Methods for enhancing graft survival by modulating heme oxygenase activity Number:7,151,090 from the United States Patent and Trademark Office (PTO) owispatent

Title: Methods for enhancing graft survival by modulating heme oxygenase activity

Abstract: Methods are provided wherein the survival of an organ transplant is enhanced by introducing into cells of the transplant a nucleic acid molecule that modulates heme oxygenase-I activity therein. Nucleic acid molecules that modulate heme oxygenase-I activity and therefore find use in the described methods include, for example, molecules that encode a polypeptide that itself exhibits heme oxygenase-I activity or antisense oligonucleotides that act to inhibit heme oxygenase-I activity in a cell.

Patent Number: 7,151,090 Issued on 12/19/2006 to Buelow,   et al.

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Inventors:	Buelow; Roland (Palo Alto, CA), Woo; Jacky (San Jose, CA), Iyer; Suhasini (San Ramon, CA)
Assignee:	Sangstat Medical Corporation (Fremont, CA)
Appl. No.:	10/782,260
Filed:	February 18, 2004

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Related U.S. Patent Documents

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	Application Number	Filing Date	Patent Number	Issue Date
	09515582	Feb., 2000	6861414
	PCT/US99/30089	Dec., 1999
	09216005	Dec., 1998

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Current U.S. Class:	514/44 ; 424/93.2; 424/93.21; 435/320.1; 435/325; 435/455
Current International Class:	A61K 31/70 (20060101); A01N 63/00 (20060101); A61K 48/00 (20060101)

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References Cited [Referenced By]

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U.S. Patent Documents

	4829984		May 1989		Gordon
	5563132		October 1996		Bodaness
	5756492		May 1998		Buelow et al.
	6013641		January 2000		Lussow et al.
	6060467		May 2000		Buelow
	6861414		March 2005		Buelow et al.

Foreign Patent Documents

	WO 96/09038		Mar., 1996		WO
	WO 98/09618		Mar., 1998		WO
	WO 98/09618		Mar., 1998		WO
	WO 99/23215		May., 1999		WO
	WO 99/23215		May., 1999		WO
	WO 00/12118		Mar., 2000		WO
	WO 00/12118		Mar., 2000		WO

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Primary Examiner: Li; Q. Janice
Attorney, Agent or Firm: Lorenz; Todd A. Dorsey & Whitney LLP

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Parent Case Text

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CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 09/515,582, filed Feb. 29, 2000, now U.S. Pat. No. 6,861,414, which is a continuation-in-part of U.S. application Ser. No. 09/216,005, filed Dec. 17, 1998, now abandoned, and is a continuation of International Application No. PCT/US99/30089, filed Dec. 17, 1999.

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Claims

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What is claimed:

1. A method for increasing the heme oxygenase level in cells of an organ transplant, comprising: contacting cells of an organ transplant with a viral vector encoding a polypeptide having heme oxygenase activity, wherein said viral vector comprises a nucleic acid having at least 80% sequence identity to nucleotides 81 944 of the human heme oxygenase-I nucleic acid sequence of SEQ ID NO:1, whereby the heme oxygenase level is increased.

2. The method of claim 1, wherein said nucleic acid comprises nucleotides 81 944 of the human heme oxygenase-I nucleic acid sequence of SEQ ID NO:1.

3. The method of claim 1, wherein said contacting is ex vivo.

4. The method of claim 1, wherein said contacting is in vivo.

5. The method of claim 1, wherein said organ transplant is an allograft.

6. The method of claim 5, wherein said allograft is a heart.

7. The method of claim 5, wherein said allograft is a liver.

8. The method of claim 5, wherein said allograft is a kidney.

9. The method of claim 1, wherein said contacting is prior to transplantation of said organ.

10. The method of claim 1, wherein said contacting is subsequent to transplantation of said organ.

11. The method of claim 1, wherein said contacting is by direct injection of said viral vector into said organ transplant.

12. A method for increasing the heme oxygenase level in cells of an organ transplant, comprising: contacting cells of an organ transplant with an adenoviral vector comprising a nucleic acid encoding a polypeptide with at least 80% amino acid sequence identity with the human heme oxygenase-I encoded by nucleotides 81 944 of the nucleic acid sequence of SEQ ID NO:1, wherein said polypeptide has heme-oxygenase activity, and whereby the level of heme oxygenase is increased.

13. The method of claim 12, wherein said polypeptide comprises human heme oxygenase encoded by nucleotides 81 944 of the nucleic acid of SEQ ID NO:1.

14. The method of claim 12, wherein said contacting is ex vivo.

15. The method of claim 12, wherein said contacting is in vivo.

16. The method of claim 12, wherein said organ transplant is an allograft.

17. The method of claim 16, wherein said allograft is a heart.

18. The method of claim 16, wherein said allograft is a liver.

19. The method of claim 16, wherein said allograft is a kidney.

20. The method of claim 12, wherein said contacting is prior to transplantation of said organ.

21. The method of claim 12, wherein said contacting is subsequent to transplantation of said organ.

22. The method of claim 12, wherein said contacting is by direct injection of said adenoviral vector into said organ.

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Description

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BACKGROUND ART

The inflammatory process is an extraordinarily complex process, varying with the cause of inflammation, the site of the inflammation, and the nature of the insult. Numerous different types of leukocytes are attracted to the site where the inflammatory process is initiated. The different leukocytes initiate different biological processes to respond to the insult. While in many situations, the inflammatory response is healthy in destroying a pathogen, in other situations, such as autoimmune diseases and transplantation, the inflammatory response is undesirable. In the latter case, this leads to rejection and loss of the implanted organ, which in most cases will be fatal.

A number of different avenues have been investigated to encourage the retention of allografts. For the most part, these avenues have involved general immunosuppression, using drugs such as cyclosporin and FK506. Extensive efforts have been directed to inducing anergy toward the foreign tissue. Also, the role of various factors has been investigated, where by modulating the level of those factors, the immune response may be diminished. For the most part, the primary approach has been the use of drugs which suppress the entire immune system, therefore leaving the patient vulnerable to adventitious infection.

Because of the restricted availability of donor organs, consideration has been given to using xenografts for temporary maintenance, while an acceptable allogenic organ is identified. The xenografts not only differ as to the MHC, but will also have numerous other epitopes differing from the host. Therefore, additional rejection mechanisms are brought to bear against the xenograft.

Heme oxygenases (HO) are the rate-limiting enzymes that catalyze the conversion of heme to biliverdin, carbon monoxide (CO) and free iron, the first step in the oxidative conversion of heme to bilirubin. Recently, great interest has been placed on the role of heme oxygenase in cellular responses to stress and insult, including ischemic and immunogenic effects. All of the end products of heme degradation, including biliverdin, bilirubin, and CO, are known to modulate immune effector functions. Biliverdin has also been shown to inhibit human complement in vitro. Bilirubin inhibits human lymphocyte responses, including PHA-induced proliferation, IL-2 production, and antibody-dependent and -independent cell-mediated cytotoxicity. In addition, heme oxygenase-I (HO-1) upregulation correlates with increased production of nitric oxide (NO), an important effector molecule involved in inflammation and immune regulation. On the other hand, NO is also known to induce HO-1 expression, while CO directly inhibits nitric oxide synthase (NOS) activity by binding to the heme moiety of the NOS enzyme and thus downregulating NO production. Like NO, CO contributes to endothelium-dependent vasodilation and inhibits platelet aggregation by elevating intracellular cGMP levels. The deleterious effects of hyperoxia are thought to be mediated by reactive oxygen species. Both biliverdin and bilirubin are efficient peroxyl radical scavengers that inhibit lipid peroxidation. Bilirubin scavenges peroxyl radicals as efficiently as .alpha.-tocopherol, which is regarded as the most potent antioxidant of lipid peroxidation. On the other hand, oxygen radicals may trigger cascade of antiapoptotic events, including those that involve activation of bcl-2 protooncogene. All these factors point to a complex picture of putative regulatory interactions between the HO system and the host cytokine network set in motion through the biological activity of heme degradation products.

There is a pressing need to find alternative modalities which will enhance and extend transplant survival. These modalities may find use in conjunction with other drugs, where lower levels of other drugs having significant side effects may be used effectively, to reduce the detrimental side effects. Thus, there is substantial interest in developing new approaches to improving transplant outcome, where a drug may act by itself or in conjunction with other drugs.

BRIEF DESCRIPTION OF THE RELEVANT LITERATURE

Heme oxygenase has been the subject of numerous studies as evidenced by the review article, Abraham et al., Int. J. Biochem. 20(6):543 558 (1988). Recently, modulation of heme oxygenase activity has been described in Raju and Maines, Biochimica et Biophysica Acta 1217:273 280 (1994); Neil et al., J. of Ocular Pharmacology and Therapeutics 11(3):455 468 (1995); Haga et al., ibid., 1316:29 34 (1996); Willis et al., Nature Medicine 2(1):87 90 (1996); and Agarwal et al., Transplantation 61(1):93 98 (1996).

SUMMARY

In one embodiment of the present invention, methods are provided for extending the survival of an organ transplant in a recipient, wherein those methods comprise contacting the organ transplant with a nucleic acid that functions to modulate heme oxygenase-I activity in those cells, whereby the survival time of the organ transplant in the recipient is extended. In one embodiment, the nucleic acid encodes a heme oxygenase polypeptide.

Yet another embodiment of the present invention is directed to methods for extending the survival of an organ transplant in a recipient, wherein the methods comprise contacting cells of the organ transplant with a nucleic acid encoding a polypeptide having heme oxygenase activity, wherein the nucleic acid is expressed in the cells in an amount sufficient to increase heme oxygenase activity therein, whereby the survival time of the transplant is extended. Additional embodiments will become evident upon a reading of the present specification.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a graph of the inhibition of target cell lysis by treatment with metalloprotoporphyrins. T-cell mediated cell lysis was evaluated in the presence of varying amounts of Zn- and Co-protoporphyrin in a four hour chromium release assay.

FIG. 2 is a graph showing the prolongation of heart allograft survival following metalloprotoporphyrin therapy. CBA recipients of C57B1/6 heart allografts were either untreated or treated as follows: Zn-protoporphyrin group (n=4); Zn-protoporphyrin was administered at 10 mg/kg/day on day -1 before transplantation and on days 1 9 post transplantation. Co-protoporphyrin group (n=4); Co-protoporphyrin was administered at 20 mg/kg/day on days 0 5 post-transplantation; Zn-protoporphyrin pretreatment group (n=3); heart donors were treated one day before transplantation with 50 mg/kg Zn-protoporphyrin.

FIG. 3 shows the nucleic acid sequence (SEQ ID NO:1) of a cDNA encoding human heme oxygenase-I (nucleotides 81 944).

FIG. 4 shows results demonstrating prolongation of liver isograft survival. Lean Zucker rats served as recipients of liver transplants from obese Zucker donors. Donor rats were either pretreated with CoPP or Ad-HO-1 or remained untreated before liver procurement followed by 4 hours of cold ischemia. Control animal survival at 14 days was 40% (.diamond-solid.) versus 80% (.box-solid.) and 81.8% (.tangle-solidup.) in the CoPP and the Ad-HO-1 group, respectively (n=10 11 rats/group).

FIG. 5 shows bile production in fatty livers perfused for 2 hours on the isolated perfusion rat liver apparatus after 6 hours of cold ischemia. Animals were pretreated with metalloporphyrins, or with Ad-HO-1 gene transfer, or left untreated. Bile production at 30-minute intervals throughout the reperfusion period was significantly higher in the CoPP/Ad-HO-1 groups (*P<0.05) as compare d with untreated, ZnPP-, or Ad-.beta. Gal--pretreated controls. These data represent the mean.+-.SE of 4 10 independent perfusions for each group. *P<0.05 versus untreated/ZnPP-treated controls.

DESCRIPTION OF SPECIFIC EMBODIMENTS

Methods are herein provided for prolonging the survival of transplants in a mammalian host. In a preferred embodiment, the methods comprise contacting cells of the organ transplant with a nucleic acid molecule that functions to modulate heme oxygenase-I (HO-1) activity in cells of the organ transplant, whereby the survival time of the organ transplant in the recipient is extended. For the most part, nucleic acid molecules that function to modulate HO-1 activity in cells will be nucleic acid molecules that encode a polypeptide that exhibits at least one biological activity that is normally associated with the human HO-1 polypeptide encoded by nucleotides 81 944 of the nucleic acid shown in FIG. 3 (SEQ ID NO:1) or will be antisense oligonucleotides whose sequences are derived from and/or based upon nucleotides 81 944 of the human heme oxygenase-I nucleotide sequence shown in FIG. 3 (SEQ ID NO:1) or non-coding sequences of a heme oxygenase-encoding nucleic acid molecule.

By "heme oxygenase-I", "HO-1" and grammatical equivalents thereof is meant the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1) and homologs thereof which exhibit at least one biological activity that is normally associated with the human heme oxygenase-I enzyme. Preferably, the heme oxygenase-I activity exhibited by the polypeptides is the ability to catalyze the first step in the oxidative degradation of heme to bilirubin (Tenhunen et al., J. Biol. Chem. 244:6388 6394 (1969) and Tenhunen et al., J. Lab. Clin. Med. 75:410 421 (1970)). In this regard, Applicants note that quick, easy and reliable assays are known in the art to determine whether a polypeptide exhibits heme oxygenase-I activity, wherein those assays may be routinely employed to test the ability of any polypeptide for the presence of heme oxygenase-I activity. For example, the production of bilirubin from heme can be determined using a spectrophotometer, whereby the increase in optical density at 468 m.mu. in a mixture of the peptide, hemin, biliverdin reductase and NADPH indicates heme oxygenase activity.

The terms "polypeptide" and "protein" may be used interchangeably throughout this application and mean at least two covalently attached amino acids, which includes proteins, polypeptides, oligopeptides and peptides. The protein may be made up of naturally occurring amino acids and peptide bonds, or synthetic peptidomimetic structures. Thus "amino acid", or "peptide residue", as used herein means both naturally occurring and synthetic amino acids. For example, homo-phenylalanine, citrulline and noreleucine are considered amino acids for the purposes of the invention. "Amino acid" also includes imino acid residues such as proline and hydroxyproline. The side chains may be in either the (R) or the (S) configuration. In the preferred embodiment, the amino acids are in the (S) or L-configuration. If non-naturally occurring side chains are used, non-amino acid substituents may be used, for example to prevent or retard in vivo degradations.

Also encompassed by "heme oxygenase-I", "HO-1", etc. are homolog polypeptides having at least about 80% sequence identity, usually at least about 85% sequence identity, preferably at least about 90% sequence identity, more preferably at least about 95% sequence identity and most preferably at least about 98% sequence identity with the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1) and which exhibit at least one biological activity that is normally associated with the human heme oxygenase-I enzyme.

By "nucleic acid molecules that encode NO-1", "nucleic acid molecules encoding a polypeptide having heme oxygenase-I activity" and grammatical equivalents thereof is meant the nucleotide sequence of human heme oxygenase-I as shown nucleotides 81 944 of FIG. 3 (SEQ ID NO:1) as well as nucleotide sequences having at least about 80% sequence identity, usually at least about 85% sequence identity, preferably at least about 90% sequence identity, more preferably at least about 95% sequence identity and most preferably at least about 98% sequence identity with nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1) and which encode a polypeptide that exhibits at least one biological activity that is normally associated with the human heme oxygenase-I enzyme.

As is known in the art, a number of different programs can be used to identify whether a protein or nucleic acid has sequence identity or similarity to a known sequence. Sequence identity and/or similarity is determined using standard techniques known in the art, including, but not limited to, the local sequence identity algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the sequence identity alignment algorithm of Needleman and Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Drive, Madison, Wis.), the Best Fit sequence program described by Devereux et al., Nucleic Acids Res. 12:387 395 (1984), preferably using the default settings, or by inspection. Preferably, percent identity is calculated by FastDB based upon the following parameters: mismatch penalty of 1; gap penalty of 1; gap size penalty of 0.33; and joining penalty of 30, "Current Methods in Sequence Comparison and Analysis," Macromolecule Sequencing and Synthesis, Selected Methods and Applications, pp 127 149, Alan R. Liss, Inc. (1988).

An example of a useful algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng and Doolittle, J. Mol. Evol. 35:351 360 (1987); the method is similar to that described by Higgins and Sharp, CABIOS 5:151 153 (1989). Useful PILEUP parameters including a default gap weight of 3.00, a default gap length weight of 0.10, and weighted end gaps.

Another example of a useful algorithm is the BLAST algorithm, described in Altschul et al., J. Mol. Biol. 215:403 410, (1990) and Karlin et al., Proc. Natl. Acad. Sci. USA 90:5873 5787 (1993). A particularly useful BLAST program is the WU-BLAST-2 program which was obtained from Altschul et al., Methods in Enzymology 266:460 480 (1996) (available at world wide web site blast.wust/edu/blast/README.html). WU-BLAST-2 uses several search parameters, most of which are set to the default values. The adjustable parameters are set with the following values: overlap span=1, overlap fraction=0.125, word threshold (T)=11. The HSP S and HSP S2 parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched; however, the values may be adjusted to increase sensitivity.

An additional useful algorithm is gapped BLAST as reported by Altschul et al., Nucleic Acids Res. 25:3389 3402. Gapped BLAST uses BLOSUM-62 substitution scores; threshold T parameter set to 9; the two-hit method to trigger ungapped extensions; charges gap lengths of k a cost of 10+k; X.sub.u set to 16, and X.sub.g set to 40 for database search stage and to 67 for the output stage of the algorithms. Gapped alignments are triggered by a score corresponding to .about.22 bits.

A percent (%) amino acid or nucleic acid sequence identity value is determined by the number of matching identical residues divided by the total number of residues of the "longer" sequence in the aligned region. The "longer" sequence is the one having the most actual residues in the aligned region (gaps introduced by WU-Blast-2 to maximize the alignment score are ignored).

The alignment may include the introduction of gaps in the sequences to be aligned. In addition, for sequences which contain either more or fewer amino acids than the amino acid sequence of the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1), it is understood that in one embodiment, the percentage of sequence identity will be determined based on the number of identical amino acids in relation to the total number of amino acids. Thus, for example, sequence identity of sequences shorter than that of the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1), as discussed below, will be determined using the number of amino acids in the shorter sequence, in one embodiment. In percent identity calculations relative weight is not assigned to various manifestations of sequence variation, such as, insertions, deletions, substitutions, etc.

In one embodiment, only identities are scored positively (+1) and all forms of sequence variation including gaps are assigned a value of "0", which obviates the need for a weighted scale or parameters as described below for sequence similarity calculations. Percent sequence identity can be calculated, for example, by dividing the number of matching identical residues by the total number of residues of the "shorter" sequence in the aligned region and multiplying by 100. The "longer" sequence is the one having the most actual residues in the aligned region.

Heme oxygenase-I having less than 100% sequence identity with the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1) will generally be produced from native heme oxygenase-I nucleotide sequences from species other than human and variants of native heme oxygenase-I nucleotide sequences from human or non-human sources. In this regard, it is noted that many techniques are well known in the art and may be routinely employed to produce nucleotide sequence variants of native heme oxygenase-I sequences and assaying the polypeptide products of those variants for the presence of at least one activity that is normally associated with a native heme oxygenase-I polypeptide.

Polypeptides having heme oxygenase-I activity may be shorter or longer than the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1). Thus, in a preferred embodiment, included within the definition of heme oxygenase-I polypeptide are portions or fragments of the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1). In one embodiment herein, fragments of the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1) are considered heme oxygenase-I polypeptides if a) they have at least the indicated sequence identity; and b) preferably have a biological activity of naturally occurring heme oxygenase-I, as described above.

In addition, as is more fully outlined below, heme oxygenase-I can be made longer than the polypeptide encoded by nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1); for example, by the addition of other fusion sequences, or the elucidation of additional coding and non-coding sequences.

The heme oxygenase-I polypeptides are preferably recombinant. A "recombinant polypeptide" is a polypeptide made using recombinant techniques, i.e., through the expression of a recombinant nucleic acid as described below. In a preferred embodiment, the heme oxygenase-I of the invention is made through the expression of nucleotides 81 944 of the nucleotide sequence shown in FIG. 3 (SEQ ID NO:1), or fragment thereof. A recombinant polypeptide is distinguished from naturally occurring protein by at least one or more characteristics. For example, the polypeptide may be isolated or purified away from some or all of the proteins and compounds with which it is normally associated in its wild type host, and thus may be substantially pure. For example, an isolated polypeptide is unaccompanied by at least some of the material with which it is normally associated in its natural state, preferably constituting at least about 0.5%, more preferably at least about 5% by weight of the total protein in a given sample. A substantially pure polypeptide comprises at least about 75% by weight of the total polypeptide, with at least about 80% being preferred, and at least about 90% being particularly preferred. The definition includes the production of a heme oxygenase-I polypeptide from one organism in a different organism or host cell. Alternatively, the polypeptide may be made at a significantly higher concentration than is normally seen, through the use of an inducible promoter or high expression promoter, such that the polypeptide is made at increased concentration levels. Alternatively, the polypeptide may be in a form not normally found in nature, as in the addition of amino acid substitutions, insertions and deletions, as discussed below.

As used herein and further defined below, "nucleic acid" may refer to either DNA or RNA, or molecules which contain both deoxy- and ribonucleotides. The nucleic acids include genomic DNA, cDNA and oligonucleotides including sense and anti-sense nucleic acids. Such nucleic acids may also contain modifications in the ribose-phosphate backbone to increase stability and half-life of such molecules in physiological environments.

The nucleic acid may be double stranded, single stranded, or contain portions of both double stranded or single stranded sequence. As will be appreciated by those in the art, the depiction of a single strand ("Watson") also defines the sequence of the other strand ("Crick"); thus the sequences depicted in FIGS. 1 and 3 also include the complement of the sequence. By the term "recombinant nucleic acid" herein is meant nucleic acid, originally formed in vitro, in general, by the manipulation of nucleic acid by endonucleases, in a form not normally found in nature. Thus an isolated nucleic acid, in a linear form, or an expression vector formed in vitro by ligating DNA molecules that are not normally joined, are both considered recombinant for the purposes of this invention. It is understood that once a recombinant nucleic acid is made and reintroduced into a host cell or organism, it will replicate non-recombinantly, i.e., using the in vivo cellular machinery of the host cell rather than in vitro manipulations; however, such nucleic acids, once produced recombinantly, although subsequently replicated non-recombinantly, are still considered recombinant for the purposes of the invention.

In one embodiment, the present invention provides nucleic acids encoding heme oxygenase-I variants. These variants fall into one or more of three classes: substitutional, insertional or deletional variants. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in nucleotides 81 944 of the nucleic acid shown in FIG. 3 (SEQ ID NO:1), using cassette or PCR mutagenesis or other techniques well known in the art, to produce DNA encoding the variant, and thereafter expressing the DNA in a transplant graft, as described below, or a recombinant cell culture as outlined above. Amino acid sequence variants are characterized by the predetermined nature of the variation, a feature that sets them apart from naturally occurring allelic or interspecies variation of the heme oxygenase-I amino acid sequence. The variants typically exhibit the same qualitative biological activity as the naturally occurring analogue, although variants can also be selected which have modified characteristics as will be more fully outlined below.

While the site or region for introducing a sequence variation is predetermined, the mutation per se need not be predetermined. For example, in order to optimize the performance of a mutation at a given site, random mutagenesis may be conducted at the target codon or region and the expressed variants screened for the optimal desired activity. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, for example, M13 primer mutagenesis and PCR mutagenesis. Another example of a technique for making variants is the method of gene shuffling, whereby fragments of similar variants of a nucleotide sequence are allowed to recombine to produce new variant combinations. Examples of such techniques are found in U.S. Pat. Nos. 5,605,703; 5,811,238; 5,873,458; 5,830,696; 5,939,250; 5,763,239; 5,965,408; and 5,945,325, each of which is incorporated by reference herein in its entirety. Screening of the mutants is done using assays of heme oxygenase activities, as described above.

Amino acid substitutions are typically of single residues; insertions usually will be on the order of from about 1 to 20 amino acids, although considerably larger insertions may be tolerated. Deletions range from about 1 to about 20 residues, although in some cases deletions may be much larger.

Substitutions, deletions, insertions or any combination thereof may be used to arrive at a final derivative. Generally these changes are done on a few amino acids to minimize the alteration of the molecule. However, larger changes may be tolerated in certain circumstances. When small alterations in the characteristics of the heme oxygenase-I are desired, substitutions are generally made in accordance with the following chart:

TABLE-US-00001 Chart I Original Residue Exemplary Substitutions Ala Ser Arg Lys Asn Gln, His Asp Glu Cys Ser Gln Asn Glu Asp Gly Pro His Asn, Gln Ile Leu, Val Leu Ile, Val Lys Arg, Gln, Glu Met Leu, Ile Phe Met, Leu, Tyr Ser Thr Thr Ser Trp Tyr Tyr Trp, Phe Val Ile, Leu

Substantial changes in function or immunological identity are made by selecting substitutions that are less conservative than those shown in Chart I. For example, substitutions may be made which more significantly affect: the structure of the polypeptide backbone in the area of the alteration, for example the alpha-helical or beta-sheet structure; the charge or hydrophobicity of the molecule at the target site; or the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in the polypeptide's properties are those in which (a) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine.

The variants typically exhibit the same qualitative biological activity and will elicit the same immune response as the naturally occurring analogue, although variants also are selected to modify the characteristics of the heme oxygenase-I as needed. Alternatively, the variant may be designed such that the biological activity of the protein is altered.

One type of covalent modification of a polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of the polypeptide. "Altering the native glycosylation pattern" is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence heme oxygenase-I polypeptide, and/or adding one or more glycosylation sites that are not present in the native sequence polypeptide.

Addition of glycosylation sites to polypeptides may be accomplished by altering the amino acid sequence thereof. The alteration may be made, for example, by the addition of, or substitution by, one or more serine or threonine residues to the native sequence polypeptide (for O-linked glycosylation sites). The amino acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids.

Removal of carbohydrate moieties present on the polypeptide may be accomplished by mutational substitution of codons encoding for amino acid residues that serve as targets for glycosylation.

To produce HO-1 protein to test for heme oxygenase activity, heme oxygenase-I is cloned and expressed as outlined below. Thus, probe or degenerate polymerase chain reaction (PCR) primer sequences may be used to find other related heme oxygenase-I polypeptides from humans or other organisms. As will be appreciated by those in the art, particularly useful probe and/or PCR primer sequences include the unique areas of the nucleic acid sequence shown in FIG. 3 (SEQ ID NO:1). As is generally known in the art, preferred PCR primers are from about 15 to about 35 nucleotides in length, with from about 20 to about 30 being preferred, and may contain inosine as needed. The conditions for the PCR reaction are well known in the art. It is therefore also understood that provided along with the sequences provided herein are portions of those sequences, wherein unique portions of 15 nucleotides or more are particularly preferred. The skilled artisan can routinely synthesize or cut a nucleotide sequence to the desired length.

Once isolated from its natural source, e.g., contained within a plasmid or other vector or excised therefrom as a linear nucleic acid segment, the recombinant nucleic acid can be further-used as a probe to identify and isolate other nucleic acids. It can also be used as a "precursor" nucleic acid to make modified or variant nucleic acids and proteins.

Using the nucleic acids of the present invention which encode a protein, a variety of expression vectors can be made. The expression vectors may be either self-replicating extrachromosomal vectors or vectors which integrate into a host genome. Generally, these expression vectors include transcriptional and translational regulatory nucleic acid operably linked to the nucleic acid encoding the protein. The term "control sequences" refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.

Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. As another example, operably linked refers to DNA sequences linked so as to be contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice. The transcriptional and translational regulatory nucleic acid will generally be appropriate to the host cell used to express the heme oxygenase-I; for example, transcriptional and translational regulatory nucleic acid sequences from Bacillus are preferably used to express the heme oxygenase-I in Bacillus. Numerous types of appropriate expression vectors, and suitable regulatory sequences are known in the art for a variety of host cells.

In general, the transcriptional and translational regulatory sequences may include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences. In a preferred embodiment, the regulatory sequences include a promoter and transcriptional start and stop sequences.

Promoter sequences encode either constitutive or inducible promoters. The promoters may be either naturally occurring promoters or hybrid promoters. Hybrid promoters, which combine elements of more than one promoter, are also known in the art, and are useful in the present invention.

In addition, the expression vector may comprise additional elements. For example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, for example in mammalian or insect cells for expression and in a procaryotic host for cloning and amplification. Furthermore, for integrating expression vectors, the expression vector contains at least one sequence homologous to the host cell genome, and preferably two homologous sequences which flank the expression construct. The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. Constructs for integrating vectors are well known in the art.

In addition, in a preferred embodiment, the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selection genes are well known in the art and will vary with the host cell used.

A preferred expression vector system is a retroviral vector system such as is generally described in WO 97/27212 and WO 97/27213, both of which are hereby expressly incorporated by reference.

Proteins of the present invention are produced by culturing a host cell transformed with an expression vector containing nucleic acid encoding the protein, under the appropriate conditions to induce or cause expression of the protein. The conditions appropriate for protein expression will vary with the choice of the expression vector and the host cell, and will be easily ascertained by one skilled in the art through routine experimentation. For example, the use of constitutive promoters in the expression vector may require optimizing the growth and proliferation of the host cell, while the use of an inducible promoter requires the appropriate conditions for induction. In addition, in some embodiments, the timing of the harvest is important. For example, the baculoviral systems used in insect cell expression are lytic viruses, and thus harvest time selection can be crucial for product yield.

Appropriate host cells include yeast, bacteria, archaebacteria, fungi, and insect and animal cells, including mammalian cells. Of particular interest are Drosophila melanogaster cells, Saccharomyces cerevisiae and other yeasts, E. coli, Bacillus subtilis, SF9 cells, C129 cells, 293 cells, Neurospora, BHK, CHO, COS, and HeLa cells, fibroblasts, Schwanoma cell lines, immortalized mammalian myeloid and lymphoid cell lines, tumor cell lines, and B lymphocytes.

In a preferred embodiment, the proteins are expressed in mammalian cells. Mammalian expression systems are also known in the art, and include retroviral systems. A mammalian promoter is any DNA sequence capable of binding mammalian RNA polymerase and initiating the downstream (3') transcription of a coding sequence for a protein into mRNA. A promoter will have a transcription initiating region, which is usually placed proximal to the 5' end of the coding sequence, and a TATA box, using a located 25 30 base pairs upstream of the transcription initiation site. The TATA box is thought to direct RNA polymerase II to begin RNA synthesis at the correct site. A mammalian promoter will also contain an upstream promoter element (enhancer element), typically located within 100 to 200 base pairs upstream of the TATA box. An upstream promoter element determines the rate at which transcription is initiated and can act in either orientation. Of particular use as mammalian promoters are the promoters from mammalian viral genes, since the viral genes are often highly expressed and have a broad host range. Examples include the SV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirus major late promoter, herpes simplex virus promoter, and the CMV promoter.

Typically, transcription termination and polyadenylation sequences recognized by mammalian cells are regulatory regions located 3' to the translation stop codon and thus, together with the promoter elements, flank the coding sequence. The 3' terminus of the mature mRNA is formed by site-specific post-translational cleavage and polyadenylation. Examples of transcription terminator and polyadenlytion signals include those derived form SV40.

The methods of introducing exogenous nucleic acid into mammalian hosts, as well as other hosts, is well known in the art, and will vary with the host cell used. Techniques include dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, protoplast fusion, electroporation, viral infection, encapsulation of the polynucleotide(s) in liposomes, and direct microinjection of the DNA into nuclei.

Proteins may be expressed in bacterial systems. Bacterial expression systems are well known in the art.

A suitable bacterial promoter is any nucleic acid sequence capable of binding bacterial RNA polymerase and initiating the downstream (3') transcription of the coding sequence of cell cycle protein into mRNA. A bacterial promoter has a transcription initiatio