# Patent

## Title
Composition and method for inhibiting tumor cell growth

## Abstract

Polynucleotides encoding a secreted mutant human carboxylesterase enzyme and polypeptides encoded by the polynucleotides which are capable of metabolizing a prodrug and inactive metabolites thereof to active drug are provided. Compositions and methods for sensitizing cells to a prodrug agent, inhibiting cell growth, treating drug addiction, and facilitating the metabolism of an organophosphate with this enzyme are also provided. In addition, a screening assay for identification of drugs activated by this enzyme is described.

## Background
INTRODUCTION
This application is a continuation-in-part of U.S. Ser. No. 13/356,776, filed Jan. 24, 2012, which is a divisional of U.S. Ser. No. 13/020,871 filed Feb. 4, 2011, now issued as U.S. Pat. No. 8,124,393, which is a divisional of U.S. Ser. No. 12/306,031 filed Jan. 28, 2009, now issued as U.S. Pat. No. 7,906,637, which is the U.S. National Phase of PCT/US2007/071640 filed Jun. 20, 2007 which claims benefit of U.S. Provisional Ser. No. 60/805,643, filed Jun. 23, 2006, the contents of which are incorporated herein by reference in their entireties.


This invention was made with government support under grant numbers CA76202, CA79763, CA98468, CA108775, DA18116 awarded by National Institutes of Health and grant number P30 CA 21765 awarded by Cancer Center Core. The government has certain rights in the invention.


BACKGROUND
Development of effective human anti-cancer drugs has often been hindered by the inability of tested agents to selectively target tumor cells over non-tumor cells. This lack of selectivity of many anti-cancer drugs often leads to unwanted and often serious side effects in patients that can limit the dose of the drug administered. A goal of all human drug therapies, regardless of the disease or condition being treated, is to be able to administer the lowest dose of a drug that produces the desired clinical effect. Therefore, strategies for more efficient drug delivery are continuously sought.
In the case of certain anti-cancer drugs, one strategy has been development of prodrug forms of active compounds that can increase the bioavailability of the drug and increase its ability to effectively kill tumor cells. One example of this prodrug strategy has been the development of carboxylesterase (CE) pro-drugs (Roosebaum, et al. 2004. Pharmacol. Rev. 56:53-102).
CEs are ubiquitous serine esterase enzymes that catalyze conversion of carboxylic esters to an alcohol and a carboxylic acid as well as hydrolyzing amides, thioesters, phosphoric acid esters and acid anhydrides. In some cases, CE enzyme activity is responsible for the detoxification of xenobiotics. CEs are present in high levels in both normal and tumor tissue, especially in liver, kidney, testis, lung and plasma. In addition to their known ability to detoxify certain chemicals, recent research has focused on the ability of these enzymes to be used in design of prodrug forms of certain cytostatic drugs (Roosebaum, et al. 2004. Pharmacol. Rev. 56:53-102). Examples of the application of CE activity to prodrug development are CPT-11, paclitaxel-2-ethylcarbonate, and capecitabine. In all three of these cases, CE activity leads to production of an active cytostatic drug, SN-38, paclitaxel, and 5′-DUFR, respectively. In addition, a particular human CE known as hCE1 has been shown to catalyze the hydrolysis of certain drugs of abuse, specifically heroin and cocaine, and to catalyze the transesterification of cocaine in the presence of ethanol to its toxic metabolite, cocaethylene (Redinbo, et al. 2003. Biochem. Soc. Trans. 31:620-624). hCE1 is also being developed by the United States military as a prophylactic agent for treating potential exposures to chemical weapons such as the organophosphates Sarin, Soman, Tabun, and VX gas (Redinbo, et al. 2003. Biochem. Soc. Trans. 31:620-624).
CPT-11 (irinotecan, 7-ethyl-10-[4-(1-piperidino)-1-piperidino]carbonyloxycamptothecin) is a prodrug that has been investigated for the treatment of cancer, and is converted to the active drug known as SN-38 (7-ethyl-10-hydroxy-camptothecin) (Tsuji, et al. 1991. J. Pharmacobiol. Dynamics 14:341-349; Satoh, et al. 1994. Biol. Pharm. Bull. 17:662-664). SN-38 is a potent inhibitor of topoisomerase I (Tanizawa, et al. 1994. J. Natl. Cancer Inst. 86:836-842; Kawato, et al. 1991. Cancer Res. 51:4187-4194), an enzyme whose inhibition in cells results in DNA damage and induction of apoptosis (Hsiang, et al. 1989. Cancer Res. 49:5077-5082). In addition to metabolism to SN-38, in humans CPT-11 is also metabolized to a compound known as APC (Haaz, et al. 1998. Cancer Res. 58:468-472). APC has little, if any, anti-tumor activity and is not converted to an active metabolite in humans (Rivory, et al. 1996. Cancer Res. 56:3689-3694). CPT-11 has demonstrated remarkable anti-tumor activity in pre-clinical models and Phase I/II clinical trials (Furman, et al. 1999. J. Clin. Oncol. 17:1815-1824; Houghton, et al. 1996. Clin. Cancer Res. 2:107-118; Houghton, et al. 1995. Cancer Hcemother. Pharmacol. 36:393-403), and as such is being tested against a variety of human malignancies. However, myelosuppression and secretory diarrhea limit the amount of drug that can be administered to patients. Accordingly, before this promising anti-cancer agent can be used successfully, these dose-limiting toxicities must be overcome. CPT-11 is currently approved for use in human colon cancer.
The active anti-tumor agent of CPT-11, SN-38, can be detected in the plasma of animals and humans minutes after the administration of CPT-11 (Stewart, et al. 1997. Cancer Chemother. Pharmacol. 40:259-265; Kaneda, et al. 1990. Cancer Res. 50:1715-1720; Rowinsky, et al. 1994. Cancer Res. 54:427-436), suggesting that a CE enzyme present in either serum or tissues can convert the camptothecin analog to its active metabolite. When CPT-11 is administered to humans, typically less than 5% of the drug is converted to SN-38, which is in contrast to mice where greater than 50% of the drug is hydrolyzed to SN-38 within the first hour of dosing (Morton, et al. 2005. Cancer Chemother. Pharmacol. 56:629-636). This may be due to either the different levels of CEs expressed in these species, or the proficiency of drug hydrolysis of the different CEs.
Since the activation of CPT-11 in humans is relatively inefficient, CE enzyme prodrug therapy approaches have been examined. For example, an enzyme/prodrug therapy approach using a rabbit liver CE (rCE) which is much more efficient at drug activation has been developed (Danks, et al. 1999. Cancer Res. 5:917-924; Meck, et al. 2001. Cancer Res. 61:5083-5089; Potter, et al. 1998. Cancer Res. 52:2646-2651; Wagner, et al. 2002. Cancer Res. 62:5001-5007; Wierdl, et al. 2001. Cancer Res. 61:5078-5082). Using the rCE in therapy, increased sensitivity to CPT-11 was accomplished in human tumor cells grown in culture and in xenografts in immune-deprived mice. It has been suggested, however, that the application of the rCE to human therapy may be limited due to the potential immunogenicity of the lagomorph protein. Human CE enzymes have been examined, but, in vitro studies suggest that human intestinal CE (hiCE) is not as efficient at drug activation when compared to rCE (Humerickhouse, et al. 2000. Cancer Res. 60:1189-1192; Khanna, et al. 2000. Cancer Res. 60:4725-4728). Additionally, while sensitization of cells to CPT-11 expressing hiCE has been reported (e.g., Khanna, et al. 2000. Cancer Res. 60:4725-4728), studies indicate that the levels and duration of hiCE expressed are much lower than can be achieved with rCE.
The development of new effective treatment strategies for cancer is dependent upon the availability of specific drug screening assays. Specific drug screening assays can involve isolated target tissue models, i.e., isolated heart, ileum, vasculature, or liver from animals such as rabbits, rats, and guinea pigs, wherein the target tissue is removed from the animal and a selected activity of that target tissue is measured both before and after exposure to the candidate drug. An example of a selected activity measured in drug screening assays to identify new cancer agents is the activity of enzymes such as topoisomerase I or II, which are known to modulate cell death. Such assays can also be used to screen for potential prodrugs which are converted to the active metabolite in selected tissues or to identify selected tissues capable of converting prodrug to its active metabolite.
However, any molecular event that is shown to be modified by a novel class of compounds can be developed as a screening assay for selection of the most promising compounds for therapeutic development. In fact, the idea of modulating cells at the genomic level has been applied to the treatment of diseases such as cancer. Gene therapy for treatment of cancer has been the focus of multiple clinical trials approved by the National Institutes of Health Recombinant DNA Advisory Committee, many of which have demonstrated successful clinical application (Hanania, et al. 1995. Am. Jour. Med. 99:537-552; Johnson, et al. 1995. J. Am. Acad. Derm. 32(5):689-707; Barnes, et al. 1997. Obstetrics and Gynecology 89:145-155; Davis, et al. 1996. Current Opinion in Oncology 8:499-508; Roth and Cristiano 1997. J. Natl. Canc. Inst. 89(1):21-39). To specifically target malignant cells and spare normal tissue, cancer gene therapies must combine selective gene delivery with specific gene expression, specific gene product activity, and, possibly, specific drug activation. Significant progress has been made in recent years using both viral (retrovirus, adenovirus, adeno-associated virus) and nonviral (liposomes, gene gun, injection) methods to efficiently deliver DNA to tumor sites. Genes can be transfected into cells by physical means such as scrape loading or ballistic penetration, by chemical means such as coprecipitation of DNA with calcium phosphate or liposomal encapsulation; or by electro-physiological means such as electroporation. The most widely used methods, however, involve transduction of genes by means of recombinant viruses, taking advantage of the relative efficiency of viral infection processes. Current methods of gene therapy involve infection of organisms with replication-deficient recombinant viruses containing the desired gene. The replication-deficient viruses most commonly used include retroviruses, adenoviruses, adeno-associated viruses, lentiviruses and herpes viruses. The efficacy of viral-mediated gene transfer can approach 100%, enabling the potential use of these viruses for the transduction of cells in vivo.
Adenovirus vector systems in particular have several advantages. These include the fact that non-dividing cells can be transduced; transduced DNA does not integrate into host cell DNA, thereby negating insertional mutagenesis; the design of adenoviral vectors allows up to 7 kb of foreign DNA to be incorporated into the viral genome; very high viral titers can be achieved and stored without loss of infectivity; and appropriate plasmids and packaging cell lines are available for the rapid generation of infectious, replication-deficient virus (Yang 1992. Crit. Rev. Biotechnol. 12:335-356). The effectiveness of adenoviral-mediated delivery of genes into mammalian cells in culture and in animals has been demonstrated.
To increase the specificity and safety of gene therapy for treatment of cancer, expression of the therapeutic gene within the target tissue must also be tightly controlled. For tumor treatment, targeted gene expression has been analyzed using tissue-specific promoters such as breast, prostate and melanoma specific promoters and tumor-specific responsive promoters such as carcinoembryonic antigen, HER-2/neu, Myc-Max response elements, DF3/MUC (Dachs, et al. 1997. Oncol. Res. 9:313-25). For example, the utility of herpes simplex virus thymidine kinase (HSV-TK) gene ligated with four repeats of the Myc-Max response element, CACGTG, as a gene therapy agent for treatment of lung cancer with ganciclovir was examined in c-, L- or N-myc-overexpressing small cell lung cancer (SCLC) cell lines (Kumagai, et al. 1996. Cancer Res. 56(2):354-358). Transduction of the HSV-TK gene ligated to this CACGTG core rendered individual clones of all three SCLC lines more sensitive to ganciclovir than parental cells in vitro, thus suggesting that a CACGTG-driven HSV-TK gene may be useful for the treatment of SCLC overexpressing any type of myc family oncogene. Additional experiments with c-myc have focused on the use of the ornithine decarboxylase (ODC) promoter gene. Within the first intron of the ODC gene are two CACGTG “E boxes” that provide binding sites for the c-myc protein when bound to its partner protein known as max. Mutation of the E box sequence results in the inability of c-myc to transactivate the ODC promoter. Previous reports indicate that reporter constructs containing the ODC promoter fused upstream of the chloramphenicol acetyltransferase gene immediately adjacent to the second exon were activated in cells that overexpress c-myc (Bello-Fernandez, et al. 1993. Proc. Natl Acad. Sci. USA 90:7804-7808). In contrast, transient transfection of promoter constructs in which the E boxes were mutated (CACGTG to CACCTG) demonstrate significantly lower reporter gene activity. These data suggest that it is possible to activate transcription of specific genes under control of the c-myc responsive ODC promoter. In the case of N-myc, N-myc protein is a basic helix-loop-helix (BHLH) protein that can dimerize with proteins of the same class. N-myc dimerizes with the BHLH protein max to form a complex that binds to the CACGTG motif present in gene promoters, such as ODC, resulting in transactivation and expression of specific genes containing this sequence (Lutz, et al. 1996. Oncogene 13:803-812). Studies in a neuroblastoma cell line and tumors have shown that binding of N-myc to its consensus DNA binding sequence correlates with N-myc expression, data that indicate that the level of N-myc in neuroblastoma cells is a determining factor in expression of proteins under control of promoters containing the CACGTG sequence (Raschella, et al. 1994. Cancer Res. 54:2251-2255). Inhibition of expression of the c-myc gene via antisense oligonucleotides as a means for inhibiting tumor growth has also been disclosed (Kawasaki, et al. 1996. Artif. Organs 20(8):836-48).
In the present invention, a mutant human CE has been developed that can activate CPT-11 as efficiently as CE from rabbit liver (rCE). Polynucleotides encoding this mutated human carboxylesterase enzyme or active fragments thereof and polypeptides encoded thereby, which are capable of metabolizing the chemotherapeutic prodrug CPT-11 to active drug SN-38, are disclosed. This mutant human carboxylesterase enzyme also has potential applications to treatments involving other potential substrates such as certain drugs of abuse (e.g., cocaine and heroin) and certain types of chemical weapons (e.g., organophosphates). It has also been found that compositions comprising a polynucleotide of the present invention and a disease-specific responsive promoter can be delivered to selected tumor cells to sensitize the tumor cells to the chemotherapeutic prodrug CPT-11, thereby inhibiting tumor cell growth.
SUMMARY OF THE INVENTION
The present invention relates to a polynucleotide encoding a secreted mutant human carboxylesterase capable of metabolizing a chemotherapeutic prodrug and inactive metabolites thereof to active drug. A polypeptide encoded by the polynucleotide is also embraced by the present invention as is a vector containing the polynucleotide and a host cell harboring a vector which expresses a secreted mutant human carboxylesterase.
Methods of sensitizing a tumor cell to a chemotherapeutic prodrug and inhibiting the growth of a tumor cell by contacting a tumor cell with a secreted mutant human carboxylesterase and a chemotherapeutic prodrug are also provided.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A through 1B depict rCE and hCE1 amino acid and nucleic acid sequences. FIG. 1A shows the amino acid sequence alignment of residues 356-371 and 448-465 from rCE and hCE1 that form the missing loops from the former enzyme, and a list of hCE1 mutants that were constructed. Underlined residues indicate amino acids that were substituted by mutagenesis. FIG. 1B shows the alignment of full-length wild-type hCE1 (SEQ ID NO:1) and rCE (SEQ ID NO:2) proteins with loop regions of FIG. 1A indicated.
FIG. 2 depicts the in vitro stability of hCE1, hCE1m6 and hiCE. Enzymes were aliquoted in 50 mM Hepes, stored at 20° C. and CE activities were determined at various time intervals, up to 11 weeks. Data are expressed as the amount of active CE remaining as compared to day 0.
FIG. 3 depicts the growth inhibition curves for COS7 cells treated with CPT-11.
FIG. 4 depicts growth inhibition curves for U373MG cells (brain tumor cell line) expressing either the intracellular (u373IRESmut6) or the secreted form (U373IRESmut6C) of hCE1mut6, which were treated with CPT-11.
FIG. 5 depicts growth inhibition curves with CPT-11 treatment in untransfected U373MG cells incubated with the media harvested control cells (pIRESneo) or cells expressing the secreted form of hCE1mut6 (pIRESmut6C).
FIG. 6 shows growth inhibition curves for U373MG cells transduced with AdVC, ADCMVrCE, or ADCMVhCE1m6, following treatment with CPT-11. The IC50 values for these cells with CPT-11 are 26.8 μM, 0.3 μM and 0.04 μM, respectively.



DETAILED DESCRIPTION OF THE INVENTION
CPT-11 is a promising anti-cancer prodrug, that when given to patients, is converted to its active metabolite SN-38 by a human carboxylesterase. However, the wild-type human enzyme is relatively inefficient and less than 5% of the prodrug is metabolized to SN-38 (Rivory, et al. 1997. Clin. Cancer Res. 3:1261-1266). In patients, this prodrug is also metabolized to APC (Haaz, et al. 1998. Cancer Res. 58:468-472). APC has little, if any, active anti-tumor activity and is not converted to an active metabolite in humans (Rivory, et al. 1996. Cancer Res. 56:3689-3694). Accordingly, high concentrations of this prodrug must be administered to achieve effective levels of active drug in vivo. However, myelosuppression and secretory diarrhea limit the amount of prodrug that can be administered to patients.
In the present invention, a method of sensitizing tumor cells to reduce the effective dose of a prodrug required to inhibit tumor cell growth is provided which involves transfecting selected tumor cells with a mutated human CE, in particular a secreted mutant human CE, encoded by a polynucleotide.
In accordance with the present invention, a polynucleotide is provided which encodes a mutant human carboxylesterase capable of metabolizing a chemotherapeutic prodrug and inactive metabolites thereof to active drug. By “polynucleotide” it is meant to include any form of DNA or RNA such as cDNA or genomic DNA or mRNA, respectively, encoding this mutated human enzyme or an active fragment thereof which are obtained by cloning or produced synthetically by well-known chemical techniques. DNA can be double- or single-stranded. Single-stranded DNA can include the coding or sense strand or the non-coding or antisense strand. Thus, the term polynucleotide also includes polynucleotides which hybridize under stringent conditions to the above-described polynucleotides. As used herein, the term “stringent conditions” means at least 60% homology at hybridization conditions of 60° C. at 2×SSC buffer. In a particular embodiment, the polynucleotide is a mutant human cDNA or a homologous sequence or fragment thereof which encodes a polypeptide having similar activity to that of rabbit liver CE enzyme. Due to the degeneracy of the genetic code, polynucleotides of the present invention can also include other nucleic acid sequences encoding this enzyme and derivatives, variants or active fragments thereof. The present invention also relates to variants of this polynucleotide which may be naturally occurring, i.e., allelic variants, or mutants prepared by well-known mutagenesis techniques.
In particular embodiments, the mutant human CE protein of the present invention contains at least the following mutations in reference to a wild-type human CE (set forth herein as SEQ ID NO:1): Leu358Ile, Leu362Met, Met363Leu, Ser364Gly, Phe448Tyr, Gln449Arg, Lys459Arg and insertion of Gln after Met361 (see FIG. 1A). These mutations, when introduced into wild-type human CE produce a polypeptide having similar activity to that of rabbit liver CE enzyme (SEQ ID NO:2). An exemplary mutant human CE polypeptide containing these mutations is set forth herein as SEQ ID NO:3.
Mutation of the wild-type hCE1 protein (SEQ ID NO:1) can be achieved using any conventional mutagenesis approach including site-directed mutagenesis methods well-known in the art with nucleic acids encoding wild-type hCE1 protein as a template. An exemplary wild-type hCE1-encoding nucleic acid molecule is set forth herein as SEQ ID NO:4.
The present invention also provides vectors which harbor polynucleotides of the present invention and host cells which are genetically engineered with vectors of the present invention to produce mutant human CE or active fragments of this enzyme. Generally, any vector suitable to maintain, propagate or express polynucleotides to produce the enzyme in the host cell can be used for expression in this regard. In accordance with this aspect of the invention the vector can be, for example, a plasmid vector, a single- or double-stranded phage vector, or a single- or double-stranded RNA or DNA viral vector. Such vectors include, but are not limited to, chromosomal, episomal and virus-derived vectors, e.g., vectors derived from bacterial plasmids, bacteriophages, yeast episomes, yeast chromosomal elements, and viruses such as baculoviruses, papova viruses, SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, cosmids and phagemids. Selection of an appropriate promoter to direct mRNA transcription and construction of expression vectors are well-known. In general, however, expression constructs will contain sites for transcription initiation and termination, and, in the transcribed region, a ribosome binding site for translation. The coding portion of the mature transcripts expressed by the constructs will include a translation initiating codon at the beginning and a termination codon appropriately positioned at the end of the polypeptide to be translated. Examples of eukaryotic promoters routinely used in expression vectors include, but are not limited to, the CMV immediate early promoter, the HSV thymidine kinase promoter, the early and late SV40 promoters, the promoters of retroviral LTRs, such as those of the Rous Sarcoma Virus (RSV), and metallothionein promoters, such as the mouse metallothionein-I promoter. Vectors comprising the polynucleotides can be introduced into host cells using any number of well-known techniques including infection, transduction, transfection, transvection and transformation. The polynucleotides can be introduced into a host alone or with additional polynucleotides encoding, for example, a selectable marker. Host cells for the various expression constructs are well-known, and those of skill can routinely select a host cell for expressing the mutated human CE enzyme in accordance with this aspect of the present invention. Examples of mammalian expression systems useful in the present invention include, but are not limited to, the C127, 3T3, CHO, HeLa, human kidney 293 and BHK cell lines, the COS-7 line of monkey kidney fibroblasts, and stem and progenitor cells.
Stem and progenitor cells may be stably or transiently transformed with a polynucleotide encoding a mutant human CE by any suitable means, with or without the use of a vector as described above. Suitable stem and progenitor cells and methods and vectors for their transformation, propagation, formulation and administration are known. Examples include but are not limited to those set forth in U.S. Pat. Nos. 6,368,636; 6,387,367; 7,022,321; 8,034,329; 8,057,789; 8,216,566; and 8,518,390, and U.S. Patent Application Nos. 20050019313 and 20050169897. Stem and progenitor cells may be collected from any suitable tissue or biological fluid, such as placenta, amniotic fluid, blood, umbilical cord blood, etc. In general, stem cells may be embryonic, adult, or induced pluripotent stem cells, with the specific choice of stem cell depending upon the specific condition and/or tissue for which they are intended.
The present invention also relates to compositions containing a polynucleotide of the present invention which have been found to be useful in sensitizing tumor cells to CPT-11 cytotoxicity by combination therapy of the prodrug and a CE enzyme. The present invention thus provides methods for sensitizing tumor cells to a prodrug oncologic agent. In this context, by “sensitizing” it is meant that the effective dose of the prodrug can be reduced when the compositions and methods of the present invention are employed. In a case where the prodrug's therapeutic activity is limited by the occurrence of significant toxicities, or dose-limiting toxicities, sensitization of tumor cells to the prodrug is especially useful.
While rabbit CE (rCE) and human liver CE, (hCE1) are structurally similar, demonstrating 81% amino acid identity (Danks, et al. 1999. Clin. Cancer Res. 5:917-924) and only a  ̃1.0 Å RMSD variation over 455 residues of the α-carbon trace (Danks, et al. 1999. Clin. Cancer Res. 5:917-924; Bencharit, et al. 2002. Nat. Struct. Biol. 9:337-342; Bencharit, et al. 2003. Chem. Biol. 10:341-349), the latter enzyme is very inefficient at CPT-11 activation (100- to 1000-fold lower than rCE. In a comparison of the x-ray crystal structures of rCE and hCE1, two loops in rCE (amino acids 356-371 and 450-465; see FIGS. 1A and 1B) were identified that were apparently missing from the crystal structure of hCE1. These loops formed the entrance to the active site of the protein, and it was assumed that the structures of these domains could not be determined due to enhanced flexibility and thermal motion. It has been reported that the substrate specificity of CEs is in part determined by the constraints enforced by loops that surround the active site entrance (Wadkins, et al. 2001. Mol. Pharmacol. 60:355-362). Thus, the more rigid structure of these domains in hCE1 protein may significantly impact the ability of the protein to activate CPT-11. A series of hCE1 mutants was developed that contained multiple amino acid substitutions in these loop regions such that the sequence in these regions was identical to rCE. The five mutants constructed are listed in Table 1 (hCE1mut2 through hCE1mut6). The mutants were inserted into a plasmid, pCIneo, which was obtained from Promega (Madison, Wis.). The cDNAs for the wild-type enzymes are found in Genbank: hCE1, Genbank Accession No. M73499 (SEQ ID NO:4); rCE, Genbank Accession No. AF036930 (SEQ ID NO:5).










TABLE 1







Name
Mutations









pCIhCE1mut2
L362M, M363L



pCIhCEmut3
L362M, M363L, K459R



pCIhCEmut4
L362M, M363L, K459R, F448Y, Q449R



pCIhCEmut5
L362M, M363L, K459R, F448Y, Q449R, L358I,




S364G



pCIhCEmut6
L362M, M363L, K459R, F448Y, Q449R, L358I,




S364G, Q362 insertion










Site-directed mutagenesis was used to produce the hCE1 mutants. All mutants were subjected to DNA sequence analysis to confirm the identity of the clones. The mutant cDNAs were expressed from pCIneo in Cos7 cells. In addition to the hCE1 mutants listed in Table 1, a plasmid containing wild-type hCE1 cDNA was constructed (pCIhCE1), and mutant rCE plasmids were also constructed as listed in Table 2.










TABLE 2







Name
Details









pCIrCEmut2
I357L, R459K



pCIrCEmut3
I357L, R459K, M362L



pCIrCEmut4
I357L, R459K, M362L, L363M, Q364S,




Y448F, R449Q



pCIrCEmut5
I357L, R459K, M362L, L363M, Q364S,




Y448F, R449Q, Q361 deletion










The CE mutants were then tested to characterize their ability to activate CPT-11. To assess CPT-11 activation by the hCE1 mutant proteins, the cDNAs had been ligated into the expression vector pCIneo and transiently produced the protein in Cos7 cells. Whole cell sonicates were monitored for CE activity. Results were expressed as nmoles o-nitrophenol produced per minute per milligram of total protein. To correct for differences in CE expression within transfected cells, the enzyme activity values were corrected for the level of immunoreactive CE protein as determined using a western blot analysis. The results of the analysis are shown in Table 3. Following transfection with all hCE1-containing plasmids, all extracts demonstrated CE activity, and all had similar levels of CE protein as determined by western blot analysis using an anti-hCE1 antibody. However, only hCE1mut6 was capable of converting CPT-11 to SN-38.











TABLE 3









CPT-11 Converting




CE Activity
Activity



Plasmid
(nmol/min/mg)
(pmol/hr/mg CE)




















pCIneo
  5.5 ± 0.1
Not detected (ND)



hCE1
 119.0 ± 5.0
ND



hCE1mut2
  267.2 ± 65.2
ND



hCE1mut3
158.4.5 ± 20.2
ND



hCE1mut4
  450.8 ± 45.7
ND



hCE1mut5
  369.5 ± 26.8
ND



rCE (wild-type)
  332.7 ± 17.2
41



hCE1mut6
  202.8 ± 10.3
40.5










To directly compare the ability of hCElm6 and rCE to activate CPT-11, both proteins were expressed in COS-7 cells and the ability of extracts to hydrolyze the drug was assessed. In these studies, the levels of CPT-11 activation were corrected for the amounts of CE protein in the cell extracts by western analysis. This was necessary since it was unclear whether the mutations would influence the ability of the CEs to metabolize o-NPA, which is used as a measure of enzyme activity. As indicated in Table 3, hCE1m6 and rCE were essentially equally efficient at CPT-11 hydrolysis.
Since mutation of the loop domain in hCE1 with residues present in rCE increased the ability of the wild-type hCE1 protein to hydrolyze CPT-11, it was postulated that the converse mutations (i.e., hCE1 residues substituted into rCE) would reduce the ability of rCE to activate. CPT-11. This panel of mutant rCE proteins is listed in Table 2. The ability of these mutants to convert CPT-11 to SN-38 was then assessed using the methods described above. The results are listed in Table 4.











TABLE 4









CPT-11 Converting




CE Activity
Activity



Plasmid
(nmol/min/mg CE)
(pmol/hr/mg CE)




















rCE (wild-type)
 243.1 ± 17.0
75.6



rCEmut2
333.1 ± 7.0
52.5



rCEmut3
 170.7 ± 11.0
47.4



rCEmut4
141.4 ± 1.8
41.7



rCEmut5
219.9 ± 5.8
11.5



hCE1 (wild-type)
 329.2 ± 11.6
Not Detected










Substitution of the amino acids present within loops of rCE with corresponding residues from hCE1 resulted in a gradual reduction in the ability of the protein to hydrolyze CPT-11. A mutant that contained eight amino acid changes, rCEmut5, was 7-fold less efficient at drug activation than wild-type rCE. Mutants with intermediate numbers of amino acid substitutions demonstrated intermediate abilities to hydrolyze CPT-11. These data demonstrate that there was a gradient of catalytic activity, where the mutant with the smallest number of substitutions demonstrated the lowest reduction in ability to hydrolyze CPT-11.
To directly compare the abilities of the mammalian CEs to hydrolyze CPT-11, a series of biochemical studies were carried out using the purified proteins in vitro. These experiments determined the Km, Vmax, kcat and kcat/Km values for the different enzymes. As indicated in Table 5, hCE1m6 was  ̃70-fold more efficient at CPT-11 hydrolysis as compared to the hCE1. In addition, hCE1m6 was almost as effective at CPT-11 hydrolysis as hiCE. It should be noted that both hiCE and hCE1m6 were less efficient at drug activation than rCE, however since hiCE has been effectively used in prior enzyme/prodrug therapy approaches (Oosterhoff, et al. 2005. Br. J. Cancer 92:882-887; Oosterhoff, et al. 2002. Br. J. Cancer 87:659-664; Oosterhoff, et al. 2005. Gene Ther. 12:1011-1018; Oosterhoff, et al. 2003. Mol. Cancer Ther. 2:765-771), hCElm6 is expected to be efficacious in CPT-11 activation in vivo.











TABLE 5









Ratio






kcat/Km as



Km
Vmax
kcat/Km
compared


Enzyme
(μM)
(nmol/min/mg)
(mM−1 min−1)
to hCE1



















hCE1a
82.8 ± 9.6 
0.36 ± 0.017
0.28
1


hCE1m6
6.25 ± 0.59
2.11 ± 0.06 
19.8
71


rCEa
6.20 ± 0.63
18 ± 0.9 
180.0
650


hiCE
3.35 ± 0.34 
1.49 ± 0.04 
25.2
91





aData taken from Wadkins, et al. 2001. Mol. Pharmacol. 60:355-362 (29).






In previous biochemical experiments, it was noted that in vitro purified hiCE was much less stable than hCE1. Therefore, the loss of CE activity was evaluated in preparations of these proteins, as well as hCElm6 that had been stored at room temperature. In these studies, purified protein was aliquoted in 50 mM Hepes pH7.4, and enzyme activity was determined over a period of 12 weeks. As indicated in FIG. 2, hiCE was the least stable protein, losing 50% of its activity by  ̃30 days. In contrast, both hCElm6 and hCE1 were relatively stable under these conditions with predicted half-lives of 129 and 440 days, respectively.
In in vivo studies, it was observed that expression of hiCE following plasmid-mediated transfection was frequently lower than that seen with rCE or hiCE. Therefore, U373MG cells expressing hiCE, hCE1 or hCElm6 were developed using the plasmid pIRESneo, and CE expression in the derived lines was monitored over an extended time period. Since expression of the transgene from this expression vector is co-regulated with the neo gene via an IRES sequence, selection with similar concentrations of G418 should result in cell lines that express approximately equal levels of recombinant protein. However, the average levels of CE activity in U373hiCE, U373hCE1 and U373hCE1m6 cells were 287.6±76.6, 1077.1±77.5, and 466.5±52.6 nmoles/min/mg, respectively. Since high level expression of the prodrug-activating protein would be necessary for effective application of enzyme/prodrug therapy, hiCE may not be the best CE for activating CPT-11.
The sensitivity of mammalian cells to CPT-11 following expression of hCE1mut6 was then determined by constructing cell growth inhibition curves for human tumor cells expression the mutant protein. Cos7 cells transiently transfected with hCE1mut6, as described above, were contacted with increasing concentrations of CPT-11 in order to determine the concentration of drug required to inhibit cell growth by 50% (IC50). FIG. 3 shows that cells expressing the hCE1mut6 protein were equally as sensitive to CPT-11 as cells expressing rCE. Both populations of cells had similar IC50 values for CPT-11, approximately 12 to 20 micromolar. This value was 5-fold less that the IC50 value for cells expressing wild-type hCE1 (IC50=77.1 micromolar).
Experiments were also performed in human brain tumor cells (U373MG) where the growth of the cells was examined in cells that expressed the mutant form of the human CE enzyme. As indicated in Table 6, cells expressing hCElm6, hiCE or rCE were sensitized to CPT-11 due to intracellular conversion of the drug to SN-38. Cells expressing hCE1 were not sensitized, consistent with the lack of CPT-11 hydrolysis observed in the biochemical studies. Furthermore, U373MG cells expressing hCElm6 were equally as sensitive to CPT-11 as cells expressing rCE, with IC50 values ranging from 0.18-0.40 μM. These values were  ̃18- to 86-fold less than cells expressing wild-type hCE1 (IC50 value=15.5 μM). These results indicate that hCE1mut6 can efficiently convert CPT-11 to SN-38 intracellularly and sensitize cells to the drug.












TABLE 6









CPT-11
Fold




Enzyme
CE activity
IC50
decrease


Cell line line
Adenovirus
expressed
(nmol/min/mg ± SD)
(μM)
in IC50*




















U373IRES
—
None
10.0 ± 00.3
24.0
—


U373hCE1
—
hCE1
1016.4 ± 45.5 
15.5
—


U373hiCE
—
hiCE
408.2 ± 5.6 
0.84
18


U373rCE
—
rCE
601.0 ± 20.5
0.40
39


U373hCE1m6
—
hCE1m6
437.3 ± 37.5
0.18
86


U373MG
AdVC
None
10.0 ± 0.5
26.8
—



AdCMVrCE
rCE
1076.8 ± 67.3 
0.3
89



AdCMVhCE1m6
hCE1m6
5999.8 ± 162.5
0.04
670


Rh30
AdVC
None
 4.6 ± 0.3
64.3
—



AdCMVrCE
rCE
665.6 ± 52.0
3.4
29



AdCMVhCE1m6
hCE1m6
2757.6 ± 87.5 
2.0
32


SK-N-As
AdVC
None
 6.9 ± 0.3
31.7
—



AdCMVrCE
rCE
2150.3 ± 105.9
0.6
53



AdCMVhCE1m6
hCE1m6
6225.0 ± 113.4 
0.5
63





*value as compared to U373MGhCE1 or cell line + AdVC.






Experiments were also performed to determine whether cells expressing a secreted form of hCElm6 (SEQ ID NO:16) produced media that had CE activity. U373MG cells expressing either the intracellular (u373IRESmut6) or the secreted form (U373IRESmut6C) of hCE1mut6 were treated with CPT-11. There was an approximate 130-fold reduction in the IC50 value for CPT-11 in the cells expressing hCE1mut6 (either form). However, cells expressing the secreted form of the protein had an intermediate IC50 for CPT-11 (7.08 μM) because the intracellular levels of the CE were lower due to the secretion into the culture media (FIG. 4).
Growth inhibition of untransfected U373MG cells was also examined following incubation with the media harvested control cells (pIRESneo) or cells expressing the secreted form of hCE1mut6 (pIRESmut6C) and CPT-11. Since the enzyme was secreted into the media and able to activate CPT-11, the active metabolite SN-38 was produced, resulting in cytotoxicity to cells that did not express the mutant CEs. This effect was not observed with the control media. The difference in the IC50 values was approximately 150-fold (FIG. 5). These results are indicative of a bystander or collateral effect.
E1A, E3-deleted replication-deficient adenovirus expressing hCElm6 were also generated and the ability of this vector to sensitize cells to CPT-11 was determined. As shown in Table 6, in all human tumor cell lines, expression of hCElm6 significantly decreased the CPT-11 IC50 values as compared to vector transduced cells. In SK-N-As and Rh30 cell lines, the CPT-11 sensitivity was comparable to cells transduced with AdCMVrCE (adenovirus containing the rabbit liver CE cDNA), with IC50 values of 2 nM and 0.6 nM, respectively. However, the human astrocytoma cell line U373MG, was 7.5-fold more sensitive to CPT-11 after AdCMVhCE1m6 transduction, than after exposure to AdCMVrCE. This resulted in an overall reduction in the IC50 for CPT-11 of  ̃670-fold for U373MG cells (FIG. 6), the greatest sensitization observed using this enzyme/prodrug approach. Overall, these results indicate that AdCMVhCE1m6 can sensitize cells to CPT-11 as effectively as AdCMVrCE, and that the former vector should be suitable for enzyme/prodrug therapy with this drug.
Thus, one embodiment of the present invention embraces transfecting selected tumor cells with the polynucleotide of the present invention, which expresses mutant human CE. The polynucleotide can expressed via a well-known promoter such as the CMV promoter or, more preferably, via a disease-specific responsive promoter which specifically targets the selected tumor cells. Targeted gene expression in tumor cells has been achieved using disease-specific responsive promoters such as carcinoembryonic antigen, HER-2/neu, Myc-Max response elements, and DF3/MUC. Thus, a composition containing the mutant CE disclosed herein and a disease-specific responsive promoter such as these can be used to transfect and sensitize tumor cells containing the disease-specific responsive promoter. Accordingly, the present invention provides a means for exploiting tumor-specific expression associated with a disease-specific responsive promoter to provide for selective therapy of tumors.
Since myc expression is deregulated in a wide variety of human tumors, myc is an attractive target for chemotherapeutics. No known drug specifically interacts with either the c-myc or N-myc protein. However, cells overexpressing a myc oncogene can be targeted with compositions of the present invention containing a polynucleotide of the present invention under the control of a myc specific promoter. Thus, using the present invention the tumor-specific overexpression of c-myc and N-myc can be exploited to produce selective killing with a chemotherapeutic agent.
A broad variety of different tissues, including neoplastic and non-neoplastic, are known targets for stem cell treatment. See, e.g., Segers & Lee. 2008. Nature 451:937-942; Kim & de Vellis. 2009. J. Neurosci. Res. 87:2183; Caplan. 2005. Tissue Engineering 11:1198-1211. Accordingly, in some embodiments, a stem or progenitor cells is transformed with a polynucleotide encoding a secreted mutant human CE (e.g., with or without a vector), and used in the treatment and/or sensitization of a neoplastic or cancer tissue to chemotherapeutic prodrug. Such cancer tissue can include, but is not limited to, brain cancer tissue or tumors (e.g. gliomas such as glioblastoma multiforme, meningiomas, pituitary adenomas, nerve sheath tumors, etc.), breast cancer tissue or tumors, skin cancer tissue or tumors (e.g., melanoma, basal cell skin cancer, squamous cell skin cancer, etc.), prostate cancer tissue or tumors, lung cancer tissue or tumors, ovarian cancer tissue or tumors, colon and colorectal cancer tissue or tumors, pancreatic cancer tissue or tumors, etc.
In vivo efficacy of the CE of the present invention to sensitize tumor cells to CPT-11 is examined in different types of tumor cells as well as in a mouse model to demonstrate that the mutant human CE of the present invention is capable of sensitizing cells to the growth inhibitory effects of CPT-11.
For example, the ability of the mutant human CE, hCE1mut6, to sensitize Rh30 rhabdomyosarcoma human tumor cells grown as xenografts in immune-deprived mice can be examined. This is a well-accepted preclinical model, where expression of the transfected cDNA for hCE1mut6 can first be established. Following establishment of tumors in the animals, treatment with CPT-11 begins. Tumor growth is examined and compared in animals treated with CPT-11 when the tumor cells had been transfected with the mutant human CE versus the growth seen in tumor cells not transfected with this mutant human CE, or those transfected with other CE forms, such as rCE. The in vivo effects of the hCE1mut6 protein can also be examined in a model such as mice with human U373 glioblastoma xenografts, where the xenografts express hCE1mut6. Again, the sensitivity of these tumor cells to CPT-11 can be compared to xenografts transfected with a control plasmid.
The data described herein support the use of the combination of polynucleotide encoding a mutant human CE of the present invention and CPT-11 to reduce the amount of CPT-11 needed to produce inhibition of tumor cell growth, or to sensitize the tumor cells to CPT-11. These data can also be used to support the use of the present invention to allow for decreased dosage with CPT-11 in cancer patients, thus reducing the likelihood of dose-limiting toxicity.
The present invention thus also relates to a method for treating cancer with reduced side effects. In some embodiments, a polynucleotide of the present invention is introduced into a host cell (e.g., stem or progenitor cell) or tumor cell, with or without a vector and used in the treatment of cancer. When using a vector, preferably the polynucleotide encoding the mutant human CE is inserted into a viral vector. Preferred viral vectors include, but are not limited to, retroviral, adenoviral, herpesvirus, vaccinia viral and adeno-associated viral vectors. In this embodiment, it is preferred that the vector further include a disease-specific responsive promoter. The vectors can then be injected into a host cell, a tumor cell or the site of tumor removal along with systemic administration of a prodrug such as CPT-11 to inhibit tumor growth or recurrence, e.g., due to residual tumor cells present after surgical resection of a tumor.
Alternatively, the viral vector can be used to purge bone marrow of contaminating tumor cells during autologous transplant. Bone marrow purging via a viral vector such as adenovirus which expresses a CE of the present invention is performed ex vivo. Efficiency of removal of contaminating tumor cells is determined by PCR assays of purged samples. Data indicate that the method of the present invention is applicable to an animal model for purging bone marrow of neuroblastoma cells such as that described in Example 6. Methods for preparation of the vectors, modes of administration, and appropriate doses of prodrug are well-known to those of skill in the art. Other methods of gene delivery such as chemical and liposome-mediated gene transfer, receptor-mediated DNA uptake, and physical transfer by gene guns or electroporation can also be employed.
Another method for delivering CEs to selected tumor cells involves antibody-directed enzyme prodrug therapy (ADEPT). In this method, human tumors are targeted by conjugation of tumor-specific marker antibody with a molecule such as hCE1mut6. Cellular internalization of the complex and release of active CE is achieved, leading to CPT-11 activation that is specific for cells expressing the marker antigen. Since the array of marker molecules expressed upon the cell surface is different for each tumor type, markers specific for each targeted tumor type can be selected as appropriate. Similarly, the use of avidin-biotin-conjugated molecules to target tumor cells (Moro, et al. 1997. Cancer Res. 57:1922-1928) is also applicable for localization of the CE protein of the present invention to the cell surface followed by drug activation at the targeted cell.
Liver CE is localized in the endoplasmic reticulum. An 18-amino acid NH2-terminal hydrophobic signal peptide is responsible for the localization of CE to the endoplasmic reticulum. Further, the COOH-terminal amino acids HIEL prevent secretion of the protein from the cell. Enzymatic activity is lost by removing the NH2-terminal domain; however, active enzyme is detected in the culture media of cells expressing the COOH-terminally truncated protein (Potter et al. 1998. Cancer Res. 58:3627-32). Secretion of CEs lacking the six COOH-terminal amino acids can be prevented with brefeldin A, confirming that the truncated enzyme is processed and released from cells by endoplasmic reticulum-mediated exocytosis. Double-truncation mutant enzymes lacking both NH2- and COOH-terminal sequences demonstrate immunostaining patterns similar to those of the NH2-terminally truncated proteins and also lack CE activity. Both the secreted and the endoplasmic reticulum-localized protein can convert CPT-11 to SN-38. See Potter et al. 1998. Cancer Res. 58:3627-32. Therefore, the potential exists for a bystander effect from cells expressing the secreted enzyme. A similar bystander effect has been demonstrated for other enzyme/prodrug combinations, such as HSVtk and ganciclovir (Dilber, et al. 1997. Cancer Res. 57:1523-1528), and results in increased cytotoxicity. Extracellular activation of CPT-11 may result in more efficient eradication of MRD in that uninfected neighboring tumor cells would be killed by exogenously produced SN-38. Gene therapy protocols with a secreted CE in combination with CPT-11 can therefore be more appropriate for the elimination of residual tumor tissue. Accordingly, in particular embodiments, the polynucleotide of the invention encodes a polypeptide which is secreted, i.e., a polypeptide lacking the six C-terminal amino acid residues (Thr-Glu-His-Ile-Glu-Leu). In other embodiments, the polynucleotide encodes a polypeptide lacking the six N-terminal amino acid residues. An exemplary mutant human CE protein lacking the six C-terminal amino acid residues is set forth herein as SEQ ID NO:16.
Additionally, recent reports indicate that the tethering of drug activating enzymes to the extracellular cell surface can result in anti-tumor activity in human tumor xenografts when combined with appropriate prodrug (Marais, et al. 1997. Nature Biotech. 15:1373-1377). A tethered enzyme generates a local bystander effect since the protein is not free to circulate in the plasma. Attachment of a CE of the present invention to the cell surface should result in local extracellular activation of CPT-11 to SN-38 and enhance local cell kill. Purging bone marrow of contaminating tumor cells will be accomplished by an intracellular enzyme, whereas eradication of MRD is better achieved by an enzyme that activates CPT-11 at an extracellular location.
Another aspect of the present invention that is contemplated is the application of the mutant human CE enzyme in the treatment of drug addiction. This use is contemplated based on work that has shown the ability of human CE to catalyze the hydrolysis of drugs such as heroin and cocaine (Redinbo, et al. 2003. Biochemi. Soc. Trans. 31:620-624; Bencharit, et al. 2003. Nat. Struct. Biol. 10:349-356). As such, the use of the instant mutant human CE enzyme to affect drug metabolism can be exploited as a method for treatment of drug addiction, as would be appreciated by one of skill in the art. In general, this application of the mutant human CE enzyme would be in a manner similar to the use of the enzyme in treatment of cancer.
In yet another aspect of the present invention that is contemplated based on the results described herein, the mutant human CE enzyme could be used in a method for metabolizing certain types of chemical weapons agents, specifically organophosphate compounds. It has been shown that organophosphates can be efficiently hydrolyzed by human CE after a single point mutation in its active site (Redinbo, et al. 2003. Biochemi. Soc. Trans. 31:620-624). In this regard, the enzyme of the present invention can be administered to a subject in need of treatment, e.g., a subject exposed to or suspected of being exposed to a chemical weapon agent, and used as a preventative treatment against the toxicity resulting from exposure to organophosphates.
The CE of the present invention cleaves the COOC bond present as an ester linkage in CPT-11 to generate SN-38. Since this enzyme can also catalyze the activation of other compounds that contain such a linkage, the present invention also provides assays for screening for compounds that contain this and related moieties. In one embodiment, the assay of the present invention is conducted in a cell system using, for example, yeast, baculovirus, or human tumor cell lines. In this embodiment, compounds activated by CE are identified and assessed for anticancer activity by growth inhibition or clonogenic cell survival assays using cells expressing or lacking a CE of the present invention. Alternatively, compounds can be screened in cell-free assays using a CE of the present invention isolated from host cells expressing this enzyme. In this embodiment, the ability of the enzyme to cleave a COOC ester linkage of a candidate compound is measured directly in a standard enzyme assay buffer system containing a CE of the present invention. Known concentrations of candidate compounds can be added to assay tubes containing a biological buffer such as HEPES at pH 7.4 and the enzyme and incubated at 37° C. for a selected amount of time. The reaction is then terminated by addition of methanol. The assay tubes are then centrifuged and the supernatant analyzed for the presence of cleaved compound fragment. Analysis of the supernatant can be performed by any number of well-known techniques including, but not limited to, spectrofluorometric analysis, high pressure liquid chromatography or mass spectrometry.
Compounds which can be screened in accordance with the instant assay include small organic compounds as well as derivatives or analogs of known compounds which contain the COOC ester linkage (e.g., CPT-11). Compounds identified in these screening assays as potential anticancer prodrugs may require chemical modification for optimize their anti-tumor activity.
The following non-limiting examples are provided to further illustrate the claimed invention.
EXAMPLE 1
Materials and Methods
Cell Lines, Plasmids and Adenoviral Vectors. Cell lines were grown in 10% fetal bovine serum and 2 mM glutamine in an atmosphere of 10% CO2 at 37° C.
Plasmids containing the cDNAs encoding hCE1, hiCE and rCE are known in the art (Danks, et al. 1999. Clin. Cancer Res. 5:917-924; Potter, et al. 1998. Cancer Res. 52:2646-2651; Khanna, et al. 2000. Cancer Res. 60:4725-4728). The Genbank accession numbers for these sequences are M73499 (Munger, et al. 1991. J. Biol. Chem. 266:18832-18838), Y09616 (Schwer, et al. 1997. Biochem. Biophys. Res. Comm. 233:117-12) and AF036930 (Potter, et al. 1998. Cancer Res. 52:2646-2651), respectively. The plasmids, cell lines and adenoviral vectors used in these studies are listed in Table 7.









TABLE 7





Name
Description
Details







PCIneo*
Mammalian
Obtained from Promega



expression vector



pCIhCE1*
pCIneo containing
From Danks, et al. 1999. 



wild-type hCE1
Clin. Cancer Res. 



cDNA
5:917-924


pCIrCE*
pCIneo containing
From Potter, et al. 1998. 



wild-type rCE cDNA
Cancer Res. 52:2646-2651


pCIhCE1m2*
pCIneo containing
L362M, M363L



mutant hCE1 cDNA



pCIhCE1m3*
pCIneo containing
L362M, M363L, K459R



mutant hCE1 cDNA



pCIhCE1m4*
pCIneo containing
L362M, M363L, K459R, 



mutant hCE1 cDNA
F448Y, Q449R


pCIhCE1m5*
pCIneo containing
L362M, M363L, K459R, 



mutant hCE1 cDNA
F448Y, Q449R, L358I, 




S364G


pCIhCE1m6*
pCIneo containing
L362M, M363L, K459R,



mutant hCE1 cDNA
F448Y, Q449R, L358I, 




S364G, Q362 insertion


pIRESneo*
Mammalian
Contains G418 resistance 



expression vector
gene coupled to an IRES




sequence


pIRESrCE*
pIRESneo
From Potter, et al. 1998. 



containing rCE
Cancer Res. 52:2646-2651



cDNA



pIREShCE1*
pIRESneo
From Danks, et al. 1999. 



containing hCE1
Clin. Cancer Res. 



cDNA
5:917-924


pIREShiCE*
pIRESneo
Expresses hiCE following



containing hiCE
transfection and selection 



cDNA
with G418


pIREShCE1m6*
pIRESneo
Contains mutations as listed 



containing hCE1m6
above for pCIhCE1m6



cDNA



COS-7#
African green
Obtained from the America 



monkey kidney cell 
Type Culture Collection



line



U373MG#
Human astrocytoma
Obtained from the America 



cell line
Type Culture Collection


U373IRES#
U373MG transfected 
G418 resistant but lacking



with pIRESneo
exogenous CE expression


U373hCE1#
U373MG transfected
U373MG expressing hCE1



with pIREShCE1



U373rCE#
U373MG transfected 
U373MG expressing rCE



with pIRESrCE



U373hiCE#
U373MG transfected
U373MG expressing hiCE



with pIREShiCE



U373hCE1m6#
U373MG transfected
U373MG expressing 



with pIREShCE1m6
hCE1m6


293#
Human embryo 
Obtained from the America 



kidney cell line
Type Culture Collection


Rh30#
Rhabdomyosarcoma
From Douglass, et al. 1987.



cell line
Cytogenet. Cell Genet. 




45:148-155


SK-N-AS#
Neuroblastoma cell 
Obtained from the America 



line
Type Culture Collection


AdVC†
Adenovirus vector
E1, E3-deleted Ad vector



based upon Ad5



AdCMVrCE†
Adenovirus
Expresses high levels of 



containing rCE
rCE under control of CMV 



cDNA
promoter


AdCMVhCE1m6†
Adenovirus
Expresses high levels of 



containing hCE1m6
hCE1m6 under control of 



cDNA
CMV promoter





*plasmid;


#cell line;


†adenovirus.






Analysis of Carboxylesterase Crystal Structures. The x-ray crystal structures of rCE (PDB 1K4Y; Bencharit, et al. 2002. Nat. Struct. Biol. 9:337-342)) and hCE1 (PDB 1MX5; Bencharit, et al. 2003. Chem. Biol. 10:341-349; Bencharit, et al. 2003. Nat. Struct. Biol. 10:349-356) were overlaid and examined using ICM Pro software (Molsoft, San Diego Calif.).
Site-Directed Mutagenesis. Site-directed mutagenesis was achieved using a QuickChange site-directed mutagenesis kit (Stratagene, La Jolla, Calif.) with custom primers designed to produce the desired mutations. All mutants were subjected to DNA sequencing to confirm the identity of the clones.
Carboxylesterase Assays. CE activity was determined using a spectrophotometric assay with 3 mM o-nitrophenyl acetate (o-NPA) as a substrate (Potter, et al. 1998. Cancer Res. 52:2646-2651; Wierdl, et al. 2001. Cancer Res. 61:5078-5082; Beaufay, et al. 1974. J. Cell Biol. 61:188-200). Data were expressed as nmoles o-nitrophenol produced per minute per milligram of protein. To correct for differences in CE expression within transfected cells, the enzyme activity values were corrected for the level of immuno-reactive CE protein as determined from western analyses.
Transfection of Cell Lines. Transient transfection of Cos7 cells was achieved by electroporation (Potter, et al. 1998. Cancer Res. 52:2646-2651). For the generation of stable cell lines, cDNAs were ligated into pIRESneo and U373MG cells were electroporated under similar conditions. Transfectants were selected in media containing 400 μg/ml of G418. Since the CE cDNA was linked via an internal ribosome entry sequence (IRES) to the neomycin gene, selection of individual G418-resistant clones was not necessary. Routinely, whole cell sonicates obtained from these pooled populations of cells contained 200-500 nmoles/min/mg of CE activity.
CPT-11 Conversion Assays. Conversion of CPT-11 to SN-38 was monitored by incubating cell extracts with 5 μM CPT-11 for 1 hour in 50 mM Hepes pH7.4 at 37° C. An equal volume of acidified methanol was added to terminate the reactions and particulate matter was removed by centrifugation at 100,000 g for 5 minutes at 4° C. Concentrations of both drugs in the supernatant were then determined by HPLC (Guichard, et al. 1998. Clin. Cancer Res. 4:3089-3094; Morton, et al. 2000. Cancer Res. 60:4206-4210).
Protein Purification. Secreted forms of hCE1, rCE and mutant human CE (SEQ ID NO:1) were expressed in Spodoptera frugiperda Sf9 cells and purified from serum-free culture media according to known methods (Morton & Potter. 2000. Mol. Biotechnol. 16:193-202). For hiCE, an alternative purification procedure was developed using DEAE chromatography and elution with a pH/salt gradient.
Determination of Kinetic Parameters for Substrate Hydrolysis. Km, Vmax and kcat values for the hydrolysis of CPT-11 by the recombinant purified proteins were determined using standard methods (Wadkins, et al. 2001. Mol. Pharmacol. 60:355-362).
Western Analysis. Cell extracts were separated in 4-20% pre-cast SDS-PAGE gels (Invitrogen, Carlsbad, Calif.) and following transfer to Immobilon-P membranes by electroblotting (Matsuidaira. 1990. Methods Enzymol. 182:602-613), western analysis was performed using known methods (Morton & Potter. 1998. J. Pharmacol. Expt. Therap. 286:1066-1073). CEs were identified using an anti-peptide antibody raised against the C-terminal amino acids CEKPPQTEHIEL (SEQ ID NO:15) of hCE1, and ECL detection (Amersham Life Sciences, Arlington Heights, Ill.). In all experiments, membranes were re-probed with an anti-TFIID antibody to confirm equal loading, and to correct for any differences in total protein. The molecular weight of immuno-reactive bands was determined using pre-stained molecular weight protein markers (Pierce, Rockford, Ill.). Densitometric quantitation of CE expression was performed using One-Dscan gel analysis software (Scanalytics Inc, Fairfax, Va.).
Construction of Adenovirus. Replication-deficient adenovirus expressing hCElm6 or rCE were constructed using standard protocols (Wierdl, et al. 2001. Cancer Res. 61:5078-5082). Multiplicity of infection (moi) was defined as the number of plaques produced in 1×106 293 cells in a total volume of 1 ml of media after incubation with virus for 1 hour. Typically for IC50 determinations an moi of 5 was used, however, using these conditions in U373MG cells resulted very high levels of transgene expression, leading to toxicity, Therefore an moi of 1 was used for this cell line.
Growth Inhibition Assays. Growth inhibition assays using CPT-11 were performed in triplicate in 6 well multiwell plates as previously described (Wierdl, et al. 2004. Biochemistry 43:1874-1882). The concentrations of drug required to inhibit cell growth by 50% (IC50 values) were calculated using Prism software (GraphPad Software, San Diego, Calif.).
EXAMPLE 2
In Vitro Biological Activity of CE
The in vitro activity of rabbit liver CE can be examined in tumor cell lines. The growth inhibition of CPT-11 is compared in cells with and without hCE1mut6. The cells used can be Rh30 cells (107) that have been electroporated with a plasmid DNA or plasmid containing CE cDNA in a volume of phosphate-buffered saline. The cells are plated into 75-cm2 flasks in fresh media and G418 added hours following transfection to select for cells expressing the neo gene and the CE. Cells are grown for a minimum of 10 days before use in growth inhibition experiments.
In one type of assay, CPT-11 is pre-incubated with hCE1mut6 to produce SN-38 prior to exposure of the cells to drug. For example, 0.5 to 5 units of hCE1mut6 are incubated with 1 M CPT-11 at 37° C. in DMEM medium for 2 hours. Each reaction mixture is filter-sterilized and Rh30 cells exposed to drug for one hour, at which time the medium is replaced with drug-free medium containing serum. Enzyme that has been inactivated by boiling for five minutes prior to incubation with drug or CPT-11 to which no enzyme has been added is used as negative controls. Cells are allowed to grow for three cell doubling times and cell numbers are determined.
In another type of growth inhibition assay, Rh30 cells transfected with either parent plasmid DNA or the plasmid containing the mutant human CE cDNA are exposed to different concentrations of CPT-11. Drug is added to tissue culture medium of each of the stably transfected cell lines for two hours, after which time the medium is replaced with drug-free medium. Cells are then allowed to grow for three cell doublings as before. Results are expressed as the concentration of drug required to reduce cell growth to 50% of control cells, or IC50.
EXAMPLE 3
Use of CE in an In Vivo Model for Minimal Residual Disease (MRD)
A xenograft model for MRD has been developed to demonstrate the effectiveness of the combination of hCE1mut6 and prodrug in the prevention of MRD. In this model, immune-deprived mice, i.e., SCID mice, bearing human NB-1691 xenografts are treated with 10 mg/kg CPT-11 daily for 5 days on two consecutive weeks and tumor regression is examined. However, within 4-6 weeks, tumors are palpable in the exact position where the original xenograft was implanted. Since these tumors arise from cells that survived the initial cycle of chemotherapy, this model therefore mimics results seen in patients following surgical resection of the primary tumor and subsequent regrowth at the same site.
Experiments are performed in this model to compare the responses of mice bearing human Rh30 xenografts as well as xenografts expressing the hCE1mut6 protein. Rh30 rhabdosarcoma xenografts are transfected with a plasmid containing the cDNA for hCE1mut6 and with G418. Expression of CE is confirmed by biochemical assay using the CE substrate o-NPA and maintained for at least 12 weeks. Two groups of SCID mice are injected with the transfected cells subcutaneously into the flanks. A third group of control mice is injected in identical fashion with Rh30 cells not transfected with the plasmid. When the tumors reach a size of approximately 1 cm3, 2.5 mg CPT-11/kg/day is administered five days each week for two weeks (one cycle of therapy), repeated every 21 days for a total of three cycles (over 8 weeks) to one group of mice injected with the transfected xenograft cells and the third group of control mice. Tumor regression is examined.
Experiments can also be performed employing U373 glioblastoma cells transfected with a control plasmid or with a plasmid containing the cDNA for the hCE1mut6 protein. Expression of CE in the tumor cells is confirmed by biochemical assay using the substrate o-NPA. Cells are injected subcutaneously into the flanks of the SCID mice. When tumors reach approximately 1 cm3 in size, CPT-11 is administered daily for five days each week as described above, for three cycles, at a dose of 7.5 mg/kg/day. Again, tumor regression is examined.
EXAMPLE 4
Use of a Human CE/prodrug Combination to Purge Bone Marrow of Tumor Cells
Intravenous injection of human neuroblastoma NB-1691 tumor cells into immune-deprived mice results in the development of widespread metastatic disease with death occurring on days 36-38. Since both synaptophysin and tyrosine hydroxylase expression are specific for neuroblastoma cells, RT/PCR analysis of these mRNAs can detect tumor cells present in mixed populations of cells. Circulating neuroblastoma cells can be detected in the peripheral blood of these animals 36 days after injection with NB-1691. Studies then determine whether the bone marrow of these same animals contains neuroblastoma cells. The success of ex vivo purging of bone marrow with the hCE1mut6/CPT-11 combination is demonstrated by transplanting purged bone marrow into lethally irradiated mice. If mice remain disease free for extended periods of time, this indicates that the CE/prodrug purging therapy kills neuroblastoma cells in the donor marrow.
EXAMPLE 5
Treatment of Minimal Residual Disease (MRD) in Humans
The mutant human CE in combination with CPT-11 or other prodrug(s) activated by this enzyme are used to purge bone marrow of residual tumor cells prior to autologous bone marrow transplants to prevent recurrence of local MRD following removal of bulk tumor by surgery or chemotherapy. Following debulking of the primary tumor, adenovirus containing the mutant human CE under the control of a tumor-specific responsive promoter is applied to the tumor margins at either the time of surgery, by stereotaxic injection, or by implantation of a time-release polymer or other material. Anti-tumor effect of single application at time of surgery is compared with the effect produced by repetitive or time-release use of adenoviral constructs. Adenovirus dose ranges from 106 to 1010 plaque-forming units as has been reported to be effective for intratumoral injection of adenovirus (Heise, et al. 1977. Nature Med. 3:639-645). CPT-11 is administered over the next one to six weeks to elicit tumor selective cell kill. Doses and schedules of CPT-11 are determined in clinical trials of CPT-11 by itself and in human xenograft model systems to produce maximal tumor effect.
EXAMPLE 6
Purging Bone Marrow of Tumor Cells in Humans
Tumor cells that contaminate bone marrow used for autologous transplant contribute to relapse of disease. Therefore, the mutant human CE can be used in combination with a suitable prodrug to eradicate tumor cells in marrow samples to be used for transplant. This approach maintains the viability of hematopoietic cells required for reconstitution. Bone marrow samples are transduced ex vivo with adenovirus containing the mutant human CE cDNA, using a multiplicity of infection (moi) that will infect 100% of the tumor cells. Typically, a moi of 0.5 to 10 is adequate for tumor cells, while a moi of 100 to 1,000 is required to transduce a majority of hematopoietic progenitor cells. Two days following adenoviral transduction, cells are exposed for two hours to a range of CPT-11 concentrations, usually varying from 50 nM to 100 μM. Two days after exposure to drug, the marrow sample is harvested and stored for reinfusion into the patient and reconstitution of a tumor-free marrow.

## Claims

1. An isolated polynucleotide encoding the secreted mutant human carboxylesterase as set forth in SEQ ID NO:3 , further having deletion of sequences corresponding to six-amino acids from the N- or C-terminus of the human carboxylesterase protein, wherein said secreted mutant human carboxylesterase is capable of metabolizing a chemotherapeutic prodrug and inactive metabolites thereof to active drug.

2. A vector comprising the polynucleotide of claim 1 and a translation initiating codon.

3. An isolated host cell comprising the vector of claim 2.

4. The host cell of claim 3, wherein said host cell is a stem or progenitor cell.