WO1999055839A1 - Host defense enhancement - Google Patents

Abstract

Nucleic and amino acid sequences for a novel cell surface transmembrane glycoprotein designated C1qRp are taught. A method by which the nucleic acid sequence encoding C1qRp may be used to modulate the role of the immune system is also described. Transgenic animals created with heterologous DNA sequence encoding C1qRp are described as well as antibodies directed against the C1qRp protein. A method of hybridization for C1qRp nucleic acid using oligonucleotide probes based on the C1qRp nucleic acid sequence and methods for detecting a hybrid probe: target C1qRp duplex are also taught including a kit for such detection.

Description

HOST DEFENSE ENHANCEMENT

The present invention was made with Government support by the National Institutes of Health/National Cancer Institute Training Program in Carcinogenesis (5T32-C- A09054) and National Institutes of Health Grant # AI-41090. The government has certain rights associated with the invention. This application is a Continuation-in-Part of Application Serial number 08/751,305 filed on November 18, 1996.

BACKGROUND OF THE INVENTION

1. Field of the Invention

This invention relates generally to compositions, and methods of employing these compositions for the enhancement of host defense. More specifically, it relates to the use of various forms of the human and murine ClqR_P receptor, their use in enhancing host defense, methods of detection, methods of hybridization and methods of determining novel homologous ClqR_P receptors and ligands and transgenic animals thereof.

2. Description of Related Art

The following is a general description of art relevant to the present invention. None is admitted to be prior art to the invention. Generally, this art relates to observations of the complement receptors of the immune system.

Introduction

Phagocytosis is a major host defense mechanism by which potentially deleterious material (both pathogenic organisms and cellular debris) is cleared from circulation and tissue, and made accessible to inactivation. The phagocytic capacity/potential of a cell can be modulated by cytokines which trigger cellular differentiation or by other activation ligands. This activation is probably relevant at sites of inflammation where -2-

Clq and/or other regulatory molecules may accumulate and enhance the phagocytic capacity of acute inflammatory cells.

The complement component protein designated Clq, is part of a family of host defense proteins with similar macromolecular structures which include a collagen-like region contiguous with a globular domain. Clq is composed of covalently linked subunits of three distinct polypeptide chains each with N-terminal collagen-like regions: Clq is the recognition subunit of the Cl component of the classical complement pathway (CCP) in that it binds to the Fc region of antibodies in immune complexes, as well as a variety of non-immunoglobulin substances, and can initiate the classical complement pathway of the immune system.

Clq can enhance both FcR- and CR1 -mediated phagocytosis by monocytes. Specifically, the collagen-like fragment of Clq (Clq-CLF) is the region of the Clq molecule that mediates enhanced phagocytosis, since the phagocytic response can be triggered by the pepsin-resistant fragment only, and not by the pepsin-sensitive, collagenase-resistant fragments.

Enhancement of phagocytosis triggered by the Clq protein can be inhibited by monoclonal antibodies R139 and R3, indicating that the antigenic region of the Clq receptor protein which is recognized by these antibodies is a critical, functional component of the Clq receptor protein. These antibodies (R139 and R3) bind to a 126,000 M_r (reduced) glycoprotein which is highly expressed on the surfaces of phagocytic cells, but not on B or T lymphoblastoid cells. Since these antibodies first described the Clq receptor that modulates monocyte phagocytosis, the protein (126,000 M_τ) is designated ClqR_P. The antibodies that recognize ClqR_p (R139 and R3) are also able to inhibit a myeloid cell response (enhanced monocyte phagocytosis), indicating a functional role for the ClqR_P protein in myeloid cell types. -3-

SUMMARY OF THE INVENTION

The invention provides human and murine Clq receptor (ClqR_p) sequences and nucleic acid sequences which encode the novel cell surface transmembrane glycoprotein receptor designated ClqR_P. This receptor plays a role in stimulating the classic complement component of the immune system, specifically in stimulating phagocytosis in cells without a concomitant increase in inflammation. A method of hybridization based on the ClqR_P nucleic acid sequence is provided as well as methods for detecting novel ligands for the ClqR_P, including those which function as agonists or antagonists. Additionally, methods of determining compositions which effect the formation of an affinity complex between the C 1 qR_P and its ligand are provided as well as methods for determining compositions which modulate signal transduction via the ClqR_P. The nucleic acid sequence encoding ClqR_p or recombinant ClqR_P protein may be used to effect the role of this classical complement component of the immune system. Transgenic animals can be created using ClqRp DNA sequences to aid in the study of the role of ClqR_P during growth and metabolism and as a model for disease states in which the normal level of ClqR_P is effected.

The invention provides substantially pure human and murine ClqR_p polypeptides, fragments thereof, nucleic acid sequences encoding ClqR_P or fragments thereof, methods of detecting novel ligands of the ClqR_P, methods of administering formulations capable of gene delivery and gene expression of ClqR_P nucleic acid, methods of hybridization for ClqR_P nucleic acid, and transgenic animals created using ClqR_P nucleic acid sequences.

The details of the preferred embodiment of the present invention are set forth in the accompanying drawings and the description below. Once the details of the invention are known, numerous additional innovations and changes will become obvious to one skilled in the art. -4-

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1. Affinity purified ClqR_P. Immobilized purified monoclonal antibody R3 (IgM) was used to affinity purify the receptor antigen from detergent extracts of U937 cells. Eluted protein was concentrated and subjected to SDS-PAGE (7.5%) under reducing conditions followed by Coomassie Blue staining (left). Mature 126,000 M_r ClqRp is indicated by the arrow. Breakdown fragments are indicated by the arrowhead and asterisk. Molecular weight markers are shown in the right lane.

Figure 2. ClqR_P PCR and λgtll clones. Positions of the three PCR fragments and isolated λgtll clones are shown. After the PCR1, PCR2 and clone 15 were sequenced, clones 2, 3, 7 and 16 were sequenced at the 5' and 3' ends to determine their positions. Clone 3 was then sequenced in its entirety. PCR3 was generated by the 5'-RACE PCR method.

Figure 3. cDNA and deduced amino acid sequence of ClqR_P. (SEQ ID NO.: 1) Nucleotides are numbered with the first base of the initiator methionine as +1. The amino terminus of the mature protein and internal peptides determined by amino acid sequencing are underlined. The single putative N-glycosylation site is in italics starting at position N325. The transmembrane domain is double underlined.

Figure 4. Structural domains of ClqR_P. Shown is a schematic diagram indicating the domains contained within ClqR_P which include a 21 amino acid signal peptide (SP) and a C-type carbohydrate recognition domain (CRD) at the N-terminus, five

Epidermal Growth Factor (EGF)-like domains, numbered, including three calcium binding (cb) EGF domains, and a single transmembrane (TM) domain. The putative N-linked glycosylation site is indicated within the second EGF domain.

Figure 5. Anti-peptide antibody recognizes ClqR_P. R3 purified ClqR_P was subjected to SDS-PAGE under nonreducing (lanes 1-3) and reducing (lanes 4-6) conditions, then transferred to nitrocellulose. The blot was probed with monoclonal antibody R139 (lanes 1 and 4), polyclonal anti-peptide antiserum (lanes 2 and 5) and with polyclonal anti-ClqR_P antiserum QR1 (lanes 3 and 6). Isotype and species matched antibodies were used as probes in parallel and resulted in no reactivity similar to lane 4 (not shown). Arrows indicate the intact receptor, whereas breakdown fragments are indicated by the arrowheads and asterisks. Molecular weights are indicated on the left.

Figure 6. Southern blot analysis of human genomic DNA for ClqR_P. DNA was digested with Bam HI, Eco Rl, Hind III and Pst I. After agarose gel electrophoresis and transfer, the DNA was hybridized to a ³²P-labeled probe generated by random priming of the λgtll clone 15 insert. Positions of size markers (in base pairs) are indicated at the far left.

Figure 7. Northern blot analysis of mRNA for ClqR_P. Messenger RNA was separated by agarose gel electrophoresis and transferred to nylon. The blot on the left was probed for ClqR_P and the blot on the right was probed for GAPDH as a control for RNA levels. Positions of the 0.24-9.49 Kb RNA ladder are indicated on the far right.

Figure 8. Nucleotide sequence (SEQ ID NO:34) and encoded amino acid sequence (SEQ ID NO:35) of murine ClqR_P.

Figure 9. Comparison of the amino acid sequence of human ClqR_P (SEQ ID NO:2) and murine ClqR_P (SEQ ID NO:35). The amino acid sequences of human and mouse ClqRp were aligned using the MegAlign program in DNASTAR. Identical residues are indicated by shading. The mouse sequence is 66% identical and 77% similar to the human sequence.

Like reference numbers and designations in the various drawings indicate like elements. -6-

DETAILED DESCRIPTION OF THE INVENTION

Before the present nucleic and amino acid sequences, compositions, formulations and methods and uses thereof are described, it is to be understood that this invention is not limited to the particular compositions, formulations, sequences and methodologies described herein as such compositions, formulations, sequences and methodologies may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and that the terminology used herein is not intended to limit the scope of the present invention which will be limited only by the appended claims.

It must be noted that as used herein and in the appended claims, the singular forms "a," "an," and "the," include plural referents unless the context clearly indicates otherwise. Thus, for example, reference to "a formulation" includes one or more of such different formulations, reference to "an antibody" includes one or more of such different antibodies, and reference to "the method" includes reference to equivalent steps and methods known to those of ordinary skill in the art which could be modified or substituted for the methods described herein.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention belongs. Although any methods, compositions, formulations, sequences similar or equivalent to those described herein can be used in the practice or testing of the invention, the preferred methods and materials are described herein. All publications mentioned herein are incorporated herein, including all figures, graphs, equations, illustrations, and drawings, to describe and disclose specific information for which the reference was cited in connection with.

The publications discussed above are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of -7-

prior invention. Throughout this description, the preferred embodiment and examples shown should be considered as exemplars, rather than as limitations on the present invention.

The invention describes human and murine ClqR_P nucleic acids, encoded amino acid sequences and functional domain structures of the ClqR_P protein. The ClqR_P protein plays a critical role in mediating cell signaling resulting in enhanced phagocytic capabilities of the signaled cell. The ClqR_P protein contains the necessary molecular components needed to transduce a cell signal and it may play a critical role as a receptor of the immune system and in the complement branch of the immune system by functioning in the clearance of cells or cellular debris.

The ability to regulate the phagocytic capacity of myeloid cells via the regulation of cell surface expression and function of ClqR_P will be valuable as a prophylactic treatment for individuals at risk for infection, such as individuals with genetic immunodeficiencies, or individuals infected with HIV, patients undergoing cancer chemotherapy, or patients undergoing high risk surgery.

Additionally, in vitro evidence indicates that ClqR_P does not induce proinflammatory cytokines. This evidence suggests that monocyte activation of increased phagocytosis by employing the ClqR_P sequences of the instant invention will be advantageous due to the selectivity of the ClqR_P response and the ability of ClqR_P not to induce an inflammatory reaction. Furthermore, ClqR_P does not increase the levels of mRNA encoding for, or protein secretion of cytokines TNF-α, IL-lβ or IL-6 which have been shown to increase inflammation.

The enhancement of the host immune system via activation of cells employing formulations encoding the ClqR_P or employing formulations comprising recombinant ClqRp protein, as taught herein, may be more advantageous than employing pharmacologic agents which increase the risk of provoking proinflammatory cytokine release (Testerman et al, J. Leuk. Biol. 58 365, 1995). For example, the -8-

proinflammatory cytokine, Tumor Necrosis Factor alpha (TNFα), enhances the expression of the human immunodeficiency virus (HIV). Thus, initiating a cytokine response such as TNFα would be extremely undesirable when trying to enhance the microbicidal activity in a patient with a compromised immune system. The present invention overcomes such limitations by increasing host resistance to microbial invasion without creating an increased inflammatory response. Furthermore, the increase in the ClqR_P phagocytosis response occurs rapidly, approximately within 5 minutes after interaction of a ClqRp expressing cell with the Clq protein or other ligand for Clq.

In addition to a lack of C 1 qR_P-mediated induction of proinflammatory cytokines, ClqR_P substantially decreased existing elevated levels of the cytokines IL-lα, IL-lβ, TNF-α and IL-6 mRNA levels and IL-lβ, TNF-α and IL-6 protein secretion levels under certain conditions in vitro. Therefore, ClqR_P mediated expression may be used prophylactically in treating immuno-compromised individuals and also as a means of effecting the levels of cytokines in a patient.

The invention provides substantially pure polynucleotides encoding the human and murine ClqR_P protein or fragments thereof. These polynucleotides include DNA, cDNA and RNA sequences which encode ClqR_P. All polynucleotides encoding all or a portion of ClqR_P are also included herein, as long as they encode a polypeptide with C 1 qR_P activity or a functional fragment of a C 1 qR_P molecule. C 1 qR_P polypeptide fragments or portions thereof must comprise a segment of at least 5 consecutive amino acids that are conserved in any of ClqR_P amino acid sequences listed herein. Such polynucleotides include naturally occurring, synthetic, and intentionally manipulated polynucleotides. For example, ClqR_P polynucleotide may be subjected to site-directed mutagenesis. The polynucleotide sequence for ClqR_P also includes antisense, nonsense, or missense sequences. The polynucleotides of the invention include sequences that are degenerate as a result of the genetic code. There are 20 natural amino acids, most of which are specified by more than one codon. Therefore, all degenerate nucleotide sequences are included in the invention as long as the amino acid sequence of ClqR_P polypeptide or a part thereof encoded by the nucleotide sequence is functionally unchanged.

The invention also provides isolated nucleic acid molecules that encode the ClqR_p polypeptides described above, as well as fragments thereof. These nucleic acids can contain naturally occurring nucleotide sequences (see Figure 3), or sequences that differ from those of the naturally occurring nucleic acids that encode ClqR_P, but encode the same amino acids, due to the degeneracy of the genetic code. The nucleic acids of the invention can contain DNA or RNA nucleotides, or combinations or modifications thereof.

The invention further provides an isolated nucleic acid molecule the sequence of which being at least about 65% identitical to SEQ ID NO:l or SEQ ID NO:34 and encoding a polypeptide having a biological activity associated with ClqR_p.

Definitions

By "isolated nucleic acid" is meant a nucleic acid, e.g., a DNA or RNA molecule, that is not immediately contiguous with the 5' and 3' flanking sequences with which it normally is immediately contiguous when present in the naturally occurring genome of the organism from which it is derived. The term thus describes, for example, a nucleic acid that is incorporated into a vector, such as a plasmid or viral vector; a nucleic acid that is incorporated into the genome of a heterologous cell (or the genome of a homologous cell, but at a site different from that at which it naturally occurs); and a nucleic acid that exists as a separate molecule, e.g., a DNA fragment produced by PCR amplification or restriction enzyme digestion, or an RNA molecule produced by in vitro transcription. The term also describes a recombinant nucleic acid that forms part of a hybrid gene encoding additional polypeptide sequences that can be used, for example, in the production of a fusion protein.

The nucleic acid molecules of the invention can be used as templates in standard methods for production of ClqR_P gene products (e.g., ClqR_P RNAs and ClqR_P -10-

polypeptides; see below). In addition, the nucleic acid molecules that encode ClqR_P polypeptides (and fragments thereof) and related nucleic acids, such as (1) nucleic acids containing sequences that are complementary to, or that hybridize to, nucleic acids encoding ClqR_P polypeptides, or fragments thereof (e.g., fragments containing at least 9, 12, 15, 20, or 25 nucleotides); and (2) nucleic acids containing sequences that hybridize to sequences that are complementary to nucleic acids encoding ClqR_P polypeptides, or fragments thereof (e.g., fragments containing at least 9, 12, 15, 20, or 25 nucleotides); can be used in methods focused on their hybridization properties. For example, as is described in further detail below, such nucleic acid molecules can be used in the following methods: PCR methods for synthesizing ClqR_P nucleic acids, methods for detecting the presence of ClqR_P nucleic acid in a sample using oligonucleotide probes based on the ClqR_P nucleic acid sequences supplied herein, which under stringent hybridization conditions will form ClqR_P probe: ClqR_P target duplexes without detectable formation of ClqR_P probe:non-ClqR_P target duplexes, and methods for detecting the hybrid ClqR_P probe:ClqR_P target duplex formed after successful hybridization of a ClqR_P probe to its complementary target nucleic acid sequence can be supplied in a kit form, screening methods for identifying nucleic acids encoding new ClqR_P family members or identifying test compounds or compositions which affect the binding to the ClqR_P can also be supplied in a kit form, and therapeutic methods. The term sample, as used herein, comprises fluid, blood, serum, plasma, cells, tissue, swabs, or secretions or other clinical samples as are commonly familiar to those of ordinary skill in the clinical arts.

The term "kit" as used herein refers to any combination of elements or interrelated parts that are necessary for: detecting and determining the presence of ClqR_P nucleic acid in a sample, screening for identifying nucleic acids encoding new ClqR_P family members, or screening for identifying test compounds or compositions which affect binding to the ClqR_P. One skilled in the art would realize that although the physical characteristics of the kit or its contents are not characterized, those features necessary for the formation of a kit and its physical instantiation are supplied by the teachings of -l i¬

the disclosure herein, the attached claims, and the common knowledge concerning kits possessed by one of common skill in the art.

The term "substantially pure" is used herein to describe a molecule, such as a polypeptide (e.g., a ClqR_P polypeptide, or a fragment thereof) that is substantially free of other proteins, lipids, carbohydrates, nucleic acids, and other biological materials with which it is naturally associated. For example, a substantially pure molecule, such as a polypeptide, can be at least 60%, by dry weight, the molecule of interest. One skilled in the art can purify ClqR_P polypeptides using standard protein purification methods and the purity of the polypeptides can be determined using standard methods including, e.g., polyacrylamide gel electrophoresis (e.g., SDS- PAGE), column chromatography (e.g., high performance liquid chromatography (HPLC)), and amino-terminal amino acid sequence analysis.

Also included in the invention are polypeptides having sequences that are "conservative variations" of the sequence of a ClqR_P polypeptide. A "conservative variation" amino acid sequence is a sequence that differs from a reference sequence only by conservative amino acid substitutions, for example, substitutions of one amino acid for another of the same class (e.g., substitution of one hydrophobic amino acid, such as isoleucine, valine, leucine, or methionine, for another, or substitution of one polar amino acid for another, such as substitution of arginine for lysine, glutamic acid for aspartic acid, or glutamine for asparagine), or by one or more non- conservative substitutions, deletions, or insertions, provided that the polypeptide retains at least one ClqR_P-specific activity or a ClqR_P-specific epitope. For example, one or more amino acids can be deleted from a ClqR_P polypeptide, resulting in modification of the structure of the polypeptide, without significantly altering its biological activity. For example, amino- or carboxyl-terminal amino acids that are not required for ClqR_P biological activity, can be removed. Such modifications can result in the development of smaller active ClqR_P polypeptides. -12-

The term "ClqR_P" is used in accordance with its conventional definition. Such receptors are cell surface receptors that typically modulate monocyte phagocytosis by transducing signals from extracellular environments (e.g., the Clq protein) to intracellular environments. ClqR_P, is a novel cell surface transmembrane glycoprotein receptor that mediates an activation signal that results in an enhanced phagocytotic capacity of the ligated cell. Cell stimulation of the ClqR_P is induced by the ligand protein Clq, or by a family of Clq-like proteins such as mannose binding lectin (MBL) or pulmonary surfactant protein A (SPA). The ClqR_P glycoprotein is highly expressed on the surfaces of phagocytic cells, but not on B or T lymphoblastoid cells. This molecule has the necessary molecular components needed to transduce a signal and can be postulated to be a critical receptor of the innate immune system, as well as functioning in immune complex clearance and/or clearance of cellular debris. Antibodies to ClqR_P (R3 and R139) inhibit Clq-, MBL-, and SPA- mediated, but not fibronectin-mediated, enhancement of phagocytosis. The ClqR_P response does not trigger the release of proinflammatory cytokines in vitro suggesting that activation of the monocyte ClqR_P by Clq and its other ligands is selective.

A "test composition", as used herein, is any composition such as a polypeptide, peptide fragment or composition created through the use of a combinatorial library or other combinatorial process that can be assayed for its ability to function in a given capacity (e.g., as a ClqR_P ligand, or ClqR_P antagonist or ClqR_P agonist or modulator of signal transduction using the ClqR_P) or compound which mimics the activity of polypeptide (e.g., peptidomimetics). Often, such a test composition or polypeptide is, because of its sequence or structure, suspected of being able to function in a given capacity. Nonetheless, randomly chosen "test" polypeptides and compositions also can be used, and art-known techniques, such as expression of polypeptides from nucleic acid libraries, or PCR combinatorial generated polypeptides can be used to this end. A "ligand" is any composition (e.g., a polypeptide, polypeptide derivative, or peptidomimetic) that is capable of inducing signal transduction in a cell by contacting a ClqR_P. Included are compositions that naturally induce signal transduction via the ClqR_p; also included are compositions that do not naturally induce signal transduction -13-

(e.g., artificial compositions and natural compositions that serve other purposes). Compositions that merely bind a ClqR_P without inducing signal transduction are not encompassed by the term ligand. The term "agonist" as used herein means any composition that is capable of increasing the ability of a ligand to bind a ClqR_P or itself to bind to the ClqR_P and induce signal transduction. Such an agonist need not bind the ligand to increase the ability of a ligand to bind the ClqR_P or to modulate signal transduction via the ClqR_P. The term "antagonist" as used herein means any composition that is capable of decreasing the ability of a ligand to bind a ClqR_P or to bind to the ClqR_P itself to inhibit signal transduction via the ClqR_P (e.g., by functioning as a competitive inhibitor of a C 1 q protein). An antagonist need not directly bind, or compete with, the ligand in order to modulate signal transduction via the ClqRp pathway.

"Formulation" means a composition capable of gene delivery and gene expression, that is, capable of delivering a nucleotide sequence to, or directly into, a target cell whereupon the formulation containing the nucleotide sequence is incorporated on the cytoplasmic side of the outermost membrane of the target cell and capable of achieving gene expression so that detectable levels of gene expression of the delivered nucleotide sequence are expressed in the target cell. More preferably, after delivery into the cytoplasmic side of the cell membrane the composition is subsequently transported, without undergoing endosomal or lytic degradation, into the nucleus of the target cell in a functional state capable of achieving gene expression so that detectable levels of gene expression of the delivered nucleotide sequence are expressed in the target cell. Expression levels of the gene or nucleotide sequence inside the target cell are capable of providing gene expression for a duration of time and in an amount such that the nucleotide product therein is capable of providing a biologically beneficially effective amount of gene product or in such an amount as to provide a functionally beneficial biological effect on the target cell. As used herein, the term formulation can refer to, but is not limited by (either explicitly or implicitly) the following examples: (1) liposome or liposome formulations or liposomal compositions either cationic, anionic or neutral in net character and net charge; (2) -14-

DNA, nucleic acid or a nucleic acid expression vector ionically complexed with a polycation/s and a ligand/s such that after attachment of the [DNA + Polycation + Ligand] composition to a cell surface receptor on a target cell via the ligand, the [DNA + Polycation + Ligand] composition is capable of being endocytosed into the target cell and the DNA is subsequently decoupled from the ligand and polycation and delivered to the cell nucleus in a functional condition for subsequent expression. Various alterations in the composition can be envisioned by those of ordinary skill in the art such as including peptide sequences which (a) protect the composition from endosomal lysis after incoφoration into the target cell by allowing the composition to leave the lysosomal vesicle, or (b) which act as a nuclear targeting agent, chaperoning the nucleic acid through the pores of the nuclear envelope and into the nucleus of the cell. Similar formulations, which have been previously described, are the asialoglycoprotein-polylysine conjugation (Wu and Wu, J. Biol. Chem. 263:14621. 1988; Wu et al, J. Biol. Chem. 264:16985, 1989); One of ordinary skill in the art would realize that the C 1 q ligand could be adopted to such formulations to enhance gene delivery to endothelial cells, macrophages and monocytes; (3) naked nucleic acid; (4) compacted nucleic acid or a compacted formulation; or (5) plasmid or naked DNA which can be microinjected (Wolff et al, Science 247:1465. 1990); (6) nucleic acid in a viral or retroviral vector compositions; and (7) colloidal dispersions (Feigner et al, Proc. Natl. Acad. Sci. USA 84:7413, 1987; Ono et al, Neuroscience Lett. 117:259, 1990; Brigham et al, Am. J. Med. Sci. 298:278, 1989; Staubinger and Papahadjopoulos, Meth. Enz. 101:512. 1983). One of ordinary skill in the art will recognize that other compositions for the delivery of nucleotide sequences to target cells may be envisioned.

"Gene delivery" means transportation or transfer of a composition or formulation inside of or into contact with a target cell so that the composition or formulation is capable of being taken up by means of a cytotic process (i.e., pinocytosis, endocytosis, phagocytosis, macrocytosis etc.) into the interior or cytoplasmic side of the outermost cell membrane of the target cell where it can subsequently be transported into the nucleus of the cell in such functional condition that it is capable of achieving -15-

detectable gene expression for a period of time and in such an amount to produce a detectable biologically beneficial effect.

"Gene expression" means the process, after delivery into a target cell, by which a nucleotide sequence undergoes successful transcription and translation such that detectable levels of the delivered nucleotide sequence are expressed in an amount and over a time period so that a functional biological effect is achieved. As used herein, gene expression can refer to, but is not restricted by (either explicitly or implicitly) the following examples. A ClqR_P nucleic acid sequence is delivered and expressed in targeted cells such that the targeted cells increase, decrease, or are inhibited in the production of ClqR_P protein or ClqR_P RNA, thus: either enhancing phagocytosis, inhibiting phagocytosis, enhancing the complement portion of the immune system or dampening the complement portion of the immune system and subsequently leading to a beneficially detectable biological effect or outcome.

"Expressible genetic construct" means a construct which has the ClqR_P gene positioned for expression.

"Operably linked" means that a gene and a regulatory sequence(s) are connected to permit expression of the ClqR_P gene when the appropriate molecules (e.g., transcriptional activator proteins) are bound to the regulatory sequence(s).

"Transformed" means a cell into which (or into an ancestor of which) has been introduced, by means of recombinant nucleic acid techniques, a heterologous nucleic acid molecule. "Heterologous" refers to a nucleic acid sequence that either originates from another species or is modified from either its original form or the form primarily expressed in the cell.

"Transgene" means any piece of DNA which is inserted by artifice into a cell, and becomes part of the genome of the organism (i.e., either stably integrated or as a stable extrachromosomal element) which develops from that cell. Such a transgene may -16-

include a gene which is partly or entirely heterologous (i. e. , foreign) to the transgenic organism, or may represent a gene homologous to an endogenous gene of the organism. Included within this definition is a transgene created by the providing of an RNA sequence which is transcribed into DNA and then incorporated into the genome. The term "transgenic" as used herein additionally includes any organism whose genome has been altered by in vitro manipulation of the early embryo or fertilized egg or by any transgenic technology to induce a specific gene knockout. The term "gene knockout" as used herein, refers to the targeted disruption of a gene in vivo with complete loss of function that has been achieved by any transgenic technology familiar to those in the art. In one embodiment, transgenic animals having gene knockouts are those in which the target gene has been rendered nonfunctional by an insertion targeted to the gene to be rendered non-functional by homologous recombination. As used herein, the term "transgenic" includes any transgenic technology familiar to those in the art which can produce an organism carrying an introduced transgene or one in which an endogenous gene has been rendered nonfunctional or "knocked out."

"Promoter" means the minimal nucleotide sequence sufficient to direct transcription. Also included in the invention are those promoter elements that are sufficient to render promoter-dependent gene expression controllable for cell-type specific, tissue specific, or inducible by external signals or agents; such elements may be located in the 5 ' or 3' regions of the native gene.

"Detectably-labeled" means any means for marking and identifying the presence of a molecule, e.g., an oligonucleotide probe or primer, an antibody or fragment thereof, a protein or fragment thereof, a gene or fragment thereof, or a cDNA molecule. Methods for detectably-labeling are well known in the art and include, without limitation, radioactive labeling (e.g., with an isotope such as ³²P or ³⁵S) and nonradioactive labeling (e.g., chemiluminescent labeling, fluorescent labeling). -17-

"Purified antibody" means antibody which is at least 60%, by weight, free from proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably 90%, and most preferably at least 99%), by weight, antibody, e.g. , a ClqR_P specific antibody. A purified antibody may be obtained, for example, by affinity chromatography using recombinantly-produced protein or conserved motif peptides and standard techniques. The invention can employ not only intact monoclonal or polyclonal antibodies, but also an immunologically-active antibody fragment, such as a Fab, Fab' or (Fab')₂ fragment, or a genetically engineered Fv fragment (Ladner et αl , U.S. Patent No. 4,946,788).

"Specifically binds" means an antibody which recognizes and binds a specified protein but which does not substantially recognize and bind other molecules in a sample, e.g., a biological sample, which naturally includes protein.

Due to the expression of ClqR_P in immune cells and tissue, there are a variety of applications using the polypeptide, polynucleotide, and antibodies of the invention, related to these cells or tissues. Such applications include treatment of disorders involving either the complement component of the immune system or immunodeficiencies. In addition, ClqR_P may be useful in various gene delivery and expression procedures, such as to enhance nucleotide uptake by endothelial cells and macrophages/monocytes.

"Therapeutically effective" as used herein, refers to an amount of formulation that is of sufficient quantity to ameliorate the state of the patient so treated. "Ameliorate" refers to a lessening of the detrimental effect of the disease state or disorder in the patient receiving the therapy. The subject of the invention is preferably a human, however, it can be envisioned that any animal can be treated in the method of the instant invention. The term "modulate" means enhance, inhibit, alter, or modify the expression or function of ClqR_P mRNA, nucleic acid, polypeptide or protein. -18-

Methods known to one of ordinary skill in the art for detecting a change in signal transduction in a cell via an extracellular receptor can be used in the invention. In one preferred embodiment, a change in signal transduction can be detected as a change in inositol phosphate levels in a cell. In another preferred embodiment, an intracellular calcium signal that is induced by activation via the ClqR_P can be measured with fluorescent calcium indicators, such as fluor3, or fura2. Such methods are well known to those of ordinary skill in the art.

The invention also provides a method for determining whether a test agent or composition modulates signal transduction in a cell. The method can be performed by (i) providing a cell that has a ClqR_P; (ii) contacting the cell with a test agent or composition and a ligand that, in the absence of the test agent or composition, activates the ClqR_P in the cell; and (iii) detecting a change in the cell. In practicing the invention, the cell can be contacted with the test agent or composition and ligand either simultaneously or sequentially. An increase in signal transduction indicates that the test agent or composition is an agonist of the ClqR_P while a decrease in signal transduction indicates that the test agent or composition is an antagonist of the ClqR_P. If desired, the above-described method for identifying ligands can be used to identify ligands of ClqR_P for use in this aspect of the invention. Any agent or composition can be used as a test agent or composition in practicing the invention; a preferred test agent or composition includes polypeptides and small organic agent or compositions. Although sequence or structural homo logy can provide a basis for suspecting that a test agent or composition can modulate the ClqR_P in a cell, randomly chosen test agent or compositions also are suitable for use in the invention. Art-known methods for randomly generating an agent or compositions (e.g., expression of polypeptides from nucleic acid libraries) can be used to produce suitable test agent or compositions. Those skilled in the art will recognize alternative techniques can be used in lieu of the particular techniques described herein. -19-

The invention also provides a method for detecting novel ligands which bind ClqR_P which comprises contacting a sample comprising the ClqR_P with test compositions and measuring the interaction of the receptor with the test composition.

The ClqR_P protein of the instant invention is useful in a screening method for identifying test compounds or test compositions which affect the binding to the ClqRp. Thus, in another embodiment, the invention provides a method for screening test compositions comprising incubating components, which include the test composition, the ClqR_P and the ligand of the ClqR_P, under conditions sufficient to allow the components to interact, then subsequently measuring the effect the test composition has on the formation of the affinity complex. Such screening identification can be supplied in the form of a kit as discussed above. The observed effect on the formation of the affinity complex between the ClqR_P and its ligand may be either agonistic or antagonistic. Preferably, the polypeptide encoding the ClqR_P is the polypeptide or functional fragment thereof of SEQ ID NO: 1 or SEQ ID NO: 34, or a synthetic peptide which has the biological activity of the ClqR_P protein. Methods for measuring the effect of the composition on the binding of the ligand to the ClqR_P will be known to those of ordinary skill in the art. For example, the effect of binding of a ligand to the ClqR_P can be analyzed by measuring the internalization of radiolabeled or photoaffinity labeled Clq protein.

The invention also includes fragments of ClqR_P polypeptides, that retain at least one ClqRp-specific activity or epitope. For example, a ClqR_P polypeptide fragment containing, e.g., at least 8-10 amino acids, can be used as an immunogen in the production of ClqR_p-specific antibodies. Such fragments can easily be identified by comparing the sequence of ClqR_p by reference to Figure 3. In addition to their use as peptide immunogens, ClqR_p fragments can be used in immunoassays, such as ELISAs, to detect the presence of ClqR_p-specific antibodies in samples.

The ClqRp polypeptides of the invention can be obtained using any of several standard methods. For example, ClqR_p polypeptides can be produced in a standard -20-

recombinant expression systems (see below), chemically synthesized (this approach may be limited to small ClqR_P peptide fragments), or purified from tissues in which they are naturally expressed (see, e.g., Ausubel, et al, supra).

The invention also provides isolated nucleic acid molecules that encode the ClqR_P 5 polypeptides described above, as well as fragments thereof. These nucleic acids can contain naturally occurring nucleotide sequences (see Figure 3), or sequences that differ from those of the naturally occurring nucleic acids that encode ClqR_Ps, but encode the same amino acids, due to the degeneracy of the genetic code or amino acids which are conservative variations. The nucleic acids of the invention can 10 contain DNA or RNA nucleotides, or combinations or modifications thereof.

The nucleic acid molecules of the invention can be used as templates in standard methods for production of ClqR_P gene products (e.g., ClqR_P and ClqR_P polypeptides; see below). In addition, the nucleic acid molecules that encode ClqR_P polypeptides (and fragments thereof) and related nucleic acids, such as (1) nucleic

15 acids containing sequences that are complementary to, or that hybridize to, nucleic acids encoding ClqR_P polypeptides, or fragments thereof (e.g., fragments containing at least 9, 12, 15, 20, or 25 nucleotides); and (2) nucleic acids containing sequences that hybridize to sequences that are complementary to nucleic acids encoding ClqR_P polypeptides, or fragments thereof (e.g., fragments containing at least 9, 12, 15, 20, or

20 25 nucleotides); can be used in methods focused on their hybridization properties. For example, as is described in further detail below, such nucleic acid molecules can be used in the following methods: PCR methods for synthesizing ClqR_P nucleic acids, methods for detecting the presence of a ClqR_P nucleic acid in a sample, screening methods for identifying nucleic acids encoding new ClqR_P family members, and

25 therapeutic methods. The invention further provides an isolated nucleic acid molecule the sequence of which being at least about 65% identitical to SEQ ID NO:l or 34 and encoding a polypeptide having a biological activity associated with ClqR_p and about 65%, more preferably 75% similar. -21-

The invention also includes methods for identifying nucleic acid molecules that encode members of a ClqR_P polypeptide family. In these methods, a sample, e.g., a nucleic acid library, such as a cDNA library, that contains a nucleic acid encoding a ClqRp polypeptide is screened with a ClqRp-specific probe, e.g., a ClqRp-specific nucleic acid probe. ClqR_P-specifιc nucleic acid probes are nucleic acid molecules (e.g., molecules containing DNA or RNA nucleotides, or combinations or modifications thereof) that specifically hybridize to nucleic acids encoding ClqR_P polypeptides, or to complementary sequences thereof. The term "ClqR_P-specific probe," in the context of this method of invention, refers to probes that bind to nucleic acids encoding ClqR_P polypeptides, or to complementary sequences thereof, to a detectably greater extent than to nucleic acids encoding homologous ClqR_P receptor family sequences, or to complementary sequences thereof. The term "ClqRp-specific probe" thus includes probes that can bind to nucleic acids encoding ClqR_P polypeptides (or to complementary sequences thereof), but not to nucleic acids encoding homologous ClqR_P receptor family sequences (or to complementary sequences thereof), to an appreciable extent.

The invention facilitates production of ClqR_P-specifιc nucleic acid probes. Methods for obtaining such probes can be designed based on the amino acid sequence alignments shown in Figure 3. The probes, which can contain at least 9, e.g., at least 12, 15, 25, 35, 50, 100, or 150 nucleotides, can be produced using any of several standard methods (see, e.g., Ausubel, et al, supra). For example, preferably, the probes are generated using PCR amplification methods, such as those described below. In these methods, primers are designed that correspond to ClqR_P sequences, which can include ClqRp-specific amino acids, and the resulting PCR product is used as a probe to screen a nucleic acid library, such as a cDNA library.

As is known in the art, PCR primers are typically designed to contain at least 15 nucleotides, for example 15-30 nucleotides. The design of ClqR_P-specifιc primers containing 21 nucleotides, which encode ClqR_p peptides containing 7 amino acids, are described as follows. Preferably, most or all of the nucleotides in such a probe -22-

encode ClqR_P-conserved amino acids, including ClqR_P-specific amino acids. For example, primers containing sequences encoding for at least 40% ClqR_P-conserved amino acids can be used. Such a primer, containing 21 nucleotides, can include nucleotide sequences encoding for at least 3 out of 7 ClqR_P-conserved amino acids or 4 out of 7, or 5 out of 7 ClqR_P-conserved amino acids. As can be determined by analysis of Figure 3, in the case of a 21 nucleotide primer, encoding 7 amino acids, up to 5 amino acids can be ClqR_P-specific. Thus, the primer can contain sequences encoding at least one ClqRp-specific amino acid, for example, up to 5 ClqR_p-specific amino acids. Once ClqRp-specific amino acid sequences are selected as templates against which primer sequences are to be designed, the primers can be synthesized using, e.g., standard chemical methods. As is described above, due to the degeneracy of the genetic code, such primers should be designed to include appropriate degenerate sequences, as can readily be determined by one skilled in the art.

Based on the guidelines presented above, examples of ClqR_P-conserved amino acid peptides that can be used as templates for the design of C 1 qR_P-specific primers. Additional examples can be found by analysis of sequence alignments of ClqR_P polypeptides. Primers can be designed, for example, based on 5-10 amino acid regions of the ClqR_P peptide, depending on the lengths of the primers desired. It is understood that such primers can be designed based on the available human or murine amino acid or nucleic acid sequences. The following are provided as illustrative examples of amino acid segments useful for designing primers:

1. PK Y G C N F N N G G C H Q D C F E G G D G S F L C G C R P GFRLLD DLVTCA (SEQ ID NO.: 2) (corresponding to amino acids 260-301 of human ClqR_P EGF-1)

2. S RNP C S S S P CRGGATCVLGPHGKNYTC RC P

Q GYQ LD S S QLD CV (SEQ ID NO.: 3) (corresponding to amino acids 302-344 of human ClqR_P-EGF-2)

3. DVDE C QD S P CA Q E CVNTP G GF RC E C WV GY EPGGP GEGACQ (SEQ ID NO.: 4) (corresponding to amino acids 345-384 of human ClqR_P-EGF-3) -23-

4. GGP GQVTYTTPF Q TT S S S LEAVP FA S AANV

A C GE (SEQ ID NO.: 5)

(corresponding to amino acids 194-227 of human ClqR_P-l) For example, a specific primer based on this PCR product, SEQ ID NO.:29, 5'CAAGGAGGAACTGGTGGTCTGG-3', and a degenerate primer based on the sequenced amino terminus starting at amino acid 2, 5'- GGIGCIGA(tc)ACIGA(ag)GC-3', were designed and used to amplify by RT- PCR a cDNA corresponding to the amino terminus of the ClqR_P protein from U937 cDNA.

5. D V D E C A L G R S P C A Q G C T N T D G S F H C S C E E GYVLAGED GTQ C Q (SEQ ID NO.: 6; corresponding to amino acids 385-426 of human ClqR_P-EGF-4)

6. LLLFYILGTVVAILLLLALAL GLLV (SEQ ID NO.:

7) (corresponding to amino acids 581 -605 of human C 1 qR_P- Transmembrane)

7. DV D E CV GP GGPL C D S L C F N T Q G S F H C G C L P G W V L A P N G V S C T (SEQ ID NO.: 8; corresponding to amino acids 427-468 of human ClqR_P-EGF-5)

8. YRKRRAKREEKKEKKPQNAADSYSWVPE RAESRAMENQYSPTPGTDC (SEQ IDNO.: 9; corresponding to amino acids 606-652 of human ClqR_P- cytoplasmic tail)

As is described above, ClqR_P-specific primers, for example primers based on the ClqR_P-specifιc peptides shown above, or portions thereof, can be used in PCR reactions to generate ClqRp-specific probes, which can be used in standard screening methods to identify nucleic acids encoding ClqR_P family members (see, e.g., Ausubel, et al, supra).

In addition to ClqRp-specific nucleic acid probes, ClqR_P-specifιc polypeptide probes, such as ClqRp-specific antibodies, can be used to screen samples, e.g., expression libraries, for nucleic acids encoding novel ClqR_P polypeptides, or portions thereof. For example, an antibody that specifically binds to a ClqR_P-specifιc peptide can be used in this method. Methods for carrying out such screening are well known in the art (see, e.g., Ausubel, et al, supra). -24-

The sequences of a pair of nucleic acid molecules (or two regions within a single nucleic acid molecule) are said to be "complementary" to each other if base pairing interactions can occur between each nucleotide of one of the members of the pair and each nucleotide of the other member of the pair. A pair of nucleic acid molecules (or two regions within a single nucleic acid molecule) are said to "hybridize" to each other if they form a duplex by base pairing interactions between them. As is known in the art, hybridization between nucleic acid pairs does not require complete complementarity between the hybridizing regions, but only that there is a sufficient level of base pairing to maintain the duplex under the hybridization conditions used.

Hybridization reactions are typically carried out under low to moderate stringency conditions, in which specific and some non-specific interactions can occur. After hybridization, washing can be carried out under moderate or high stringency conditions to eliminate non-specific binding. As is known in the art, optimal washing conditions can be determined empirically, e.g., by gradually increasing the stringency. Condition parameters that can be changed to affect stringency include, e.g. , temperature and salt concentration. In general, the lower the salt concentration and the higher the temperature, the higher the stringency. For example, washing can be initiated at a low temperature (e.g., room temperature) using a solution containing an equivalent or lower salt concentration as the hybridization solution. Subsequent washing can be carried out using progressively warmer solutions having the same salt solution. Alternatively, the salt concentration can be lowered and the temperature maintained in the washing step, or the salt concentration can be lowered and the temperature increased. Additional parameters can be altered to affect stringency, including, e.g., the use of a destabilizing agent, such as formamide.

In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting -25-

hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.

An example of progressively higher stringency conditions is as follows: 2 x SSC/0.1% SDS at about room temperature (hybridization conditions); 0.2 x SSC/0.1% SDS at about room temperature (low stringency conditions); 0.2 x SSC/0.1% SDS at about 42 °C (moderate stringency conditions); and 0.1 x SSC at about 68 °C (high stringency conditions). Washing can be carried out using only one of these conditions, e.g., high stringency conditions, or each of the conditions can be used, e.g., for 10-15 minutes each, in the order listed above, repeating any or all of the steps listed. However, as mentioned above, optimal conditions will vary, depending on the particular hybridization reaction involved, and can be determined empirically.

The nucleic acid molecules of the invention can be obtained by any of several standard methods. For example, the molecules can be produced using standard recombinant, enzymatic (e.g. , PCR or reverse transcription (RTVPCR methods), and chemical (e.g., phosphoramidite-based synthesis) methods. In addition, they can be isolated from samples, such as nucleic acid libraries and tissue samples, using standard hybridization methods. For example, as described above, using standard methods, genomic or cDNA libraries can be hybridized with nucleic acid probes corresponding to ClqR_P nucleic acid sequences to detect the presence of a homologous nucleotide sequence in the library (see, e.g., Ausubel, et al, supra). These methods are described in more detail above. Also as described above, nucleic acids encoding polypeptides containing at least one ClqR_P epitope, such as a ClqRp- specific epitope, can also be identified by screening a cDNA expression library, such as a library contained in lambda gtl 1 , with a C 1 qR_P-specific antibody as a probe. Such antibodies can be either polyclonal or monoclonal and are produced using standard methods (see, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1988). -26-

ClqRp-specific antibodies and nucleic acids can be used as probes in methods to detect the presence of a ClqR_P polypeptide (using an antibody) or nucleic acid (using a nucleic acid probe) in a sample, such as a biological fluid (e.g., synovial fluid , such as an arthritic joint) or a tissue sample (e.g., CNS tissue, thymus tissue or endothelial tissue). In these methods, a ClqR_P-specifιc antibody or nucleic acid probe is contacted with a sample from a patient suspected of having a ClqR_P-associated disorder, and specific binding of the antibody or nucleic acid probe to the sample detected. The level of ClqR_P polypeptide or nucleic acid present in the suspect sample can be compared with the level in a control sample, e.g., an equivalent sample from an unaffected individual, to determine whether the patient has a ClqR_P- associated disorder. ClqR_P polypeptides, or fragments thereof, can also be used as probes in diagnostic methods, for example, to detect the presence of ClqRp-specific antibodies in samples. Additionally, ClqRp-specific antibodies could be used to detect novel ligands which have formed an affinity complex with a ClqR_P receptor or fragment thereof.

The ClqRp-specific nucleic acid probes can be labeled with a compound that facilitates detection of binding to the ClqR_P nucleic acid in the sample. For example, the probe can contain biotinylated nucleotides, to which detectably labeled avidin conjugates (e.g., horse-radish peroxidase-conj ugated avidin) can bind. Radiolabeled nucleic acid probes can also be used. These probes can be used in nucleic acid hybridization assays to detect altered levels of ClqR_Ps in a sample. For example, in situ hybridization, RNase protection, and Northern Blot methods can be used. Other standard nucleic acid detection methods that can be used in the invention are known to those of skill in the art (see, e.g., Ausubel, et al, supra). In addition, when the diagnostic molecule is a nucleic acid, it can be amplified prior to binding with a ClqR_P-specifιc probe. Preferably, PCR is used, but other nucleic acid amplification methods, such as the ligase chain reaction (LCR), ligated activated transcription (LAT), and nucleic acid sequence-based amplification (NASBA) methods can be used. -27-

Additionally, ClqR_P-specifιc nucleic acid probes could be used to detect unique polypeptide expression clones from nucleic acid libraries such as expression libraries for fragments of the ClqR_P nucleic acid sequence or homologues of the ClqR_P nucleic acid sequence. ClqRp-specific nucleic acid probes could be used to detect expression clones used to randomly generate compounds (e.g., expression of polypeptides from nucleic acid libraries) that can be used to produce suitable test compounds of the instant invention. A cDNA expression library can be screened indirectly for ClqR_P peptides having at least one epitope, using antibodies specific for ClqRp as described herein. Such antibodies can be either polyclonally or monoclonally derived and used to detect expression product indicative of the presence of ClqRp cDNA.

Specifically disclosed herein is a 3.46 Kb cDNA sequence containing the active portion of the human ClqR_P coding sequence and the 4.062 Kb cDNA sequence of the murine ClqR_P coding sequence. The cDNA clones from which these sequences were obtained contain the entire coding sequence for ClqR_P. The amino acid sequence disclosed for human ClqR_P includes a C-type carbohydrate recognition domain at the N-terminus, five Epidermal Growth Factor (EGF)-like domains, including three calcium binding (cb) EGF domains, a single transmembrane (TM) domain and a cytoplasmic tail. A putative N-linked glycosylation site is located within the second EGF domain at amino acid position N325. The predicted molecular weight of the mature protein Clq based on the amino acid sequence is 66,495 Da. The cDNA and deduced amino acid sequence of ClqR_P are shown in Figure 3. Nucleotides and amino acids are numbered based on the initiator methionine.

The polynucleotide encoding ClqR_P includes the nucleotide sequence in Figure 3 (SEQ ID NO: 1) and Figure 8 (SEQ ID NO:34), as well as nucleic acid sequences complementary to those sequences. A complementary sequence may include an antisense nucleotide. When the sequence is RNA, the deoxynucleotides A, G, C, and T of Figure 3 are replaced by ribonucleotides A, G, C, and U, respectively. Also included in the invention are fragments of the above-described nucleic acid sequences -28-

that are at least 9 bases in length, which is sufficient to permit the fragment to selectively hybridize to DNA that encodes the protein of Figure 3 (SEQ ID NO: 2) or Figure 8 (SEQ ID NO:35) under physiological conditions.

DNA sequences of the invention can be obtained by several methods. For example, the DNA can be isolated using hybridization techniques which are well known in the art. These include, but are not limited to: 1) hybridization of genomic or cDNA libraries with probes to detect homologous nucleotide sequences, 2) polymerase chain reaction (PCR) on genomic DNA or cDNA using primers capable of annealing to the DNA sequence of interest, and 3) antibody screening of expression libraries to detect cloned DNA fragments with shared structural features. Therefore, given a partial DNA sequence of the gene of interest, one of skill in the art would be able to prepare probes for isolation of a full length cDNA clone, without undue experimentation (see e.g., Ausubel, et al, Current Protocols in Molecular Biology, Units 6.3-6.4, Greene Publ., current edition; Maniatis, et al, Molecular Cloning, Cold Spring Harbor Laboratories, current edition).

The development of specific DNA sequences encoding ClqR_P can also be obtained by: 1) isolation of double-stranded DNA sequences from the genomic DNA; 2) chemical manufacture of a DNA sequence to provide the necessary codons for the polypeptide of interest; and 3) in vitro synthesis of a double-stranded DNA sequence by reverse transcription of mRNA isolated from a eukaryotic donor cell. In the latter case, a double-stranded DNA complement of mRNA is eventually formed which is generally referred to as cDNA.

DNA sequences encoding ClqR_P can be expressed in vitro, in vivo or ex vivo by DNA transfer into a suitable target cell. "Target cells" are cells in which a vector can be propagated and its DNA expressed or in which a formulation can be delivered into a cell for subsequent gene expression. The term also includes any progeny of the subject target cell. It is understood that all progeny may not be identical to the parental cell since there may be mutations that occur during replication. However, -29-

such progeny are understood to be included when the term "target cell" is used. Methods of stable transfer, meaning that the foreign DNA is continuously maintained in the host, are known in the art. Determination of ClqR_P mRNA expression levels in targeted cells can be determined by one of ordinary skill in the art by comparing either or both C 1 qR_P RNA or C 1 qR_P protein levels before and after treatment of the target cells. Such methods of analysis employing techniques like Northern or Western analysis are common in the art. Other common techniques to determine levels of RNA or protein in such ClqR_? target cells will be known to those in the art.

In the present invention, the ClqR_P polynucleotide sequences may be inserted into a recombinant expression vector. The term "recombinant expression vector" refers to a plasmid, virus or other vehicle known in the art that has been manipulated by insertion or incoφoration of the ClqR_P genetic sequences. Such expression vectors contain a promoter sequence which facilitates the efficient transcription of the inserted genetic sequence of the host. The expression vector typically contains an origin of replication, a promoter, as well as specific genes which allow phenotypic selection of the transformed cells. Vectors suitable for use in the present invention include, but are not limited to the T7-based expression vector for expression in bacteria (Rosenberg et al, Gene 56:125, 1987), the pMSXND expression vector for expression in mammalian cells (Lee and Nathans, J. Biol. Chem. 263:3521. 1988) and baculovirus-derived vectors for expression in insect cells. The DNA segment can be present in the vector operably linked to regulatory elements, for example, a promoter (e.g., 11, metallothionein I, or polyhedrin promoters).

Polynucleotide sequences encoding ClqR_P can be expressed in either prokaryotes or eukaryotes. Hosts can include microbial, yeast, insect and mammalian organisms. Methods of expressing DNA sequences having eukaryotic or viral sequences in prokaryotes are well known in the art. Biologically functional viral and plasmid DNA vectors capable of expression and replication in a target cell are known in the art. Such vectors are used to incoφorate DNA sequences of the invention. -30-

Transformation of a target cell with recombinant DNA may be carried out by conventional techniques as are well known to those skilled in the art. Where the target is prokaryotic, such as E. coli, competent cells which are capable of DNA uptake can be prepared from cells harvested after their exponential growth phase and subsequently treated by the CaCl₂ method using procedures well known in the art. Alternatively, MgCl₂ or RbCl can be used. Transformation can also be performed after forming a protoplast of the target cell if desired.

When the target cell is a eukaryote, such methods of transfection of DNA as calcium phosphate co-precipitates, conventional mechanical procedures such as microinj ection, electroporation, insertion of a plasmid encased in liposome or liposome formulations, or virus vectors may be used. Eukaryotic cells can also be co- transformed with DNA sequences encoding the ClqR_P of the invention, and a second foreign DNA molecule encoding a selectable phenotype, such as the heφes simplex thymidine kinase gene. Another method of transformation is to use a eukaryotic viral vector, such as simian virus 40 (SV40) or bovine papilloma virus, to transiently infect or transform eukaryotic cells and express the protein, (see e.g., Eukaryotic Viral Vectors, Cold Spring Harbor Laboratory, Gluzman ed., 1982).

Isolation and purification of microbial expressed ClqR_P polypeptide, or fragments, or conservative variants thereof, provided by the invention, may be carried out by conventional means including preparative chromatography and immunological separations involving monoclonal or polyclonal antibodies.

The ClqRp polypeptides of the invention can also be used to produce antibodies which are immunoreactive or bind to epitopes of ClqR_P polypeptides. Antibody which consists essentially of pooled monoclonal antibodies with different epitopic specificities, as well as distinct monoclonal antibody preparations are provided. Monoclonal antibodies are made from antigen containing fragments of the ClqR_P protein by methods well known in the art (Kohler et al, Nature 256:495, 1975; Current Protocols in Molecular Biology, Ausubel et al, ed., 1989). -31-

The term "antibody" as used in this invention includes intact molecules as well as fragments thereof, such as Fab, Fab', F(ab')₂, and Fv which are capable of binding the epitopic determinant. These antibody fragments retain some ability to selectively bind with its antigen or receptor and are defined as follows:

(1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain;

(2) Fab', the fragment of an antibody molecule can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab' fragments are obtained per antibody molecule;

(3) (Fab')₂, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab')₂ is a dimer of two Fab' fragments held together by two disulfide bonds;

(4) Fv, defined as a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and

(5) Single chain antibody ("SCA"), defined as a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule.

Methods of making these fragments are known in the art. (See for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (current edition), incoφorated herein by reference). -32-

As used in this invention, the term "epitope" means any antigenic determinant on an antigen to which the paratope of an antibody binds. Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteris- tics, as well as specific charge characteristics.

Antibodies which bind to the ClqR_P polypeptide of the invention can be prepared using an intact polypeptide or fragments containing small peptides of interest as the immunizing antigen. The polypeptide or peptide used to immunize an animal can be derived from translated cDNA or chemical synthesis which can be conjugated to a carrier protein, if desired. Such commonly used carriers which are chemically coupled to the peptide include keyhole limpet hemocyanin (KLH), thyroglobulin, bovine serum albumin (BSA), and tetanus toxoid. The coupled peptide is then used to immunize the animal (e.g., a mouse, rat, goat, sheep or rabbit).

If desired, polyclonal or monoclonal antibodies can be further purified, for example, by binding to and elution from a matrix to which the polypeptide or a peptide to which the antibodies were raised is bound. Those of skill in the art will know of various techniques common in the immunology arts for purification and/or concentration of polyclonal antibodies, as well as monoclonal antibodies (See e.g., Coligan, et al, Unit 9, Current Protocols in Immunology, Wiley Interscience, current edition, incoφorated by reference).

It is also possible to use the anti-idiotype technology to produce monoclonal antibodies which mimic an epitope. For example, an anti-idiotypic monoclonal antibody made to a first monoclonal antibody will have a binding domain in the hypervariable region which is the "image" of the epitope bound by the first mono- clonal antibody.

The present invention identifies a nucleotide sequence that can be expressed in an altered manner as compared to expression in a normal cell, therefore it is possible to -33-

design appropriate therapeutic or diagnostic techniques directed to this sequence. Thus, where a disorder is associated with the altered expression of ClqR_P, nucleic acid sequences that interfere with ClqR_P expression at the transcriptional or translational level can be used. This approach utilizes, for example, antisense, missense or nonsense, nucleic acid and ribozymes to block translation of a specific ClqRp mRNA, either by masking that mRNA with an antisense nucleic acid or by cleaving it with a ribozyme. Such ClqR_P disorders may include diseases such as vasculitis and sepsis, for example. One of ordinary skill in the art can determine without undue experimentation if the delivery and expression of ClqR_P mRNA in target cells has altered the level of ClqR_p polypeptide or nucleic acid by comparing the levels of ClqR_P polypeptide or nucleic acid present in ClqR_P target cells before and after treatment or by comparing target cells with equivalent non-target controls. Such techniques as Northern or Western analysis are common to those in the art and would be useful in making such determinations. Although, other techniques useful for such comparisons are commonly known to one of ordinary skill in the art.

Antisense nucleic acids are DNA or RNA molecules that are complementary to at least a portion of a specific mRNA molecule (Weintraub, Scientific American 262:40. 1990). In the cell, antisense nucleic acids hybridize to a corresponding mRNA, forming a double-stranded molecule. The antisense nucleic acids interfere with the translation of the mRNA, since the cell will not translate a mRNA that is double- stranded. Antisense oligomers of about 15 nucleotides are preferred, since they are easily synthesized and are less likely to cause problems than larger molecules when introduced into the target ClqR_P-producing cell. The use of antisense methods to inhibit the in vitro translation of genes is well known in the art (Marcus-Sakura, Anal. Biochem. 172:289, 1988).

Ribozymes are RNA molecules possessing the ability to specifically cleave other single-stranded RNA in a manner analogous to DNA restriction endonucleases. Through the modification of nucleotide sequences which encode these RNAs, it is possible to engineer molecules that recognize specific nucleotide sequences in an -34-

RNA molecule and cleave it (Cech, Amer. Med. Assn. 260: 3030, 1988). A major advantage of this approach is that, because they are sequence-specific, only mRNAs with particular sequences are inactivated.

The present invention also provides gene delivery and gene expression for disorders mediated by ClqR_P protein. Such gene delivery and gene expression achieves its beneficial effect by altering the levels of ClqR_P mRNA in a cell. This may entail delivery and expression of ClqR_P antisense to target cells or the delivery and expression of heterologous ClqR_P receptors to target cells to enhance the function of the Clq component of the immune system. Delivery and expression of ClqR_P nucleic acid can be achieved by a variety of means known to those in the art. A preferred means is using a recombinant expression vector such as a chimeric virus or a colloidal dispersion system. Especially preferred for therapeutic delivery of antisense sequences is the use of formulations containing liposome or liposome formulations or liposomal-like agents capable of being targeted to particular cells or receptors. Various viral vectors which can be utilized for gene therapy as taught herein include adenovirus, heφes virus, vaccinia, or, preferably, an RNA virus such as a retrovirus.

Another targeted delivery system for ClqR_P antisense polynucleotides is a colloidal dispersion system. Colloidal dispersion systems include macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposome or liposome formulations. The preferred colloidal system of this invention is a liposome or liposomal formation. Liposome or liposome formulations are artificial membrane vesicles or formulations containing liposomal compositions that can be complexed with other compositions. These formulations may have net cationic, anionic or neutral charge characteristics are useful characteristics with in vitro, in vivo and ex vivo delivery methods.

It has been shown that large unilamellar vesicles (LUV), which range in size from 0.2- 4.0 μm can encapsulate a substantial percentage of an aqueous buffer containing large macromolecules. RNA, DNA and intact virions can be encapsulated within the -35-

aqueous interior and be delivered to cells in a biologically active form (Fraley et al, Trends Biochem. Sci. 6:77, 1981). Additionally, non-membrane bound liposomal formulations can be used for delivery and expression of nucleic acids (Feigner et al, Proc. Natl. Acad. Sci. USA 84: 7413, 1987). In addition to mammalian cells, liposome or liposome formulations have been used for delivery of polynucleotides in plant, yeast and bacterial cells. For a liposome or liposome formulation to be an efficient gene transfer vehicle, the following characteristics should be present: (1) encapsulation of the genes of interest at high efficiency while not compromising their biological activity; (2) preferential and substantial binding to a target cell in comparison to non-target cells; (3) delivery of the aqueous contents of the vesicle or of the nucleic acid of the formulation to the target cell cytoplasm at high efficiency without degradation and in a functional state capable of permitting gene expression at such levels as to achieve a detectable biological effect; and (4) accurate and effective expression of genetic information which has been delivered (Mannino et al, Biotechniques 6:682, 1988).

A well-characterized "on/off" switch for use in a recombinant expression vector is the antibiotic (tetracycline) regulated promoter system. Means for construction of such a system are well-known in the art; for review in this regard, those of skill in the art may wish to consult Furth et al, Proc. Natl. Acad. Sci. USA, 91 :9302, 1994 (tetracycline regulated control of gene expression in transgenic mice).

In addition, a transgenic animal model can be developed which is especially predictive of the impact on the defense/clearance system in which ClqR_p activity has been increased or decreased according to the method of the invention. Protocols useful in producing such ClqR_p transgenic animals are described below. The protocol generally follows conventional techniques for introduction of expressible transgenes into mammals. Those of ordinary skill in the art will be familiar with these applications and will be able to apply the techniques in the context of the present invention without undue experimentation. -36-

For example, embryonal target cells at various developmental stages can be used to introduce transgenes. Different methods are used depending on the stage of development of the embryonal target cell. The zygote is the best target for microinj ection. In the mouse, the male pronucleus reaches the size of approximately 20 micrometers in diameter which allows reproducible injection of l-2pl of DNA solution. The use of zygotes as a target for gene transfer has a major advantage in that in most cases the injected DNA will be incoφorated into the host gene before the first cleavage (Brinster et al, Proc. Natl. Acad. Sci. USA 82:4438, 1985). As a consequence, all cells of the transgenic non-human animal will carry the incoφorated transgene. This will in general also be reflected in the efficient transmission of the transgene to offspring of the founder since 50% of the germ cells will harbor the transgene. Microinj ection of zygotes is the preferred method for incoφorating transgenes in practicing the invention.

Retroviral infection can also be used to introduce transgene into a non-human animal. The developing non-human embryo can be cultured in vitro to the blastocyst stage. During this time, the blastomeres can be targets for retroviral infection (Jaenisch, Proc. Natl. Acad. Sci. USA 73:1260, 1976). Efficient infection of the blastomeres is obtained by enzymatic treatment to remove the zona pellucida (Hogan, et al, Manipulating the Mouse Embryo, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y, 1986). The viral vector system used to introduce the transgene is typically a replication-defective retrovirus carrying the transgene (Jahner et al, Proc. Natl. Acad. Sci. USA 82:6927, 1985; Van der Putten et al, Proc. Natl. Acad. Sci. USA 82: 6148, 1985). Transfection is easily and efficiently obtained by culturing the blastomeres on a monolayer of virus-producing cells (Van der Putten supra; Steward et al, EMBO J. 6: 383, 1987).

Alternatively, infection can be performed at a later stage. Virus or virus-producing cells can be injected into the blastocoele (Jahner et al, Nature 298: 623, 1982). Most of the founders will be mosaic for the transgene since incoφoration occurs only in a subset of the cells which formed the transgenic non-human animal. Further, the -37-

founder may contain various retroviral insertions of the transgene at different positions in the genome which generally will segregate in the offspring. In addition, it is also possible to introduce transgenes into the germ line, albeit with low efficiency, by intrauterine retroviral infection of the midgestation embryo (Jahner et al, supra).

A third type of target cell for introduction of heterologous C 1 qR_p nucleic acid sequences is the embryonal stem cell (ES). ES cells are obtained from pre- implantation embryos cultured in vitro and fused with embryos (Evans et al, Nature 292:154, 1981 ; Bradley et al, Nature 309: 255, 1984; Gossler et al, Proc. Natl. Acad. Sci. USA 83:9065, 1986; and Robertson et al, Nature 322:445, 1986). Transgenes can be efficiently introduced into the ES cells by DNA transfection or by retrovirus- mediated transduction. These transformed ES cells can thereafter be combined with blastocysts from a non-human animal. The ES cells will thereafter colonize the embryo and contribute to the germ line of the resulting chimeric animal (see for review. Jaenisch, Science 240:1468, 1988).

Construction of C 1 qR_P transgenes can be performed by those of ordinary skill in the art using the teachings concerning the ClqR_P nucleotide sequences herein. One of ordinary skill in the art can "knock out" the ClqR_P enhancement of phagocytic function in mice by targeted disruption of the murine ClqR_P gene. This can be accomplished by homologous recombination in murine embryonic stem (ES) cells using standard techniques. The clinical and cellular consequences of targeted disruption of ClqR_P can be investigated in multiple genetic backgrounds including inbred strains, strains with many undefined nonsense alleles, and strains of known mutant genotype to determine if: (a) targeted disruption of ClqR_p can effect a loss of the ClqR_P derived enhancement of phagocytic function; (b) loss of the ClqR_P enhancement of host defense and clearance of cellular or foreign debris can have an phenotype consequences (i.e., the creation of knockout phenotypes), (c) loss of the ClqRp enhancement of phagocytic function unmasks the effects of other complement components heretofore unknown. -38-

Transgenic murine cells can be generated by using a vector for ClqR_P gene targeting by homologous recombination. The vector contains a large genomic fragment of the murine ClqR_P gene. The exons can be deleted and substituted for by a Neomycin resistance expression cassette. A thymidine kinase gene can be inserted at the end of the long arm of homology to assist in the selection of bona fide-homologous recombinants. Transfection and stable selection of murine SV/129 cells will allow identification of a clonal colony of cells harboring one inactivated ClqR_P allele. These cells can be injected into mouse blastocysts to create chimeras. Chimeras can be bred to yield animals heterozygous for the targeted allele. Finally, heterozygotes can be bred to create homozygotes. Mice with characterized phenotypes can be bred to mice deficient for the ClqR_P enhancement of phagocytic function. If necessary, the identical approach of homologous recombination-based targeting of endogenous genes can then be used in cultured human cells. This would require a second phase of transfection and selection, using a different selectable marker, to target both alleles. Only minor modifications in the methods used for murine cells, all previously employed for other puφoses, will be necessary to permit one of ordinary skill in the art to completely inhibit ClqR_P expression in cultured human cells. One example of such a method of transgenic construction is described below. However, this example is not meant to be limiting as other transgenic constructions can be used which are commonly known to those in the art.

Insertion of the 1.2kb Pol H-neomycin resistance cassette into an early exon of the ClqR_P gene will disrupt the translational reading frame for ClqR_p with the creation of an in-frame premature termination codon (PTC). Insertion of the PTC in an early exon will prevent translation of the C-terminus of ClqR_P and will result in a complete loss of function. An alternate strategy is to target the very first exon eliminating the start-site for translation. N-terminal epitopes can also be used to determine whether a truncated protein is expressed from stabilized transcripts from the knockout allele. -39-

Construction of a targeting vector: A large fragment of murine ClqR_P cDNA is cloned, (-20kb) murine (129/Sv) genomic clone spanning the five Epidermal Growth Factor-like domains, and characterized. A detailed restriction map of the clone and localizing intron-exon boundaries through a combination of the subcloning of relatively large (6-12kb) restriction fragments into plasmid vector (pBlueprint II-SK) is determined, restriction analysis accompanied by Southern transfer and hybridization of radiolabeled oligonucleotide complementary to cDNA sequences, and direct sequencing of genomic subclones using cDNA primers can be done. Subsequently, a targeting vector is constructed using a (6-12kb) genomic fragment which contains the exon of interest is subcloned into a suitable plasmid. Preferably, the exon is somewhat asymmetrically placed in the insert, with a minimum of -2kb of sequence at either end (Deng, et al, Mol Cell Biol L2: 3365-71, 1992). Genomic sequences that immediately flank the insert at the 5' and 3' ends are retained for use as probes in Southern analysis to confirm homologous recombination at a later time. The 1.2kb Pol H-neomycin resistance expression cassette (Wang, et al., Nat Genet 11: 185-190, 1995) is inserted into the exon of interest using a suitable restriction site. The PGKtk expression cassette is added distal to the long arm of homology to enrich for homologous recombinants by FIAU selection (Li, et al, Cell 69: 915-26, 1992) (Andrikopoulos, et al., Nat Genet 9: 31-36 1995). The resultant construct is linearized and band-purified by CsCI₂ ultracentrifugation (Wang, et al. , Nat Genet 11: 185-190, 1995).

Additionally, recent advances in the efficiency of targeted gene delivery in cultured somatic cells can be used by one of ordinary skill in the art. Briefly, promoterless cDNAs that encode antibiotic resistance factors are used in targeting vectors such that expression can be driven by the promoter of the targeted allele upon homologous recombination. Enrichment ratios (homologous recombinants vs. random insertions) of up to 5,000 to 10,000-fold can be achieved compared to conventional methods (Hanson, et al, Mol Cell Biol 15: 45-51, 1995), thus efficiently inactivating both alleles by sequential gene targeting using two targeting vectors that contain different selectable genes. -40-

Generation of targeted mice: Pluripotent Jl ES cells derived from the inner cell mass of 129/Sv blastocysts are cultured under standard conditions (Li, et al, Cell 69: 915- 26, 1992). Approximately 1 x 10⁷ cells are transfected with 10-20μg of linearized construct by electroporation at 230mV, 500μF using a Bio-Rad Gene Pulser and are replated on a feeder layer of γ-irradiated G418-resistant primary mouse embryonic fibroblasts in Delbecco's modified Eagle's media supplemented with 5% FBS, 0.1 mM non-essential amino acids, 0.1 mM βME and 1000 U/ml leukemia inhibitory factor (Li, et al, Cell 69: 915-26, 1992). Selection with G418 and FIAU commences 24 hours after plating and is maintained for seven to ten days. An aliquot of each resistant colony (~90%>) is frozen for later use and the remainder are replated and grown to confluence for DNA extraction. Identification of recombinant clones is accomplished by Southern analysis and facilitated by a single EcoRI site in the Neo cassette and the probes that flank the homologous sequences are used for gene targeting as above. The 5'-flanking probe is used to detect a restriction fragment unique to the targeted allele. DNA from all positive clones are subsequently screened with the 3' probe to confirm bonafide homologous recombination (Wang, et al, Nat Genet l 185-190, 1995). Northern analysis are performed on RNA extracted from +/+ and +/- colonies. By observing the size and abundance of hybridizing species of ClqR_P RNA one of ordinary skill in the art can learn early valuable information regarding the influence of the haplo-insufficiency state for ClqR_P upon the efficiency of the ClqRp expression of mRNA. In addition, the transcription rate and transcript stability can be determined using nuclear run-on analysis and Northern or RNase- protection analysis of RNA extracted at various intervals after the addition of actinomycin D (5μg/ml) to inhibit new transcription (Urlaub, et al, Mol Cell Biol 9: 2868-80, 1989; Cheng et al, Mol Cell Biol 13: 1892-902, 1993). These parameters can be determined on an allele-specific basis by observing differences in transcript size or by using fusion probes which contain both ClqR_P and Neo sequences.

Approximately 15 cells from each targeted ES cell clone are microinj ected into each

C57B1/6J blastocysts (-15) collected at 3.5 days post coitus. Chimeric offspring are identified by agouti (ES-derived) coat color. Male chimeras are bred with C57B1/6J -41-

females. Homozygotes for the targeted allele are be generated by the breeding of heterozygotes. The genotype of all mice are determined by Southern analysis or a PCR-based assay.

Characterization of resultant mice: The genetic complement of all initial mice are composed solely of the genomes of two well characterized inbred stains. Therefore, the murine genomes carry no deleterious recessive nonsense alleles other than the targeted ClqR_P allele. Litter size, sex ratio, and genotyping of all newborn mice are used to monitor embryonic lethality. Mice of all 3 genotypes (+/+, +/- and -/-) are examined carefully over time for any phenotypic differences including birth weight, growth, activity, and congenital or acquired anomalies. Non- viable mice undergo autopsy.

Molecular analysis of mice of all three genotypes are performed. First, the character and steady state level of ClqR_P transcripts are determined by Northern analysis and RNase protection. Second, the level and distribution of reactive protein are determined by Western analysis and immunohistochemistry. Experiments can be performed to determine the allele-specific ClqR_P transcription rates and transcript stabilities. A simultaneous analysis is performed on total, nuclear, and cytoplasmic RNAs (Daar, et al, Mol Cell Biol 8: 802-13, 1988). Gene dosage effects on ClqR_P expression will be observed to determine the degree of reduction of ClqR_P protein expression on hetereozygote cells (ClqR_P ^+/") compared with wild type. Finally, fetal fibroblast cultures are established and transfected with a construct expressing wild- type ClqR_P to determine whether reconstitution with ClqR_P can rescue an abnormal phenotype. Additionally, the functional consequences of ClqR_P loss of expression (ClqRp^"'^") to more clearly define the role of ClqR_P in host defense against infection in vivo. To assess the effect of ClqR_P deficiency on host defense, mice are challenged with intraperioteneal injection of virulent Escherichia coli (OI 8:K1 :H7) (Cross et al. , J. Exp. Med. 169, 2021 (1989); Lowrance et al, J. Exp. Med., 180, 1693 (1994)). ClqRp deficient mice are monitored to establish dose response mortality over time compared to wild-type and heterozygous (ClqR_P ^+/) littermates. Cellular infiltrate and -42-

bacterial colony counts are established to determine if the influx of other immune system cellular components (e.g., Polymoφhonuclear leucocytes (PMN)) are impaired or enhanced. Quantitation of bacterial colony-forming units reveal when and if a defect in the control of bacterial growth is apparent after challenge.

Outcrossing of homozygous null (-/-) mice and further experimentation: To determine the phenotypic consequence of loss of the ClqR_P enhancement of phagocytic function in different genetic backgrounds. The results can be compared to the tissue-specific expression pattern of ClqR_P to determine whether the level of ClqRp is a limiting factor in the determination of tissue-specific components of the classical complement pathway of the immune system efficiency. Mice of all genotypes are analyzed, and the genotype-specific results can be compared.

If homozygosity for the targeted allele is incompatible with embryonic development, but heterozygosity is not associated with a phenotype, it is possible to generate dominant-negative or relative loss-of- function alleles. The size and character of such mutations would be influenced by expression studies using mammalian cells. The process of generating subtle (e.g. missense) mutations in the genome of ES-cells is well described and quite effective (Stacey, et al, Mol Cell Biol H: 1009-16, 1994). Briefly, a targeting vector is first used to replace a defined region of the target gene in HPRT-deficient ES cells with an HPRT minigene. After selection for the HPRT + phenotype, a second round of targeting is used to replace the HPRT minigene with a desired DNA fragment that harbors a site-specified mutation. Enrichment for homologous recombinants is achieved by selection for reversion to the HPRT phenotype. Mice heterozygous for a dominant-negative mutation or homozygous for a relative loss-of-function mutation may have sufficient impairment of ClqR_P efficiency to show a phenotype yet be viable. All potential mutations can be assessed in for their relative impact on host response to pathogenic challenge, immunocomplex clearance and kinetics of removal of cellular debris, and a select few can be used in transgenic experimentation. -43-

Additionally, if homozygosity for the targeted ClqR_P allele is incompatible with embryonic development, one of ordinary skill in the art can apply inducible gene targeting under the control of the CxdloxP recombination system of bacteriophage PI (Sauer, et al, Proc Natl Acad Sci USA 85: 5166-70, 1988). The Cre recombinase directs site-specific recombination between two short recognition sequences (loxP) without additional co-factors. Cre recognizes the loxP sites and nicks them on opposite strands, leaving behind a single loxP site after recombination. This process deletes or inverts the intervening ("floxed") DNA sequence when the loxP sites are placed in a head-to-tail or head-to-head orientation, respectively. In vivo gene inactivation can be restricted to a specific development stage or tissue by crossing a mouse strain harboring a floxed allele to a transgenic strain of activation (Gu, et al, Science 265: 103-6, 1994; Kuhn, et al, Science 269: 1427-1429, 1995). Alternatively, an inducible promoter can be used to drive Cre expression. First, an exon or region of ClqR_P would be flanked by two loxP sites using gene targeting methods described above. A resistance-conferring gene is included between the loxP sites but outside of the coding region for ClqR_P to allow for positive selection of recombinant clones. Resulting mice are bred to homozygosity for this targeted, albeit functionally intact, allele. Resulting homozygotes are bred to a transgenic strain that expresses Cre under the control of a promoter with desirable characteristics. By bypassing certain critical developmental stages or tissues, one of ordinary skill in the art can create a viable and useful model of ClqR_P deficiency despite the inherent essential nature of the gene product. The choice of the promoter for Cre expression can be an interferon-inducible promoter of the mouse Mxl gene (Kuhn, et al, Science 269: 1427-1429, 1995) .

The present invention may ameliorate mutations in ClqR_P genes found in sites of pathogenic invasion, wounds, abrasions, epithelial intrusion, cellular debris or inflammation. Because the presence of mutant ClqR_P polypeptide may correlate with vasculitis or sepsis, the ClqR_P nucleic acid may find use in gene therapy to enhance phagocytosis for the treatment of diseases in which rapid clearance and/or inactivation -44-

of detrimental substances is required. In preferred therapies, the ClqR_P regulating gene product is preferentially expressed in those cells where enhanced phagocytosis is required. Alternatively, therapy can be provided by administration of a peptidomimetic or other composition which mimics the biological activity of wild- type ClqR_P polypeptides or which modifies the defect, such as a conformational defect, in a mutant ClqR_P polypeptide to thereby restore the wild-type biological activity to the mutant polypeptide. Additionally, the ClqR_P sequences taught herein can be used to effect the levels of various cytokines in a patient.

A preferred method of gene therapy is direct gene transfer, /. e. , local application of a formulation containing the ClqR_P polypeptide-encoding nucleic acid into an afflicted site or other region. A variety of well known vectors can be used to deliver the ClqR_P gene to targeted cells in a location like an endothelial lining, including but not limited to adenoviral vectors, adeno-associated vectors or formulations targeting endothelial cells. In addition, naked DNA, liposome formulations delivery methods, or other novel formulations developed to deliver the ClqR_P gene to target cells are also preferred.

For any of the above approaches, the therapeutic ClqR_P polynucleotide construct can be applied to the site where enhanced phagocytosis is desirable (e.g., by injection), but the ClqRp formulation may also be applied to tissue in the vicinity of the needed phagocytosis event, to a blood vessel supplying the cells where phagocytosis is desirable or even systemically.

In the ClqRp gene delivery formulation of the instant invention, polynucleotide expression is directed from any suitable promoter (e.g., the human cytomegalovirus, simian virus 40, actin or adenovirus constitutive promoters; or the cytokine or metalloprotease promoters for activated synoviocyte specific expression).

Furthermore, ClqR_P polynucleotide production may be regulated by any desired mammalian regulatory element. For example, if desired, enhancers known to direct preferential gene expression in fibroblasts or macrophages may be used to direct -45-

ClqRp gene expression. Such enhancers include, without limitation, those enhancers which are characterized as tissue or cell specific in their expression.

Alternatively, if a ClqR_P-gene regulating genomic clone is utilized as a therapeutic construct, expression is regulated by its cognate regulatory sequences or, if desired, by regulatory sequences derived from a heterologous source, e.g., any of the promoters or regulatory elements described above.

Less preferably, gene therapy is accomplished by direct administration of the ClqR_P- regulating gene mRNA to a cell either in vitro, ex vivo, or in vivo. This mRNA may be produced and isolated by any standard technique, but is most readily produced by in vitro transcription using a cDN A under the control of a high efficiency promoter (e.g., the T7 promoter). Administration of mRNA to accumulated cells is carried out by any of the methods for direct nucleic acid administration described above.

Ideally, the production of the ClqR_P protein by any gene therapy approach described herein results in a cellular level of the ClqR_P polypeptide that is at least functionally equivalent to the normal, cellular level in a normal individual. Treatment by any gene therapy approach described herein may also be combined with more traditional therapies.

Another therapeutic approach included within the invention involves direct administration of recombinant ClqR_P protein by any conventional recombinant protein administration techniques, to the site of infection, at the site where pathogenic cells accumulate (for example, by injection), or administered systemically. The ClqR_P protein may also be targeted to specific cells or receptors by any of the methods described herein to target ClqR_P nucleic formulations. The actual dosage of protein depends on a number of factors, including the size and health of an organism, however one of one of ordinary skill in the art can use the following teachings describing the methods and techniques for determining clinical dosages (Spilker B., Guide to Clinical Studies and Developing Protocols, Raven Press Books, Ltd., New -46-

York, 1984, pp. 7-13, 54-60; Spilker B., Guide to Clinical Trials, Raven Press, Ltd., New York, 1991, pp. 93-101; Craig C, and R. Stitzel, eds., Modern Pharmacology, 2d ed., Little, Brown and Co., Boston, 1986, pp. 127-33; T. Speight, ed., Avery's Drug Treatment: Principles and Practice of Clinical Pharmacology and Therapeutics, 3d ed., Williams and Wilkins, Baltimore, 1987, pp. 50-56; R. Tallarida, R. Raffa and P. McGonigle, Principles in General Pharmacology, Springer- Verlag, New York, 1988, pp. 18-20) to determine the appropriate dosage to use; but, generally, between O.lmg and 1 OOmg inclusive are administered per day to an adult in any pharmaceutically-acceptable carrier.

In one embodiment, the invention provides a method of treating a patient having or at risk of having early stage infection when little or no antibody is present to attack antigenic or pathogenic agents or under conditions in which an individual is immuno- compromised as a result of genetic deficiency, disease or clinical treatment or the condition has an etiology associated with a defective phagocytosis-regulating gene or polypeptide, deficient ClqR_P or level thereof, or an inability to overcome infection (e.g., such as a post-operative patient), the method comprising administering to the patient a therapeutically effective amount of a formulation or composition which modulates the expression of the ClqR_P gene or polypeptide or triggers functional activation of the ClqR_P receptor such that the state of the patient is ameliorated. Furthermore, since it has been demonstrated that Clq enhances macrophage mediated tumor cell killing in vitro, one of ordinary skill in the art would recognize that modulation of ClqR_P (e.g., through upregulation of ClqR_P by administration of a ClqR_P formulation) could become part of a treatment for various forms of cancer.

Therapeutic applications also include utilizing a selective survival technique taking advantage of those cells specifically expressing the wild-type protein, e.g., ClqR_P . Such treatment kills or inactivates the cell that contains a defective ClqR_P gene, while leaving cells containing the wild type or normal ClqR_P gene/polypeptide unharmed. Several approaches for selective killing include but are not limited to: 1) infection with a viral vector to induce expression of the endogenous, normal ClqR_P -47-

gene,; 2) contact a cell having a mutant ClqR_P protein with an agent that specifically binds to the mutant and not the wild-type protein; and 3) contact a cell having a mutant ClqR_P protein with a first agent that protects the wild-type ClqR_P and then a second agent that is toxic to a mutant ClqR_p.

EXAMPLES

The following examples are intended to illustrate but not admitted to limit the invention in any manner, shape, or form (either explicitly or implicitly). While they are typical of those that might be used, other procedures, methodologies, or techniques known to those skilled in the art may be used alternatively.

MATERIALS AND METHODS

Reagents and Cell Culture

The ImmunoPure IgM Purification Kit, ReactiGel (6x) Support and NP-40 were purchased from the Pierce Chemical Co., Rockford, IL. Protein A-Sepharose and CNBr-Sepharose were from Pharmacia Biotech Inc. (Piscataway, NJ). TPCK-trypsin was purchased from Worthington (Freehold, NJ). The RPMI 1640 medium,

Dulbecco's modified eagle medium, Superscript Preamplification System for First Strand cDNA Synthesis Kit, DNAZOL Reagent, RadPrime DNA Labeling System, herring sperm DNA and 0.24-9.5 Kb RNA Ladder were obtained from GIBCO BRL (Grand Island, NY). Except where noted otherwise, all other reagents were purchased in the highest quality from Sigma Chemical Company (St. Louis, MO). The human histiocytic cell line, U937, was grown in suspension at 37° C, in RPMI 1640 medium containing 10% supplemented bovine calf serum (Hyclone, Logan, UT) and 10 mM HEPES, pH 7.4. The human acute lymphoblastic leukemia cell line, CEM, was grown in Dulbecco's modified eagle medium supplemented with 10% FCS (Hyclone). RPMI 1640 medium was purchased from Gibco (Long Island, N.Y). HL-1 medium (serum free) was purchased from Ventrex Laboratories (Portland, ME). Fetal calf serum (FCS) was purchased from Hyclone (Logan, Utah). L-glutamine and gentamicin were obtained from M.A. Bioproducts (Walkersville, MD). The human -48-

serum albumin (HSA) used for the elutriation buffer obtained from the American Red Cross was prepared by Baxter Healthcare Coφoration (Glendale, CA). Human recombinant γ-interferon was a gift from Dr. Krishna Tewari (UC, Irvine and ICGEB, New Delhi, India).

Antibodies

The R3 mAb and 710 polyclonal antiserum were generated by immunization with Clq-CLF binding proteins isolated from U937 cell extracts as previously described (Guan et al. J. Immunol. 152: 4005, 1994). Polyclonal antiserum QRl was generated by immunization of a rabbit with the 126,000 M_τ ClqR_P band extracted from agarose gels after separation by electrophoresis using the ProSieve Gel System (FMC

BioProducts, Rockland, Maine) according to manufacturer's instructions. The anti- peptide polyclonal antiserum was generated by immunization with a mixture of two peptides, VGGGEDTPYSN (SEQ ID NO.: 10) and VGGGEDTPYSNK (SEQ ID NO.: 11) (to allow conjugation at the C-terminal amino acids), conjugated to keyhole limpet hemocyanin using glutaraldehyde as the crosslinker as described (Current Protocols in Immunology). Purified R3 IgM was obtained from ascites fluid using the ImmunoPure IgM Purification Kit according to manufacturer's instructions. 710 IgG was purified by affinity chromatography using protein A-Sepharose as described (Andrew and Titus Curr. Prot. Immun. Wiley Interscience, N.Y, p 2.7.4., 1991).

Protein Isolation and Amino Acid Sequencing

Purified 710 IgG was coupled to CNBr-activated Sepharose 4B and purified R3 IgM was coupled to ReactiGel (6x) according to manufacturer's directions. For a single preparation, approximately 6 x 10⁸ U937 cells were washed once in ice cold RPMI 1640, then once in ice cold PBS, pH 7.4. The pelleted cells were resuspended to a concentration of 10⁸ cells/mL in extraction buffer (10 mM triethanolamine, pH 7.4, ImM CaCl₂, ImM MgCl₂, 0.15M NaCl, 0.3% NP-40, lμg/mL pepstatin, 5 μg/mL leupeptin, 1 μg/mL aprotinin and ImM phenylmethylsulfonyl fluoride (PMSF)). After a 1 hr incubation on ice with occasional agitation, the cell extract was centrifuged at 4°C at 12,000 g for 10 min to pellet insoluble material. The extract -49-

was pre-cleared by incubation for 1 hr on ice with 40% (v/v) packed Sepharose CL- 4B. The Sepharose was removed, the lysate diluted five fold with 20 mM Tris pH 7.4, 0.15M NaCl, ImM PMSF to dilute the NP-40 to a final concentration of 0.05%, then applied to the antibody column at 4°C. After washing with 10 column volumes of 20mM Tris, pH 7.4, 0.5M NaCl, 0.05% NP-40, ImM PMSF, the bound antigen was eluted with 0.1M glycine, pH 2.4, 0.5M NaCl, 0.5% NP-40, ImM PMSF. ClqR_P containing fractions were pooled and concentrated by ultrafiltration using Centricon 30 concentrators (Amicon, Inc., Beverly, MA). The protein was then precipitated overnight on ice using trichloroacetic acid at a concentration of 10%), and the precipitate washed with ice cold acetone. The pellet was resuspended in 20 μL Laemmli loading buffer (Laemmli, Nature 227: 680, 1970), boiled for 5 min, and subjected to SDS-PAGE (7.5% acrylamide) under reducing conditions. In some instances, the gels were stained directly with Coomassie blue, and the 126,000 M_τ band was excised from the gel. Gel slices containing protein isolated from the 710 column was sent to the W.M. Keck Foundation Biotechnology Resource Laboratory at Yale University for endoproteinase Lys-C (endo-Lys-C) digestion and subsequent amino acid sequencing, resulting in peptide sequences 112 and 115 (Table 1). Gel slices containing receptor isolated by R3 affinity chromatography were digested in situ using TPCK-trypsin using the procedure of (Ward et al, J. Chromatog. 519: 1990). After isolation of the peptide fragments using a C₄ reverse phase column (Vydac, Hesperia, CA), the peptide-containing peaks were subjected to protein sequencing by the Edman degradation method carried out on a Hewlett-Packard Protein Sequencing System, model G1005A, with an on-line analyzer of the amino acid derivatives. The resulting peptide sequences are labeled in Table 1 as beginning with the letters AH. Other preparations of the protein after SDS-PAGE were electrophoretically transferred to nitrocellulose as described by Towbin et al. (Towbin et al , Proc. Nat. Acad. Sci. 76: 4350, 1979) for 2-3 h, with the addition of 0.02% SDS to the transfer buffer. The membrane was then stained for 10 min in 0.5% Ponceau S in 1% acetic acid, then destained with O.lmM acetic acid. Both the 126,000 M_r and 90,000 M_r bands were cut from the nitrocellulose subjected to either N-terminal sequencing or -50-

internal peptide sequencing after endo-Lys-C digestion and separation of peptides by HPLC ("BB" peptides in Table 1).

Table 1. ClqR_P Peptides Determined by Amino Acid Sequencing

Peptide ID Sequence^a

Endo Lys-C Digestion 112 FWIGLQREK (SEQ ID NO.: 12)

115^b GFSXVGGGEDTPYSNXHK

(SEQ ID NO.: 13)

N-terminus BBN VGADTEAVVXXGTATYRIHXKL (SEQ ID NO.: 14)

Endo Lys-C Digestion BB3 XGATVPQAATASPTGGPEGV (SEQ ID NO.: 15)

BB7 ATPTTSRPSL (SEQ ID NO.: 16)

BB10^b GFSWVGGGEDTPXSNXHK

(SEQ ID NO.: 17)

BB14 APDVFDWGSXGPLXVY (SEQ ID NO.: 18)

BB17 AMXXPLALGGPGQVTYTTPFQXT (SEQ ID NO.: 19)

Trypsin Digestion AH28 KPQNAADSYSWVPER (SEQ ID NO.: 20)

AH31 VLAQLLR (SEQ ID NO.: 21)

AH37 FWIGLQR (SEQ ID NO.: 22)

AH39^b GFSWVGGGEDTPYSNWHK (SEO ID

NO.: 23)

AH45 TTPFQTTSSSLEAVPFASAANVAAGEG (SEQ ID NO.: 24)

AHA^C YGXNFXNG (SEQ ID NO.: 25)

AHBc PQGYQLDXXQ (SEQ ID NO.: 26)

AHCc MLAP (SEQ ID NO.: 27) ^a Discrepancies from deduced amino acid sequence are indicated as bold residues. ^b Peptide sequence (underlined) used to generate anti-peptide antiserum. ^c New peptide sequences identified from sequencing data of the peptide mixtures.

Clq was isolated from plasma-derived human serum by the method of Tenner et al. (Tenner, et al,, J. Immunol, 127:648. 1981) and modified as described in Young, et al, J. Immunol, 146:3356. 1991. The preparations used were fully active as -51-

determined by hemolytic titration and homogeneous as assessed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Protein concentration was determined using an extinction coefficient (E^1%) at 280 nm of 6.82 for Clq. All proteins were stored at -70°C. Purified human fibronectin was generously provided by Drs. Sheila Huff and Kenneth Ingham (American Red Cross Holland Laboratory, Rockville, Md.), and human SPA isolated from alveolar proteinosis patients was a generous gift from Dr. Jo Rae Wright, Duke University, Durham, N.C.

PCR and Library Screening Generation of PCR3 To obtain the 5' region of the cDNA, the 5 'RACE System for Rapid Amplification of cDNA Ends was used according to manufacturer's instructions. The gene-specific primer 1 (GSP1) used to generate the cDNA from 1.75 μg of U937 total RNA was 5'- TTGGCCGCAGAGGCAAAGGGCA-3' (SEQ ID NO.: 28). The primary PCR reaction was done with the supplied 5' RACE Abridged Anchor Primer and a nested primer, GSP2, of the SEQ ID NO.: 29, 5'-CAAGGAGGAACTGGTGGTCTGG-3' . The reaction products from this primary PCR was used as the template for a final PCR reaction using the supplied Abridged Universal Amplification Primer and another nested primer, GSP3, of the SEQ ID NO.: 30: 5'- TGGGCCTCGGCAGCGCTCAGCT-3'. The resulting 297 bp PCR product was cloned into the pGEM-T vector and sequenced.

A trypsin cleavage in the protein after a tyrosine residue allowed for the overlap of peptides BB17 and AH45, which includes the sequence, SEQ ID NO.: 5: GGPGQVTYTTPFQTTSSSLEAVPFASAANVACGE. Based on this sequence, two degenerate primers were synthesized and used for RT-PCR using cDNA generated with the Superscript Preamplification System for First Strand cDNA Synthesis Kit according to manufacturer's instructions from mRNA isolated from U937 cells as template. The forward oligonucleotide was SEQ ID NO.: 31: 5'- GG(agct)GG(agct)CC(agct)GG(agct)CA(ag)GT(agct)AC-3' and the reverse was SEQ ID NO.: 32: 5'-TC(agct)CC(agct)GC(agct)GC(agct)AC(ag)TT(agct)GC-3'. The PCR -52-

product of 101 bp was isolated on a 12% polyacrylamide gel (Sambrook et al, 1989), cloned into the pGEM-T vector (Promega Coφoration, Madison, WI) and sequenced using the Sequenase Quick-Denature Plasmid Sequencing Kit (USB, Cleveland, OH) to confirm that it encoded the expected peptide. A specific primer based on this PCR product, SEQ ID NO.: 29: 5'-CAAGGAGGAACTGGTGGTCTGG-3', and a degenerate primer based on the sequenced amino terminus starting at amino acid 2, SEQ ID NO.: 32: 5*-GGIGCIGA(tc)ACIGA(ag)GC-3', were used to amplify by RT- PCR the cDNA corresponding to the amino terminus of the protein from U937 mRNA. This 570 bp PCR product was also cloned into the pGEM-T vector and sequenced, and then was used to screen a λgtl 1 U937 cDNA library (Clontech, Palo Alto, CA), using conventional techniques. The 1458 bp Eco Rl insert from a positive phage (clone 15) was cloned into pBluescriptII-KS(+) (Stratagene, La Jolla, CA), sequenced, then used to rescreen the U937 λgtl 1 cDNA library. Four new positive phage were isolated and both ends of each insert was sequenced using the frnol DNA Sequencing System (Promega) to determine their position relative to clone 15. Clone 3, which contains a 1832 bp insert that extends the farthest downstream, was then cloned into pBluescriptII-KS(+) and sequenced in its entirety. Sequencing of the phage clone inserts 3 and 15 were done using the Erase-a-Base System (Promega) and the Sequenase Quick-Denature Plasmid Sequencing Kit to obtain unambiguous overlapping readings from both strands. Computer analysis of the sequencing data was done using the Lasergene DNASTAR for Windows software.

Sequence Analysis

The National Center of Biotechnology Information (NCBI) electronic mail server BLAST was used to search for homologous sequences in the non-redundant compilation of the protein databases. Motif searches were done using the Motifs program of the GCG computer package, Version 8 (Madison, WI) and the transmembrane domain was predicted using the TMpred program (Hoffmann and Stoffel, J. Biol Chem.. 347:166. 1993). -53-

Western Blot

After R3 affinity purified ClqR_P was transferred to nitrocellulose (described above), the membrane was blocked with 3% nonfat dry milk in Tris-buffered saline, containing 0.05% Tween 20 (TBST). R139 and control IgG_2b were diluted to 5 μg/mL and the rabbit antisera were diluted 1 : 1000 in the blocking buffer. Bound antibodies were detected using peroxidase-conjugated anti-mouse IgG or anti-rabbit IgG and the peroxidase was detected using 4-chloro-l-naphthol (Bio-Rad Laboratories, Hercules, CA).

Southern Blot Analysis Human genomic DNA was isolated from whole blood using DNAZOL Reagent according to manufacturer's directions. For each digest, 10 μg of DNA was restricted with either Bam HI, Eco Rl, Hind III or Pst I, then separated by electrophoresis on a 0.7%) agarose gel in 0.5x TBE. The DNA was fractionated, transferred overnight in lOx SSPE to Maximum Strength Nytran (Schleicher and Schuell, Inc., Keene, NH), and immobilized using a Stratalinker UV Crosslinker (Stratagene). The clone 15 insert was used as the template to make a ³²P labeled probe generated by the random priming method using the RadPrime DNA Labeling System. Hybridization of the probe was carried out for 16 hrs at 42°C in 50% formamide, 6x SSPE, 5x Denhardt's reagent, 0.5% SDS and 0.5 mg/mL herring sperm DNA. Washing was done as follows: twice in 7x SSPE, 0.5% SDS for 15 min each at room temperature, twice in lx SSPE, 0.1% SDS for 15 minutes each at 37°C, then finally once for 30 min at 55 °C in O.lx SSPE, 0.5% SDS. The membrane was wrapped in plastic wrap and exposed to autoradiographic film for two days at -70 °C.

Northern Blot Analysis Messenger RNA was isolated from U937 and CEM cells using the Micro-FastTrack mRNA isolation kit (Invitrogen, San Diego, CA). One μg of each RNA was separated in each of two lanes on a denaturing 1% agarose gel containing formaldehyde. The RNA was transferred overnight in 20x SSPE to Maximum Strength Nytran, UV crosslinked to the membrane, then probed with the clone 15 insert as in the Southern -54-

blot. A 0.24-9.5 Kb RNA Ladder was used as a size marker. After washing twice in 6x SSPE, 0.1% SDS for 15 min each at room temperature, twice in lx SSPE, 0.1% SDS for 15 min at 37°C and once in lx SSPE, 0.1% SDS for 30 min at 50°C, bound probe was detected by autoradiography for 3 days at room temperature.

Cells

Human peripheral blood monocytes were isolated by counterflow elutriation using a modification of the technique of Lionetti et al. (Lionetti et al, Methods of Cell Separation, Plenum Publishing Coφ. New York, p. 141, 1980) as described (Bobak et al, J. Immunol, L36:4604, 1986). Blood units were collected into CPDA1 at the UCI Medical Plaza, Irvine, CA. Greater than 95% of the cells in each preparation were monocytes according to size analysis on a Coulter Channelyzer. Cells were cultured in RPMI 1640 supplemented with 10% FCS or in HL-1 medium. One- well Lab Tek chambers (Nunc, Naperville, IL) were coated with Clq , SPA or other control or test proteins (8-16 μg/mL) in coating buffer (0.1 M carbonate, pH 9.6), and incubated at 37°C for 2.5 h. After washing chambers twice with PBS, monocytes (2 ml of 10⁶/ml) were added to chambers and cultured for various periods of time at 37°C in 5% CO₂ air. Where indicated, LPS (100 ng/ml) or INFγ (100U-300U/ml) was added directly to the monocytes.

Phagocytosis Assay Sheep erythrocytes (E) bearing either IgG anti sheep red blood cells (EA_lgG) or IgM anti sheep red blood cells and C4b (EA _C4b) were prepared as previously described (Bohnsack et al, J.Exp.Med. 16J_.:912, 1985). Eight-well Lab Tek chambers were coated with varying concentrations of Clq, SPA, iron-saturated transferrin (Sigma) or HSA (Bobak et al, Eur. J. Immunol. Jj>^*:2001, 1988). Monocytes or macrophages (6.25 x 10⁴ cells/well) are added to each chamber, the cells centrifuged at 600 rpm (RT6000, Dupont Sorvall) for 3 min and subsequently placed at 37°C in 5% CO₂ for times noted. Targets were then added (10⁷/100 μl), the slides again subjected to centrifugation (600 rpm, 3 min), and incubated for 30 min at 37°C. After removing EA_IgG or EA_C4b not cell-associated by washing, non-ingested targets were removed by -55-

hypotonic lysis (Bobak et al, supra). After fixation in 1% glutaraldehyde and staining with Giemsa, phagocytosis was quantitated using light microscopy. The number of E-targets ingested per 100 effector cells was defined as the phagocytic index, whereas the percentage of effector cells ingesting at least one E-target was defined as the percent phagocytosis. Each experiment, performed on separate days with different donors, used duplicate sample wells per condition. Controls of unopsonized E were not ingested by monocytes or macrophages under any conditions.

RNase protection assay At various culture times, total RNA was extracted from both adherent monocytes and nonadherent monocytes (recovered by centrifugation of cell supernatants), using the TRIzol™ reagent (GIBCO BRL, Grand Island, NY) following manufacturer's direction. The ribonuclease protection assay (RPA) was performed exactly as described (Hobbs et al, J. Immunol. 8: 3602 1993.). Briefly, 50 ng of EcoRI linearized template for each cytokine was used in an in vitro transcription reaction (Promega , Madison, WI ) using [α -³²P]-UTP (3000 ClqRp/mmol, Amersham, Arlington Heights, IL) to generate the radiolabeled riboprobe template set, HL-14. The HL-14 template set was previously described (Rochford, et al, manuscripts submitted) and contains linearized templates specific for IL-6 (320 bases protected mRNA), IL-10 (294 bases), IL-lα (269 bases), TNF-β (220 bases), GM-CSF (208 bases), TGF-βl (170 bases), IL-lβ (149 bases), TNF-α (124 bases), and φL32 (76 bases). Labeled antisense RNA was hybridized overnight with the total RNA. Yeast tRNA was added to each sample to bring the final RNA content to 5-10 μg. Unprotected (single stranded) RNA was then digested by addition of 2 μl RNase Tl (2000 U/μl, GIBCO BRL). In initial experiments 5μl RNase A (100 μg/ml, Sigma) was also added, but was discontinued since no advantage was seen. Protected fragments were analyzed by electrophoresis in 5% acrylamide/8 M urea gels. Dried gels were placed on XAR film (FUJI Medical film) with intensifying screens, and were developed at -70°C. For signal quantitation, in some experiments dried gels were analyzed with the GS-250 Molecular Imager ™ (Bio-Rad) and volume measurements of each protected band was determined. -56-

ELISA

The levels of human IL-lβ, IL-6, and TNF-α in culture supematants were measured by using two-site sandwich ELISA. The TNF-α cytokine standard, rabbit anti-rhTNF-α IgG and rabbit HRP-anti-TNF-α IgG were a gift from Dr. Gale Granger (University of California, Irvine, CA), and the ELISA assay used was as described (Choi et al, Cell. Immunol.1996.). Microtiter plates were coated with 100 μl of rabbit anti- rhTNF-α IgG at 5 μg/ml in 0.05 M carbonate buffer, pH 9.6. After overnight incubation at 4°C, the plates were washed with PBS containing 0.2% Tween 20 (PBS- Tween). After washing, serial dilutions of the test supematants and the TNF-α standard (in 1%BSA/PBS) were added (100 μl/well). Following overnight incubation, wells were washed 3 times with PBS -Tween and incubated with rabbit HRP-anti-TNF-α IgG at 2 μg/ml in 1% BSA/PBS for 1 h, 37°C. Finally, after washing, 100 μl of ABTS (lmg/ml in 0.1 M Acetate buffer, pH 4.2 and 0.03% H₂O₂) was added to each well, and the change in A₄₀₅ was monitored using a thermoregulated (24°C) Molecular Devices microplate reader. Comparison with log- log plots of absorbance vs standard cytokine concentration were used to calculate cytokine levels in supematants. Alternatively, TNF-α was measured using an ELISA kit from PerSeptive Diagnostics. The levels of IL-lβ and IL-6 in culture supematants was measured using commercially available test kits (R&D Systems, Minneapolis, MN and PerSeptive Diagnostics, Cambridge, MA).

EXAMPLE 1

PURIFICATION. CHARACTERIZATION, AND PEPTIDE

SEQUENCING OF THE ClqR„ RECEPTOR PROTEIN

To gain a further understanding of how ClqR_P functions to enhance phagocytosis triggered by its known ligands, the structure of the receptor is required. Accordingly, the ClqRp receptor protein was isolated to obtain amino acid (aa) sequence data to design degenerate oligonucleotide probes and/or PCR primers. -57-

Purified 710 or R3 antibodies were used to affinity purify ClqR_P from NP-40 detergent extracts of U937 cells. The eluted material was concentrated by ultrafiltration, precipitated with trichloroacetic acid, then separated by SDS-PAGE under reducing conditions.

The mature protein migrates with an apparent molecular weight of 126,000. Two additional bands with apparent molecular weights of 90,000 and 60,000 were variably seen and are most likely breakdown fragments resulting from the purification procedure since both fragments are also reactive with anti-ClqR_P antibodies. Additionally, the 90,000 M_τ fragment shares the identical N-terminus, as well as certain internal peptides as the mature protein.

The 126,000 M_r receptor protein was excised from SDS-PAGE gels and subjected to either trypsin or endo-Lys-C digestion and subsequent peptide sequencing. In another approach, both the 126,000 M_r and 90,000 _r proteins were transferred to nitrocellulose for N-terminal sequencing, as well as internal peptide sequencing following endo-Lys-C digestion. The sequenced peptides are summarized in Table 1. One sequence, FWIGLQREK, is found among other membrane receptors that are reported to modulate endocytosis, including the human and murine mannose macrophage receptor (Ezekowitz et al, J. Exp. Med. 172: 1785, 1990), chicken hepatic lectin (Drickamer et al. J. Biol. Chem. 261:6878. 1986) and the beta subunit of human fibronectin receptor (Argraves et al, J. Cell Biol, 105:1183, 1987). This finding is consistent with the fact that ClqR_P plays a role in modulating monocyte phagocytosis.

EXAMPLE 2 CLONING OF THE ClqR_P cDNA

A trypsin cleavage within the purified protein at the C-terminus of a tyrosine residue resulted in the peptide AH45 (Table 1). The beginning of this peptide overlaps the last seven amino acids of peptide BB17, resulting in a 44 amino acid sequence. -58-

Degenerate oligonucleotide primers were used to amplify, by RT-PCR, a 101 bp cDNA fragment from U937 mRNA corresponding to 34 amino acids of the overlapping peptide sequences AH45 and BB17. Specific primers based on this 101 bp cDNA were used in combination with another degenerate primer corresponding to the amino terminus of the protein, starting at the second amino acid, to amplify a 570 bp cDNA of ClqR_P. This 570 bp fragment was used to screen a U937 λgtl 1 cDNA library. A phage was identified (clone No. 15) which contained a 1458 bp insert that overlapped the 570 bp PCR product by 165 bp.

The insert from clone No. 15 was used to rescreen the U937 λgtl 1 cDNA library and four additional, distinct phage inserts were identified. Clone No. 3 contained a 1832 bp insert that overlapped clone No. 15 by 449 bp. To obtain the 5' end of the cDNA, specific primers based on sequences derived from the 570 bp PCR product were used in 5' RACE-PCR reaction to amplify a 297 bp product which overlaps the 570 bp cDNA by 83 bp.

Nucleic acid encoding murine ClqR_P (SEQ ID NO:34) was identified by screening a murine genomic library (129SVEV) obtained from Clontech with a nucleic acid probe for the coding region of human ClqR_P.

EXAMPLE 3 SEQUENCING THE ClαR_P RECEPTOR NUCLEOTIDE CLONES

The PCR products and clones Nos. 15 and 3 were sequenced in their entirety on both strands and a 3460 bp of total cDNA was translated. The open reading frame of the cDNA encodes a 652 amino acid protein, which, excluding the 21 amino acid signal peptide (based on the N-terminal sequence) has a predicted molecular weight of 66,495 Daltons and a pi of 5.24. The amino terminal sequence starting at the second amino acid, as well as all ten of the sequenced intemal peptides are found within the predicted amino acid sequence, indicating that this cDNA corresponds to the isolated ClqR_P protein. -59-

The stop codon for the protein is located 54 bp downstream of the most C-terminal peptide determined by amino acid sequencing. The nucleotide sequence has been configured by re-sequencing both strands of the cDNA three separate times.

EXAMPLE 4 SEQUENCE ANALYSIS OF ClqR_P

Homology searches of the protein and nucleotide data bases indicate that ClqR_P is a novel protein whose structural domains are shown in Figure 4. There is a single C- type carbohydrate recognition domain at the amino terminus, containing seven of the 18 nearly invariant residues (Drickamer J. Biol Chem. 263:9557, 1988), including the four cysteine residues that are involved in disulfide bonds within the domain. The protein also contains a set of five epidermal growth factor (EGF)-like domains, the last three of which contain an asparagine hydroxylation motif consistent with calcium binding EGF domains (Rees et al, Embo J. h 2053, 1988).

ClqRp shows homology to the other diverse, non-related, extracellular proteins due to their EGF domains, including fibrillin, thrombomodulin, and fibulin.

There is a single putative N-linked glycosylation site at residue N325 (Figure 3, italics). At the carboxy terminus, there is a single 25 amino acid transmembrane domain (Figure 3, double underline), and finally a short, 47 amino acid cytoplasmic tail. Within the cytoplasmic tail, there is a tyrosine residue at position Y644 that is part of a consensus motif which is recognized by tyrosine kinases (Patschinsky et al, Proc. Natl. Acad. Sci. 79:973, 1982). Once the cDNA was translated and the primary amino acid sequence known, amino acid sequence data of HPLC peaks containing peptide mixtures derived from the trypsin digest of ClqR_P were reexamined. In addition to re-identifying 11 of the peptides previously sequenced, three new peptide sequences were found (Table 1), further confirming that the cloned cDNA encodes the isolated, monoclonal antibody reactive protein. -60-

EXAMPLE 5 WESTERN BLOT ANALYSIS OF ClqR_r

A synthetic peptide (SEQ ID NO.: 10, VGGGEDTPYSN), based on the intemal peptide sequence encoded in the cloned ClqR_P cDNA, was synthesized by three independent facilities using three different protocols and subsequently used to generate a rabbit polyclonal ClqR_P anti-peptide antiserum. Using western blot analysis on purified ClqR_P transferred to nitrocellulose, the anti-peptide ClqR_P antibody reacted with the 126,000 _r ClqR_P receptor in both its reduced and nonreduced forms. The anti-peptide ClqR_P antibodies also recognized the 90,000 M_r C 1 qRp breakdown fragment, but not the smaller 60,000 M_r C 1 qR_P fragment, indicating that the 60,000 M_r ClqR_P fragment does not contain the N-terminus of the ClqR_P protein. The fact that the anti-peptide antiserum reacted with two forms of the ClqRp receptor (the 126,000 M_r full length and its 90,000 M_τ breakdown fragment) in both reduced as well as nonreduced mobility shifted forms, and that the synthetic peptide encoded by the cloned C 1 qR_P cDNA (SEQ ID NO. : 10, VGGGEDTPYSN), was sequenced by three separate facilities using different protocols to generate the peptide fragments, strongly suggests that the cloned ClqR_P cDNA encodes the native ClqRp protein.

EXAMPLE 6 ANALYSIS OF GENOMIC ClαR_P DNA BY SOUTHERN BLOT

To characterize the genomic organization and expression of ClqR_P, Southern blotting was done using a probe based on the insert of clone No. 15. Clone No. 15 corresponds to 486 amino acids of the coding region, beginning at position P136.

Human genomic DNA, isolated from whole blood, was digested with restriction enzymes and separated by agarose gel electrophoresis. The DNA was transferred to a nylon membrane and hybridized to a probe generated by the random priming method. A single band hybridized in three of the four digests indicating that the gene encoding -61-

for ClqR_p is present as a single copy in the human genome. Two bands were visible in digests using Eco Rl. These two band are inteφreted as being present as a result of the presence of restriction site(s) within a ClqR_P intron, since no such Eco Rl restriction enzyme sites are present in the cDNA insert of clone No. 15 .

EXAMPLE 7

ANALYSIS OF ClqR_P mRNA BY NORTHERN BLOT

To determine the size of the mRNA of ClqR_P, mRNA was isolated from U937 cells, separated by agarose gel electrophoresis and transferred to a nylon membrane. Using a probe generated as in the Southern blot of Example 6, the mRNA for ClqR_P was found to be a single species that was 6.7 Kb in size.

In contrast, a ClqR_P probe did not hybridize to mRNA isolated from CEM cells which are of a different cell type than U937 cells. The specificity of ClqR_P mRNA to a particular cell type is consistent with our previous work demonstrating that while the ClqR_P protein is expressed on the surface of U937 cells it is not expressed on the surface of CEM cells (Guan et al. J. Immunol. 152:4005, 1994).

EXAMPLE 8 ClqR_P DOES NOT TRIGGER CYTOKINE mRNA EXPRESSION

To determine the efficacy of using ClqR_P to bolster the complement component of the immune system we attempted to determine if ClqR_P also stimulated an inflammatory response since co-stimulation of an inflammatory response with stimulation of phagocytosis would not be desirable. Therefore, we performed an analysis of the effect of ClqRp interaction with monocytes on the subsequent mRNA expression of selected cytokines in cells cultured in HL-1 media. -62-

HL-1 media is a defined low protein synthetic medium, chosen to exclude possible effects of external proteins on cytokine synthesis and to mimic more closely the serum-free assay conditions under which ClqR_P enhances phagocytosis of opsonized targets.

Cytokine mRNA expression was examined using an RNase protection assay after incubation of monocytes with no stimulus or in ClqR_P-coated wells, in the absence or presence of LPS for 1 h (a time at which ClqR_P-enhanced phagocytosis is evident) and for 18 h (to assess the long term effect of ClqR_P). LPS was added to the media as a positive control since it is well established that LPS stimulates monocytes to synthesize TNF-α, IL-lβ, and IL-6 which are known to promote inflammation.

Control cells, cultured in uncoated wells, expressed substantial levels of mRNA for the cytokines TNF-α, IL-lβ and TGF-βl at both 1 h and 18 h of culture. IL-6 and IL- lα mRNA expression, while nearly undetectable at 1 h, was quite prominent by 18 h of culture. Exposure of monocytes to LPS increased IL-lα, IL-lβ, IL-6 and TNF-α mRNA levels relative to untreated cells at 1 h and significantly (3-10 fold relative to untreated controls) after 18 h of culture.

In contrast, at lh ClqR_P had a slight, but consistent, suppressive effect on the levels of detectable cytokine mRNA relative to the basal level of cytokine mRNA synthesis by cells in HL-1 media alone. After 18 h of incubation, cytokine mRNA levels in cells exposed to ClqR_P were greatly reduced when compared both to the 1 h time point and compared to the control cells at 18 h. The IL-6 mRNA level was 20-fold lower and IL-lβ and TNF-α mRNA levels 10-fold less in monocytes cultured in Clq-coated dishes relative to cells cultured in uncoated wells. Similar effects were seen in all other experiments performed with ClqR_P (n = 5). This decrease cannot be attributed to a toxic effect on the cells as the mRNA for the ribosomal protein L-32, a housekeeping gene, was present in these cells at levels comparable to those in control cells. -63-

EXAMPLE 9

ClqRp NEGATIVELY INFLUENCES THE LIPOPOLYSACCHARIDE (LPS)

BINDING PROTEIN MEDIATED UPREGULATION

OF SPECIFIC CYTOKINES

To determine whether C 1 qR_P was merely nonstimulatory or, alternatively, if it actively inhibited cytokine synthesis, we compared cytokine mRNA levels in monocytes exposed to LPS and adhered to ClqR_P-coated wells to that seen in LPS- treated cells adhered to uncoated control wells. Adherence to ClqR_P resulted in a substantial inhibition of the stimulatory effect of LPS on mRNA levels (n = 5) at both 1 h and 18 h of culture for all cytokines detected except for IL-10. The level of IL-lα, IL-lβ, TNF-α and IL-6 mRNA in LPS-treated monocytes adhered to ClqR_P at 18 h increased only 2.0-, 3.7-, 1.7- and 2-fold, respectively, in contrast to the 7.5-, 10-, 3- and 6.7-fold higher levels seen in the presence of LPS, all relative to an untreated control. TGF-βl mRNA expression was enhanced to a lesser degree (2-fold increase) by LPS. However, even this enhancement was inhibited by adherence of monocytes to ClqR_P-coated surfaces. Interestingly, the induction of IL-10 mRNA by LPS at 18 h was not suppressed by ClqR_P, but rather was increased by ClqR_P relative to LPS alone.

The inhibitory effects of ClqR_P on cytokine synthesis were observed using several different ClqR_P preparations, suggesting that the inhibition was directly caused by ClqR_P and not by contaminating molecules. Furthermore, the pepsin resistant, collagen-like fragment of ClqR_P which is known to bind to cells and induce enhanced phagocytosis, inhibited cytokine synthesis as well as the intact ClqR_P molecule. Cells incubated under these different conditions were viable and expressed comparable levels of L-32 mRNA. -64-

EXAMPLE 10

ClqRp NEGATIVELY INFLUENCES THE INCREASE IN IL-lα. IL-lβ AND

TNF-α mRNA LEVELS INDUCED BY INTERFERON-γ

The effect of ClqR_P on another known modulator of monocyte cytokine synthesis, interferon-γ (INF-γ), was assessed to determine if the ability of ClqR_P to suppress LPS -induced cytokine expression was a specific effect on LPS cell signaling or if ClqRp could modulate cytokine synthesis induced by more than one activator.

At one hour after addition of INF-γ (100 U/ml or 300 U/ml), mRNA levels of IL-lα, IL-lβ and TNF-α were increased similar to that following LPS stimulation of monocytes in two of four experiments (in two experiments, cytokine levels were elevated but to a lesser degree than the LPS-treated cells). In all four experiments, adherence to ClqR_P resulted in greatly reduced levels of cytokine mRNA in the INF- γ-treated cells after only one hour of incubation, suggesting a potential regulatory role for ClqR_P in the induction of these proinflammatory cytokines. Again, induced IL-10 mRNA levels were relatively unchanged by adherence to ClqR_P. After 18 h, mRNA levels in the presence of INF-γ with or without ClqR_P were unchanged or lower than that of cells in control media.

EXAMPLE 11 ClqRp INFLUENCES THE SECRETION OF CYTOKINES IL-6. IL-lβ AND TNF-α

The results in Example 10 indicated that ClqR_P contributes to the regulation of mRNA expression of the proinflammatory cytokines, IL-lβ, IL-6 and TNF-α. To determine if there was any correlation of mRNA levels with the secretion of IL-6, IL- lβ and TNF-α under these conditions, the level of these cytokines present in the cell culture media was assessed by ELISA. -65-

Supematants from monocytes cultured in serum-free media adhered to ClqR_P or SCR1-A or to uncoated wells in the presence or absence of LPS were collected and assayed for IL-lβ, TNF-α and IL-6. After 1 h of culture, levels of cytokines in the monocyte supematants under all conditions were very low (i.e., baseline levels). However, by 18 h of incubation, the concentration of IL- 1 β and TNF- α in control cultures was elevated over the 1 h time point, and LPS greatly enhanced the concentration of all three cytokine levels. As anticipated from the measured levels of cytokine mRNA after 18 hours, levels of IL-lβ (n=6) and TNF-α (n=4) in the media of LPS-treated cells cultured in ClqR_P-coated wells were suppressed relative to LPS- stimulated cells in uncoated wells.

Incubation of monocytes for 18 h with SCR1-A also blocked secretion of TNF-α (n=2) and IL-lβ (n=3) relative to control cultured monocytes, again consistent with results of RNase protection assay.

EXAMPLE 12 ClqRp INFLUENCES CYTOKINE mRNA EXPRESSION IN RPMI MEDIUM

SUPPLEMENTED WITH 10% FCS

To determine if ClqR_P affects cytokine synthesis in media containing serum, monocytes were cultured in 10% FCS in the presence or absence of ClqR_P. Total RNA was isolated and ribonuclease protection assays performed.

After 1 h of culture, levels of TGF-βl, IL-lβ and TNF-α mRNA were nearly identical in the control and Clq-adherent monocytes. Similarly, after 18 hours in culture, levels of mRNA for the cytokines assayed were barely detectable in either the control cells or cells adhered to ClqR_P. Cells incubated under these different conditions showed distinct moφhology by microscopic observation, but all were viable. Thus, in both serum-free defined media and serum-containing media, ClqR_p does not activate the monocyte/macrophage to produced these proinflammatory cytokines. -66-

EXAMPLE 13 ClqR_p EFFECT ON LPS UPREGULATION OF CYTOKINE EXPRESSION

Fetal calf serum is known to contain LBP, a LPS binding protein, which results in an increased functional response to LPS in cells expressing CD 14. We therefore investigated whether ClqR_P was able to modulate the LPS-mediated upregulation of cytokine expression when cells were cultured in serum-containing media.

Monocytes incubated with LPS demonstrated a robust stimulation of all cytokine mRNA levels (except TNF-β and GM-CSF), which was either not inhibited by the adherence of cells to Clq-coated surfaces at either 1 h or 18 h of culture or only minimally inhibited. Thus, the data suggest that in serum-containing media, LPS triggers a dominant stimulating effect on cytokine gene expression in monocytes which is not altered by ClqR_P. Stimulation of these mRNA levels by LPS was also not inhibited by SCR1-A, HSA or fibronectin at 1 h or 18 h of culture in the presence of serum (n = 2).

Finally, the effect of C 1 qR_P on the levels of IL-6, IL- 1 β and TNF-α in culture supematants of monocytes in serum-containing media were assayed. Cytokine levels of cells adherent to ClqR_P were found to be near baseline levels in control cultures at 1 h and did not increase after 18 h of culture. In LPS-stimulated cells, after one hour of incubation, the level of TNF-α , but not IL-lβ, was increased in cell supematants, even though LPS triggered enhanced levels of mRNA for both cytokines at the early time point. After 18 h, as expected, LPS treatment significantly increased IL-6, IL-lβ and TNF-α levels relative to the unstimulated control samples. ClqR_P did not have any inhibitory effect on LPS-induced secretion of these cytokines in monocytes cultured in serum-containing media, consistent with its minimal modulation of the LPS-induced mRNA levels of these cytokines in cells in serum. -67-

A number of embodiments of the present invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, it is to be understood that the invention is not to be limited by the specific illustrated embodiment, but only by the scope of the appended claims.

Claims

-68-What is claimed is:

1. A substantially pure C 1 qR_p polypeptide.

2. The polypeptide of claim 1 , wherein the polypeptide comprises a segment of at least 5 consecutive amino acids that are conserved in the amino acid sequence of human ClqR_P (SEQ ID NO:2) or murine ClqRp (SEQ ID NO:35).

3. An isolated nucleic acid molecule encoding a ClqR_P polypeptide.

4. An isolated nucleic acid molecule, wherein the nucleic acid has a sequence having at least 65% sequence identity to SEQ ID NO:l and wherein said nucleic acid molecule encodes a polypeptide having a biological activity of ClqR_p.

5. An isolated nucleic acid molecule selected from the group consisting of: a) the nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO:34, where T can also be U; b) a nucleic acid sequence that hybridizes to the complement of the nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO:34; and c) a fragment of a) or b) that comprises at least 9 nucleotides and hybridizes to a nucleotide sequence encoding SEQ ID NO:2 or SEQ ID NO:35; and d) SEQ ID NO: 1 or SEQ ID NO:34.

6. An isolated nucleic acid molecule that hybridizes to a nucleic acid of claim 3.

7. An isolated nucleic acid molecule that hybridizes to a nucleic acid of claim 5.

8. An isolated nucleic acid molecule of claim 3, wherein the nucleic acid is mammalian. -69-

9. An isolated nucleic acid molecule of claim 8, wherein the nucleic acid is human.

10. An isolated nucleic acid molecule of claim 8, wherein the nucleic acid is murine.

11. An expression vector containing a nucleic acid of claim 3.

12. A pharmaceutical composition for gene delivery and gene expression of a nucleic acid of claim 3 in a pharmaceutically acceptable carrier.

13. An recombinant cell containing a vector of claim 11.

14. A method of identifying a test composition which binds a C 1 qR_P, the method comprising: a) incubating components comprising the test composition and the ClqR_P, and; b) measuring the binding of the test composition to C 1 qR_P.

15. The method of claim 14, wherein the C 1 qR_P is encoded by a polypeptide comprising a segment of at least 8 consecutive amino acids that are conserved in the amino acid sequence of human ClqR_P (SEQ ID NO:2) or murine ClqRp (SEQ ID NO:35).

16. The method of claim 14, wherein the ClqR_P is encoded by a nucleic acid having a nucleotide sequence that has at least 65%> sequence identity to the nucleotide sequence of human C 1 qR_P (SEQ ID NO : 1 ) or murine ClqRp (SEQ

ID NO:34). -70-

17. The method of claim 14, wherein the ClqR_P is encoded by a nucleic acid having a nucleotide sequence consisting of the nucleotide sequence of SEQ ID NO.: 1 oe SEQ ID NO:34.

18. A method of identifying a test composition which effects the ability of binding of a ligand of a C 1 qR_P, the method comprising: a) incubating components comprising the test composition, the ClqR_P and the ligand of the ClqR_P wherein the incubating is carried out under conditions sufficient to permit the components to interact; and b) measuring the effect of the test composition on the binding of the ligand to the ClqRp.

19. The method of claim 18, wherein the ligand is C 1 q, MBP or SPA.

20. A method for determining whether a test composition modulates C 1 qR_P mediated intracellular signaling, the method comprising: a) providing a cell expressing a functional ClqR_P; b) contacting the cell with a ligand that in the absence of a test compound transmits a ClqR_P intracellular signal after binding of the ligand to the ClqR_P; and c) detecting a change in the intracellular signaling of the cell.

21. A method of detecting a C 1 qR_P associated disorder, wherein the method comprises contacting a sample from a subject having or suspected of having a disorder with a reagent that detects expression of the polypeptide and detecting the binding of the reagent in the sample.

22. The method of claim 21 , wherein the reagent is an antibody.

23. The method of claim 21 , wherein the reagent is a nucleic acid. -71-

24. The method of claim 23, wherein the nucleic acid hybridizes to a nucleic acid of claim 3 or claim 5.

25. The method of claim 21 , wherein the reagent comprises a detectable label.

26. A non-human transgenic animal created utilizing a human ClqR_P nucleotide 5 sequence.

27. A method for affecting the level of ClqR_P mRNA in a target cell, wherein the method comprises: a) delivering a composition comprising ClqR_P nucleic acid into a target cell; and 10 b) expressing said composition inside of the target cell.

28. The method of claim 27, further comprising detecting a change in the level of ClqRp mRNA in the target cell subsequent to step b).

29. The method of claim 27, wherein a composition comprising ClqR_P nucleic acid is introduced into the target cell in vitro.

15 30. The method of claim 27, wherein a composition comprising C 1 qR_P nucleic acid is introduced into the target cell in vivo.

31. The method of claim 27, wherein a composition comprising C 1 qR_P nucleic acid is introduced into the target cell ex vivo.

32. An antibody which binds to a polypeptide of claim 1.

20 33. The antibody of claim 32, wherein the antibody is monoclonal.

34. The antibody of claim 32, wherein the antibody is polyclonal. -72-

35. The nucleic acid molecule of claim 3, wherein said nucleic acid molecule encodes the amino acid sequence set forth in SEQ ID NO:2 or SEQ ID NO:35.

36. An in vivo cell containing a vector of claim 10.

37. An ex vivo cell containing a vector of claim 10.

38. The method of claim 27, wherein a composition comprising C 1 qR_p nucleic acid is introduced into the target cell in vitro.