [29] and INF-γ [28] stabilize the HIF-1α heterodimer (protecting the α subunit from ubiquitin-dependent proteolysis) and induce HIF-1α gene expression. A mouse line with tissue-specific deletion of HIF-1α expression in intestinal epithelial cells was more susceptible to trinitrobenzene sulfonic acid (TNBS)-induced colitis [32]. Furthermore, mice with constitutive activation of HIF-1α (via mutation of von Hippel-Lindau gene) exhibit increased expression of HIF-1α-regulated barrier-protective genes: multi-drug resistance gene-1 (MDR-1), intestinal trefoil factor (ITF) and CD73, resulting in attenuated loss of barrier function during colitis [32]. In addition to its induction of numerous pro-inflammatory agents, HIF-1α can also mediate lymphocyte development, myeloid cell function, and also appears to play a critical role in the hypoxia- induced upregulation of adhesion molecules involved in leukocyte recruitment [43].

[00129] Although severe ischemia can be produced in CDAD/PMC, the inventors have shown that HIF-1α signaling in epithelial cells can be induced with direct stimulation by C. difficile toxins, independent of oxygen status. This finding could reflect an intrinsic attempt by the host to control the severity of the inflammatory response and/or to promote mucosal healing in the injured intestine. CDAD/PMC is associated with a profound inflammatory cell infiltrate

that is mediated in part by the ability of the C. difficile toxins to induce a potent chemokine and cytokine response. Recruitment of neutrophils to the site of infection is thought to occur both via direct interaction with TcdA and as a result of secondary events mediated by inflammatory mediators. TcdA has been shown to activate mitogen-activated protein kinases in human THP- 1 monocytes, in a process that appeared to be independent of Rho and linked to the production of the cytokine, interleukin (IL)-8 [44]. Interestingly, HIF-1α also regulates IL-8 secretion in colonic cancer cells through an NFKB- dependent process [45]. The role of NFKB in CDAD/PMC is complex; mice that cannot activate NFKB (i.e. IKKβ-/- mice) had more severe TcdA-induced intestinal injury. However, whether HIF-1α acts in a complementary manner to NFKB in this process remains to be defined.

Example 2

[00130] The inventors have initiated a study of HIF-1α impact on smooth muscle contractility with intestinal epithelium-targeted, HIF-1α(-/-) mice. The preliminary examination of short-term Cdif toxin exposure (4 h) indicates that interplay exists between the epithelial HIF-1 pathway and the contractile properties of the intestinal smooth muscle. Following Cdif toxin challenge, Ca2+ sensitization in HIF-1 α(-/-) mice was increased (CCh/K+ contractile ratio: 5.3-fold (Fig 7) versus 3.1 fold (Fig 7A), for HIF-1 α(-/-) and VW mice respectively). The contribution of ROK (Rho-associated kinase), which was elevated in Cdif toxin-treated ileal loops from WT mice, was not increased as profoundly in HIF-1 α(-/-) mice (Fig 8). These results suggest that epithelium- dependent HIF-1 α signaling can influence smooth muscle Ca2+ sensitization via ROK signaling during challenge with Cdif toxin.

[00131] While the present application has been described with reference to what are presently considered to be the preferred examples, it is to be understood that the application is not limited to the disclosed examples. To the contrary, the application is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.

[00132] All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety.

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