# Patent

## Title
Antibody binding microbial heparin binding motif to retard or prevent microbial biofilm formation on implanted medical devices

## Abstract

Methods and reagents for ameliorating biofilm formation on a surface of an indwelling or implanted device in a patient resulting in decreased virulence of microorganisms such as Candida species and/or Staphylococcus species.

## Background
This application is a Continuation-In-Part of co-pending PCT/US2013/031499 filed Mar. 14, 2013, which claims priority to U.S. application Ser. No. 61/636,243 filed Apr. 20, 2012, each of which is expressly incorporated by reference herein in its entirety.


A novel interaction between Candida albicans (C. albicans) surface proteins and heparin, a drug commonly used in patients at risk for catheter-associated biofilms and candidemia, is disclosed with an antibody that reduced or prevented a microorganism surface protein from binding to heparin, and reduced catheter-associated biofilm formation, where the reduction in biofilm formation can reduce the microorganism's virulence in a patient, with reduction encompassing any level of decrease.
Heparin is a highly sulfated, non-branched, anionic disaccharide composed of uronic acid, predominantly iduronic acid, in 1,4 linkage with glucosamine. Heparin is a known anticoagulant that is often infused in indwelling catheters to prevent the blood flowing through the catheter from clotting. Heparan sulfate is composed of the same disaccharide but is less sulfated and has a more varied structure than heparin. Heparan sulfate linked to core proteins, such as syndecans or glypicans, forms heparan sulfate proteoglycans (HSPGs). HSPGs are widely expressed on mammalian cell surfaces and in the extracellular matrix. Heparin binding motifs can bind to both heparin and heparan sulfate.
Several microbial proteins bind heparin and heparan sulfate, e.g., HIV-1 gp120, CypA, and Tat; hepatitis C envelope glycoprotein E2; herpes simplex virus glycoproteins B, C, and D; dengue virus envelope protein; Plasmodium falciparum circumsporozoite (CS) protein, Listeria monocytogenes ActA, and LcI of Legionella pneumophila (1-11). Such microbial protein interactions with surface HSPGs typically promote binding and entry of the microbial organism into the mammalian cell (except for HIV-1 gp120 and Tat), but the mechanisms by which individual microbial proteins recognize heparin or heparan sulfates are largely undefined. Positively charged tripeptides containing Lys or Arg in the amino terminus of L. monocytogenes ActA (aa 40-230) and in L. pneumophila LcI (aa 69-349) were shared with tripeptides in a number of heparin-binding mammalian proteins such as EGF-like growth factor and vonWillebrand factor, but the precise amino acids that mediated binding to heparin were not defined for ActA or LcI (10-11).
Eukaryotic proteins that bind heparin express either linear or conformational heparin binding motifs (HBM). Linear heparin binding motifs are short, conserved peptides containing both basic (B) and hydropathic (X) amino acids in specific patterns first identified by Cardin (XBBXBX) and Weintraub (XBBBXXBX) and subsequently expanded by Sobel (XBBBXXBBBXXBBX) (12-14). Molecular modeling studies suggested that basic amino acids such as lysine, arginine, and histidine were critical for interaction with anionic sulfate or carboxylate groups in heparin through electrostatic and hydrogen bonds. For example, substituting alanine for basic amino acids in linear HBM in the morphogen sonic hedgehog abolished binding to heparin (15). However, because many heparin-binding proteins failed to exhibit linear motifs, the concept of spatial orientation of basic residues was propounded (16). The CPC clip motif, a structural signature in which two cationic residues surround one polar residue, was conserved in eukaryotic heparin binding proteins, as well as in vaccinia complement protein and papillomavirus 18 capsid protein (17)
Because of its propensity to form biofilms in implanted medical devices such as indwelling central venous catheters, Candida albicans (C. albicans) is a leading pathogen in infections of indwelling catheters. A biofilm is a multilayered structure of microbes embedded in a polysaccharide matrix that forms on central venous catheters as well as implanted prosthetic joints, contact lenses, and other such medical devices (18, 19). A biofilm is undesirable because antibiotics and host defenses cannot penetrate it, thus a biofilm prevents elimination of microorganisms that have attached or adhered to a surface of an implanted medical device. For example, because of the high flow-through in a central venous catheter, sessile projections from a biofilm break off and are carried into the bloodstream to cause infection that can be carried by the blood to other sites in the body.
Heparin is a known anticoagulant, and catheters are often infused with heparin to prevent blood flowing through the catheter from clotting (20). Because heparin inhibited attachment of C. albicans to extracellular matrix proteins (21), the inventors hypothesized that C. albicans interacted with heparin through linear heparin binding motifs (HBMs): conserved sequences of basic (Arg, Lys, H is) and hydropathic amino acids in prescribed patterns.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 schematically illustrates the internal lumen of an indwelling catheter.
FIGS. 2A-E demonstrate lack of an effect by heparin on wild type Candida albicans (C. albicans) planktonic growth and morphology.
FIGS. 3A-D demonstrate C. albicans binding to heparin and heparin analogs in vitro.
FIGS. 4A-C show that two lysine residues in linear heparin binding Motif 1 in C. albicans Int1 mediate binding to heparin, as measured by an ELISA assay in vitro. FIG. 4A discloses SEQ ID NOS 1, 40, 48, 2, 3, 52 and 53, respectively, in order of appearance. FIG. 4B discloses SEQ ID NO: 2. FIG. 4C discloses SEQ ID NOS 52-53, respectively, in order of appearance.
FIG. 5 compares pre-immune rabbit IgG with affinity-purified IgG raised against the sequence HKQEKQKKHQIHKV (SEQ ID NO:4) for ability to inhibit binding of C. albicans to heparin.
FIGS. 6A-C show consequences of heparin binding in vitro. FIG. 6A discloses SEQ ID NO: 65. FIG. 6B discloses SEQ ID NO: 66. FIG. 6C discloses SEQ ID NO: 67.
FIGS. 7A-B show consequences of heparin binding in vitro.
FIGS. 8A-F demonstrate that heparin binding motifs contribute to biofilm formation in vivo.
FIG. 9 demonstrates that affinity-purified IgG raised against the sequence HKQEKQKKHQIHKV (SEQ ID NO:4) substantially inhibited biofilm production in jugular venous catheters in rats. FIG. 9 discloses SEQ ID NO: 6.
FIG. 10 schematically illustrates the internal lumen of an indwelling catheter in the presence of antibody against heparin binding motifs on cell wall proteins of C. albicans. 
FIG. 11 shows Anti-KKHQ specific binding to Candida species.
FIGS. 12A-C show Anti-KKHQ effect on biofilm progression.



Thirty-four C. albicans surface proteins encoding at least one linear heparin binding motif (HBM) were identified from a sequence-based search. Twelve of these 34 proteins flanked recently described transcriptionally active regions that are involved in biofilm production. Thirty-three of these 34 proteins are known targets of master biofilm regulators (22).
C. albicans binding to 2.5 units (12.5 μg) solid-phase heparin in an ELISA assay was significantly decreased by desulfation of heparin at the 2-O or 2-N groups, and by preincubation of C. albicans with heparin. The protein Int1 contained the largest number of HBMs; Int1 is a surface protein that is involved in adhesion, filamentation, and antigenic recognition. In the Int1 sequence 804QKKHQIHK (SEQ ID NO: 1), alanine mutation of lysine residues at positions 805/806 significantly reduced binding of the Int1 mutant to heparin. Rabbit IgG recognizing the polypeptide 799HKQEKQKKHQIHKV812 (SEQ ID NO: 4) inhibited C. albicans binding to heparin by 19%; pre-immune rabbit IgG had no effect.
Consequences of heparin binding in vitro included removal of C. albicans surface antigens such as Eno1, Pgk1, Tdh3, and Ssa1/2, which themselves contain putative HBMs; impairment of histatin-mediated killing; and modulation of gene expression. In vivo, substitution of alanine residues for lysines at positions 805/806 in 804QKKHQIHK (SEQ ID NO: 1) markedly attenuated biofilm formation in central venous catheters in rats. In addition, pre-incubation of C. albicans with rabbit IgG recognizing the polypeptide 799HKQEKQKKHQIHKV812 (SEQ ID NO: 4) inhibited biofilm formation in vivo; pre-immune IgG had no inhibitory effect. These results identify linear HBM in C. albicans surface proteins, characterize specific lysine residues that mediate heparin binding, and demonstrate relevance for innate and adaptive immunity in vitro and biofilm formation in vivo.
The inventive method and composition ameliorated this undesirable situation by using antibodies against a specific heparin-binding motif that is expressed by surface proteins on C. albicans; other microorganisms also express similar heparin binding motifs. Without being held to a single theory, the disclosed antibodies reduce or prevent the undesirable biofilm from forming on the surface of a medical device, particularly a plastic device, implanted in a patient. Microorganisms include bacteria, yeast, fungi, etc. as known to one skilled in the art. Medical devices include those implanted or implantable in a patient, particularly plastic medical devices, including but not limited to catheters and central lines but excluding current non-plastic implanted joints, pacemakers, pacemaker wires, and spinal rods.
In one embodiment of the inventive method, antibodies were produced against a linear heparin binding motif that was expressed by a surface protein of Candida albicans (C. albicans). Related heparin binding motifs occur in surface proteins from Staphylococcus epidermidis (S. epidermidis) and Staphylococcus aureus (S. aureus).
Linear heparin binding motifs are sequential amino acids that conform to one of three consensus motifs (Cardin, Sobel, or Weintraub motifs); they have been identified in multiple mammalian proteins that bind heparin. While conformational heparin binding motifs also occur in some proteins, they must be identified by crystal structure of the protein. Antibodies to these linear heparin binding motifs inhibited C. albicans from adhering to heparin bound to a plastic surface (a microtiter plate).
Of the six million patients who have a central line implanted each year, more than 75,000 will develop bloodstream infections (23). Central line-associated blood stream infections (CLABSI) are a major source of hospital-acquired infection; over 43,000 CLABSI occurred among patients hospitalized in U.S. intensive care units (ICUs) in 2001, which is 3.2 infections for every 1000 line days. With a protocol for their sterile insertion and daily maintenance, CLABSI in ICUs dropped to 18,000 in 2009, but even with these improvements in ICUs procedures, more than 23,000 CLABSI occurred in patients on inpatient wards and 37,000 CLABSI occurred in outpatient hemodialysis patients in 2009. Even with a 50% reduction in CLABSI in ICU patients, the annual cost of these infections across the U.S. is more than $13 billion (23)
Staphylococcus epidermidis is the most common cause of CLABSI in central lines, with gram-negative rods second, S. aureus third; and Candida species fourth (24). In peripherally inserted central catheters (PICC), i.e., central lines inserted through peripheral veins in the arm, Candida species are the second most common cause of line infection (25). Candida spp. are equivalent to S. aureus in infections in central lines in the ambulatory setting (26). Among Candida spp, C. albicans is the most common cause of CLABSI (24).
When Candida species infect a central venous catheter, the organism enters the bloodstream to cause candidemia. Hosts at highest risk of candidemia, include burn patients and patients on a pump during coronary artery bypass procedures (27). Neutropenic oncology patients, premature newborns, and patients with major abdominal surgery such as intestinal resections are also high-risk patients with 8- to 16-fold the number of infections of other patient groups (27).
A major risk factor in candidemia is the presence of central lines (28-33), whose lumens are a site for formation of microbial biofilms that are effectively shielded from antimicrobial agents and host defenses. A second commonality is the use of heparin as an anticoagulant in most catheters. The amount of heparin is often considerable; e.g., a premature newborn in a neonatal intensive care unit may receive 150 units/kg/day, compared to 2.8 units/kg for a 70 kg adult receiving a 100 unit flush twice a day (20).
The ability to bind heparin is a unifying feature among S. epidermidis, S. aureus, and, Candida albicans (34-36), three of the leading causes of catheter-associated bloodstream infections. In experiments with S. aureus, high concentrations of heparin have been shown to increase S. aureus biofilm formation in vitro (37).
A first step in biofilm formation is microorganism adhesion or adherence to a surface of the implanted device, such as a catheter (38). In FIG. 1, negatively charged heparin molecules (circles) injected into the catheter lumen bind to the positively charged catheter surface, and heparin sulfate moieties (curved lines) are exposed on vascular endothelium lining catheter lumens. Linear heparin binding motifs present on the surface of microorganisms, such as C. albicans, interact either with heparin (A) or with heparin sulfate (B) and enable the organism to attach to the inside of the catheter. As the attached microorganisms replicate, they form the multilayered structure of a biofilm (C) and secrete the polysaccharide mortar-like matrix that holds the biofilm together. The inventors hypothesize that interactions between heparin and surface proteins on microorganisms such as C. albicans facilitate biofilm formation, and subsequent infection of the bloodstream when projections from biofilm break off into the catheter lumen and enter the bloodstream.
Heparin is associated with central line infections, particularly those due to Candida spp. In a randomized trial of 260 central lines, 128 were coated with chlorhexidine and 132 were coated with heparin; all Candida colonization and all candidemias occurred in patients whose central lines were coated with heparin (39). A second study in renal dialysis patients showed that those patients who received 5000 units of heparin in the middle of dialysis had considerably more catheter loss due to infection compared to patients not treated with heparin. Although staphylococcal infections were most common in this patient group, candidemia also occurred (40).
One mechanism by which heparin interacts with proteins is through linear heparin binding motifs, conserved sequences of basic amino acids such as lysine, arginine, and histidine interspersed with hydropathic amino acids (14). Microbial heparin-binding proteins are identified by short consensus motifs of basic (B) and hydropathic (X) amino acids, as defined by Cardin [XBBXBX], Weintraub [XBBBXXBX], or Sobel [XBBBXXBBBXBBX].
In the invention, a computer-based algorithm examined all 400 C. albicans surface and cell wall proteins for heparin binding motifs (HBM). Of the 6,000 known Candida albicans proteins, about 400 are localized to the cell wall of yeast or hyphae, depending upon the extraction technique (41). A sequence-based search identified putative Cardin, Sobel, or Weintraub motifs in 159 C. albicans proteins. Table 1 shows HBM in cell surface proteins expressed by C. albicans. The 34 proteins in Table 1 include only those that have the attribution “cell surface”, “fungal cell wall”, “yeast cell wall”, or “hyphal cell wall” as the cellular component in the Candida Genome Database, where *=Weintraub motif; #=Cardin motif; ‡=Identified by molecular modeling studies; A=“cell wall” in protein description (as of January 2011); obtained from Candida Genome Database (CGD); B=“cell wall” in Gene Ontology (GO) annotation (as of January 2011); obtained from CGD; C=cell wall proteins as reviewed by Alberti-Segui (42) and D=cell wall proteins as reviewed by Chaffin (41).
The following procedure was used to identify a set of cell wall proteins in C. albicans with HBM. The first step combined evidence to identify possible cell wall proteins in C. albicans. Specifically, using “cell wall” as keywords, 154 putative cell wall proteins were identified from protein descriptions, and another 245 unique cell wall proteins were identified from Gene Ontology functional annotations from Candida Genome Database (www.candidagenome.org; Assembly 21). Also included were 125 non-redundant cell wall proteins identified by Alberti-Segui (50) and another 174 reported by Chaffin (22) and mapped annotations to Assembly 21. The second step screened for consensus HBM in protein ORF sequences of these cell wall proteins from Assembly 21. Three types of consensus motifs were included: Weintraub (XBBBXXBX), Sobel (XBBBXXBBBXXBBX), and Cardin (XBBXBX) motifs, where B is a basic amino acid and X is a hydropathic amino acid. In the algorithm, basic amino acids are H, K, and R. Hydropathic amino acids are W, F, Y, L, I, C, M, G, V, S, T, A, N, P, and Q. A total of 159 cell wall proteins were identified that have possible HBM, and some have multiple motifs. The 159 proteins that met the search criteria were then manually curated to select only those proteins whose cell wall localization was confirmed by manual or computational methods in the Candida Genome Database.
Proteins with GPI anchoring sequences within these 159 cell wall proteins with HBM were further identified. Three Web servers were used to perform GPI anchoring sequence prediction: SignalP (43), GPI-SOM (44), and PredGPI (45). Combined results of these three prediction methods indicated that 15 out of these 159 proteins had GPI anchoring sequences, four of which overlapped with reviewed GPI anchoring proteins (46).
The algorithm identified 34 cell wall proteins with potential linear heparin binding sequences that matched the Cardin, Weintraub, and Sobel motifs. The 34 identified cell wall proteins were Ahp1, Als7, Atcl, Bud2, Cat1, Cef3, Chs1, Crh12, Dot4, Not5, Pdi1, Pga4, Pgk1, Phr3, Rbt1, Rps6A, Sam2, Srb1, Ssa2, Ssb1, Tdh3, Eft2, Eno1, Gap1, Gph1, Gpm2, Hem13, Hsp104, Hsp70 (also called Ssa1), Ino1, Int1, Ipp1, Ugp1, Xyl2. Three of these proteins, Als7, Pga4, and Rbt1, have GPI anchors. The genes encoding eleven of these proteins, Als7, Cat1, Dot4, Eno1, Gph1, Ino1, Rbt1, Sam2, Srb1, Ssa2, and Ugp1, are located in newly defined transcriptionally active regions that are critically involved in biofilm formation (22). Moreover, many of these proteins are known to be regulated by at least one of six master biofilm regulators; by RNA-seq, where RNA-seq is defined as the use of high-throughput sequencing techniques to sequence cDNA in order to get sequence information about the transcriptome, the sample's RNA content; CAT1, GAP1, GPH1, and HSP104 are up-regulated in biofilm formation, while CHS1, EN01, GPM2, HEM13, INO1, IPP1, PGK1, RPS6A, SAM2, SRB1, SSA2, SSB1, and TDH3 are down-regulated (22)
Given the presence of putative HBM among C. albicans surface proteins and the possible interactions with heparin in central venous catheters or with heparin sulfate proteoglycans expressed on host tissues such as vascular endothelium, the biochemical determinants and immunologic consequences of this interaction were defined. The protein Int1 (SEQ ID NO: 5) (accession number P53705.2; GI 187608862) had the highest number of HBM (five). Int1 (SEQ ID NO: 5) spans 1711 amino acids and is localized to the cell wall of the bud neck in C. albicans. It mediates adhesion, hyphal formation, and virulence, defined as the ability to cause disease such as bloodstream infection (47). Using the same search technique, HBM were also detected in surface proteins of S. epidermidis and S. aureus.















TABLE 1 





Gene ID


# of







(Assembly 21)
Protein
Ref.
motifs
Motif 1
Motif 2
Motif 3
Motif 4
Motif 5







orf19.4257
Int1
C
5
804QKKHQIHK‡
1383THKGRF#
1530MKRGKP#
1593FKKRFFKL*
1612SHKTRA#






(SEQ ID NO: 1)
(SEQ ID NO: 40)
(SEQ ID NO: 48)
(SEQ ID
(SEQ ID









NO: 2)
NO: 3)


 


orf19.1738
Ugp1
B, D
3
176SHRIRV#
310IKKFKY#
368IRHFKG#








(SEQ ID NO: 7)
(SEQ ID NO: 41)
(SEQ ID NO: 49)




 


orf19.3370
Dot4
B
3
442NKKGKS#
519CHKCHN#
635FKRFKF#








(SEQ ID NO: 8)
(SEQ ID NO: 42)
(SEQ ID NO: 50)




 


orf19.3651
Pgk1
A, B, D
3
136GKKVKA#
146VKKFRQ#
168AHRAHS#








(SEQ ID NO: 9)
(SEQ ID NO: 43)
(SEQ ID NO: 51)




 


orf19.4660
Rps6A
B, D
2
185QRKRALKA*
192AKKVKN#









(SEQ ID NO: 10)
(SEQ ID NO: 44)





 


orf19.5107
Not5
B
2
114QKRSRF#
333VKKLKP#









(SEQ ID NO: 11)
(SEQ ID NO: 45)





 


orf19.5130
Pdi1
D
2
210NKKFKN#
301GKKYRG#









(SEQ ID NO: 12)
(SEQ ID NO: 46)





 


orf19.6387
Hsp104
D
2
53VKRARY#
199ARRSKS#









(SEQ ID NO: 13)
(SEQ ID NO: 47)





 


orf19.1065
Ssa2
B, D
1
258LRRLRT#










(SEQ ID NO: 14)






 


orf19.1067
Gpm2
B
1
45IKKNHL#










(SEQ ID NO: 15)






 


orf19.1327
Rbt1
A, B, C
1
121GKKVKQ#










(SEQ ID NO: 16)






 


orf19.2762
Ahp1
B, D
1
171LKRIHN#










(SEQ ID NO: 17)






 


orf19.2803
Hem13
B, D
1
257IRRGRY#










(SEQ ID NO: 18)






 


orf19.3590
Ipp1
B, D
1
74TKKGKL#










(SEQ ID NO: 19)






 


orf19.377
Phr3
B, C
1
115PHHHLNRY*










(SEQ ID NO: 20)






 


orf19.395
Eno1
B, D
1
141AKKGKF#










(SEQ ID NO: 21)






 


orf19.3966
Crh12
A, B, C
1
420TKHIHN#










(SEQ ID NO: 22)






 


orf19.4035
Pga4
B, C, D
1
259AKRPRP#










(SEQ ID NO: 23)






 


orf19.4152
Cef3
B
1
623LRKYKG#










(SEQ ID NO: 24)






 


orf19.4304
Gap1
B
1
72QRKLKT#










(SEQ ID NO: 25)






 


orf19.4980
Ssa1
B, D
1
259LRRLRT#










(SEQ ID NO: 26)






 


orf19.5188
Chs1
B, C
1
126PKRQKT#










(SEQ ID NO: 27)






 


orf19.5788
Eft2
B, D
1
581NKHNRI#










(SEQ ID NO: 28)






 


orf19.6190
Srb1
B, D
1
123FHKAHG#










(SEQ ID NO: 29)






 


orf19.6214
Atc1
A, B
1
959PKRVKV#










(SEQ ID NO: 30)






 


orf19.6229
Cat1
B
1
82GKKTRI#










(SEQ ID NO: 31)






 


orf19.6367
Ssb1
B, D
1
263LRRLRT#










(SEQ ID NO: 32)






 


orf19.657
Sam2
B, D
1
380PKKLKF#










(SEQ ID NO: 33)






 


orf19.6814
Tdh3
B, D
1
70GHKIKV#










(SEQ ID NO: 34)






 


orf19.7021
Gph1
B, D
1
656TKHHIPKA*










(SEQ ID NO: 35)






 


orf19.7400
Als7
B, C
1
1482SKRNKN#










(SEQ ID NO: 36)






 


orf19.7585
Ino1
B, D
1
161MKRAKV#










(SEQ ID NO: 37)






 


orf19.7676
Xyl2
A, B, D
1
330THRFKF#










(SEQ ID NO: 38)






 


orf19.940
Bud2
B
1
716LRKGKS#










(SEQ ID NO: 39)









Heparin effect on Candida albicans growth and morphology was determined. A single colony of BWP17 wt was inoculated into 3 ml YPD medium and incubated overnight at 30° C. with shaking at 225 rpm. Overnight cultures were diluted to an OD600 of 0.1 in 5 ml of YPD (yeast) or RPMI-HEPES (hyphae) in a 50 ml conical polypropylene tube and incubated in the presence or absence of 100 units/ml preservative-free pharmaceutical heparin at 30° C. for six hours. Cells (1 ml) were fixed with an equal volume of 4% formaldehyde in FACS buffer at 4° C. for one hour, then pelleted (7,000 rpm for 3 minutes) and washed with PBS. After reconstitution in 0.5 ml PBS, filipin (50 mg/ml stock solution in DMSO) was added to a final concentration of 100 μg/ml and incubated with cells at room temperature for five minutes. Cells were pelleted, washed with PBS and mounted on a slide using Fluoromount G. For calcofluor white staining, after six hours incubation, 1 μl of 1 mg/ml stock solution of calcofluor white in 0.1 N NaOH was added to 100 μl cells to a final calcofluor white concentration of 10 μg/ml.
Microscopy was performed by imaging filipin, PKH26, DAPI, and heparin-Alexa Fluor 488 on a Nikon Ti-E inverted microscope with a 100×CFI APO oil NA 1.49 objective. Filipin was excited with a Prior Lumen 200 metal halide light source set at 10% light output. This light was further attenuated by ND4 and ND8 neutral density filters in series to reduce light output to approximately 3% of output from the liquid light guide. The filters used for imaging were EX 360/40, dichroic 400 nm Ip, EM 460/50. Images were acquired with an Andor iXon emccd camera. Exposure times were 391 ms. Excitation of PKH26/DAPI/Heparin-Alexa Fluor 488 triple staining was accomplished with a Nikon A1R si laser scanning confocal. DAPI was imaged with 405 nm excitation and a 450/50 filter with a laser power of 16.3 and a photomultiplier tube (pmt) voltage of 92. Alexa Fluor 488 was imaged with 488 nm excitation from an Argon-ion laser and a 525/50 filter with a laser power of 6.0 and a pmt voltage of 84. PKH26 was imaged with 561 nm excitation and a 595/50 filter with a laser power of 13.2 and a pmt voltage of 108. Gains were kept below 110 to eliminate contribution from C. albicans autofluorescence; lack of autofluorescence was confirmed by comparison to a control sample without heparin-Alexa Fluor 488. Images were processed with Nikon NIS-Elements AR 4.11.00 64-bit software. Calcofluor white slides were examined using a Zeiss Axiovert 200M fluorescent microscope equipped with a Plan-Apochromat 63×/1.40 oil objective lens with 1.6× optivar and DAPI filter at 350 nm excitation and 460 nm emission. Images were captured using a Zeiss Axiocam color camera and processed with Axiovision version 4.8.2.
Flow cytometry was performed by inoculating a single colony of BWP17 wt into 3 ml YPD medium and incubating overnight at 30° C. with shaking at 225 rpm. Overnight cultures were diluted to OD600 of 0.1 in 5 ml of YPD or RPMI-HEPES and incubated in the presence or absence of 100 units/ml preservative-free pharmaceutical heparin at 30° C. for one hour. One ml aliquots of each mixture were removed, pelleted (7,000 rpm for 3 min), washed twice with PBS, and reconstituted in 1 ml PBS. Flow cytometry analysis was performed using the ImagestreamX flow cytometer (Amnis, Seattle Wash.) equipped with a 405 nm, 488 nm, 653 nm, laser and multi-mag function. The 40× magnification, 10 mm/sec flow rate, and 488 nm laser were used to collect SSC and Brightfield parameters. The flow cell allows particles up to 100 μm wide (height unlimited) to be collected in the instrument. INSPIRE (v.6.0) software was used to acquire events. Software analysis using IDEAS (v5.0) identified percent hyphae using aspect ratio, height and width features using the side scatter (Channel 6) and brightfield (Channel 1) parameters. Objects were selected within each file and tagged to use as identification of truth sets within the population.
For growth curves in the presence or absence of soluble heparin, a single colony of BWP17 wt was inoculated into 3 ml YPD medium and incubated overnight at 30° C. with shaking at 225 rpm. Overnight cultures were diluted to an OD600 of 0.1 in 5 ml of YPD, RPMI-MOPS, RPMI-HEPES or CSM in a 50 ml conical polypropylene tube. Preservative-free pharmaceutical heparin (1000 units/ml) was added to yield a final concentration of 100 units/ml in the heparin-treated samples. Cultures were grown at 30° C. with shaking and OD600 measured periodically. Doubling times (td) were calculated based on the equation td=ln 2/μ (μ=specific growth rate (48). One hundred units/ml heparin, the concentration recommended to prevent clotting of central venous catheters (20), had no effect on doubling times of planktonic yeast cells grown in YPD, RPMI-HEPES, RPMI-MOPS or CSM, as shown in FIGS. 2A and 2B.
FIGS. 2A-E demonstrate lack of an effect by heparin on wild type Candida albicans (C. albicans) planktonic growth and morphology.
FIG. 2A shows that growth curves in the presence (open circles) or absence (closed diamonds) of soluble heparin were identical.
FIG. 2B shows that doubling times in various media at 30° C. in the absence and presence of heparin (100 units/ml) were identical.
FIG. 2C shows that percent hyphae as determined by flow cytometry did not differ after incubation with or without heparin (100 units/ml) under conditions that favor yeast (YPD, 30° C.) or hyphae (RPMI-HEPES, 37° C.).
FIGS. 2D-E show that the integrity of membrane sterols identified with filipin (FIG. 2D) and the location of septin rings identified with calcofluor white staining (FIG. 2E) were identical between untreated and heparin-treated organisms. Thus, concentrations of heparin commonly used to maintain patency of central venous catheters (100 units/ml) did not lead to readily observable differences in growth or cellular architecture of the organism.
Binding of heparin by C. albicans was examined in vitro. Heparin was labeled with Alexa Fluor 488 by a method modified from Osmond (49). Briefly, 5 mg heparin (Sigma) was dissolved in 0.5 ml MES buffer (0.1M 2-(N-morpholino)ethanesulfonic acid hydrate, pH 4.5, Sigma), then mixed with a solution of 1 mg Alexa Fluor 488 hydrazide (Life Technologies) in 0.4 ml MES buffer. After adding 0.2 ml of EDC solution (15 mg 1-ethyl-3-(3-dimethylaminopropyl) carbo-diimide/ml water, Thermo Scientific), the mixture was stirred at room temperature for 30 min. A second 0.2 ml aliquot of EDC solution was added and the mixture stirred at room temperature for an additional 30 min. After adding 1.3 ml NaOAc (1 M, pH 4.8) and stirring at room temperature for one hour, heparin-Alexa Fluor 488 was purified on a PD-10 desalting column (GE Healthcare) equilibrated in autoclaved nanopure water. Fractions containing the labeled material detected at 490 nm were combined and dried overnight on a SpeedVac concentrator (Savant) with heating. The resulting solid was dissolved in autoclaved nanopure water to 10 mg/ml and stored at 4° C.
Heparin-Alexa Fluor 488 bound to PKH26- and DAPI-labeled C. albicans. A single colony of BWP17 wt was inoculated into 3 ml YPD medium and incubated overnight at 30° C. with shaking at 225 rpm. Using a PKH26 Red Fluorescent Cell staining kit (including PKH26 dye and diluent C, Sigma), 2×107 cells were mixed with 1 ml diluent C. To this solution was added a mixture of 4 μl PKH26 dye in 1 ml diluent C, and the mixture allowed to stand at room temperature for 3 min. After adding 10 ml 3% BSA, the mixture was centrifuged at 3,000 rpm for 7 min. The resultant magenta-colored cells were washed with 10 ml each of 1% BSA and PBS, with centrifugation after each step. After supernatant removal, the cells were reconstituted in 10 ml fresh PBS. Two 1 ml (2×106 cells) aliquots were placed in separate 15 ml conical tubes, centrifuged, and supernatants removed. Each was reconstituted with 2 ml YPD, and heparin-Alexa Fluor 488 (0.1 ml of above 10 mg/ml solution) was added to the experimental sample. Control and experimental samples were incubated at 30° C. with shaking (225 rpm) for 30 min, at which time 0.4 ml aliquots of each were removed, pelleted (10,000 rpm for 3 min), and washed twice with PBS. After reconstitution with 0.5 ml PBS, DAPI (4′,6-diamidino-2-phenylindole dihydrochloride (Sigma, stock solution of 5 mg/ml) was added to a final concentration of 1 μg/ml and the solution allowed to stand at room temperature for 10 min. Cells were pelleted and washed twice with PBS, then mounted on a microscope slide using Fluoromount G.
To measure the binding of C. albicans to solid-phase heparin, a heparin-binding ELISA assay was developed, as follows. A single colony of each C. albicans wild type or mutant strain from a YPD plate was inoculated into 3 ml YPD medium and incubated overnight at 30° C. with shaking at 225 rpm. Sigma heparin (fresh solution made daily), diluted to 25 units/ml in autoclaved, sterile-filtered PBS was added as 0.1 ml aliquots to each well of an allyl amine-coated 96-well heparin binding microtiter plate (BD Biosciences). The plate was incubated at room temperature overnight in the dark (50). In the morning, the plate was washed with acetate buffer (100 mM NaCl, 50 μM NaOAc, 0.2% Tween 20, pH 7.2), incubated with 3% bovine serum albumin (BSA) in PBS at 30° C. for 1 hour, then washed with PBS. In the meantime, overnight cultures of C. albicans were subcultured by dilution to OD600 of 0.2 in 25 ml of YPD, and grown at 30° C. to mid-log phase (OD600 0.6-0.7). Cells were pelleted (3,000 rpm for 7 minutes), washed twice with PBS and reconstituted in RPMI-HEPES to 4×105, 2×105, and 1×105CFU/ml, respectively. One hundred μl of each C. albicans dilution was applied to the microtiter wells; experiments for each strain were performed in quadruplicate. The plate was incubated at 30° C. for one hour and washed with PBS to remove non-adherent C. albicans. One-tenth ml of a biotinylated polyclonal rabbit anti-C. albicans antibody raised against soluble proteins in a C. albicans lysate (Meridian Life Science), which had been diluted 1:2500 in FACS-Tween (0.05% Tween 20 in FACS buffer consisting of 0.3% BSA), was added to each well. The plate was incubated at 30° C. for one hour, then washed with PBS-Tween (0.05% Tween 20 in PBS). One-tenth ml streptavidin alkaline phosphatase (Biolegend) diluted 1:10,000 in FACS-Tween was then added to each well, and the plate was incubated at 30° C. for 30 minutes. After washing with PBS-Tween and AKP buffer (100 mM Tris base, 50 μM MgCl2, 100 mM NaCl, pH 9.5.), 0.1 ml alkaline phosphatase substrate (KPL) was added to each well. After 45 minutes, absorbance at 595 nM was read on a Beckman Coulter DTX 880. When desulfated heparin analogs, chondroitin sulfate, or dermatan sulfate were used, equimolar amounts of the analogs (with respect to heparin) were applied to the allyl amine-coated 96-well plate instead of heparin.
The ability of soluble heparin to inhibit C. albicans binding to plate-bound heparin was demonstrated by pre-incubating 1×106 CFSE-labeled C. albicans with 200 units heparin at 37° C. for one hour in wells of a 96-well black plate. C. albicans was labeled with carboxyfluorescein succinimidyl ester (CFSE), succinimidyl ester (CFSE; Invitrogen), which is used to track cell division and therefore does not kill the organism (28), as follows. A single colony of C. albicans was suspended in CSM to an OD600 of 0.1, diluted 1:200 into 25 ml CSM and grown at 30° C. overnight to mid-log phase (OD600 0.6-0.7). Cells were washed twice in sterile PBS and suspended in PBS at 2×107 CFU/ml. Carboxyfluorescein succinimidyl ester (Life Technologies) was dissolved in DMSO, diluted in PBS to 50 μM, and 0.5 ml CFSE mixed with 0.5 ml C. albicans suspension. The mixture was incubated for 20 min at room temperature on a rotator, washed once with FACS buffer, once with PBS, then suspended in 1 ml FACS buffer. Intensity of labeling was determined as the mean fluorescence intensity using a BD Accuri C6 cytometer (San Jose, Calif.) with excitation at 488 nm and a 533/30 emission filter. Wells of a black 96-well microtiter plate were incubated with 0.1 mg poly-D-lysine for one hour at room temperature, washed three times with PBS, then incubated with 200 units of heparin in 100 μl RPMI-HEPES overnight at room temperature. The following afternoon, C. albicans wild type strain and mutants were labeled with CFSE as follows: after growth of C. albicans to mid-log phase in CSM medium, organisms were washed two times in PBS and suspended in PBS at a concentration of 2×107/ml. 0.5 ml cells was mixed with 0.5 ml CFSE, covered in foil, and rotated on a mixer for 20 minutes at room temperature. CFSE-labeled C. albicans cells were pelleted in a minifuge at 3000 rpm for four minutes, washed once with FACS buffer (0.3% bovine serum albumin in PBS), washed again with PBS, and then suspended in 1 ml FACS buffer at a concentration of 1×107/ml. 100 μl CFSE-labeled C. albicans (1×106) were deposited in test wells for 60 minutes at room temperature. At the end of the incubation period, wells were washed three times with PBS, and fluorescence in each well was measured (Beckman Coulter Multimode detector DTX880).
FIGS. 3A-D demonstrate C. albicans binding to heparin in vitro. FIG. 3A shows confocal microscopy of C. albicans in the presence of heparin-Alexa Fluor 488, with (i) C. albicans cell wall stained with PKH26, (ii) nucleus stained with DAPI, (iii) cell wall outlined by heparin-Alexa Fluor 488, and (iv) arrows indicating co-localization of heparin with C. albicans cell surface. Incubation of C. albicans with 100 units/ml heparin-Alexa Fluor 488 for 30 mins at 30° C. demonstrated co-localization of heparin with the C. albicans cellular surface (FIG. 3A). Heparin deposition was seen at the interface of adjoining yeast cells and in individual cells.
FIG. 3B shows binding of 10,000 colony-forming units (CFU) C. albicans (OD595) to increasing concentrations of heparin immobilized on an allyl amine-coated 96-well microtiter plate; values are ±SD of duplicate wells. Binding of C. albicans at 10,000 CFU/well did not change over heparin concentrations ranging from 1.25 units/well (6.3 μg/well) to 20 units/well (100 μg/well) (FIG. 3B), indicating saturation of the allyl amine plate by heparin in low concentrations.
FIG. 3C shows the linear dose-response for the heparin binding ELISA assay with 2.5 units/well heparin and increasing C. albicans input from 10,000 (left-most bar), 20,000 (center bar), and 40,000 (right-most bar) CFUs; the graph represents mean±SD of four experiments, *p<0.007 for all inputs. FIG. 3C shows that the OD595 of the ELISA assay increases linearly as input of C. albicans increased from 10,000 colony forming units (CFU)/well to 40,000 CFU/well.
FIG. 3D shows binding of C. albicans (40,000 CFU/well) to equimolar amounts of heparin analogs desulfated at the 2-O (second from the left bar), 2-N (second from the right bar), or 6-O (right-most bar) positions versus heparin control (left-most bar) (normalized to 100%), with the graph representing mean±SD of three experiments, performed in triplicate *p≦0.003, **p=0.20 vs. heparin control. With equimolar amounts of desulfated heparins, binding of C. albicans was decreased by 11% when heparin was desulfated at the 2-0 position of iduronic acid (p=0.003), and by 21% when heparin was desulfated at the 2-N position of glucosamine (p=0.002) (FIG. 3D). Removal of the sulfate group at the 6-O position of glucosamine did not significantly reduce binding.
Pre-incubation of CFSE-labeled C. albicans with 100 units/ml heparin decreased binding to heparin by 27% (p=0.022; data not shown). C. albicans also recognizes the related structures of chondroitin sulfate and dermatan sulfate. Binding of C. albicans to heparin and to chondroitin sulfate was equivalent, but binding to dermatan sulfate was reduced (p=0.019; data not shown). These results confirmed that the binding of C. albicans to heparin and similar glycosaminoglycans (chondroitin sulfate and dermatan sulfate) could be reproducibly measured and, in the case of heparin, specifically inhibited by pre-incubating the organisms with heparin. These results also suggested that surface components of C. albicans may mediate C. albican binding to heparin.
Location of HBM in Int1 (SEQ ID NO: 5) were determined. Five overlapping polypeptides spanning amino acids 51-1711 of Int1 were expressed with a 6×His tag (SEQ ID NO: 54) in S. cerevisiae BJ3501 and purified by affinity chromatography (HisTrap column; GELifesciences). Fractions containing the His-tagged polypeptide were pooled, diluted with loading buffer (10 mM phosphate, pH 7.0 plus 250 mM NaCl) and applied to a heparin sepharose column (HiTrap Heparin HP; GE Lifesciences). Heparin-binding polypeptides were eluted with a step gradient of NaCl (0.5-2 M) in loading buffer. Eluted fractions were analyzed by SDS-PAGE and immunoblot using anti-His tagged antibody (Santa Cruz) and chemiluminescent detection (SuperSignal West Pico Mouse IgG Detection Kit, Pierce) according to manufacturers' instructions. Polypeptides spanning aa 656-1193 and aa 1548-1711 bound to heparin-Sepharose and were eluted with NaCl, indicating that the HBM in those domains, schematized as Motif 1 (SEQ ID NO: 1), Motif 4 (SEQ ID NO: 2), and Motif 5 (SEQ ID NO: 3) (FIG. 4A), were candidates for mediating binding to heparin. Bolded letters represent basic amino acids in heparin binding motifs; unbolded letters represent hydropathic residues. Polypeptides spanning aa 51-385, aa 385-659, and 1188-1551 failed to bind to a heparin-Sepharose column.
The linear polypeptide spanning aa 656-1193 contains one potential heparin binding site, 804QKKHQIHK (SEQ ID NO: 1) (basic residues shown in red) (Motif 1 in Table 1 and FIG. 4A). The linear polypeptide spanning aa 1548-1711 contains a canonical Weintraub motif 1593FKKRFFKL (SEQ ID NO: 2) (Motif 4 in Table 1 and FIG. 4A) and a canonical Cardin motif 1612SHKTRA (SEQ ID NO: 3) (Motif 5 in Table 1 and FIG. 4A). Sequence homology search using BLAST indicated that aa 1548-1711 contains a Pleckstrin homology domain (PHD), which is structurally resolved. Using homology-based 3-D modeling, we found that the three lysine residues and single arginine residue in Motif 4 were located on the rim of the PHD and might facilitate binding to a strong anion such as heparin by electrostatic interaction (FIG. 4B, arrows). The Cardin motif (Motif 5) did not share this conformation.
To test whether 804QKKHQIHK (SEQ ID NO: 1) (Motif 1) and/or 1593FKKRFFKL (SEQ ID NO: 2) (Motif 4) mediated the binding of heparin to C. albicans, standard PCR-mediated mutagenesis (51) was used to construct a set of isogenic INT1 disruptants and mutants (Table 2).










TABLE 2





Strain
Abbreviation
Genotype
Source







BWP17
—
ura3::imm434/ura3::imm434 his1::hisG/his1::hisG
[27]




arg4::hisG/arg4::hisG


BWP17WT
WT
BWP17 plus arg4::ARG4::URA3/his1::hisG::HIS1
[27]


VBIDM2
—
as BWP17 plus int1::ARG4/int1::URA3
[60]


VBIDM6-2
DD
as VBIDM2 plus his1::hisG/HIS1
[60]


KO503
Motif 4
VBIDM2 plus his1::hisG::HIS1-INT1 (KK1595AA)
current


KO507
Motif 1
VBIDM2 plus his1::hisG::HIS1-INT1(KK804AA)
current


KO508
Motifs 1&4
VBIDM2 plus his1::hisG::HIS1-INT1(KK804AA, KK1595AA)
current


KO509
Reint
VBIDM2 plus his1::hisG::HIS1-INT1 (WT)
current









Construction of mutants was as follows. C. albicans genomic DNA was isolated from saturated overnight cultures using glass beads as described (52). A lithium acetate method was used to transform C. albicans (41). Plasmids and PCR products were purified using kits (Fermentas/ThermoFisher, Pittsburg Pa.) or established methods (53). Pfu enzyme (New England Biolabs) with High Fidelity buffer was employed for all amplifications. Products were sequenced to affirm fidelity prior to use. Primers are described in Table 3.










TABLE 3 





Primer
Internal reference
Sequence
Purpose







1
SAC2035UP
gggagctcGTTACTTGTCATTAATTAGTTACTTCC
SacI 5′ INTI




(SEQ ID NO: 55)



 


2
MLU3′UTR
ggacgcgtTTTTATCTTTTTATGTAAATATATACTA
MluI 3′INT1




(SEQ ID NO: 56)



 


3
INT1 KR1595AA F
ATTGTCCAATTTTTAAGGCTGCTTTTTTCAAATTAAT
mutate Motif 1




GGG (SEQ ID NO: 57)



 


4
INT1 KR1595AA R
CCATTAATTTGAAAAAAGCAGCCTTAAAAATTGGAC
mutate Motif 1




AATC (SEQ ID NO: 58)



 


5
INT1 KK805AA F
GCATAAACAAGAAAAGCAGGCCGCCCATCAAATTC
mutate Motif 4




ATAAAGTTCC (SEQ ID NO: 59)



 


6
INT1 KK805AA R
GGAACTTTATGAATTTGATGGGCGGCCTGCTTTTC
mutate Motif 4




TTGTTTATGC (SEQ ID NO: 60)



 


7
GHISR
CTCCCGGCCGCCATGGCCGC (SEQ ID NO: 61)
check





integration


 


8
HIS3AMP
GTTGGTGTGGCCCAGAGACTCT (SEQ ID NO: 62)
check





integration









A single copy of Int1, including 1450 bp upstream and 548 bp downstream from the Int1 open reading frame (www.candidagenome.org, Assembly 21), was integrated into the hisG locus of the int1−/− strain VBIDM2 (54) to produce the reconstituted strain KO509. Briefly, a copy of Int1 was generated by PCR, using primers 1 and 2 with BWP17 wt DNA as template and cloned into the SacI/MluI sites of pGEMHIS (51) to create pKO509. pKO509 was digested with SwaI and transformed into VBIDM2 to create the reconstituted strain KO509. PCR-mediated overlap extension mutagenesis (55) was used to produce copies of Int1 mutated at putative heparin binding domains. Briefly, primer pairs 1+3 and 2+4 (or 1+5 and 2+6) were used to produce two overlapping fragments of INT1 in which putative heparin binding domains were mutated (FKKRFFKL (SEQ ID NO: 2)→FKAAFFKL (SEQ ID NO: 53) or KQKKHQ (SEQ ID NO: 64)→KQAAHQ (SEQ ID NO: 63)), and a full length mutated sequence generated in a third per using primers 1+2 with the fragments as template. The mutated sequences were cloned into the SacI/MluI sites of pGEMHIS to create pKO503 and pKO507, respectively. A construct mutated at both sites (pKO508) was produced using primers 1+5 and 2+6 with plasmid DNA from pKO503 as template. Full length mutated products cloned into pGEMHIS and used to transform VBIDM2 as above, producing strains KO503, KO507, and KO508. The correct insertion and orientation of all constructs was confirmed by PCR. In growth curves performed with and without 100 units/ml heparin at 30° C. in RPMI-HEPES, there was no difference in the doubling times of the wild type, Δint1 mutant, INT1 reintegrant, or the reintegrants containing alanine substitutions in Motif 1 (804QKKHQIHK (SEQ ID NO: 1) to QAAHQIHK (SEQ ID NO: 52)), Motif 4 (1593FKKRFFKL (SEQ ID NO: 2) to FKAAFFKL (SEQ ID NO: 53)), or Motifs 1 and 4. Percent binding of each mutant to heparin in the ELISA assay was compared to the wild type according to the formula [Absorbance595 mutant]/[Absorbance595 wild type]×100.
The ELISA assay used a commercially available 96-well microtiter plate coated with polymerized allylamine (BD Biosciences) (27), in which wells were inoculated with 2.5 units (12.5 μg) heparin in 100 μl phosphate buffered saline (PBS) per well. The plate was covered and allowed to stand at room temperature overnight, then washed with acetate buffer (100 mM NaCl, 50 mM NaOAc, 0.2% Tween, pH 7.2). Wells were washed three times with PBS, then inoculated with 1×104 to 4×104 Candida albicans yeast cells that were grown overnight at 30° C. in yeast peptone dextrose (YPD) broth, washed, and resuspended in RPMI-HEPES at 1×107 organisms/ml. The plate was then incubated at 30° C. for one hour, then washed with PBS-Tween (PBST, PBS/0.05% Tween). A commercially available biotinylated anti-Candida antibody (Meridian Life Science, Memphis Tenn.) was diluted 1:1500 in FACS-TWEEN (0.3% BSA/0.05% Tween), added to the wells, incubated at 30° C. for one hour, then washed with PBST. Streptavidin-alkaline phosphatase (BioLegend, San Diego Calif.) was then added to the wells at a 1:10,000 dilution in FACS-TWEEN and incubated at 30° C. for 30 min, then washed with PBST and AKP buffer (100 mM Tris, 100 mM NaCl, 50 mM MgCl2*6H2O). BluePhos@ microwell substrate (Kirkegaard and Perry Laboratories, Gaithersburg Md.) was added to the wells and allowed to react for 45 min at room temperature. The color change was read spectrophotometrically at absorbance of 595 nm.
FIGS. 4A-D show that linear heparin binding motifs in C. albicans Int1 mediate binding to heparin.
FIG. 4A illustrates the five putative heparin binding sites in Int1. Mutations were made by substituting alanine residues in Motif 1: 804QKKHQIHK (SEQ ID NO: 1) to QAAHQIHK (SEQ ID NO: 52) (Table 1, Motif 1) and in Motif 4: 1593FKKRFFKL (SEQ ID NO: 2) to FKAAFFKL (SEQ ID NO: 53) (Table 1, Motif 4). A third reintegrant had alanine substitutions at both sites.
FIG. 4B shows molecular modeling of Motif 4, which predicts that the three lysine residues and the single arginine residue (arrows) might facilitate binding to a strong anion like heparin.
FIG. 4C shows heparin binding of C. albicans WT (normalized to 100%), Δint1 double disruptant (DD), and four single-copy reintegrants: (1) Reint contains one wild type copy of Int1; (2) Motif 1 mutant contains alanine substitutions for lysine residues at positions 805/806 (804QAAHQIHK (SEQ ID NO: 52)); (3) Motif 4 mutant contains alanine substitutions for lysine 1595 and arginine 1596 (1593FKAAFFKL (SEQ ID NO: 53)), and (4) Motif 1&4 mutant contains alanine substitutions at both sites. Binding to heparin was highest for the wild-type C. albicans strain that expressed both copies of the INT1 gene. Disruption of both copies of INT1 (DD) reduced the binding of heparin by 40% (p=0.031) despite removing just one of the 34 C. albicans genes encoding putative linear HBM. Reintegration of one copy of the wild type INT1 gene (Reint) partially restored the ability of C. albicans to bind to heparin. Differences in heparin binding among the WT, Reint and DD strains were statistically significant (p=0.031 in all cases). Among the three isogenic strains with alanine mutations in putative heparin binding sites, mutation of Motif 1 was associated with the largest reduction in heparin binding, compared to the wild type strain (p=0.031), to the Motif 4 mutant (p=0.036), and to the Motif 1&4 mutant (p=0.031). Results with the Motif 1 mutant were not significantly different from the percent binding observed with the double disruptant (p=0.063) or the reintegrant (p=0.115), nevertheless, this trend of reduced binding suggested that lysine residues in Motif 1 might be likely mediators of heparin binding. Results are presented as mean±SD for n=5 experiments performed in quadruplicate, *p=0.031, **p=0.036.
Because Motif 1 in Int1 appeared to mediate a considerable proportion of the binding of C. albicans to heparin, a peptide encompassing this motif HKQEKQKKHQIHKV (SEQ ID NO: 4) was used to immunize rabbits with a commercial protocol (Pacific Immunology). Affinity-purified immune IgG and IgG from pre-immune rabbit serum (both from Pacific Immunology) were compared for the ability to inhibit binding of C. albicans to heparin (FIG. 5). Antibody and heparin inhibition studies were performed as follows. Antibody was produced and tested by Pacific Immunology, Ramona, Calif. (www.pacificimmunology.com; NIH Animal Welfare Assurance Number A41820-01; USDA License 93-R-283). A peptide corresponding to amino acids 799-812 of Int1 (HKQEKQKKHQIHKV (SEQ ID NO: 4)), encompassing Motif 1, was conjugated to KLH via an N-terminal cysteine residue and used to immunize two NZW rabbits. The animals were immunized once with conjugated peptide in a proprietary formulation of Freund's complete adjuvant and boosted 3 times with conjugated peptide in Freund's incomplete adjuvant. The same peptide was conjugated to CNBr-Sepharose and used for affinity purification of epitope-specific IgG. The final serum titer for both animals was >1:100,000 by ELISA. Both pre-immune rabbit serum and serum from bleed 3 were chromatographed on a 2 ml Protein A column (Thermo Scientific) to yield pre- and post-immune IgG and brought to a concentration of 1.6 mg/ml. 100 μl poly-D-lysine (MP Biomedicals, Solon Ohio) diluted as 1 mg in 10 ml distilled water was added to each well of black 96-well plates (Costar) and incubated at room temperature for 60 min. After three washes with PBS, 100 μl pharmacologic heparin (2000 units/ml in RPMI-HEPES) was added to each well and incubated overnight at room temperature in the dark. In the morning, the plate was washed three times with PBS, then a 1:1000 dilution of pre- or post-immune IgG in PBS was added to each well and incubated for 30 min at room temperature. After overnight growth to mid-exponential phase in CSM, C. albicans wild type and double disruptant strains were labeled with CFSE as above. After labeling, samples of each strain were removed to determine the intensity of labeling by flow cytometry, as described above. CFSE-labeled C. albicans were diluted in RPMI-HEPES to yield 1×106 cells per 100 μl and added to each well for 60 min at 30° C. The plate was washed three times with PBS; fluorescence in each well was measured with a Beckman DTS 880. Experiments were performed in triplicate. For heparin inhibition studies, wild type C. albicans were grown as above, labeled with CFSE, and washed to remove excess CFSE. Organisms were pelleted, the supernatant was removed, and the pellets were suspended in 2 ml pharmacologic heparin (20,000 units/ml) diluted with RPMI-HEPES to a concentration of 250 units/ml (1.3 mg/ml). CFSE-labeled C. albicans were incubated with heparin for 60 min at 37° C. with shaking at 400 RPM, then added to the wells of a black plate, incubated for 60 min at RT, and washed three times with PBS; fluorescence in each well was measured with a Beckman DTS 880. The assay was performed in a 96-well black plate with CFSE-labeled C. albicans. Wells were coated with poly-D-lysine, 100 μg/100 μl PBS for 60 min at room temperature, then 200 units heparin in 50 μl RPMI-HEPES were added to each well. The plate was incubated overnight at room temperature. The following afternoon, pre-immune IgG and post-immune IgG were diluted in PBS to a final concentration of 13.2 μg/ml. 50 μl of pre- or post-immune IgG was deposited in the appropriate well for 30 min at room temperature, then 1×106 CFSE-labeled C. albicans in 50 μl RPMI-HEPES were added for two hours at room temperature. After this incubation, the wells were washed three times with PBS, and fluorescence was measured on the multimode detector as previously described.
Polyclonal IgG to the HKQEKQKKHQIHKV (SEQ ID NO: 4) motif in domain 3 of Int1 blocked 19% of binding of wild type C. albicans (WT) to heparin. FIG. 5 shows heparin binding of wild type C. albicans preincubated with pre-immune IgG (left closed circles) and wild type C. albicans pre-incubated with post-immune IgG raised to the polypeptide HKQEKQKKHQIHKV (SEQ ID NO: 4) (right closed circles), where data represent mean±SD of n=15 experiments performed in duplicate, *p=0.023, by paired statistics. These results confirmed the importance of Motif 1, as a mediator of heparin binding in C. albicans. 
In other systems, heparin has been reported to cleave surface proteins (56), change protein conformation (57), and bind trypsin-sensitive lysine and arginine residues in histone H1 (58). In order to understand whether incubation with heparin changed the conformation of C. albicans surface proteins, 1×107 C. albicans were incubated for one hour at 3° C. on a rotator with pharmacologic heparin (20,000 units/ml) diluted in RPMI-HEPES to a working concentration of 250 units/ml. C. albicans 1×107 C. albicans in an equal volume of RPMI-HEPES served as control. Supernatants were removed. 300 μl of Hep+ and Hep− supernatants were incubated with 100 μl avidin agarose beads (Thermo Scientific) for 60 min at room temperature on a rotator in the presence of 50 units heparin (Hep+); an equal volume of RPMI-HEPES was substituted for heparin in the Hep− supernatants. Beads were pelleted, and 100 μl beads were incubated with 100 μl 3.0 M NaCl for 30 mins at room temperature on a rotator. Beads were pelleted and the supernatants were withdrawn; 100 μl TCA was added to 100 μl Hep+ or 100 μl Hep− supernatants and incubated on ice overnight at 4° C. The TCA precipitates were stored at −80° C. until analysis by mass spectroscopy.
Six biological replicates of TCA precipitated protein pellets from equal cellular equivalence of heparin-treated (Hep+) and untreated (Hep−) conditioned medium from cultures of C. albicans were each solubilized in 50 μL Laemmli gel buffer. To remove any residual TCA and to further concentrate the samples, each was subjected to buffer exchange and concentration using an Amicon ultra 3 kDa microfuge filtration cartridge at 14,000×g for 15 min with five subsequent additions of 50 μL of 1× Laemmli gel buffer between spins. The resulting retained proteins (6 Hep+ and 6 Hep−) were subsequently prepared for SDS-PAGE by combining into two pools of three samples for the Hep+ and Hep− conditioned medium. The replicate sample pools were loaded onto two 4-12% mini gels and separated using the MOPS buffer system followed by silver staining to visualize the proteins using the Sigma Proteosilver system. The proteins were prepared for identification and quantitation by mass spectrometry by gridding the gel lanes from the replicates of Hep+ and Hep− samples into 11 equal regions followed by in gel trypsin digestion and extraction of peptides as described (59)
The recovered peptides from the gridded gel sections were analyzed by liquid chromatography coupled nano-electrospray mass spectrometry (nLC-MSMS) on a TripleTOF 5600 mass spectrometer (AB Sciex, Toronto Canada) attached to an Eksigent (Dublin Calif.) nanoLC ultra nanoflow system. Recovered peptides from each fraction were loaded on to IntegraFrit Trap Column (outer diameter of 360 μm, inner diameter of 100, and 25 μm packed bed) from New Objective, Inc. (Woburn Mass.) at 2 μl/min in FA/H2O 0.4/99.2 (v/v) for 10 min to desalt and concentrate the samples. For the chromatographic separation of peptides, the trap-column was switched to align with the analytical column, Acclaim PepMap100 (inner diameter of 75 μm, length of 15 cm, C18 particle sizes of 3 μm and pore sizes of 100 Å) from Dionex-Thermo Fisher Scientific (Sunnyvale Calif.). The peptides were eluted using a linear gradient from 95% phase A (FA/H2O 0.4/99.6, v/v) to 40% phase B (FA/ACN 0.4/99.6, v/v) from 5 min to 22.5 min (2% ACN/min) at a flow of 300 mL/min. As the peptides eluted from the column they were sprayed into the mass spectrometer using NANOSpray® III Source (AB Sciex, Toronto Canada). Ion source gas 1 (GS1), ion source gas 2 (GS2) and curtain gas (CUR) were respectively kept at 7, 0 and 25 vendor specified arbitrary units. Interface heater temperature and ion spray voltage was kept at 150 C, and at 2.3 kV respectively. Mass spectrometer method was operated in positive ion mode set to go through 25 minutes, where each cycle performing one TOF-MS scan type (0.25 sec accumulation time, in a 400 to 1600 m/z window) followed by twenty information dependent acquisition (IDA)-mode MS/MS-scans on the most intense candidate ions selected from initially performed TOF-MS scan during each cycle having a minimum 150 counts. Each product ion scan was operated under vender specified high-sensitivity mode with an accumulation time of 0.05 sec and a mass tolerance of 50 mDa. Former MS/MS-analyzed candidate ions were excluded for 10 sec after its first occurrence, and data were recorded using Analyst®-TF (1.5.1) software.
NanoLC-MSMS data collected from the Hep+ and Hep− samples were converted to Mascot generic files and searched against the SwissProt fungal database on an in house server running Mascot version 2.2.07 (Matrix Science, Ltd). Specific search parameters included up to two missed tryptic cleavages, carbamidomethylation of Cys, oxidation of Met, peptide and fragmentation mass tolerance of 0.1 Da. Only proteins with a minimum of two peptides with Mascot peptide score indicating a peptide identity and a false discovery rate (FDR) against and inverse database at less than 1% were reported. Semi-quantitative measurements between the Hep+ and Hep− proteins were generated using a minimum of two tryptic peptides from each protein as surrogates for the amount of proteins from the two groups. This was accomplished by capturing extracted ion profiles for each peptide and then comparing the mono-isotopic peak intensity at the apex of the signal for the M+2H or M+3H signal for each peptide. An average ratio of the maximal peak intensity between two independent peptides for each protein presented was used to determine semi-quantitative ratios of proteins between the Hep+ and Hep− samples.
To determine the levels of these proteins in control versus heparin-treated organisms, the relative level of several tryptic peptides were used as surrogates for the protein levels.
Compared to untreated organisms, heparin treatment led to a seven-fold increase in intensity of IDVVDQAK (SEQ ID NO: 65) from Eno1 (FIG. 6A), a ten-fold increase in intensity of SLLDAAVK (SEQ ID NO: 66) from Pgk1 (FIG. 6B), and a five-fold increase in VPTTDVSVVDLTVR (SEQ ID NO: 67) from Tdh3 (FIG. 6C) in supernatants.
Other peptides from Eno1, Pgk1, and Tdh3 also exhibited increased intensities, ranging from 10-16 fold the intensity of the corresponding peptides from untreated organisms (data not shown), further validating significant increases in the protein levels in the supernatants for heparin-treated cultures. Of the 12 proteins whose peptides were found in highest concentration in the supernatant (Table 4), all but one are known to be localized to the cell wall; cellular localization of Eft1 is not known. Eight of the twelve, including Eno1, Pgk1, Tdh3 and Ssa1/2, themselves contain putative heparin binding motifs (Table 1) and are considered critical antigens for innate and adaptive immune responses against C. albicans (31-36).












TABLE 4







ID
Prot Score
Prot Mass
Peptide Matches**





















Eno1*,#
2877
47202
213



Ssa2*,#
1938
70199
73



Pgk1*,#
1826
45266
131



Tdh3*,#
1751
35508
192



Hsp90#
1666
80773
65



Ssb1*,#
1608
66562
82



Met6#
1566
85763
70



Ssa1*,#
1455
70452
61



Adh1#
1218
37255
67



Eft1
1187
50426
99



Ino1*,#
1006
57857
39



Eft2*,#
933
93865
25







*proteins with putative linear heparin binding motifs;



**total peptides identified by MSMS including duplicates; and



#cell wall proteins by Gene Ontology.






In order to evaluate the consequences of removal of Ssa1 and Ssa2 (Table 4), both targets of histatin, a histatin killing assay was performed as follows. C. albicans strains were grown to late log phase overnight in YPD. A single colony was suspended in 1 ml YPD, diluted 1:500 into 10 ml YPD, and incubated overnight at 30° C. and 225 rpm to OD600 1.0. Yeast cells were washed twice in PBS and 2×104 cells suspended in 250 μl RPMI+10 mM HEPES, pH 7.0, with or without 500 units/ml heparin (Sigma). The cells were incubated at 37° C. for one hour with shaking, washed twice with 10 mM phosphate buffer, pH 7.4, and suspended in 20 μl phosphate buffer. Histatin 5 (final concentration 15 μM; Peptides International) or 10 mM phosphate buffer was added to the preincubated cells (total volume 40 μl) and incubated further at 37° C. for 90 minutes with shaking. YPD (360 ul) was added to each tube, a 40 μl aliquot spread onto YPD plates, and colonies counted after two days. The effect of heparin treatment was determined by the formula % change=[(cfu+heparin)−(cfu−heparin)]/(cfu+heparin).
Heparin binding to trypsin-sensitive lysine and arginine residues in histone H1 unfolds chromatin and increases its accessibility (58). To test whether heparin binding could influence gene expression in C. albicans, qRT-PCR was performed on a selective set of 13 genes involved in adhesion, cell-cell interaction, and biofilm formation after incubating C. albicans with and without 100 units/ml heparin at 37° C. for 75 minutes. Gene expression studies were performed as follows. Overnight cultures (3 ml YPD at 30° C., 225 rpm) were diluted in 25 ml YPD to a nominal concentration of 8×105/ml and grown to OD600 approximately 1.0 (30° C., 225 rpm), collected by centrifugation, and washed in PBS. Cells (5×107) were suspended in 5 ml RPMI1640 with 25 mM MOPS pH7.4, with or without 100 units/ml Sigma heparin in 50 ml polypropylene tubes, and incubated at 37° C. with shaking for 75 minutes. One ml aliquots (approximately 107 cells) were collected by centrifugation, washed once with room temperature PBS, and frozen at −80°. Pellets were thawed on ice and suspended in 1 ml Tri-Reagent (MRC Research) in a 2 ml screw capped tube containing about 0.2 g acid washed glass beads (Sigma) and vortexed three times for 1 minute with a 1 minute rest on ice between each vortex. The lysates were rested for five min at room temperature, centrifuged for five min at 12,000 rpm, and RNA isolated from the supernatant using the DirectZol kit (Zymo), including DNAse digestion, per manufacturer's instructions. cDNA was produced from equivalent quantities of RNA (between 300 and 900 ng) for each treatment using the Maxima Reverse Transcriptase Kit for qRT-PCR (Fermentas). Two μl of 1:5 dilution of cDNA was used in each qPCR reaction with 500 nM of each primer and Fast SYBR Green Master Mix (Life Technologies) on a 7500 FAST Instrument (Applied Biosystems) according to manufacturer's instructions. Relative expression was determined using the ΔΔCt method (60) with 18S RNA as the reference. Primers are shown in Table 5.










TABLE 5 






Primer
Sequence
SEQ ID NO:








18S F
TCTTGTGAAACTCCGTCGTG
68


 



18S R
AGGGACGTAATCAACGCAAG
69


 



AHP1 F
TGTGCCTGGTGCTTTTACC
70


 



AHP1 R
TTAGCCCAAGCTGCCATTAC
71


 



ALS1 F
TCATTTGCCACCACTACCAC
72


 



ALS1 R
TGGCATAGGATTGTGACCAG
73


 



ALS3b F
GCTGGTGGTTATTGGCAACGTGC
74


 



ALS3b R
TGGTAAGGTGGTCACGGCGG
75


 



CDC10 F
AGATCAAGGGCAAACCTCAC
76


 



CDC10 R
ATAGGAGCATTTGGCACACC
77


 



EAP1 F
TACCCAGGCCAATACAAAGG
78


 



EAP1 R
TAATGGGCTTGACCTTGGAG
79


 



ECE1 F
CTAATGCCGTCGTCAGATTG
80


 



ECE1 R
AACATCTGGAACGCCATCTC
81


 



ENO1 F
CCATTGACAAAGCCGGTTAC
82


 



ENO1 R
TTAGATGGGTCGGATTCTGG
83


 



HGC1 F
AGGTCGCAAGCAACAACAAC
84


 



HGC1 R
AAGAAACAGCACGAGAACCAG
85


 



HWP1b F
TCCTGCCACTGAACCTTCCCCAG
86


 



HWP1b R
CCACTTGAGCCAGCTGGAGCG
87


 



HWP2 F
CCACCAAAACCAAGTGCTAC
88


 



HWP2 R
AACTCCAGATGATCCCGAAG
89


 



INT1 F
TGTGCCCACTGAAGTCAAAG
90


 



INT1 R
GCTTTACCGGTGATTTGGTC
91


 



RBT1 F
CACCTCATGCTCCAACAATG
92


 



RBT1 R
GATGATTCTGGGGCTGATTC
93


 



RBT5 F
TGCTGAAAGTTCTGCACCAG
94


 



RBT5 R
GCTTCAACGGAAACAGAAGC
95









FIG. 7A shows CFU of C. albicans WT and DD after 75-minute incubation without (left bar of each set) or with (right bar of each set) 500 units/ml heparin followed by histatin 5 (15 μM), performed in duplicate. Confirming proteomic results showing removal of Ssa1/2 (Table 3), incubation of wild type C. albicans with 500 units/ml heparin led to a 25% decrease in histatin-mediated killing (FIG. 7A); in contrast, heparin treatment of the INT1 double disruptant did not impair killing (1.5% decrease).
FIG. 7B shows relative mRNA expression of thirteen genes measured by qRT-PCR after incubation of C. albicans with heparin, with the level of expression compared to C. albicans without heparin (=1). Results showed a 2.5 to 3-fold increase in mRNA for HWP1 and HWP2.
In order to understand whether heparin binding motifs 1 and 4 influenced C. albicans pathogenesis in vivo, we employed a rat model of biofilm formation in central venous catheters inserted into the jugular vein, as previously described (61). After insertion into the jugular vein of an anesthetized female Sprague-Dawley rat, a silastic catheter was heparinized with 100 units heparin/mil and remained in place for 24 hours. At the 24 hour timepoint, 500 μl of blood was withdrawn and cultures to insure sterility, and then 1×106 CFU of the desired C. albicans strain was instilled into the catheter and allowed to dwell for 6 hours. The animal was then sacrificed, the catheter was removed aseptically and processed for scanning electron microscopy. Biofilm formation on the intra-luminal surface of the catheter was assessed by scanning electron microscopy (SEM) at 100× and 2000×.
FIGS. 8A-F demonstrated that heparin binding motifs contribute to biofilm formation in vivo.
The INT1 wild type strain (WT) produced a profuse biofilm with intertwined hyphae and visible exopolysaccharide matrix (FIG. 8A). Biofilm formation by the Int1 double disruptant was much reduced on SEM (FIG. 8B), as expected. Reintegration of one wild type copy of INT1 restored a profuse biofilm (FIG. 8C). However, alanine substitution of lysines805/806 in Motif 1 greatly impaired biofilm formation (FIG. 8D). Although alanine substitution of lysine1595 and arginine1596 in Motif 4 did not reduce biofilm formation (FIG. 8E), the Motif 1&4 mutant again produced sparse biofilm (FIG. 8F). These results showed that lysine residues 805/806 in Motif 1 were critical for biofilm formation in vivo.
Inhibition of biofilm formation by the antibody raised against the peptide sequence HKQEKQKKHQIHKV (SEQ ID NO:4) was also tested in the rat central venous catheter model. A 1:10 dilution of affinity-purified IgG against the peptide HKQEKQKKHQIHKV (SEQ ID NO: 4) was incubated with wild type C. albicans at 30° C. for one hour. A 1:10 dilution of pre-immune IgG was used as a control. The strains were then instilled into separate jugular venous catheters in individual rats. After 6 hours, catheters were removed and aseptically processed for scanning electron microscopy (100× and 2000×) as described above.
Central venous catheters from animals that received C. albicans pre-incubated with IgG against HKQEKQKKHQIHKV (SEQ ID NO:4) exhibited substantially reduced biofilm formation. FIG. 9 (left panel) shows intraluminal biofilm (100× and 2000×) from C. albicans incubated with pre-immune IgG; there is no diminution in biofilm, hyphae, or production of exopolysaccharide matrix. FIG. 9 (right panel) shows intraluminal biofilm (100× and 2000×) from C. albicans incubated with post-immune IgG recognizing the sequence HKQEKQKKHQIHKV (SEQ ID NO: 4); there is a marked diminution in biofilm with sparse hyphae and no matrix.
In vitro study results showed that C. albicans binds heparin through HBM in Int1 (FIG. 4C). The specificity of this interaction was confirmed by inhibition with heparin (data not shown) and with antibodies directed against a peptide that encompasses Motif 1 in Int1 (FIG. 5). Binding of heparin results in several consequences that could potentially impact virulence in vivo: removal of Candida surface proteins that serve as targets for innate (FIG. 7A) and adaptive (FIG. 6A-C) immune defenses and modulation of gene expression (FIG. 7B).
The in vivo studies of biofilm formation in heparinized central venous catheters in rats showed an obvious reduction in biofilm formation after mutation of lysine residues 805/806 in Motif 1 (FIGS. 8D, 8F). In addition, a rabbit IgG antibody directed against a peptide encompassing Motif 1 dramatically inhibited biofilm formation in the rat central venous catheter model as well (FIG. 9, right panel). These results not only demonstrate the central role of lysine residues in Motif 1 but also have important clinical implications because of the use of heparin in central venous catheters, in which setting Candida spp. are the fourth most common cause of infections (23, 24).
Putative linear HBM are also present in Staphylococcus epidermidis and Staphylococcus aureus (Long and Hostetter unpublished data), two organisms that are even more common causes of catheter-associated infection (43), as shown in Tables I-IV. For example, putative linear HBM were identified in the following cell wall or putative cell wall proteins, where the motif and the beginning position of the motif is indicated in parenthesis, from methicillin resistant Staphylococcus aureus, strain 252 (MRSA252): sasC (LKKNKY; 4; and IRKYKV; 11), isdB (YKKAKT; 289), sasF (SRRNKL; 618), glcB (IRKFKL; 415), sasA (MHHTHS; 1263), SAR0879 (LKKIKG; 573), SAR0986 (YRHLKP; 754), SAR1559 (IRKAHQ; 206), SAR2393 (PKRKVVKI; 149), and sasG (VRKARS; 140); from methicillin sensitive Staphylococcus aureus, strain 476 (MSSA476): SAS2383 (VRKARS; 140; and VKKSKI; 1319), SAS1682 (LKKNKY; 4; and IRKYKV; 11), SAS1063 (YKKAKT; 282), SAS1657 (YHKAKT; 484), SAS2532 (SRRNKL; 626), SAS2540 (MHHTHS; 2187), SAS0082 (LKKIKG; 573), SAS1011 (IRKAHQ; 206), SAS2035 (PKRKVVKI; 149), and SAS2424 (IRKFKL; 415); and from Staphylococcus epidermidis, strain RP62A: SERP1316 (FRKQKF; 4; VHRLKV; 352; and IHKIKP; 3234), SERP0660 (LKKWKV; 4; and IRRAHQ; 212), SERP0719 (TRKNHY; 13), SERP1482 (VKRFKN; 1730), SERP1654 (MKKSKV; 1), SERP2264 (MKRIKT; 393), SERP0207 (NRKNKN; 887), and SERP1691 (PKKIKN; 72).
In one embodiment, an antibody is generated against a linear heparin binding motif which is conserved among MSSA, MRSA, and S. epidermidis. In one embodiment, the conserved heparin binding motif is selected from the group consisting of LKKNKY, LKKNKY, LKKWKV, LKKIKG, LKKIKG, VRKARS, VRKARS, YKKAKT, YKKAKT, YHKAKT, PKRKVVKI, PKRKVVKI, IRKAHQ, IRKAHQ, and IRRAHQ.
Putative linear HBM were identified in the following cell wall or putative cell wall proteins from various yeast species, as shown in Table V where a check mark indicates that the motif is identical to the motif found in C. albicans, including C. dubliniensis (Int1 (YKKRFFKL), Eno1 (AKKGKF), and Tdh3 (GHKIKV) proteins), C. parapsilosis (Tdh3 protein (GHKIKV)), C. tropicalis (Int1 (FKRRFFKL), and Tdh3 (GHKIKV) proteins), C. glabrata (Int1 (FKKRFFTL) protein), Lodderomyces elongisporus (Int1 (FKKFIFKL) and Tdh3 (GHKIKV) proteins), and A. nidulans (Int1 (FKKRFFKL) protein). In embodiments, an antibody directed to a region of these proteins containing the putative HBM or the region of these proteins containing the putative HBM may be used in the described methods.







TABLE I 





Methicillin resistant Staphylococcus aureus, strain 252


MRSA252


























“Cell wall” 
“Cell wall”
Have
Motif

Start





in
in GO
signaling
in Se-

Loca-


GI Accession
Name
Description
Description
annotation
peptide
quence
Motif
tion





G1:49484003
sasC
putative surface anchored


Yes
Yes
LPNTG
2153




protein








GI:49483291
isdB
iron-regulated heme-iron


Yes
Yes
LPQTG
 616




binding protein








GI:49484843
sasF
putative surface anchored


Yes
Yes
LPKAG
 588




protein








GI:49484739
glcB
PTS system, glucose-



Yes
LPAAG
  22




specific IIABC component








G1:49484850
sasA
putative serine rich



Yes
LPDTG
1308




repeat containing protein








GI:49482351
SAR0879
putative myosin-



Yes
LPKAG
  57




crossreactive antigen








GI:49482500
SAR0986
putative nitric oxide



Yes
LPSAG
 230




reductase








GI:49483239
SAR1559
putative cobalt transport



Yes
LPITG
 258




protein








GI:49484356
SAR2393
hypothetical protein



Yes
LPTAG
 177



sasG
virulence associated cell










wall protein

















Ortholog


RP62A
Have heparin




in
MSSA476 ortholog 
Ortholog
orthology
binding
#of heparin


GI Accession
MSSA476
has motif?
in RP62A
has motif:
motif?
binding motifs





GI:49484003
SAS1682
Yes
SERP1316
Yes
Yes
2


GI:49483291
SAS1063
Yes


Yes
1


GI:49484843
SAS2532
Yes
SERP2264
Yes
Yes
1


GI:49484739
SAS2424
Yes


Yes
1


GI:49484850
SAS2540
Yes
GI:57865710
No
Yes
1


GI:49482351
SAS0082
Yes
GI:57866574
No
Yes
1


GI:49482500




Yes
1


GI:49483239
SAS1011
Yes
SERP0660
Yes
Yes
1


GI:49484356
SAS2035
Yes
SERP1739
Yes
Yes
1







Yes
1






Motif 1

Motif
Motif




GI Accession
type
Motif 1 seq
after
2 type
Motif 2 seq
Motif lifter





GI:49484003
Cardin
LKKNKY
3
Cardin
IRKYKV
10


 













GI:49483291
Cardin
YKKAKT
288





 


GI:49484843
Cardin
SRRNKL
617





 


GI:49484739
Cardin
IRKFKL
414





 


GI:49484850
Cardin
MHHTHS
1262





 


GI:49482351
Cardin
LKKIKG
572





 


GI:49482500
Cardin
YRHLKP
753





 


GI:49483239
Cardin
IRKAHQ
205





 


GI:49484356
Wentraub
PKRKVVKI
148






Cardin
VRKARS
139
found by








MKH


















TABLE II 





Methicillin sensitiveie Staphylococcus aureus, strain 476


MSSA476



























“Cell wall”




GI


“Cell wall” in
in GO 


ID MSSA476
refSeq
Accession
Name
Description
Description
annotation





SAS2383
YP_044496.1
GI:49487275
SAS2383
putative cell wall-
Yes
Yes






anchored protein




SAS1682
YP_043802.1
GI:49486581
SAS1682
putative surface








anchored protein




SAS1063
YP_043187.1
GI:49485966
SAS1063
iron-regulated heme-

Yes






iron binding protein




SAS1657
YP_043776.1
GI:49486555
SAS1657
haptoglobin-binding

Yes






surface anchored








protein




SAS2532
YP_044646.1
GI:49487425
SAS2532
putative surface








anchored protein




SAS2540
YP_044654.1
GI:49487433
SAS2540
putative cell wall-
Yes
Yes






anchored protein




SAS0082
YP_042206.1
GI:49484985
SAS0082
putative myosin-








crossreactive antigen




SAS1011
YP_043135.1
GI:49485914
SAS1011
putative cobalt








transport protein




SAS2035
YP_044146.1
GI:49486925
SAS2035
hypothetical protein




SAS2424
YP_044538.1
GI:49487317
SAS2424
PTS system, glucose-








specific IIABC component

























MRSA252

RP62A
Have



Have


Start
Orthlog
ortholog

orthology
heparin



signaling
Motif in

Loca-
in
has
Ortholog in
has
binding


ID MSSA476
peptide
Sequence
Motif
tion
MRSA252
motif?
RP62A
motif?
motif?





SAS2383
Yes
Yes
LPKTG
1338
sasG

aap
Yes
Yes


SAS1682
Yes
Yes
LPNTG
2150
sasC
Yes
SERP1316
Yes
Yes


SAS1063
Yes
Yes
LPQTG
609
isdB
Yes


Yes


SAS1657
Yes
Yes
LPKTG
860




Yes


SAS2532
Yes
Yes
LPKAG
596
sasF
Yes
SERP2264
Yes
Yes


SAS2540

Yes
LPDTG
2232
sasA
Yes
GI:57865710
No
Yes


SAS0082

Yes
LPKAG
57
SAR0879
Yes
GI:57866574
No
Yes


SAS1011

Yes
LPITG
258
SAR1559
Yes
SERP0660
Yes
Yes


SAS2035

Yes
LPTAG
177
SAR2393
Yes
SERP1739
Yes
Yes


SAS2424

Yes
LPAAG
22
glcB
Yes


Yes


















# of









heparin









binding
Motif 

Motif
Motif




ID MSSA476
motifs
1 type
Motif 1 seq
after
2 type
Motif 2 seq
Motif after





SAS2383
2
Cardin
VRKARS
139
Cardin
VKKSKI
1318


 


SAS1682
2
Cardin
LKKNKY
3
Cardin
IRKYKV
  10


 


SAS1063
1
Cardin
YKKAKT
281





 


SAS1657
1
Cardin
YHKAKT
483





 


SAS2532
1
Cardin
SRRNKL
625





 


SAS2540
1
Cardin
MHHTHS
2186





 


SAS0082
1
Cardin
LKKIKG
572





 


SAS1011
1
Cardin
IRKAHQ
205





 


SAS2035
1
Wentraub
PKRKVVKI
148





 


SAS2424
1
Cardin
IRKFKL
414
















TABLE III 





Staphylococcus epidermidis, strain RP62A


























“Cell wall”
“Cell wall”




GI


in
in GO


ID RP62A
refSeq
Accession
Name
Description
Description
annotation





SERP1316
YP_188888.1
GI:57867198
SERP1316
cell wall surface
Yes







anchor family protein




SERP0660
YP_188245.1
GI:57866567
SERP0660
cobalt transport








family protein




SERP0719
YP_188302.1
GI:57866639
SERP0719
cell wall surface
Yes







anchor family protein




SERP1482
YP_189048.1
GI:57867352
SERP1482
cell wall surface
Yes







anchor family protein




SERP1654
YP_189219.1
GI:57867536
SERP1654
cell wall surface
Yes







anchor family protein




SERP2264
YP_189815.1
GI:57865679
SERP2264
cell wall surface
Yes







anchor family protein




SERP0207
YP_187803.1
GI:57866125
SERP0207
sdrG protein




SERP1691
YP_189256.1
GI:57867615
SERP1691
cell division protein,








FtsW/RodA/SpoVE family










Strain RP62A (continuation)


















Have
Motif



MSSA476

MRSA252
Have
# of



sig-
in 

Start
Orthlog
ortholog
Ortholog 
orthology
heparin
heparin



naling
Se-

Loca-
in
has
in
has
binding
binding


ID RP62A
peptide
quence
Motif
tion
MSSA476
motif?
MRSA252
motif?
motif?
motifs





SERP1316
Yes
Yes
LPEAG
3654
SAS1682
Yes
sasC
Yes
Yes
3


SERP0660

Yes
LPITG
 264
SAS1011
Yes
SAR1559
Yes
Yes
2


SERP0719
Yes
Yes
LPETG
 787




Yes
1


SERP1482
Yes
Yes
LPDTG
1937




Yes
1


SERP1654
Yes
Yes
LPETG
 165




Yes
1


SERP2264
Yes
Yes
LPATG
 639
SAS2532
Yes
sasF
Yes
Yes
1


SERP0207

Yes
LPDTG
 852
SAS0521
Yes
bbp
Yes
Yes
1


SERP1691

Yes
LPITG
 352
SAS1988
Yes
SAR2371
Yes
Yes
1










Strain RP62A (continuation)

















Motif
Motif
Motif
Motif
Motif
Motif
Motif
Motif
Motif


ID RP62A
1 type
1 seq
after
2 type
2 seq
after
3 type
3 seq
after





SERP1316
Cardin
FRKQKF
3
Cardin
VHRLKV
351
Cardin
IHKIKP
3233


SERP0660
Cardin
LKKWKV
3
Cardin
IRRAHQ
211





SERP0719
Cardin
TRKNHY
12








SERP1482
Cardin
VKRFKN
1729








SERP1654
Cardin
MKKSKV
0








SERP2264
Cardin
MKRIKT
392








SERP0207
Cardin
NRKNKN
886








SERP1691
Cardin
PKKIKN
71
















TABLE IV 





Linear Heparin Binding Motifs Conserved Among 2 or 3 Staphylococcus species


























MRSA
sasC
LKKNKY
sar0879
LKKIKG
sasG
VRKARS
isdB
YKKAKT


sar2892


MSSA
sasC
LKKNYY
sas0082
LKKIKG
sas2383
VRKARS
sas1063
YKKAKT
sas1657
YHKAKT
sas2035


St.
serp0660
LKKWKV











epi















MRSA
PKRKVVKI
sari 559
IRKAHQ



MSSA
PKRKVVKI
sas1011
IRKAHQ



St. epi

serp0660
IRKAHQ
















TABLE V







Heparin Binding Motifs in various yeast species














HEPARIN-BINDING MOTIF





Lodderomyces



C. albicans XXXXXXX
C. albicans
C. dubliniensis
C. parapsilosis
C. tropicalis
C. glabrata
elongisporus
A. nidulans


















Motif
Protein









FKKRFFKL
Int1
√
YKKRFFKL
no
FKRRFFKL
FKKRFFTL
FKKFIFKL
√


LRRLRT
Ssa2/Ssb1
√




no



AKKGKF
Eno1
√
√
no
no

no



GHKIKV
Tdh3
√
√
√
√

√





√ identical






The interaction of C. albicans with heparin or heparin-like compounds may play a key role in clinical settings where heparin is used (e.g. central venous catheters, dialysis catheters) or possibly in tissues where heparan sulfates are preferentially expressed.
Because antibodies raised against a linear heparin binding motif inhibited binding of C. albicans to heparin, the heparin binding peptide HKQEKQKKHQIHKV (SEQ ID NO: 4) could be used as an immunizing antigen in immunocompetent patients to elicit antibodies that protect against heparin binding.
For example, a peptide from streptococcal M protein has been used to make a vaccine for rheumatic fever (62). Alternatively, antibodies raised against this peptide in immunized humans can be used for passive immunization. This technology is used with commercially available antibodies such as hepatitis B immune globulin (HBIG) or botulism immune globulin (BabyBIG®) (63). Hepatitis B immune globulin is commercially available; botulism immune globulin is made and distributed by the California Department of Public Health and is FDA-approved. A humanized monoclonal antibody recognizing a desired heparin binding motif could be made using technology for the production of palivizumab (Synagis®), a humanized monoclonal antibody that is given monthly to premature newborns to prevent infection with respiratory syncytial virus (64). Because similar heparin binding motifs are also found in S. epidermidis and S. aureus, using heparin binding motifs as antigens is a first step in developing vaccines against three of the most common causes of central line-associated bloodstream infection.
Antibodies raised against a linear heparin binding motif expressed by a surface protein of C. albicans inhibited adhesion of the yeast to heparin in vitro and abolished biofilm formation in vivo. Similar heparin binding motifs occur in surface proteins from S. epidermidis and S. aureus, two organisms which are also major causes of biofilm-related infections.
In one embodiment, an antibody reactive with a heparin binding motif expressed on the surface of a microorganism is administered to an individual. The microorganism may be, but is not limited to, a Candida species or a Staphylococcus species. In one embodiment, the microorganism is C. albicans, S. epidermidis and/or S. aureus. In one embodiment, the heparin binding motif is identified by a computer-based algorithm analysis of protein sequences expressed by a microorganism. In one embodiment, the heparin binding motif to which the antibody was generated is derived from Int1. In one embodiment, the antibody is directed to the peptide HKQEKQKKHQIHKV (SEQ ID NO: 4), or a fragment of this peptide. In one embodiment, the fragment is at least seven amino acids of the peptide. In one embodiment, the surface expression of the heparin binding motif depends on the life-cycle stage of the microorganism. In one embodiment, the antibody is a polyclonal antibody. In one embodiment, the antibody is a monoclonal antibody.
In one embodiment, a peptide that corresponds to a linear heparin binding motif expressed on the surface of a microorganism, or a portion of the peptide, is provided. In one embodiment, the peptide is used to generate antibodies directed against the peptide, using methods known in the art. Alternatively, a peptide is provided combined with additional carriers or as a component of a complex, e.g., an adjuvant non-toxic to humans. Such an adjuvant could be aluminum hydroxide used in Engerix-B® (commercially available hepatitis B vaccine), and in Comvax® (commercially available vaccine for Haemophilus influenzae type b and hepatitis B). The peptide corresponds to a linear heparin binding motif, or a portion of the motif, of a microorganism. In one embodiment, the microorganism is a Candida species and/or a Staphylococcus species. In one embodiment, the microorganism is C. albicans, S. epidermidis and/or S. aureus. In one embodiment, the heparin binding motif is identified by a computer-based algorithm analysis of protein sequences expressed by a microorganism. In one embodiment, the heparin binding motif is derived from Int1. In one embodiment, the peptide is HKQEKQKKHQIHKV (SEQ ID NO: 4), or a fragment of SEQ ID NO: 4. In one embodiment, the peptide is a fragment of the peptide HKQEKQKKHQIHKV (SEQ ID NO: 4), where the fragment contains at least seven amino acids of the peptide. In one embodiment, the surface expression of the heparin binding motif depends on the life-cycle stage of the microorganism. In one embodiment, the peptide is used to generate an antibody using methods known in the art.
In one embodiment, a method is provided for ameliorating biofilm formation on a surface of an implanted device in a patient. In one embodiment, the method comprises administering an antibody to a patient, and ameliorating biofilm formation on a surface of an implanted device in a patient, wherein the antibody is directed to a heparin binding motif expressed on the surface of a microorganism. In one embodiment, the antibody is administered intravenously at a dose not more than 2 grams/kg given as an infusion over 10-24 hours. Since the half-life of antibody preparations is about four weeks, antibody administration would be repeated at monthly intervals over the life of the catheter. In one embodiment, the antibody has been modified to increase safety and/or efficacy in a human patient. In one embodiment, the antibody has been humanized using methods known in the art. In one embodiment, the described antibody is provided as a pharmaceutical composition with at least one biocompatible excipient, e.g., buffers, preservatives, tonicity adjusting agents, pH adjusting agents, osmolality adjusting agents, etc, as known to one skilled in the art. Without being held to a single theory, the antibody blocks binding between a heparin binding motif-containing protein expressed on the surface of a microorganism and heparin or heparin sulfate, which is expressed by human cells lining the lumen of the implanted device (FIG. 10). Binding of the antibody to the microorganism prevented its attachment to heparin or to heparin sulfate moieties. In the rat model of Candida infection of central venous catheters, the disclosed antibody recognizing a peptide encompassing Motif 1 in Candida albicans Int1 (also called anti-KKHQ antibody (“KKHQ” disclosed as SEQ ID NO: 6)) showed excellent in vivo results. The antibody recognizing Motif 1 (anti-KKHQ antibody (“KKHQ” disclosed as SEQ ID NO: 6)) substantially inhibited biofilm production, as shown in FIG. 9. FIGS. 11 and 12A-C demonstrate the anti-KKHQ antibody is effective against various Candida species.
The administration of the described antibody is referred to as passive immunization.
In one embodiment, the method comprises administering a peptide to a patient, where the peptide encompasses a heparin binding motif, or a fragment of the motif, that is expressed on the surface of a microorganism. The peptide is 14 amino acids in length, with amino acids both preceding and following the 8 amino acids of the heparin binding motif. In one embodiment, the peptide is HKQEKQKKHQIHKV (SEQ ID NO: 4), or a fragment thereof. In one embodiment, the described peptide is provided as a pharmaceutical composition comprising at least one biocompatible excipient including but not limited to buffers, stabilizing agents, solubility enhancing agents, tonicity agents, etc. as known to one skilled in the art.
Without being held to a single theory, the peptide serves as an antigen to immunize the patient. It provides immunity by promoting endogenous generation of antibodies directed to the peptide, where the endogenously-produced antibodies block binding between heparin, which is administered through the catheter or is bound to a surface of an implanted medical device, and a heparin binding motif-containing protein expressed on a microorganism surface. Administration of the described peptide is referred to as active immunization. Peptide vaccines are typically administered subcutaneously or intramuscularly. Immunizing dose of the peptide and frequency of immunization are experimentally determined with humans.
The patient being treated may be naturally immunodeficient by having an underdeveloped immune response, e.g., a premature newborn. The patient being treated may have a normal immune response, but may be immunocompromised due to particular circumstances, e.g., as a result of treatment such as chemotherapy, or disease, or burns. In one embodiment, the disclosed antibody is administered to an immunodeficient patient. In one embodiment, the disclosed peptide is administered to an non-immunodeficient patient, e.g., an otherwise well adult or child who will receive long term antibiotics through a central line for the treatment of a serious infection, e.g., endocarditis.
In one embodiment, the implanted medical device, e.g., catheter, central line, hemodialysis catheter, peritoneal catheter, PICC line, plastic catheters such as central venous catheters, urinary tract catheters, central nervous system shunt catheters, peritoneal dialysis catheters, dialysis shunts, etc., is implanted in a vein, artery, or a body cavity. In one embodiment, the implanted medical device is a plastic device. In one embodiment, the implanted device is present in the patient's body for a period of time ranging from minutes to six weeks or longer. In one embodiment, the above described methods may be performed before the device is implanted in the patient. In one embodiment, a first dose of the antibody is administered before the medical device is implanted. In this embodiment, a peripheral intravenous line could administer this first dose of the antibody if the device to be implanted is a catheter.
In one embodiment, the described methods decrease the virulence of a microorganism, i.e., the method decrease the ability of a microorganism to cause infection in a patient.
All references cited are expressly incorporated by reference herein in their entirety.

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The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. The ASCII copy, created on Mar. 8, 2013, is named 070248_94_SL.txt and is 30,824 bytes in size.
The embodiments described in the specification are only specific embodiments of the inventors who are skilled in the art and are not limiting. Therefore, various changes, modifications, or alterations to those embodiments may be made without departing from the spirit of the invention or the scope of the following claims.

## Claims

1. A composition comprising at least one biocompatible excipient and an antibody capable of binding to peptide HKQEKQKKHQIHKV (SEQ ID NO: 4) wherein the excipient comprises a Tris buffer and wherein the antibody is a non-human humanized antibody.

2. The composition of claim 1, where the peptide HKQEKQKKHQIHKV (SEQ ID NO: 4) is a portion of a protein.

3. The composition of claim 2 where the microorganism is a Candida species or a Staphylococcus species.

4. The composition of claim 1 where the peptide is derived from Int1 protein (SEQ ID NO: 5).

5. The composition of claim 1 where the antibody is a polyclonal antibody.

6. The composition of claim 1 where the antibody is a monoclonal antibody.

7. A kit comprising
instructions for administering a composition to a patient candidate for medical device installation or implantation, and
a composition comprising at least one biocompatible excipient and an antibody capable of binding to peptide HKQEKQKKHQIHKV (SEQ ID NO: 4)
where the excipient comprises a Tris buffer and wherein the antibody is a non-human humanized antibody.

8. An antibody capable of binding to peptide HKQEKQKKHQIHKV (SEQ ID NO: 4) where the antibody is a nonhuman humanized antibody.