# Patent

## Title
ABCB1 genotyping to predict microtubule-stabilizing-agent-induced toxicity

## Abstract

The present disclosure provides methods of identifying subjects having an increased likelihood of developing one or more adverse side effects resulting from administration of a microtubule-stabilizing agent. In particular examples, the method includes determining whether the subject has an ABCB1 predictive polymorphism for microtubule-stabilizing agent-induced toxicity, wherein the presence of such a polymorphism indicates that the subject has an increased risk of developing microtubule-stabilizing agent induced adverse effects. Examples of ABCB1 predictive polymorphisms include 2677G>T/A and 3435C>T. Also provided are methods of modifying microtubule-stabilizing agent therapy in a subject identified as having one or more ABCB1 predictive polymorphisms. Kits and isolated nucleic acid molecules that can be used in the disclosed methods are also provided.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This is the U.S. Stage of International Application No. PCT/US2007/073497, filed Jul. 13, 2007 (published in English under PCT Article 21(2)), which claims the benefit of U.S. Provisional Application No. 60/807,453 filed Jul. 14, 2006, herein incorporated by reference.


FIELD
This application relates to methods of identifying subjects who are likely to have significant adverse effects from administration of taxanes or other microtubule-stabilizing agents, as well as isolated nucleic acid molecules and kits that can be used to practice these methods.
BACKGROUND
Taxanes are a family of compounds that were originally identified in extracts of the bark of the yew tree (Taxus). Paclitaxel (Taxol®) and docetaxel (Taxotere®) are taxanes with broad antitumor activity. These drugs were originally approved for use in breast or ovarian tumor subjects, but they have activity against diverse tumors including lymphoma, non-small-cell lung, head and neck, gastric, bladder, prostate, and other carcinomas. Dosing and scheduling of these drugs have been optimized throughout the last two decades. Adverse effects caused by taxane treatment include severe hypersensitivity reaction, neutropenia, peripheral neuropathy, myalgia/arthralgia, skin and nail disorders, and alopecia. Neutropenia is the major dose-limiting toxicity of treatment with paclitaxel, while the frequency of peripheral neuropathy appears to increase with cumulative dose. Although the incidence of severe hypersensitivity reactions has been reduced by the use of premedication, cumulative peripheral neuropathy and neutropenia persist as challenges to optimal treatment with taxanes.
Taxanes are part of the larger family of anti-cancer drugs whose mechanism of action targets microtubules (MTs). Both paclitaxel and docataxel bind to the f3-tubulin subunit and stabilize MTs. This stabilization of the MTs leads to mitotic arrest and subsequent apoptosis. Other compounds with a similar mechanism of action include the epothilones, discodermolide, eleutherobin, the sarcodictyins, and the laulimalides (He et al., (2001) Drug Discovery Today 6:1153-1164).
One of the primary proteins involved in taxane elimination and distribution is ABCB1 (also known as multi-drug resistance 1 (MDR1) or P-glycoprotein). ABCB1 is a member of the ATP-binding cassette family of efflux transporters that are expressed in several tissues, including tissues with excretory function, neural stem cells, the blood-brain-barrier, and hematopoietic precursor cells. Although ABCB1 has not been detected in peripheral nerve cells, the transfer of drugs across the systemic circulation to the peripheral nerves is regulated by the blood-nerve barrier consisting of capillary endothelial cells. The cells that make up the blood-nerve barrier express ABCB1 and are thought to protect the peripheral nervous tissue by transporting toxic substances from the nervous system back into the systemic circulation.
Due to the severity of adverse effects resulting from administration of taxanes and other MT-stabilizing agents, methods for identifying individuals at increased risk for these side effects prior to commencement of treatment are needed.
SUMMARY
Polymorphisms in the ABCB1 gene have been identified that are predictive for adverse effects induced by treatment with taxanes or other microtubule (MT)-stabilizing agents. Based on these observations, methods are provided for identifying a subject at increased risk for adverse effects. In some examples, subjects identified as having an increased risk of adverse MT-stabilizing agent side effects receive a modified therapy designed to reduce such undesirable side effects.
In one example, the method includes determining the subject's genotype for ABCB1 predictive polymorphisms, such as those that indicate an increased likelihood of a particular clinical outcome. Exemplary ABCB1 predictive polymorphisms include, but are not limited to, one or more of 1236C>T, 2677G>T/A, and 3435C>T, such as two, three or four of such polymorphisms (for example 2677G>T/A and 3435C>T). In particular examples, the presence of one or more of these polymorphisms, such as two or three of these polymorphisms, is predictive of increased risk for adverse effects, while the absence of such predictive polymorphisms indicates that the subject will not likely experience adverse effects. In a particular example, the MT-stabilizing agent is a taxane. In another particular example, the MT-stabilizing agent is an epothilone.
Methods are also provided to decrease the occurrence of MT-stabilizing-agent-induced adverse effects by determining the genotype of a subject for ABCB1 polymorphisms and altering the course of treatment if the subject has at least one predictive polymorphism, such as at least two or at least three of such predictive polymorphisms. In one example, the amount of MT-stabilizing agent administered to a subject is decreased, for example wherein the dosage is decreased by at least 20%. In another example, the interval between treatments with MT-stabilizing agent is increased or the duration of MT-stabilizing agent infusion is increased (for example administering the same dose of a MT-stabilizing agent over a greater period of time). In yet another example, a therapeutically effective amount of colony-stimulating factor (CSF) is administered following MT-stabilizing agent treatment in order to reduce the incidence of neutropenia. Combinations of these can also be used.
Also provided are isolated nucleic acid molecules, such as those that consist of any of SEQ ID NOs: 1-12. One skilled in the art will appreciate that such primers can include a detectable label, such as a fluorophore or enzyme. Kits are disclosed that can be used to identify a subject at increased risk for MT-stabilizing-agent-induced adverse effects. In one example, two or more primers shown in SEQ ID NOs: 1-12 are included in the kit, for example to detect the presence or absence of one or more predictive polymorphisms in the ABCB1 gene. Such kits can include additional reagents, such as buffers and reagents that permit detection of a nucleic acid molecule, for example by amplification and/or specific hybridization.
The foregoing and other objects and features of the disclosure will become more apparent from the following detailed description, which proceeds with reference to the accompanying figures.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a diagram showing the association between the risk of developing grade 3 peripheral neuropathy and ABCB1 genotype status in 22 subjects receiving paclitaxel treatment for 12 weeks. CC, ABCB1 3435CC genotype; CT, ABCB1 3435CT genotype; TT, ABCB1 3435TT genotype. The P value was obtained from an exact two-tailed log rank test.
FIG. 2 is a diagram showing the association between the risk of neutropenia and ABCB1 genotype status in 18 subjects. Data are presented as a percentage decrease in absolute neutrophil count for each genotype following 12 weeks of paclitaxel treatment. Non-double variant, wild type at both, or heterozygous at one or both of ABCB1 2677 and ABCB1 3435 alleles; double variant, ABCB1 2677TT and ABCB1 3435TT genotype. The unadjusted P value was 0.0025.
FIG. 3 is a diagram showing the association between onset of docetaxel-induced peripheral neuropathy and ABCB1 genotype status in 50 subjects receiving docetaxel once a week for 3 consecutive weeks followed by a 1 week rest period until treatment failure. Data are presented as a percentage decrease of subjects having no neuropathy for each genotype. Upper trace shows subjects having the ABCB1 2677GG genotype (wild-type a both alleles), lower trace shows subjects having the ABCB1 2677GT or 2677GA (heterozygous at the ABCB1 2677 allele) or the double variant ABCB1 2677TT genotype. The P value was 0.017 by Log-Rank Test.



SEQUENCE LISTING
The nucleic acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. In the accompanying sequence listing:
SEQ ID NO: 1 and SEQ ID NO: 2 are forward and reverse primers, respectively, used to PCR amplify ABCB1 to detect polymorphisms at nucleotide 1236.
SEQ ID NO: 3 and SEQ ID NO: 4 are forward and reverse primers, respectively, used to PCR amplify ABCB1 to detect polymorphisms at nucleotide 2677.
SEQ ID NO: 5 and SEQ ID NO: 6 are forward and reverse primers, respectively, used to PCR amplify ABCB1 to detect polymorphisms at nucleotide 3435.
SEQ ID NO: 7 and SEQ ID NO: 8 are forward and reverse primers, respectively, used to sequence PCR products encompassing ABCB1 position 1236 in order to determine genotype.
SEQ ID NO: 9 and SEQ ID NO: 10 are forward and reverse primers, respectively, used to sequence PCR products encompassing ABCB1 position 2677 in order to determine genotype.
SEQ ID NO: 11 and SEQ ID NO: 12 are forward and reverse primers, respectively, used to sequence PCR products encompassing ABCB1 position 3435 in order to determine genotype.
SEQ ID NO: 13 is an exemplary human ABCB1 cDNA sequence that can be used to identify the referenced 1236, 2677, and 3435 positions disclosed herein.
SEQ ID NO: 14 is the protein encoded by SEQ ID NO: 13.
DETAILED DESCRIPTION
Abbreviations and Terms
The following explanations of terms and methods are provided to better describe the present disclosure and to guide those of ordinary skill in the art in the practice of the present disclosure. The singular forms “a,” “an,” and “the” refer to one or more than one, unless the context clearly dictates otherwise. For example, the term “including a nucleic acid” includes single or plural nucleic acids and is considered equivalent to the phrase “including at least one nucleic acid.” The term “or” refers to a single element of stated alternative elements or a combination of two or more elements, unless the context clearly indicates otherwise. As used herein, “comprises” means “includes.” Thus, “comprising A or B,” means “including A, B, or A and B,” without excluding additional elements. For example, the phrase “mutations or polymorphisms” or “one or more mutations or polymorphisms” means a mutation, a polymorphism, or combinations thereof, wherein “a” can refer to more than one.
Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below. The materials, methods, and examples are illustrative only and not intended to be limiting.
Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes V, published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).
ABCB1: ATP-binding cassette, sub-family B (MDR/TAP), member 1 gene or protein
CSF: colony-stimulating factor
G-CSF: granulocyte colony-stimulating factor
GM-CSF: granulocyte macrophage colony-stimulating factor
MDR1: multi-drug resistance gene or protein
MT: microtubule
PCR: polymerase chain reaction
ABCB1: ATP-binding cassette, sub-family B (MDR/TAP), member 1; otherwise known as the multidrug resistance gene (MDR1), encoding the protein known as P-glycoprotein. ABCB1 is a member of the ATP-binding cassette family of efflux transporters. It was first discovered as a protein responsible for resistance against anti-cancer drugs in human cancer cells. In general, ABCB1 is expressed in many normal tissues, for example, intestinal epithelium, adrenal gland, kidney, liver, pancreas, and capillary endothelial cells of the brain and testes. It plays a role in excretion of foreign xenobiotics from the body and preventing their transfer across the placenta and the blood-brain barrier.
ABCB1 sequences are publicly available. For example, GenBank Accession number NC 000007 discloses a human ABCB1 gene sequence, and GenBank Accession numbers BC130424 and AY910577 disclose exemplary human ABCB1 cDNA sequences and AAI30425 and AAW82430 disclose exemplary human ABCB1 protein sequences. One skilled in the art will appreciate that ABCB1 nucleic acid and protein molecules can vary from those publicly available, such as ABCB1 sequences having one or more substitutions, deletions, insertions, or combinations thereof, while still retaining ABCB1 biological activity. In addition, ABCB1 molecules include fragments that retain the desired ABCB1 biological activity.
Administration: To provide or give a subject an agent, such as a composition that includes a MT-stabilizing agent, such as a taxane or an epothilone, alone or in combination with another agent, by any effective route. Exemplary routes of administration include, but are not limited to, oral, injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), sublingual, rectal, transdermal, intranasal, vaginal and inhalation routes.
Analog: A synthetic chemical compound using a common structure as a backbone (for example, where side groups have been added or such groups have been deleted from the parent structure). The analog differs in structure from the parent molecule such as by a difference in the length of an alkyl chain, a molecular fragment, by one or more functional groups, or a change in ionization. For example, an analog of paclitaxel will have the taxane ring structure (as described by Kinston et al., Progress in the Chemistry of Organic Natural Products, Springer-Verlag, 1993) with alterations in side chains as compared with paclitaxel.
Cancer: Malignant neoplasm that has undergone characteristic anaplasia with loss of differentiation, increased rate of growth, invasion of surrounding tissue, and is capable of metastasis.
Colony-stimulating factor (CSF): Any of a family of glycoproteins which promote the differentiation of hematopoietic stem cells, particularly to neutrophils or macrophages. In one particular example, a CSF is granulocyte colony-stimulating factor (G-CSF). In another example, a CSF is granulocyte macrophage colony-stimulating factor (GM-CSF). In some examples, therapeutically effective amounts of CSF can be used to treat neutropenia.
Decreased/decreasing: Becoming less or smaller, as in number, amount, or intensity. In one example, reducing the frequency of occurrence of MT-stabilizing-agent-induced adverse effects by at least 10%, at least 20%, at least 30%, or at least 50%. In another example, reducing the amount of MT-stabilizing agent administered to a subject by at least 10%, at least 20%, at least 30%, or at least 50%. In a further example, reducing the incidence, duration, or severity of adverse effects induced by MT-stabilizing agents.
Docetaxel (Taxotere®): A member of the taxane family of compounds with anti-tumor activity derived from Taxus baccata by a semi-synthetic process, with the chemical formula (2R,3S)—N-carboxy-3-phenylisoserine,N-tert-butyl ester, 13-ester with 5β-20-epoxy-1,2α,4,7β,10β,13α-hexahydroxytax-11-en-9-one 4-acetate 2-benzoate, trihydrate. Docetaxel is an anti-microtubule agent that promotes the assembly and stabilization of MTs by preventing depolymerization. Stabilization of MTs leads to mitotic arrest and cytotoxicity.
Dosing schedule: Timing of administration of a therapeutic agent, such as a MT-stabilizing agent. For example, a therapeutic agent can be administered at least one time per day, at least once per week, at least once every two weeks, at least once every three weeks, or at least once every six weeks. In a specific example, paclitaxel dosing schedule can be a three hour infusion once ever three weeks.
Epothilone: A class of microlides initially discovered from the myxobacterium Sorangium cellulosum. Epothilones have MT-stabilizing activity and may have antitumor activity. Examples include epothilone A, epothilone B, and ixabepilone.
Granulocyte colony-stimulating factor (G-CSF): A member of the family of CSFs which stimulates growth and differentiation of neutrophils from the hematopoietic precursor cell population. G-CSF can be used as an adjunct to cytotoxic chemotherapy treatment of solid tumors. It has been shown to reduce incidence of febrile neutropenia and decrease time of recovery of neutrophil levels following chemotherapy. A pegylated form of G-CSF has also been approved for use in treating neutropenia. See Komrokji and Lyman (2004) Expert Opin. Biol. Ther. 4:1897-1910.
Granulocyte macrophage colony-stimulating factor (GM-CSF): A member of the family of CSFs which stimulates proliferation of neutrophils, macrophages, and eosinophils. GM-CSF can be used to treat neutropenia that occurs as a result of cytotoxic chemotherapy for solid tumors. See Komrokji and Lyman (2004) Expert Opin. Biol. Ther. 4:1897-1910.
Increased: Greater in amount, size, or degree. In one example, the time period during which MT-stabilizing agent chemotherapy is administered is lengthened by at least two hours, such as at least 23 hours. In another example, the interval between administration of doses of MT-stabilizing agent is lengthened by at least one week, at least two weeks, or at least five weeks.
Increased risk: An elevated likelihood that a certain event will occur. For example, subjects having one or more predictive polymorphisms in the ABCB1 gene may have an increased probability of experiencing MT-stabilizing-agent-induced adverse effects, such as neutropenia or peripheral neuropathy.
Isolated: An “isolated” biological component (such as a nucleic acid molecule, protein, or cell) has been substantially separated or purified away from other components, such as other components in the cell of the organism, or the organism itself, in which the component naturally occurs, such as other chromosomal and extra-chromosomal DNA and RNA, proteins and cells. Nucleic acid molecules and proteins that have been “isolated” include nucleic acid molecules (such as DNA or RNA) and proteins purified by standard purification methods. The term also embraces nucleic acid molecules and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acid molecules and proteins.
Ixabepilone (BMS-247550): A member of the family of epothilones with the chemical structure (1S,3S,7S,10R,11S,12S,16R)-7,11-dihydroxy-8,8,10,12,16-pentamethyl-3-[(1E)-1-methyl-2-(2-methylthiazol-4-yl)ethenyl]-17-oxa-4-azabicyclo[14.1.0]heptadecane-5,9-dione.
Microtubule-stabilizing agent: A class of compounds that bind to tubulin oligomers or polymers and enhances polymerization of tubulin or stabilizes MTs. This is in contrast to agents that depolymerize MTs, such as the vinca alkaloids. In one example, a MT-stabilizing agent is a taxane, such as paclitaxel. In another example, a MT-stabilizing agent is an epothilone, such as ixabepilone. In a further example, a MT-stabilizing agent is discodermolide or eleutherobin. In another example, a MT-stabilizing agent is a sarcodictyins or a laulimalide.
Microtubule-stabilizing-agent-induced adverse effects: Negative side effects resulting from administration of a MT-stabilizing agent anti-cancer drug to a subject, such as a human. Exemplary effects include hypersensitivity reaction, hematological effects (neutropenia, leucopenia, anemia), cardiovascular effects (bradycardia, hypotension), peripheral neuropathy, myalgia/arthralgia, nausea and vomiting, alopecia, and combinations thereof. Other effects are known to skilled clinicians.
Neutropenia: A condition wherein there is a reduction in the blood neutrophil count, often leading to increased susceptibility to infection. The severity of neutropenia is generally defined by the absolute neutrophil count—mild, between 1×109/ml and 2×109/ml; moderate, between 0.5×109/ml and 1×109/ml; severe, less than 0.5×109/ml. The most common cause of neutropenia is impaired neutrophil production as a result of drug treatment, particularly anti-cancer drugs. In one example, MT-stabilizing-agent-induced neutropenia may be treated by adjusting MT-stabilizing agent treatment or by administering CSFs subsequent to MT-stabilizing agent treatment.
Paclitaxel (Taxol®) A member of the taxane family with anti-tumor activity derived from Taxus baccata by a semi-synthetic process, with the chemical formula 5β,20-Epoxy-1,2α,4,7β,10β,13α-hexahydroxytax-11-en-9-one 4,10-diacetate 2-benzoate 13-ester with (2R,3S)—N-benzoyl-3-phenylisoserine. Paclitaxel is an anti-microtubule agent that promotes the assembly and stabilization of MTs by preventing depolymerization. Stabilization of MTs leads to mitotic arrest and cytotoxicity. Paclitaxel treatment generally results in lower rates of neutropenia than docetaxel treatment.
Peripheral neuropathy: A syndrome of sensory loss, muscle weakness and atrophy, decreased deep tendon reflexes, and vasomotor symptoms, singly or in any combination. In one example, MT-stabilizing agent-induced peripheral neuropathy is most commonly characterized by numbness and parathesia in a glove-and-stocking distribution. In a further example, MT-stabilizing-agent-induced peripheral neuropathy may be treated by adjusting MT-stabilizing agent treatment.
Polymorphism: A variation in a gene sequence, such as a variation in an ABCB1 sequence. The polymorphisms can be those variations (DNA sequence differences) which are generally found between individuals or different ethnic groups and geographic locations which, while having a different sequence, produce functionally equivalent gene products. The term can also refer to variants in the sequence which can lead to gene products that are not functionally equivalent. Polymorphisms also encompass variations which can be classified as alleles and/or mutations which can produce gene products which may have an altered function. Polymorphisms also encompass variations which can be classified as alleles and/or mutations which either produce no gene product or an inactive gene product or an active gene product produced at an abnormal rate or in an inappropriate tissue or in response to an inappropriate stimulus. Further, the term is also used interchangeably with allele as appropriate.
Polymorphisms can be referred to, for instance, by the nucleotide position at which the variation exists, by the change in amino acid sequence caused by the nucleotide variation, or by a change in some other characteristic of the nucleic acid molecule or protein that is linked to the variation. For example, a 1236C>T polymorphism in ABCB1 refers to a substitution of the C at position 1236 of the ABCB1 cDNA sequence for a T, which does not result in any amino acid change in the protein. In another example, a 2677G>T/A polymorphism refers to a substitution of the G at position 2677 of the ABCB1 cDNA sequence for a T or an A, resulting in a change of alanine 893 in the protein to serine or threonine, respectively. In a further example, 3435C>T refers to a substitution of the C at position 3435 of the ABCB1 cDNA sequence for a T, which does not result in any amino acid change in the protein. The locations of these positions can be determined from an ABCB1 cDNA sequence known in the art, for example GenBank Accession No. BC130424 (SEQ ID NO: 13).
A predictive polymorphism is one that indicates an increased likelihood of a particular clinical outcome. For example, the presence of one of more of the 1236C>T, 2677G>T/A, and 3435C>T polymorphisms in the ABCB1 gene are indicative of a subject more likely to experience adverse effects from MT-stabilizing agent treatment (such as peripheral neuropathy or neutropenia) as compared to a subject not having these polymorphisms.
Sample: Includes biological samples that contain cells, genomic DNA, RNA, or proteins (or combinations thereof) obtained from a subject, such as those present in peripheral blood, urine, saliva, sputum, tissue biopsy, surgical specimen, fine needle aspirate, and autopsy material. In a particular example, a sample includes blood plasma obtained from a human subject.
Subject: Living multi-cellular vertebrate organisms, a category that includes human and non-human mammals (such as laboratory or veterinary subjects).
Subsequent to: At a time later than or after another event. For example, subsequent administration of a CSF indicates administration of a CSF at some time following administration of a MT-stabilizing agent, such as at least 24 hours after MT-stabilizing agent administration, at least 72 hours after MT-stabilizing agent administration, or at least seven days following MT-stabilizing agent administration.
Synonymous substitution: A nucleotide substitution that results in a new codon specifying the same amino acid. Such substitutions often occur at the third base position of a codon. However, base substitution at the first base position can occasionally give rise to a synonymous substitution, as in the case of some leucine and arginine codons (for example CUAUUA, CUGUUG, AGACGA and AGGCGG).
Taxane: A “taxane” is a chemical based on the taxane ring structure as described in Kinston et al., Progress in the Chemistry of Organic Natural Products, Springer-Verlag, 1993. A member of the group of complex diterpenoids derived from the bark of Taxus brevifolia or semi-synthetically from the needles of a member of the genus Taxus, such as Taxus baccata. Taxanes may also be made synthetically by total synthesis. Their mechanism of action is through binding to tubulin polymers and stabilizing the MT, resulting in cell cycle arrest and ultimately cell death. Taxanes can be used as anti-neoplastic agents in the treatment of a number of solid tumors, including breast, ovary, non-small cell lung, and prostate. In one example, a taxane is paclitaxel. In another example, a taxane is docetaxel. In a further example, a taxane is an analog of paclitaxel containing the taxane ring structure.
Therapeutically effective amount: An amount of a therapeutic agent (such as a composition that includes a MT-stabilizing agent, such as paclitaxel or ixabepilone), that alone, or together with one or more additional therapeutic agents, induces the desired response, such as treatment of a solid tumor, such as breast, ovarian, non-small cell lung, or AIDS-related Kaposi's sarcoma. In one example, it is an amount of MT-stabilizing agent needed to prevent or delay the development of a tumor, prevent or delay the metastasis of a tumor, cause regression of an existing tumor, or treat one or more signs or symptoms associated with a tumor, in a subject, such as a subject having breast cancer. Ideally, a therapeutically effective amount provides a therapeutic effect without causing a substantial cytotoxic effect in the subject. The preparations disclosed herein are administered in therapeutically effective amounts.
In one example, a desired response is to decrease the size, volume, or number (such as metastases) of a solid tumor. For example, the composition that includes a MT-stabilizing agent can in some examples decrease the size, volume, or number of tumors (such as ovarian tumors) by a desired amount, for example by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 50%, at least 75%, or even at least 90%, as compared to a response in the absence of the therapeutic composition.
In general, an effective amount of a composition that includes a MT-stabilizing agent administered to a human subject will vary depending upon a number of factors associated with that subject, for example the overall health of the subject. An effective amount of a composition that includes a MT-stabilizing agent can be determined by varying the dosage of the product and measuring the resulting therapeutic response, such as the regression of a tumor. The disclosed therapeutic agents can be administered in a single dose, or in several doses, as needed to obtain the desired response. However, the effective amount can be dependent on the source applied, the subject being treated, the severity and type of the condition being treated, and the manner of administration.
In particular examples, a therapeutically effective dose of a MT-stabilizing agent includes at least 35 mg/m2 (such as 35-300 mg/m2) of paclitaxel administered intravenously over at least 1 hour (such as 1-24 hours) at least every one week (such as every 1-3 weeks). The disclosed compositions that include a MT-stabilizing agent can be administered alone, in the presence of a pharmaceutically acceptable carrier, in the presence of other therapeutic agents (such as other anti-neoplastic agents), or both.
Treatment: Refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition related to a disease (such as a tumor, for example a breast, ovarian, or lung tumor). Treatment can also induce remission or cure of a condition, such as a tumor. Reducing a sign or symptom associated with a tumor (such as a breast, ovarian, or lung tumor) can be evidenced, for example, by a delayed onset of clinical symptoms of the disease, a reduction in severity of some or all clinical symptoms of the disease, a slower progression of the disease (for example by prolonging the life of a subject having tumor), a reduction in the number of relapses of the disease, an improvement in the overall health or well-being of the subject, or by other parameters well known in the art that are specific to the particular tumor. In another example, treatment can include a therapeutic intervention that ameliorates a MT-stabilizing agent-induced adverse effect, such as peripheral neuropathy or neutropenia, for example by altering the MT-stabilizing agent treatment regimen.
Treatment includes preventing a disease, for example by inhibiting the full development of a disease, such as preventing development of a tumor (such as a metastasis or the development of a primary tumor). Prevention does not require a total absence of a tumor. In one example, treatment includes therapeutic intervention that prevents the development of MT-stabilizing-agent-induced adverse effects such as peripheral neuropathy or neutropenia. In a particular example, if a subject is determined to have an ABCB1 polymorphism predictive for MT-stabilizing-agent-induced neutropenia, treatment can include administration of a CSF to prevent development of neutropenia.
Tumor: A neoplasm. A particular type of tumor is a solid tumor. Examples of solid tumors, such as sarcomas and carcinomas, include, but are not limited to: fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, and other sarcomas, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, lymphoid malignancy, pancreatic cancer, breast cancer, lung cancers, ovarian cancer, prostate cancer, hepatocellular carcinoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, Wilms' tumor, cervical cancer, testicular tumor, bladder carcinoma, and CNS tumors (such as a glioma, astrocytoma, medulloblastoma, craniopharyogioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, menangioma, melanoma, neuroblastoma and retinoblastoma). Certain classes of tumors respond therapeutically to treatment with a MT-stabilizing agent and this class of tumors is referred to as an MT-stabilizing agent responsive tumor.
Methods of Identifying Risk for Adverse Effects
Methods are provided for identifying a subject at increased risk for developing MT-stabilizing-agent-induced adverse effects. The subject may, for example, have a tumor that is believed to be a tumor that is responsive to a MT-stabilizing agent. In one example, the method includes determining whether the subject has at least one predictive polymorphism in an ABCB1 gene, wherein the presence of at least one predictive polymorphism in an ABCB1 gene (such as at least two predictive polymorphisms in an ABCB1 gene) indicates that the subject has an increased risk for developing MT-stabilizing-agent-induced adverse effects. In contrast, a subject not having a predictive polymorphism in an ABCB1 gene indicates that the subject does not have an increased risk for MT-stabilizing-agent-induced adverse effects.
A predictive polymorphism is one that indicates that a subject has an increased likelihood of a particular clinical outcome. For example, an ABCB1 predictive polymorphism includes one or more ABCB1 polymorphisms that can be used to determine whether a subject has an increased likelihood of developing one or more adverse effects resulting from treatment with a MT-stabilizing agent. Particular examples of predictive ABCB1 polymorphisms include, but are not limited to: 1236C>T, 2677G>T, 2677G>A, or 3435C>T, or combinations thereof.
In one example, if the subject has at least two or at least three predictive polymorphisms in an ABCB1 gene, this indicates that the subject is at increased risk for developing MT-stabilizing-agent-induced adverse effects, such as peripheral neuropathy and neutropenia. For example, if the subject has an ABCB1 3435C>T polymorphism, this can indicate an increased risk for development of peripheral neuropathy following administration of a MT-stabilizing agent. In another example, if the subject has both 2677G>T/A and 3435C>T ABCB1 polymorphisms, the subject can have an increased risk for development of neutropenia following MT-stabilizing agent treatment.
Determining ABCB1 Genotype
Nucleic acids suitable for detecting polymorphisms in ABCB1 can be obtained from numerous biological sources. Exemplary biological samples include, but are not limited to, whole blood or fractions thereof (such as plasma), buccal cells obtained by swab or mouthwash, tumor biopsy, fine needle aspirates, amniocentesis or chorionic villus samples, pathological samples, and blood spots on Guthrie cards. See, for example, Chapter 17 in Human Molecular Genetics 2. Eds. Tom Strachan and Andrew Read. New York: John Wiley & Sons Inc., 1999. In one example, DNA is isolated from plasma from a subject.
Methods to isolate nucleic acids (such as genomic DNA, cDNA, or mRNA) from a biological sample are known in the art. Although exemplary methods are provided, the methods are not limited to those listed. Particular methods of isolating nucleic acid molecules from a biological sample are well known in the art, and can include ethanol precipitation following cell lysis, column purification methods, and magnetic or glass bead-based isolation methods. In addition, commercially available kits can be used, such as QIAamp® DNA purification kits (Qiagen, Valencia, Calif.) or PUREGENE® DNA purification kits (Gentra Systems, Minneapolis, Minn.). In a particular example, genomic DNA is isolated from human plasma from a subject using a spin column method.
Methods for detecting polymorphisms (such as predictive polymorphism of ABCB1) in a nucleic acid molecule are known in the art. Although exemplary methods are provided, the methods are not so limited. Particular methods of detecting a predictive polymorphism at one or more particular nucleotides (for example in ABCB1) include, but are not limited to, restriction fragment length polymorphism (RFLP), single strand conformational polymorphism (SSCP) mapping, direct nucleic acid sequencing, hybridization, fluorescent in situ hybridization (FISH), pulsed field gel electrophoresis (PFGE) analysis, RNase protection assay, allele-specific oligonucleotide (ASO), dot blot analysis, allele-specific PCR amplification (ARMS), oligonucleotide ligation assay (OLA) and PCR-SSCP. Methods of performing such methods are routine. See, for example, Chapters 6 and 17 in Human Molecular Genetics 2. Eds. Tom Strachan and Andrew Read. New York: John Wiley & Sons Inc., 1999.
In a particular example, the presence of one or more predictive polymorphisms, such as those of ABCB1, is determined by direct nucleotide sequencing. In a further example, the presence of one or more polymorphisms is determined by a Taq polymerase assay, such as a TaqMan® assay (Holland et al. (1991) Proc. Natl. Acad. Sci. U.S.A. 88:7276-80; Lee et al. (1999) J. Mol. Biol. 285:73-83). This assay is based on the fact that Taq polymerase does not possess a proofreading 3′ to 5′ exonuclease activity, but possesses a 5′ to 3′ exonuclease activity. This assay involves the use of two conventional PCR primers (forward and reverse), which are specific for the target sequence (such as ABCB1), and a third primer, which is allele-specific, designed to bind specifically to a site on the target sequence downstream of the forward primer binding site. The third primer is generally labeled with two fluorophores, a reporter dye at the 5′ end, and a quencher dye, having a different emission wavelength compared to the reporter dye, at the 3′ end. The third primer also carries a blocking group at the 3′ terminal nucleotide, so that it cannot by itself prime any new DNA synthesis. During the PCR reaction, Taq DNA polymerase synthesizes a new DNA strand primed by the forward primer and as the enzyme approaches the third primer, its 5′ to 3′ exonuclease activity processively degrades the third primer from its 5′ end. The end result is that the nascent DNA strand extends beyond the third primer binding site and the reporter and quencher dyes are no longer bound to the same molecule. As the reporter dye is no longer near the quencher dye, the resulting increase in reporter emission intensity can be detected.
In another example, the presence of predictive polymorphisms in ABCB1 can be detected using an oligonucleotide ligation assay (OLA) method. The OLA includes two phases, a PCR amplification and an oligonucleotide ligation. In the first reaction a PCR primer is hybridized to the target sequence. The primers are designed with either the normal or mutant nucleotide(s) at the 3′ end and differing fluorescent labels at the 5′ end. The second reaction is a ligation reaction. A common primer which is complementary to the target DNA sequence immediately downstream (3′) of the SNP site is ligated to a primer which perfectly matches the 5′ sequence. The resulting ligated oligonucleotide products can be detected using capillary gel electrophoresis and fluorescent detection of the respective fluorescent tags in order to determine genotype.
In a further example, a bead-based assay utilizing hybridization of allele-specific oligonucleotides attached to a fluorescent label can be used to identify polymorphisms in ABCB1. Oligonucleotides specific to each allele, which are attached to different fluorescently labeled beads, are hybridized to amplified DNA containing the polymorphism of interest. The allele-specific oligonucleotides will only significantly hybridize if the allele is present in the sample. The hybridized beads are then captured, for example with a biotinylated detector molecule, and the relative fluorescence of the beads for each label is measured. This allows the determination of genotype for a particular polymorphism, for example in the ABCB1 gene.
Subjects
In one example, mammalian subjects are analyzed for the presence of one or more ABCB1 predictive polymorphisms, such as a human or veterinary subject. In some examples, the subject has a disorder that can be treated by administration of a MT-stabilizing agent. Examples of disorders that can be treated by administration of a MT-stabilizing agent include, but are not limited to, solid tumors, such as solid cancers of the breast, lung (such as non-small cell lung carcinoma), ovary, bladder or ureter, esophagus, head or neck, and kidney, as well as Kaposi's sarcoma.
For example, the subject can be receiving treatment for a tumor which includes administration of a MT-stabilizing agent. In another example, the subject is a candidate for administration of a MT-stabilizing agent, for example, someone who has a tumor of the MT-stabilizing agent responsive type.
Microtubule-Stabilizing Agents
Particular ABCB1 polymorphisms are associated with increased risk of occurrence of adverse effects following administration of MT-stabilizing agents, and are referred to herein as predictive ABCB1 polymorphisms. MT-stabilizing agents are compounds that bind to tubulin oligomers or polymers and enhance polymerization of tubulin or stabilize MTs, leading to cytotoxicity.
In one example, the MT-stabilizing agent is from the class of epothilones, such as ixabepilone (BMS-247550). In another example, the MT-stabilizing agent is from the class of taxanes, such as paclitaxel (Taxol®), docetaxel (Taxotere®), or a chemical analog of paclitaxel that shares the taxane ring backbone.
Adverse Effects
It is shown herein that particular polymorphisms in an ABCB1 gene are associated with increased risk for certain adverse effects induced by MT-stabilizing agents. MT-stabilizing-agent-induced adverse effects include undesirable side effects that can result from the administration of therapeutically effective amounts of a MT-stabilizing-agent. In some examples, such effects are not observed uniformly throughout a population. That is, some subjects suffer more effects or more severe effects than others. In particular examples, the disclosed methods can be used to distinguish such subjects.
In one example, the adverse effect is peripheral neuropathy. In a particular example, increased risk of developing peripheral neuropathy is predicted by the presence of the polymorphism 3435C>T. In another example, the adverse effect is neutropenia. In a particular example, increased risk of developing neutropenia is predicted by the presence of polymorphisms at both 2677G>T/A and 3435C>T.
Method for Decreasing Occurrence of Adverse Effects
Methods are provided for decreasing the occurrence of one or more MT-stabilizing-agent adverse effects, such as peripheral neuropathy and neutropenia. In one example, the genotype of a subject for ABCB1 predictive polymorphisms 2677G>T/A and 3435C>T is determined, and if the subject is determined to have at least one predictive polymorphism, thus indicating that the subject has an increased risk of developing one or more MT-stabilizing-agent adverse effects, approaches can be taken to reduce the MT-stabilizing-agent adverse effects.
For example, administration of a MT-stabilizing agent can be modified, agents can be administered that are known to treat one or more MT-stabilizing-agent adverse effects, or combinations thereof, thereby decreasing the occurrence of adverse effects in the subject having an increased risk of developing MT-stabilizing-agent adverse effects.
Microtubule-Stabilizing Agent Administration
The amount, timing, or rate of administration (or combinations thereof) of a MT-stabilizing agent can be modified to reduce the occurrence or severity of adverse effects caused by the treatment, such as peripheral neuropathy and neutropenia. In some examples the modifications are relative to routine therapeutic methods for administering an MT-stabilizing agent to a subject (such as what would be routine for a cancer patient). In one example, the amount of MT-stabilizing agent administered is decreased, for example relative to an amount routinely administered, such as a reduction of at least 10%, at least 20%, at least 30%, or at least 50%. In a particular example, the dose of paclitaxel is reduced from 175 mg/m2 to an amount less than 175 mg/m2 (such as 150 mg/m2 to 50 mg/m2, such as 140 mg/m2 to 100 mg/m2, for example 135 mg/m2). In another example, the interval between administration of doses of a MT-stabilizing agent is increased, for example relative to an interval routinely used. In particular examples the interval is increased by at least one week, at least two weeks, or at least five weeks. In a further example, the interval between doses of microtubule-stabilizing agent is increased from one week to three weeks. In another example, the rate of administration of the MT-stabilizing agent is decreased by increasing the time period of administration, for example relative to a rate routinely administered. In particular examples the time of administration is increased by at least one hour, at least two hours, or at least 23 hours. In a further example, the time of administration is increased from one hour to three hours.
Administration of Additional Treatments
Neutropenia
The incidence, severity, or duration of neutropenia in subjects identified to be at increased risk based on ABCB1 genotype can be reduced by additional treatment. In one example, a therapeutically effective amount of CSF is administered to subjects at risk for MT-stabilizing agent-induced neutropenia, for example before, during, or after administration of the MT-stabilizing agent. In a particular example, a therapeutically effective amount of CSF is administered subsequent to MT-stabilizing agent administration. In a particular example, the CSF is G-CSF. In a further example, at least 1 μg/kg/day of G-CSF (such as 4-8 μg/kg/day of G-CSF, for example 5 μg/kg/day) is administered starting at least 24 hours (such as 24-72 hours) after microtubule-stabilizing agent administration. In another example, at least 1 mg of pegylated G-CSF (such as 1-10 mg of pegylated G-CSF, for example 6 mg) is administered at least 24 hours (such as 24 hours to 7 days) following MT-stabilizing agent treatment by subcutaneous injection. In a further example, the CSF is GM-CSF. In a particular example, at least 100 μg/m2 of GM-CSF (such as 100-250 μg/m2 of GM-CSF) is administered starting at least 24 hours after microtubule-stabilizing agent administration.
In another example, CSF is administered prior to commencement of treatment with a MT-stabilizing agent. In a particular example, at least 1 μg/kg/day of G-CSF (such as 4-8 μg/kg/day of G-CSF, for example 5 μg/kg/day) is administered starting at least 24 hours (such as 24-72 hours) before MT-stabilizing agent administration. In another example, at least 1 mg of pegylated G-CSF (such as 1-10 mg of pegylated G-CSF, for example 6 mg) is administered at least 24 hours (such as 24 hours to 7 days) before MT-stabilizing agent treatment by subcutaneous injection. In a further example, at least 100 μg/m2 of GM-CSF (such as 100-250 μg/m2 of GM-CSF) is administered starting at least 24 hours before microtubule-stabilizing agent administration.
In a further example, CSF is administered concurrent with treatment with a MT-stabilizing agent. In a particular example, at least 1 μg/kg/day of G-CSF (such as 4-8 μg/kg/day of G-CSF, for example 5 μg/kg/day) is administered starting immediately after the administration of an MT-stabilizing agent. In another example, at least 1 mg of pegylated G-CSF (such as 1-10 mg of pegylated G-CSF, for example 6 mg) is administered starting immediately after the administration of an MT-stabilizing agent by subcutaneous injection. In a further example, at least 100 μg/m2 of GM-CSF (such as 100-250 μg/m2 of GM-CSF) is administered starting immediately after the administration of an MT-stabilizing agent.
Peripheral Neuropathy
The incidence, severity, or duration of peripheral neuropathy in subjects identified to be at increased risk based on ABCB1 genotype can be reduced by additional treatment. In one example, a therapeutically effective amount of amytriptyline is administered to subjects at risk for MT-stabilizing agent-induced peripheral neuropathy, for example before, during, or after administration of the MT-stabilizing agent. In a particular example, at least 5 mg (such as 10-50 mg, for example 25 mg) of amitriptyline is administered at least 24 hours after MT-stabilizing agent administration.
In another example, a therapeutically effective amount of glutamine is administered to subjects at risk for MT-stabilizing-agent-induced peripheral neuropathy for example before, during, or after administration of the MT-stabilizing agent. In a particular example, at least 5 g (such as 5-20 g, for example 10 g) of glutamine is administered orally three times per day, starting at least 24 hours (such as 24-72 hours) following MT-stabilizing agent treatment for at least 1 day (for example 4 days).
In a further example, a therapeutically effective amount of Vitamin E is administered to subjects at risk for MT-stabilizing agent-induced peripheral neuropathy for example before, during, or after administration of the MT-stabilizing agent. In a particular example, at least 100 mg (such as 100-600 mg, for example 300 mg) of Vitamin E is administered orally two times per day starting at the time of administration of MT-stabilizing agent and continuing at least 1 month (such as 1-6 months, for example 3 months) following MT-stabilizing agent treatment.
Diagnostic Reagents
Another aspect of the disclosure includes reagents that can be used to detect one or more ABCB1 polymorphism genotypes in a subject. For example, the disclosed reagents can be used to determine if a subject has one or more polymorphisms at position 1236, 2677 and 3435 of ABCB1 cDNA (e.g. SEQ ID NO: 13), such as a 1236 C>T, 2677 G>T/A or 3435 C>T polymorphism.
Isolated Nucleic Acids
Isolated nucleic acid molecules are provided that in some examples are used to determine the genotype of a subject for polymorphisms in an ABCB1 gene. Exemplary isolated nucleic acids are provided in SEQ ID NOS: 1-12. In one example, an isolated nucleic acid molecule consists of any of SEQ ID NOS: 1-12. However, one skilled in the art will appreciate that minor changes to these sequences will still permit detection of the desired polymorphism in ABCB1. For example, the disclosure provides isolated nucleic acid molecules that include any of SEQ ID NOS: 1-12 containing one or two deletions, substitutions, insertions, or combinations thereof. In a further example, isolated nucleic acid molecules that include, consist essentially of, or consist of SEQ ID NOS: 1-12 can include modified nucleotides, such as nucleotides containing phosphorothioate.
The disclosed isolated nucleic acids can also include one or more detectable labels, for example to permit detection of a nucleic acid molecule. A detectable label is an agent capable of detection, for example by ELISA, spectrophotometry, flow cytometry, or microscopy. For example, a label can be attached to the 5′- or 3′-end of any of SEQ ID NOS: 1-12, or anywhere in between. Examples of labels include, but are not limited to, radioactive isotopes, enzyme substrates, co-factors, ligands, chemiluminescent agents, fluorophores, haptens, enzymes, and combinations thereof. Methods for labeling and guidance in the choice of labels appropriate for various purposes are discussed for example in Sambrook et al. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., 1989) and Ausubel et al. (Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1998).
In a particular example, one or more of SEQ ID NOS: 1-6 are used to PCR amplify regions of an ABCB1 gene that contain known polymorphisms (such as 2, 3, 4, 5, or 6 of these sequences). In a further example, one or more of SEQ ID NOS: 7-12 are used to determine the nucleotide sequence of regions of ABCB1 that contain known polymorphisms (such as 2, 3, 4, 5, or 6 of these sequences).
Diagnostic Kits
Kits are provided that can be used to determine if a subject is at an increased risk for MT-stabilizing-agent-induced adverse effects. In one example, the kit contains one or more reagents for detecting at least one polymorphism in an ABCB1 gene. In a particular example, the one or more reagents detect the presence of one or more (such as at least two) of the following polymorphisms: 1236 C>T, 2677G>T/A, or 3435C>T. In another example, the one or more reagents include at least one of the isolated nucleic acids shown in SEQ ID NOS: 1-12, such as 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or all 12 of these sequences. In one example, the kit includes SEQ ID NOS: 1-6. In another example, the kit includes SEQ ID NOS: 7-12. In yet another example, the kit includes SEQ ID NOS: 1-12.
The disclosed kits can further include other agents, such as buffers, agents that permit amplification of a nucleic acid sequence (such a Taq polymerase or dNTPs), agents that permit sequencing of a nucleic acid sequence (such as fluorescently labeled dideoxynucleotide triphosphates or Taq polymerase), or combinations thereof. In another example the kits can further include agents that permit detection of polymorphisms by TaqMan® assay (such as fluorescently labeled primers or Taq polymerase).
Example 1
Subjects
This example describes the demographics and treatment regimen for the subjects evaluated.
Twenty-six subjects were examined. There were 14 male subjects and 12 female subjects with a median age of 59.5 years (range: 42-72). Details of their demographics are presented in Table 1. The subjects were treated with weekly one- or three-hour paclitaxel infusions. All subjects had histologically proven, locally advanced or metastatic cancer, for which paclitaxel as monotherapy was a therapeutic option.







TABLE 1







Demographics at Baseline










Characteristic
Valuea














Paclitaxel infusion duration




1-hour
12



3-hours
14



Site of primary tumor



Breast
5



Lung
9



Ovary
3



Bladder or ureter
2



Esophagus
3



Head and neck
3



Kidney
1



Prior therapy
24



Chemotherapy containing vinca
9



Chemotherapy containing platinum
14



Radiation therapy
11







aNumbers represent number of subjects.






Paclitaxel (30 mg) formulated in a mixture of Cremophor and absolute:ethanol (1:1, vol/vol) (Bristol Myers Squibb, Munich, Germany) was diluted in 500 mL of 5% (weight/vol) dextrose in water and administered to subjects via a peripheral or central venous catheter using a motor-driven programmable infusion pump. Eligible subjects were randomized between a one hour and three hour infusion duration to receive a total of six weekly intravenous infusions of paclitaxel at a dose of 100 mg/m2. After six weeks of therapy (defined as one cycle) response was evaluated bi-dimensionally, usually by computed tomography. Subjects with a stable disease, partial response or complete response after one cycle received a second cycle, provided toxic effects were not prohibitive.
Example 2
Isolation of Nucleic Acids
This example describes methods used to isolate DNA from human plasma.
Genomic deoxyribonucleic acid (DNA) was extracted from 1 mL of human plasma using the QIAamp® Ultrasensitive Virus Kit (Qiagen Inc., Valencia, Calif.), following the manufacturer's instructions. The resulting DNA was reconstituted in a buffer containing 10 mM Tris (pH 7.6) and 1 mM ethylenediamine tetra acetic acid. It will be recognized that additional methods for isolating DNA from human plasma, whole blood, or other biological specimens are well known in the art.
Example 3
Detecting ABCB1 Polymorphisms
This example describes methods used to genotype ABCB1 at positions 1236, 2677 and 3435, relative to the ABCB1 reference coding sequence (CDS) Genbank accession number NM—000927, with the translation start site designated as base position number one. Although a particular method is described, it will be recognized that additional methods for determining the genotype of a subject at a particular position are well known in the art.
For analysis of ABCB1 variants, a 50 μL reaction was prepared for polymerase chain reaction (PCR) amplification using the PCR primer combinations listed in Table 2. The reaction consisted of 1×PCR buffer, 2 mM of each of the four deoxynucleotide triphosphates (dNTPs), 1.5 mM magnesium chloride, and 1 unit of Platinum® Taq DNA polymerase (Invitrogen, Carlsbad, Calif.). PCR conditions were as follows:
94° C. for 5 minutes, followed by 40 cycles of 94° C. for 30 seconds, 68° C. for 30 seconds, and 72° C. for 30 seconds, with a final 7 minute cycle at 72° C. Direct nucleotide sequencing PCR was conducted using the BigDye® Terminator Cycle Sequencing Ready Reaction kit V3.1 (Applied Biosystems, Foster City, Calif., USA) using the sequencing primers listed in Table 2. Sequences were generated on an ABI Prism® 310 Genetic Analyzer. The genotype was called variant if it differed from the consensus sequence of BC130424.







TABLE 2







Primers Used for ABCB1 Amplification and Sequencing










PCR Primer 
Sequencing Primer 



Sequence
Sequence


SNP
(SEQ ID NO: )
(SEQ ID NO: )





1236
Fa GTTCACTTCAGTT
F GTCAGTTCCTATATC


C > T
ACCCATCTCG
CTGTGTCTG



(1)
(7)



Rb TATCCTGTCCATCAA
R TCCTGTCCATCAACA



CACTGACC
CTGACCTG



(2)
(8)


 


2677
F AGGCTATAGGTTCC
F CCCATCATTGCAAT


G > 
AGGCTTGC
AGCAGGAG


A/T
(3)
(9)



R AGAACAGTGTGAA
R GAACAGTGTGAAGAC



GACAATGGCC
AATGGCCT



(4)
(10)


 


3435
F ATCTCACAGTAA
F GCTGGTCCTGAA


C > T
CTTGGCAGTTTC
GTTGATCTGTG



(5)
(11)



R AACCCAAACAGGA
R AAACAGGAAGTGTG



AGTGTGGCC
GCCAGATGC



(6)
(12)





aForward primer; 


bReverse primer. 






All data are reported as median values with the associated 95% confidence interval (95% CI), unless specified otherwise. Genotype-frequency analysis of Hardy-Weinberg equilibrium was carried out using Clump version 1.9. The linkage between each pair of SNPs was determined in terms of the classical statistic D′. The absolute value for D′ (|D′|) of 1 denotes complete linkage disequilibrium, while a value of 0 denotes complete linkage equilibrium. All P values are two-tailed, and those less than or equal to 0.05 were considered to reflect statistically significant results.
Genetic analysis was performed to detect ABCB1 SNPs in subjects described in Example 1. As shown in Table 3, the observed ABCB1 genotype frequencies were in Hardy-Weinberg equilibrium (P>0.11), and were similar to previously published values for a predominantly white population. Strong linkage was observed between the three SNPs in ABCB1, with a D′ of 1 for the 1236C>T and 2677G>T/A loci (P<0.001); a D′ of 0.64 (P=0.007) for the 1236C>T and 3435C>T loci; and a D′ of 0.49 for the 2677G>T/A and 3435C>T loci (P=0.042). The most frequently observed haplotypes were T-T-T (40.7%), C-G-C (22.5%), and C-T-C (12.4%), although in total, 6 different haplotypes were observed.







TABLE 3







Genotype and Allele Frequencies










Genotype frequenciesa
Allele frequenciesb













Polymorphismc
Effectd
WTe
Het
Var
p
q





ABCB1 1236C > T
G411G
5 (19.2%)
17 (65.4%)
4 (15.4%)
0.52
0.48


ABCB1 2677G > T
A893S
2 (7.7%) 
13 (50.0%)
11 (42.3%) 
0.32
0.67


ABCB1 3435C > T
I1145I
4 (15.4%)
14 (53.8%)
8 (30.8%)
0.42
0.58





aNumbers represent number of subjects with percentage in parentheses; the difference in the total number of subjects is due to the fact that not all samples yielded sequencing data or showed PCR amplification;


bHardy-Weinberg notation for allele frequencies (p, frequency for wild type allele and q, frequency for variant allele);


cNumber represents position in nucleotide sequence;


dNumber represents amino acid codon;


eWT, Homozygous wild type; Het, Heterozygous; Var, Homozygous variant.






Example 4
Pharmacokinetic Analysis
This example describes analysis of pharmacokinetics of paclitaxel in treated subjects and their association with ABCB1 genotype.
Blood samples were obtained from the subjects described in Example 1 during the first paclitaxel administration at baseline and at serial time points during and after infusion. Concentrations of total paclitaxel in plasma were determined by a validated method based on reversed-phase high performance liquid chromatography with ultraviolet detection, while unbound paclitaxel plasma concentrations were determined by micro-equilibrium dialysis using a [G-3H]paclitaxel tracer. Pertinent pharmacokinetic parameters were calculated by non-compartmental methods using WinNonlin® version 5.0 (Pharsight, Mountain View, Calif., USA).
All data are reported as median values with the associated 95% CI, unless specified otherwise. Interindividual pharmacokinetic variability was assessed as the coefficient of variation, and expressed as a percentage. The associations of the variant genotypes with individual pharmacokinetic parameters were evaluated statistically with the nonparametric Kruskal-Wallis test. All P values are two-tailed, and those less than or equal to 0.05 were considered to reflect statistically significant results.
Pharmacokinetic data for total and unbound paclitaxel were available for all 26 subjects described in Example 1. The parameter describing the time during which concentrations of total paclitaxel in plasma were above 0.05 μM was only available for 25 subjects. As shown in Table 4, none of the studied ABCB1 genotypes were associated with interindividual differences in paclitaxel pharmacokinetic parameters.







TABLE 4







Association Between ABCB1 Genotype Status and Paclitaxel Pharmacokinetics














T > 0.05 μM

AUCp

AUCu




(hours)

[(ng/mL) × hr]

[(ng/mL) × hrs]


Genotype
Median (95% CI)
P
Median (95% CI)
P
Median (95% CI)
P





ABCB1 1236C > T








Wild-type (N = 5)†
20.3 (8.8-34.2)
0.67
4657 (2909-9916)
0.34
5007 (371-641) 
0.39


Heterozygous (N = 17)
 15.6 (9.3-19.3)*

5264 (3879-6235)

470 (445-519)


Variant (N = 4)†
15.6 (8.8-24.9)

3547 (2309-5600)

407 (362-522)


ABCB1 2677G > T


Wild-type (N = 2)†
15.1 (8.8-21.3)
0.97
3348 (2909-3787)
0.18
540 (507-572)
0.26


Heterozygous (N = 13)
 17.3 (9.6-20.7)*

5146 (3776-7762)

482 (371-641)


Variant (N = 11)
12.6 (8.8-19.8)

4203 (2309-5600)

445 (362-516)


ABCB1 3435C > T


Wild-type (N = 4)†
 937 (8.8-19.3)
0.23
4534 (2909-5146)
0.18
420 (313-572)
0.31


Heterozygous (N = 14)
 19.8 (10.5-21.3)*

5485 (3787-6344)

512 (432-523)


Variant (N = 8)
13.7 (8.7-18.9)

3656 (2259-5600)

448 (362-522)





*Indicates the genotype of the patient with unavailable T > 0.05 μM data;


†Indicates that 95% confidence intervals are unavailable and the range is quoted instead.


Abbreviations: T > 0.05 μM, duration of total plasma concentration of paclitaxel exceeding 0.05 μM; AUCp, area under the curve of total paclitaxel; AUCu, area under the curve of unbound paclitaxel; 95% CI, 95% confidence interval; P, Kruskal-Wallis test.






Example 5
Association of ABCB1 Genotypes and Neurotoxicity
This example describes the assessment of neurotoxicity in subjects treated with paclitaxel and association of peripheral neuropathy with ABCB1 genotype.
Clinical examination, hematological diagnostics with a complete blood cell count, and the assessment of symptoms and toxicity were performed weekly while subjects described in Example 1 were on paclitaxel therapy. Prior to therapy, and if possible after six and twelve weeks of therapy, these examinations were supplemented by the evaluation of the peripheral neuropathy score, clinical chemistries (serum creatinine, transaminases, alkaline phosphatase, and bilirubin), electrocardiogram analysis and performance status. For the assessment of neurotoxicity a standardized clinical peripheral neuropathy scoring system was used, which included questioning subjects' symptoms, requiring a clinical examination based on a tuning fork test, and an evaluation of strength and peripheral reflexes. This individual clinical score could range from 0 (best) to 12 (worst) points, and based on the inclusion criteria of this trial, peripheral neuropathy was defined as an event when the score exceeded a value of 3 for the first time. A score had to be obtained, at a minimum, prior to and after six and twelve weeks of therapy in order for subjects to be included.
All data are reported as median values with the associated 95% CI, unless specified otherwise. The probability of development of a peripheral neuropathy during paclitaxel therapy as a function of time, according to various genotypes, was analyzed using the Kaplan-Meier method. Statistical significance of the differences between Kaplan-Meier curves was determined using an exact log rank test. All P values are two-tailed, and those less than or equal to 0.05 were considered to reflect statistically significant results.
Twenty-two out of 26 subjects with genetic analyses were assessable for cumulative peripheral neuropathy, while four subjects were excluded due to incorrect infusion durations, impermissible dose reductions, or incomplete follow-up evaluation of the peripheral neuropathy score. Four of these 22 subjects experienced a single event of treatment delay (15 to 21 days) but were still considered eligible for this analysis. No subjects received dose reductions until peripheral neuropathy developed or they were taken off protocol.
As shown in FIG. 1, subjects carrying the ABCB1 3435CT or ABCB1 3435TT genotype were more likely to develop clinically significant cumulative peripheral neuropathy. The four subjects wild-type for the ABCB1 3435C>T transition did not develop peripheral neuropathy during the observation period, whereas 17 of 18 subjects carrying at least one variant allele at this position developed peripheral neuropathy. This trend approached statistical significance (P=0.09) using an exact log-rank test, unadjusted for multiple comparisons. Variant alleles were grouped based on previous observations that ABCB1 expression and activity are decreased in subjects carrying at least one ABCB1 3435T allele. Although the above data are not statistically significant, most likely due to the small sample size, it is still notable that no subjects carrying the ABCB1 3435CC (wild type) genotype developed peripheral neuropathy, whereas those subjects heterozygous or homozygous variant for this allele had a much greater propensity to develop this side effect during treatment. Similar associations were not observed for the ABCB1 2677G>T (P=0.85) genotype, or any of the haplotypes (P>0.05).
These results demonstrate that the ABCB1 3435C>T polymorphism has predictive power in the assessment of ABCB1 expression and activity at the blood-nerve barrier, and thus, taxane-induced peripheral neuropathy.
Example 6
Association of ABCB1 Genotypes and Myelotoxicity
This example describes the assessment of myelotoxicity in subjects treated with paclitaxel and association of neutropenia with ABCB1 genotype.
Clinical examination, hematological diagnostics with a complete blood cell count, as well as the assessment of symptoms and toxicity were performed weekly while subjects described in Example 1 were on paclitaxel therapy. Hematological requirements for paclitaxel administration were an absolute neutrophil count ≧1.5×109/L and a platelet count ≧75×109/L. Toxicities other than peripheral neuropathy were graded according to the National Cancer Institute common toxicity criteria guidelines, version 2.0.
All data are reported as median values with the associated 95% CI, unless specified otherwise. Hematological pharmacodynamics were evaluated by analysis of the absolute nadir values of neutrophil counts relative to the baseline value between days 1 and 36, and was expressed as a percentage. The associations of the variant genotypes with neutropenia were evaluated statistically with the nonparametric Kruskal-Wallis test. An exact Wilcoxon rank sum test was used to determine the statistical significance of the difference in percent absolute neutrophil count decline between subjects with a 2677/3435 diplotype double variant and the other subjects. It was reported after a Bonferroni adjustment to correct for an evaluation of a set of four hematologic parameters, as well as a pooling of diplotypes following an exploratory analysis.
Complete sets of neutrophil counts within the first six weeks of treatment were available for 19 out of the 26 subjects. One further patient had to be excluded due to incorrect infusion duration so that ultimately 18 subjects remained assessable for myelotoxicity analysis. Three of these 18 subjects had a single delay in their treatment delivery of 15 to 21 days but were still included. As shown in FIG. 2, consideration of four hematologic parameters, including total platelet/neutrophil counts at nadir, and percent decreases of platelet or neutrophil counts at nadir, demonstrated a significant association between the percent decrease from baseline in neutrophil count at nadir and the ABCB1 2677/3435 variant diplotype. Specifically, subjects variant at both the 2677 and 3435 loci demonstrated an approximately 1.5-fold greater percent decrease (P=0.02, after a conservative adjustment) in neutrophil count at nadir (median: 79.7%, range: 74.2-83.1, n=3) as compared to the rest of the population (median: 53.8%; range: 27.5%-73.7%, n=15). Variant alleles were grouped on the notion that both the 2677 and 3435 loci were recently determined to be important determinants of ABCB1 expression. This particular diplotype was unrelated to any of the studied pharmacokinetic parameters in the 26 subjects wherein pharmacokinetic data were available (P>0.05).
These results demonstrate that the 2677G>T/A and 3435C>T alleles in combination are able to predict the expression and activity of ABCB1 in repopulating neutrophils and thus, the likelihood of neutropenia in response to taxane chemotherapy.
Example 7
Association of ABCB1 Genotypes and Neurotoxicity
This example describes the assessment of neurotoxicity in subjects treated with docetaxel and association of peripheral neuropathy with ABCB1 genotype.
ABCB1 genotypes were evaluated in patients from a trial involving 73 men with androgen-independent prostate cancer that were treated with either docetaxel alone or docetaxel in combination with thalidomide. Patients were administered docetaxel intravenously (30 mg/m2) over 1 hour every week for 3 consecutive weeks (n=23). Some patients additionally received 200 mg of thalidomide orally each day (n=50). Toxicity was defined by Cancer Therapy Evaluation Program/National Cancer Institute Common Toxicity Criteria (version 2.0) and patients were evaluated for symptoms of toxicity weekly.
As shown in FIG. 3, there is a clear difference in the time to onset of peripheral neuropathy in subjects treated with docetaxel based on the ABCB1 2677GG vs 2677GT and 2677TT genotypes. Subjects carrying the ABCB1 2677GT, 2677TT or 2677GA genotype were more likely to develop clinically significant cumulative peripheral neuropathy. Of the 15 subjects wild-type for the ABCB1 2677G>T/A transition, 4 did not develop peripheral neuropathy during the observation period, whereas 3 of 35 subjects carrying at least one variant allele at this position did not. Of the 15 subjects wild-type for the ABCB1 2677G>T/A transition, 11 developed peripheral neuropathy during the observation period, whereas 32 of 35 subjects carrying at least one variant allele at this position developed peripheral neuropathy. This trend was statistically significant (p=0.017) using an exact log-rank test, adjusted for multiple comparisons.
As shown in Table 5, there is also a trend towards an association with double variant 2677TT+3435TT, versus all other of the ABCB1 polymorphisms at positions 1236, 2677, and 3535 and increased clinical grade of neutropenia (p=0.053 following a conservative adjustment for multiple comparisons).







TABLE 5







Association of ABCB1 Polymorphisms


and Clinical Grade of Neutropenia









# Patients with Clinical Grade of Neutropenia
















Total



Genotype
Grade 0
Grade 2
Grade 3
Patients
P-value*















2677TT +
8
0
3
11
0.053


3435TT


Other ABCB1
35
3
1
39


Genotypes





*P-value determined by the Cochran-Armitage Trend Test






Example 8
Association of ABCB1 Genotype with Neurotoxicity and Myelotoxicity Following Epothilone Treatment
This example describes the assessment of myelotoxicity and neurotoxicity in subjects treated with ixabepilone and association of neutropenia and peripheral neuropathy with ABCB1 genotype.
Subjects will receive ixabepilone (BMS-247550) as treatment for breast cancer. Subjects will receive infusions of ixabepilone at 6 mg/m2/day over one hour daily for five days every three weeks or infusions of ixabepilone at 8 mg/m2/day over one hour daily for three days every three weeks. Subjects may also receive an infusion of ixabepilone at 35-40 mg/m2 over three hours every three weeks. DNA will be isolated as described in Example 2. ABCB1 genotype will be determined as described in Example 3. Subjects will be assessed for development of peripheral neuropathy as described in Examples 5 and 7 and neutropenia as described in Example 6 during the course of ixabepilone treatment.
Example 9
ABCB1 Genotyping and MT-Stabilizing Agent Treatment
This example describes treatment decisions that can be made based on the ABCB1 genotype of a subject who is undergoing treatment with a MT-stabilizing agent.
DNA will be isolated from subjects as described in Example 2 or other suitable methods. The genotype for ABCB1 polymorphisms will be determined as described in Example 3, or other methods known in the art.
If a subject is found to have the ABCB1 genotype of 3435CT or 3435TT, it is concluded that the subject has an increased risk of developing at least one or more MT-stabilizing agent-induced adverse effects, such as peripheral neuropathy, following treatment with a MT-stabilizing agent. In this situation, the treatment regimen can be modified to decrease the likelihood of occurrence or severity of peripheral neuropathy. This can include, but is not limited to, decreasing the dosage of MT-stabilizing agent (for example decreasing the dosage by at least 20%, such as at least 50%), increasing the interval between doses of MT-stabilizing agent (for example increasing the interval by at least one day, at least seven days, at least fourteen days, or even at least 30 days), increasing the time over which a dose of MT-stabilizing agent is administered (for example by at least 1 hr, at least 12 hrs, or at least 24 hrs), or combinations thereof.
If the subject is found to have the ABCB1 double variant phenotype at both positions 2677 and 3435, it is concluded that the subject has an increased of developing at least one or more MT-stabilizing agent-induced adverse effects, such as neutropenia, following treatment with a microtubule-stabilizing agent. In this situation, the treatment regimen can be modified to decrease the likelihood of occurrence of neutropenia. This can include, but is not limited to, decreasing the dosage of MT-stabilizing agent, increasing the interval between doses of MT-stabilizing agent, increasing the time over which a dose of MT-stabilizing agent is administered (for example as described above), administering at least one therapeutically effective amount dose of CSF following administration of MT-stabilizing agent, or combinations thereof.
In contrast, if the subject is found to have wild-type ABCB1 genotype at positions 2677 and 3435, it is concluded that the subject does not have an increased of developing at least one or more MT-stabilizing agent-induced adverse effects, and thus administration of MT-stabilizing agent (such as a taxane) need not be modified.
Example 10
Accumulation of Paclitaxel in Peripheral Neurons of ABCB1 Knockout Mice
This example describes methods that can be used to assess the accumulation of paclitaxel in peripheral neurons of mice that lack expression of ABCB1. Mice that lack expression of ABCB1 (such as mdr1a −/− mice or mdr1b −/− mice) can be used to evaluate the differential accumulation of paclitaxel in peripheral neurons based on the level of ABCB1 expression. 10-30 mg/kg of paclitaxel will be administered intravenously to wild type and control mice. [14C]paclitaxel will be administered, and accumulation of paclitaxel in peripheral nervous tissue will be monitored by digital whole body autoradiography at subsequent time points, such as 1 hour, 3 hours, or 24 hours following administration Likewise, fluorescently-labeled paclitaxel will be administered to mice and uptake by peripheral neurons will be monitored by fluorescent microscopy at subsequent time points, such as 1 hour, 3 hours, or 24 hours following administration. These experiments will confirm that a decrease in expression of ABCB1 in peripheral neurons results in increased accumulation of paclitaxel in this tissue.
In view of the many possible embodiments to which the principles of the disclosed examples may be applied, it should be recognized that the illustrated embodiments are only preferred examples of the invention and should not be taken as limiting the scope of the invention. Rather, the scope of the disclosure is defined by the following claims. We therefore claim as our invention all that comes within the scope and spirit of these claims.

## Claims

1. A method for identifying a human subject at increased risk for developing microtubule-stabilizing-agent-induced adverse effects selected from the group consisting of neutropenia and peripheral neuropathy, comprising:
amplifying DNA isolated from a biological sample obtained from a human subject having a tumor that can be treated with a microtubule-stabilizing-agent or a subject who has been treated with a microtubule-stabilizing-agent using primer sequences selected from the group consisting of SEQ ID NOS: 3, 4, 5 and 6;
determining in a biological sample obtained from a human subject having a tumor that can be treated with a microtubule-stabilizing-agent or a subject who has been treated with a microtubule-stabilizing-agent that the human subject has a 2677G>T (Ala893Ser) and a 3435C>T (synonymous) predictive polymorphism in an ABCB1 gene, wherein the primer sequences consisting of SEQ ID NOS: 9 and 10 are used to detect 2677G>T and the primer sequences consisting of SEQ ID NOS: 11 and 12 are used to detect 3435C>T; and
identifying the subject as one at increased risk for developing microtubule-stabilizing agent-induced adverse effects selected from the group consisting of neutropenia and peripheral neuropathy as compared to a subject which does not have the 2677G>T (Ala893Ser) and 3435C>T (synonymous) predictive polymorphisms.

2. The method of claim 1, wherein the microtubule-stabilizing agent comprises an epothilone.

3. The method of claim 2, wherein the epothilone comprises ixabepilone.

4. The method of claim 1, wherein the microtubule-stabilizing agent comprises a taxane.

5. The method of claim 4, wherein the taxane comprises paclitaxel (Taxol®), docetaxel (Taxotere®), or an analog of paclitaxel.

6. The method of claim 1, wherein the subject has a disease that is sensitive to administration of a therapeutically effective amount of a microtubule-stabilizing agent.

7. The method of claim 6, further comprising:
administering to the subject a therapeutically effective amount of a microtubule-stabilizing agent.

8. The method of claim 7, wherein the effective amount of a microtubule-stabilizing agent is less than 100 mg/m2.

9. The method of claim 1, further comprising:
obtaining a blood sample from the subject; and
isolating DNA from the blood sample, wherein determining that the human subject has the predictive polymorphisms in the ABCB1 gene comprises determining whether the isolated DNA comprises the predictive polymorphisms in the ABCB1 gene.

10. The method of claim 9, wherein the blood sample is a plasma sample.

11. A method for decreasing occurrence of microtubule-stabilizing-agent-induced adverse effects selected from the group consisting of neutropenia and peripheral neuropathy in a human subject having a disorder which can be treated with a therapeutically effective amount of a microtubule-stabilizing agent, comprising:
amplifying DNA isolated from a biological sample obtained from a human subject having a tumor that can be treated with a microtubule-stabilizing-agent or a subject who has been treated with a microtubule-stabilizing-agent using primer sequences selected from the group consisting of SEQ ID NOS: 3, 4, 5 and 6;
determining in a biological sample obtained from a human subject having a tumor that can be treated with a microtubule-stabilizing-agent or a subject who has been treated with a microtubule-stabilizing-agent that the human subject has a 2677G>T (Ala893Ser) and a 3435C>T (synonymous) predictive polymorphism in an ABCB1 gene, wherein the primer sequences consisting of SEQ ID NOS: 9 and 10 are used to detect 2677G>T and wherein the primer sequences consisting of SEQ ID NOS: 11 and 12 are used to detect 3435C>T; and
modifying administration of a microtubule-stabilizing agent to decrease microtubule-stabilizing-agent-induced adverse effects selected from the group consisting of neutropenia and peripheral neuropathy to the human subject having the predictive polymorphisms.

12. The method of claim 11, wherein the amount of microtubule-stabilizing agent administered is decreased, an interval between microtubule-stabilizing agent administration is increased, a dosing schedule of microtubule-stabilizing agent administration is increased, a therapeutically effective amount of colony-stimulating factor is administered, or combinations thereof.

13. The method of claim 12, wherein the colony-stimulating factor comprises granulocyte colony-stimulating factor or granulocyte macrophage colony-stimulating factor.

14. The method of claim 11, wherein microtubule-stabilizing agent dosage is decreased, timing of microtubule-stabilizing agent administration is altered, dosing schedule of microtubule-stabilizing agent administration is increased, or combinations thereof.