# Patent

## Title
Method for evaluating side-effect onset risk in anticancer drug treatment, including detecting MUC4 gene polymorphism

## Abstract

The purpose of the present invention is to provide an evaluation method kit for evaluating the risk of onset of diffuse alveolar damage due to such factors as anticancer drug administration. The purpose of the present invention is also to provide a method for evaluating the risk of onset of side effects in anticancer drug treatment. An evaluation method and evaluation kit for evaluating the risk of onset of diffuse alveolar damage, including detecting gene polymorphism present in the MUC4 gene. A method for evaluating the risk of onset of side effect in anticancer drug treatment, including detecting gene polymorphism present in the MUC4 gene of a patient scheduled for anticancer drug administration.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a national phase application of PCT Application No. PCT/JP2014/054796, filed on 27 Feb. 2014, which claims benefit of Japanese Patent Application 2013-041305, filed on 1 Mar. 2013. The entire disclosure of the application identified in this paragraph is incorporated herein by reference.
REFERENCE TO A SEQUENCE LISTING
Applicant hereby submits, in compliance with sequence rules 37 C.F.R. §§1.821-1.825, the required Sequence Listing. A copy of the Sequence Listing is being submitted in computer readable format as required by 37 C.F.R. §1.182(e).
This application contains references to amino acid sequences and/or nucleic acid sequences which are being submitted concurrently herewith as the sequence listing text file 61572648_1.TXT file size 68.8 KiloBytes (KB), created on 1 Mar. 2013. The aforementioned sequence listing is hereby incorporated by reference in its entirety.
TECHNICAL FIELD
The present invention relates to: (1) a method for determining the risk of development of diffuse alveolar damage, which method includes detecting an MUC4 gene polymorphism(s); (2) a method for determining the risk of occurrence of a side effect in an anticancer drug therapy, which method includes detecting an MUC4 gene polymorphism(s); (3) a kit used for these purposes; and the like.
BACKGROUND
Administration of an anticancer drug such as Iressa (generic name: gefitinib) or Tarceva (generic name: erlotinib) causes a serious side effect called diffuse alveolar damage in some cases. Also in acute exacerbation of idiopathic pulmonary fibrosis, the serious side effect called diffuse alveolar damage is caused in some cases. Diffuse alveolar damage shows resistance to treatment, has a recurrent nature, and exhibits repeated exacerbation during treatment, resulting in serious exacerbation at an early stage. Thus, diffuse alveolar damage is a symptom to which very careful attention should be paid.
Japanese are reported to develop such diffuse alveolar damage at high frequency (Non-patent Document 1). For example, in cases of gefitinib, the frequency is 0.3% according to surveys in countries other than Japan, while the frequency is 3.98% in Japanese, which indicates a not less than 10 times higher frequency in Japanese. In cases of erlotinib, the frequency is 0.2% according to surveys on Asians, while the frequency is 2.7% according to a survey on Japanese, which again indicates a not less than 10 times higher frequency in Japanese. Further, Japanese patients with idiopathic pulmonary fibrosis are reported to show a higher rate of acute exacerbation and a higher case fatality rate than patients in other countries (Non-patent Document 2). It has been assumed that the number of deaths due to diffuse alveolar damage in Japan is as much as several thousand per year. It should be noted, of course, that death due to the side effect of drugs is a serious problem also in countries other than Japan, apart from its frequency.
PRIOR ART DOCUMENTS
Non-Patent Documents


    Non-patent Document 1: JMAJ (Japan Medical Association), vol. 50, p. 107 (2007);
    Non-patent Document 2: Am J Respir Crit Care Med. vol. 177(12), pp. 1397-1398 (2008).


SUMMARY OF THE INVENTION
Technical Problem
Anticancer drug therapy is carried out, of course, for treatment of cancer. However, as described above, there are cases where diffuse alveolar damage occurs due to administration of an anticancer drug. Since diffuse alveolar damage shows rapid progression and a high case fatality rate, it would be very useful if a method for preliminarily determining the risk of development of diffuse alveolar damage due to administration of an anticancer drug can be provided. This is because the method enables prevention of death of a cancer patient due to an anticancer drug, which should originally be administered for the purpose of saving the life of the patient.
In general, diffuse alveolar damages including those caused by administration of anticancer drugs cannot be easily distinguished from normal pneumonia based on their initial symptoms. At clinical sites, these diseases often cannot be distinguished from each other at the first visit, and, in such cases, treatment is carried out from the viewpoints of both pneumonia and diffuse alveolar damage. Since diffuse alveolar damage shows rapid progression and a high case fatality rate, it would be very useful if a method for preliminarily determining the risk of development of diffuse alveolar damage can be provided at the time point when the initial symptoms are found.
However, in spite of the past efforts by research institutes around the world, gene polymorphisms associated with diffuse alveolar damage have not been discovered. Therefore, needless to say, no gene polymorphism has been reported to have very strong association with diffuse alveolar damage so far. Although there may be many reasons for this, one of the reasons may be difficulty in obtaining samples from patients since the patients die at an early stage due to drastic exacerbation of the disease state.
Under such circumstances, the present invention aims to provide: (1) a method for determining the risk of development of diffuse alveolar damage, which method comprises detecting an MUC4 gene polymorphism(s); (2) a method for determining the risk of occurrence of a side effect in an anticancer drug therapy, which method comprises detecting an MUC4 gene polymorphism(s); (3) a kit used for these purposes; and the like.
Technical Solution
In order to solve the problems described above, the present invention has the following characteristics.
That is, an embodiment of the present invention is a method for determining the risk of development of diffuse alveolar damage, which method comprises detecting a gene polymorphism(s) present in the MUC4 gene.
In an embodiment of the present invention, the “gene polymorphism(s) present in the MUC4 gene” may be a gene polymorphism(s) present in exon 2 of the MUC4 gene.
In an embodiment of the present invention, the “gene polymorphism(s) present in exon 2 of the MUC4 gene” may be at least one single nucleotide polymorphism selected from the group consisting of the following (1) to (6):
(1) rs150551454 (C/T polymorphism at nucleotide position 195,507,491 in chromosome 3);
(2) rs62282480 (C/A polymorphism at nucleotide position 195,510,749 in chromosome 3);
(3) rs2911272 (A/G polymorphism at nucleotide position 195,510,773 in chromosome 3);
(4) rs413807 (C/T polymorphism at nucleotide position 195,510,827 in chromosome 3);
(5) rs6805660 (T/C polymorphism at nucleotide position 195,512,042 in chromosome 3); and
(6) rs62282486 (T/C polymorphism at nucleotide position 195,512,245 in chromosome 3).
In an embodiment of the present invention, the “gene polymorphism(s) present in exon 2 of the MUC4 gene” may be the following single nucleotide polymorphisms (5) and (6):
(5) rs6805660 (T/C polymorphism at nucleotide position 195,512,042 in chromosome 3); and
(6) rs62282486 (T/C polymorphism at nucleotide position 195,512,245 in chromosome 3).
In an embodiment of the present invention, the diffuse alveolar damage is caused by administration of a drug. The drug may be an anticancer drug. Such an anticancer drug may be selected from the group consisting of molecular-targeted agents, antimetabolites, and microtubule depolymerization inhibitors. Specific examples of such an anticancer drug include gefitinib, erlotinib, crizotinib, gemcitabine, irinotecan, pemetrexed, and docetaxel.
In an embodiment of the present invention, the diffuse alveolar damage may be caused by acute exacerbation of idiopathic pulmonary fibrosis.
An embodiment of the present invention relates to a method for determining the risk of occurrence of a side effect in an anticancer drug therapy, which method comprises detecting a gene polymorphism(s) present in the MUC4 gene in a patient to whom an anticancer drug is to be administered. The side effect may be diffuse alveolar damage. Specific examples of such an anticancer drug include gefitinib, erlotinib, crizotinib, gemcitabine, irinotecan, pemetrexed, and docetaxel.
An embodiment of the present invention relates to a kit for determining the risk of development of diffuse alveolar damage, which kit detects a gene polymorphism(s) present in the MUC4 gene.
Effects of the Invention
According to the present invention, a method for determining the risk of occurrence of a side effect in an anticancer drug therapy can be provided. This might enable determination of the risk of occurrence of a side effect before administration of an anticancer drug, and selection of an appropriate therapeutic method for saving the life of a cancer patient. For example, in cases where the risk of occurrence of the side effect, diffuse alveolar damage, due to an anticancer drug is found to be very high, administration of the anticancer drug may be stopped, or the dose of the anticancer drug may be reduced. The method for determining the risk of occurrence of a side effect in an anticancer drug therapy of the present invention may be also useful for patients who are already receiving the anticancer drug.
According to the present invention, a method and a kit for determining the risk of development of diffuse alveolar damage can be provided. By this, the risk of development of alveolar damage can be determined, and an appropriate treatment can be carried out for a patient.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a diagram showing an association analysis for mutations in the entire gene coding region between “Iressa ILD+Tarceva ILD” patients and normal Japanese.
FIG. 2 is a diagram showing the probabilities at which the polymorphisms satisfy epidemiological data.
FIG. 3 is a diagram showing an association analysis for mutations in the MUC4 region between “Iressa ILD+Tarceva ILD” patients and normal Japanese.
FIG. 4 is a diagram showing an association analysis for mutations in the entire gene coding region between IPF acute exacerbation patients and normal Japanese.
FIG. 5 is a diagram showing an association analysis for mutations in the MUC4 region between IPF acute exacerbation patients and normal Japanese.



DETAILED DESCRIPTION
The present invention relates to a method and a kit for determining the risk of development of diffuse alveolar damage, and a method for determining the risk of occurrence of a side effect in an anticancer drug therapy, comprising detecting an MUC4 gene polymorphism(s).
<Diffuse Alveolar Damage>
One of the most characteristic symptoms of diffuse alveolar damage (DAD) is inflammation of the entire lung
Diffuse alveolar damage may be caused by administration of a drug. Diffuse alveolar damage may also be caused by acute exacerbation of idiopathic pulmonary fibrosis.
Other possible causes of diffuse alveolar damage include the followings:
(1) irradiation pneumonitis that widely extends into areas other than the irradiation field in the lung;
(2) rapid progressive interstitial pneumonia (RPIP), which is found after administration of an anticancer drug to, or after surgery of, a patient with complication of pulmonary fibrosis;
(3) fatal rapidly progressive interstitial pneumonia found in patients with dermatomyositis;
(4) rapid progressive interstitial pneumonia found in patients with interstitial pneumonia other than idiopathic pulmonary fibrosis (IPF); and
(5) acute respiratory distress syndrome (ARDS).
<Anticancer Drugs>
As described above, diffuse alveolar damage may be caused by anticancer drugs. Specific examples of such anticancer drugs include, but are not limited to, gefitinib (trade name: Iressa and the like), erlotinib (trade name: Tarceva and the like), crizotinib (trade name: Xalkori and the like), gemcitabine, irinotecan, pemetrexed (trade name: Alimta and the like), and docetaxel (trade name: Taxotere and the like).
Among these, gefitinib, erlotinib, and crizotinib are anticancer drugs categorized as tyrosine kinase inhibitors, which are included in the so called molecular-targeted agents. Gemcitabine, irinotecan, and pemetrexed are anticancer drugs categorized as antimetabolites. Docetaxel is an anticancer drug categorized as a microtubule depolymerization inhibitor.
<Molecular-Targeted Agents>
Molecular-targeted agents are anticancer drugs that suppress the growth and the like of tumors by targeting and inhibiting molecules involved in the growth, infiltration, and metastasis of the tumors. Molecular-targeted agents can be roughly classified into low molecular weight compounds and monoclonal antibodies. Molecular-targeted agents which are low molecular weight compounds can be further classified into tyrosine kinase inhibitors, Raf kinase inhibitors, TNF-α inhibitors, and proteasome inhibitors.
<Tyrosine Kinase Inhibitors>
Examples of known tyrosine kinase inhibitors include gefitinib, erlotinib, and crizotinib as described above, and also include imatinib, dasatinib, vandetanib, sunitinib, lapatinib, and nilotinib. Both gefitinib and erlotinib are known to be anticancer drugs that suppress the growth and the like of tumors by selectively inhibiting the tyrosine kinase of epidermal growth factor receptor to block its signal transduction. Crizotinib is known as an anticancer drug that suppresses the growth and the like of tumors by inhibiting the tyrosine kinase activity of anaplastic lymphoma kinase (ALK), which is a receptor-type tyrosine kinase.
<Antimetabolites>
Antimetabolites are analogues of nucleic acid bases, and are anticancer drugs that suppress the growth and the like of tumors by being incorporated into the DNA strand to stop extension of the DNA strand or to cleave the DNA strand. Gemcitabine is an analogue of a nucleic acid base cytidine. When it is incorporated into a DNA strand, and another nucleic acid base is attached thereto, extension of the DNA strand stops. Irinotecan is a derivative of camptothecin, which is a plant alkaloid, and is an anticancer drug that suppresses the growth and the like of tumors by inhibiting recombination after cleavage of a single-strand DNA by topoisomerase I. Pemetrexed is an antifolate having a molecular structure similar to that of folic acid, and inhibits synthesis of purine and pyrimidine nucleotide precursors by inhibition of thymidylate synthase, dihydrofolate reductase, and glycinamide ribonucleotide formyl transferase.
<Microtubule Depolymerization Inhibitors>
These are anticancer drugs that suppress the growth and the like of tumors by inhibiting depolymerization of microtubules. They bind to microtubules, which are the main constituent of the mitotic apparatus formed during cell division, to prevent the microtubules from undergoing depolymerization and returning to tubulin. This causes stabilization and excessive formation of microtubules, resulting in arrest of the cell cycle in the G2/M phase, and inhibition of cell division. Representative examples of microtubule depolymerization inhibitors include docetaxel and paclitaxel.
<Idiopathic Pulmonary Fibrosis and its Acute Exacerbation>
Idiopathic pulmonary fibrosis (IPF) is a chronic disease, and is an intractable (incurable) disease specified by the Ministry of Health, Labour and Welfare. Patients with this disease suffer from chronic lung destruction, and die of respiratory failure, infection, acute exacerbation, and the like. In 1⁄3 of IPF patients, the disease state changes from a chronic state to rapidly progressive respiratory failure, leading to death of the patients. This is the acute exacerbation of idiopathic pulmonary fibrosis (IPF AE). The death rate of IPF AE is 70%, which is very high. It is known that patients with IPF die at a high rate due to development of IPF AE after the patients undergo administration of an anticancer drug, radiation therapy, surgery, or the like.
<MUC4 Gene>
The method of the present invention is a method for determining the risk of development of diffuse alveolar damage by detection of at least one gene polymorphism present in the MUC4 gene.
The MUC4 gene is known as a gene encoding the core protein of mucin expressed in the respiratory epithelium. The nucleotide sequence of the MUC4 gene is known and deposited as, for example, NM_018406 according to The National Center for Biotechnology Information (NCBI), and is present at nucleotide positions 195,473,636-195,541,844 (including the nucleotide positions of 3000 base pairs of the promoter region) of chromosome 3 in the human genome UCSC hg19 NCBI b37.3. The nucleotide sequence deposited as NM_018406 is shown in SEQ ID NO:1 as the most typical MUC4 gene coding sequence (cDNA sequence), and the amino acid sequence of the protein encoded by the nucleotide sequence is shown in SEQ ID NO:2.
In the present invention, the method for determining the risk of development of diffuse alveolar damage is a method comprising detecting an MUC4 gene polymorphism(s). The “comprising” herein means that the process of detecting the MUC4 gene polymorphism(s) is the substantial part of the method for determining the risk of development of diffuse alveolar damage, and that the method may also comprise other processes.
The detection of the MUC4 gene polymorphism(s) is preferably detection of one or more single nucleotide polymorphisms present in exon 2 of the MUC4 gene (nucleotide positions 195,518,368-195,505,661 in chromosome 3), especially preferably detection of at least one single nucleotide polymorphism selected from the group consisting of the following (1) to (6) (wherein rs means reference SNP ID):
(1) rs150551454 (C/T polymorphism at nucleotide position 195,507,491 in chromosome 3);
(2) rs62282480 (C/A polymorphism at nucleotide position 195,510,749 in chromosome 3);
(3) rs2911272 (A/G polymorphism at nucleotide position 195,510,773 in chromosome 3);
(4) rs413807 (C/T polymorphism at nucleotide position 195,510,827 in chromosome 3);
(5) rs6805660 (T/C polymorphism at nucleotide position 195,512,042 in chromosome 3); and
(6) rs62282486 (T/C polymorphism at nucleotide position 195,512,245 in chromosome 3).
<Method for Detecting Gene Polymorphism(s)>
As the method for detecting at least one single nucleotide polymorphism selected from the group consisting of the above-described (1) to (6) in the MUC4 gene, a known method which is commonly used as a method for detecting a polymorphism(s) in a nucleic acid sequence may be used as appropriate, and examples of such a method include replication or amplification of nucleic acid, and hybridization and sequencing using a probe(s).
For example, direct detection of a polymorphism(s) in the MUC4 gene is possible by amplifying a nucleic acid fragment containing the position(s) where the polymorphism(s) of the MUC4 gene is/are present, and determining the sequence of the amplified nucleic acid product using a sequencer. A preferred method for the replication or amplification of the nucleic acid is PCR. However, the method is not limited thereto, and known methods such as the LAMP method, NASBA method, LCR method, and SDA method may also be used. The polymorphism(s) of the MUC4 gene may also be detected by real-time PCR using a TaqMan probe wherein hybridization of the TaqMan probe to a specific fragment containing the MUC4 gene polymorphism(s) is detected.
In the PCR, a forward primer and a reverse primer are used. These primers can be designed based on the DNA sequence at a position where detection of the polymorphism(s) of the MUC4 gene is possible. For example, the primers may be designed such that one or more of the single nucleotide polymorphisms (1) to (6) identified in the present invention is sandwiched between the forward primer and the reverse primer. Alternatively, at least one of the forward primer and the reverse primer may be designed at the position(s) of a single nucleotide polymorphism(s) such that amplification occurs (or does not occur) only in cases where the genetic polymorphism(s) is/are present.
The length of each primer is not limited as long as a sufficient amount of amplified DNA fragments can be obtained, and depends on the GC content and the like of the sequence selected. The length of the primer sequence is preferably about 10 to 100 bases, more preferably 10 to 50 bases.
In the hybridization using a probe, a portion containing one or more of the single nucleotide polymorphisms (1) to (6) may be used as the probe. The probe may be labeled with a fluorescent substance, radioactive substance, or the like, if necessary. The probe is not limited as long as the probe can detect the single nucleotide polymorphism(s). That is, as long as the presence/absence of the single nucleotide polymorphism(s) can be determined based on the presence/absence of hybridization of the probe or based on the detected intensity, the length of the probe is not limited, and the probe may contain one or more substitution(s), deletion(s), and/or addition(s) compared to the subject sequence to be hybridized therewith. Conditions of the hybridization may be appropriately determined depending on the length and the GC content of the probe, and the like.
The detection of the single nucleotide polymorphism(s) can also be carried out by the restriction fragment length polymorphism (RFLP) method and/or electrophoresis. By performing digestion using a restriction enzyme that recognizes and specifically cleaves a sequence(s) containing the position(s) of the single nucleotide polymorphism(s), and investigating the size(s) of the obtained fragment(s) by electrophoresis, the presence/absence of the cleavage by the restriction enzyme can be detected. This allows detection of the polymorphism(s). Single strand conformation polymorphism (SSCP) analysis and/or capillary electrophoresis may also be used.
<Kit for Determining Risk of Development of Diffuse Alveolar Damage>
In the present invention, the kit for determining the risk of development of diffuse alveolar damage is a kit containing a reagent(s) to be used for the above-described method for detecting a polymorphism(s) of the MUC4 gene. Examples of the reagent(s) include those generally used in the methods for detecting gene polymorphism(s) described above, such as commercially available reagents and synthetic oligonucleotide DNAs. For example, in cases of PCR analysis, the kit may contain a forward primer and a reverse primer for amplification of the DNA fragment of interest, four kinds of deoxyribonucleoside triphosphates, DNA polymerase, and the like.
The terms used in the present description are merely for explanation of specific modes, and not intended to limit the invention.
The term “contain/comprise” used in the present description is intended to mean the presence of a described matter(s) (member(s), step(s), element(s), number(s), and/or the like), and does not exclude the presence of one or more of other matters (members, steps, elements, numbers, and the like) except for cases where the context evidently requires a different understanding.
Unless otherwise defined, all terms used herein (including technical terms and scientific terms) have the same meanings as the meanings widely understood by those skilled in the art to which the present invention belongs. Unless otherwise clearly defined, the terms used herein should be understood to have meanings consistent with the present description and with the meanings in the related technical fields, and should not be understood to have idealized meanings or excessively formal meanings.
Terms such as “first” and “second” are used to represent various elements in some cases. It is understood that these elements should not be limited by those terms. These terms are used merely for distinguishing an element from another element, and, for example, a first element may be described as a second element, or a second element may be similarly described as a first element, without departing from the scope of the present invention.
The present invention is described below more specifically by way of Examples. However, the present invention can be realized in various modes, and should not be understood as being limited by the Examples described here.
EXAMPLES
Example 1
<Patient Samples>
From 30 cooperative medical institutions throughout Japan, a total of 442 cases of patient samples, including 262 cases of patients diagnosed with drug-induced lung damage and 180 cases of patients diagnosed with interstitial lung disease, were collected.
The 180 cases of patients diagnosed with interstitial lung disease include 141 cases of IPF acute exacerbation patients.
The 262 cases of patients diagnosed with drug-induced lung damage include the following cases.
49 cases of patients with interstitial lung disease (ILD) caused by Iressa or Tarceva (hereinafter referred to as “Iressa ILD+Tarceva ILD”)
3 cases of patients with interstitial lung disease (ILD) caused by Xalkori (hereinafter referred to as Xalkori ILD)
38 cases of patients with interstitial lung disease (ILD) caused by Taxotere (hereinafter referred to as Taxotere ILD).
<Exome Analysis>
Patient data and patient images were collected for 279 cases out of the 442 cases described above, for confirmation of the diagnosis. Among definitely diagnosed cases, 98 patients (36 “Iressa ILD+Tarceva ILD” patients, 45 IPF acute exacerbation patients, 2 Xalkori ILD patients, and 15 Taxotere ILD patients) selected mainly from fulminant cases and fatal cases (who are thought to be patients who developed diffuse alveolar damage) were subjected to human entire gene coding region sequence analysis (exome analysis).
To provide controls, exome fastq data for Caucasians (53 individuals), Chinese Hans (68 individuals), and Japanese (70 individuals) were obtained from a sequence read archive database (http://www.ncbi.nlm.nih.gov/sra). All data were mapped on a human genome reference sequence (hg19) using CLC Genomics Workbench (CLC bio). After confirming that not less than 90% of the exon regions were read not less than 10 times in each patients, information on gene mutations was obtained using the Probabilistic variant detection algorithm.
As a result, among the mutations detected in any one or more of the Japanese (98 patients+70 controls), mutations that cause amino acid changes (non-synonymous mutations) were present at 180,215 positions in the whole genome.
(Example 2) <“Iressa ILD+Tarceva ILD” Patients>
(Example 2-1) <Association Analysis>
For all 180,215 polymorphisms described above, association analysis was carried out between a total of 36 “Iressa ILD+Tarceva ILD” patients and 70 normal Japanese. The results are shown in FIG. 1. Bonferroni correction was carried out, and associations with P values of not more than 0.001/180,215 were regarded as significant.
In FIG. 1, isolated points could be artifacts due to differences in the exon complement efficiency among kits. The points contained in the areas where the points aggregate in spire shapes (for example, the positions indicated by arrowheads in FIG. 1) indicate that there are differences in the polymorphism frequency between the two groups over a large chromosomal region, and are likely to suggest true associations.
(Example 2-2) <Identification of Gene Polymorphisms>
Only polymorphisms that showed significant P values in <Association Analysis> in Example 2-1 were selected, and subjected to international comparison of the frequency.
For Iressa ILD and Tarceva ILD, the following epidemiological data are known.
(1) The frequency of development in Japanese is about 4%.
(2) The frequency of development in Westerners is not more than 1/10 of the frequency in Japanese.
(3) The frequency of development in Chinese is not more than the frequency of development in Japanese.
From the viewpoint of the epidemiological data described above, each polymorphism was evaluated based on the exome data obtained in Example 1 for the Japanese (70 individuals), Caucasians (53 individuals), and Chinese Hans (68 individuals), in terms of:
the probability that the frequency of Japanese carrying the gene is not less than 4% (P1);
the probability that the frequency of Westerners carrying the gene is not more than 1/10 of the frequency of Japanese carrying the gene (P2); and
the probability that the frequency of Chinese carrying the gene is not more than the frequency of Japanese carrying the gene (P3);
and the probability that all of these are satisfied, P(P1×P2×P3), was calculated.
The probability P can be understood as the probability that each polymorphism is consistent with the epidemiological data described above. The results are shown in FIG. 2.
Each of all points with P>0.1 in FIG. 2 was studied in terms of the gene function to which it belongs and the gene expression site. As a result, MUC4 (which corresponds to the position indicated by the arrowhead in FIG. 2) was the only gene that is expressed in lung and has a function which could be associated with interstitial lung disease.
(Example 2-3) <Identification of Gene Polymorphisms in MUC4>
By the same method as in <Exome Analysis> in Example 1, all mutations in the MUC4 gene region were specified.
All these mutations were subjected to association analysis for a total of 36 “Iressa ILD+Tarceva ILD” patients and 70 normal Japanese. In <Association Analysis> in Example 2-1, only mutations that cause amino acid changes (non-synonymous mutations) were used. However, in the present analysis, all mutations were used irrespective of whether each mutation is a mutation that causes an amino acid change (non-synonymous mutation).
The results are shown in FIG. 3. Since MUC4 is present in the reverse strand, the right side corresponds to the 5′ side in FIG. 3. The part corresponding to exon 2 (nucleotide positions 195,505,661-195,518,368) contained an especially large number of mutations.
In exon 2, the following positions showed especially strong associations: rs150551454 (nucleotide position 195,507,491), rs62282480 (nucleotide position 195,510,749), rs2911272 (nucleotide position 195,510,773), rs413807 (nucleotide position 195,510,827), rs6805660 (nucleotide position 195,512,042), and rs62282486 nucleotide position 195,512,245). Among these, the following positions showed extremely strong associations: rs6805660 (nucleotide position 195,512,042) and rs62282486 (nucleotide position 195,512,245).
(Example 2-4) <Relationship Between Gene Polymorphisms and Diseases>
The frequencies of polymorphisms of rs6805660 and rs62282486, which showed the strongest associations, were studied. The results are shown in Table 1. In Table 1, Ref/Ref represents the homozygote of the human genome reference sequence; Alt/Alt represents the homozygote of the mutant sequence; and Ref/Alt represents the heterozygote.












TABLE 1










“Iressa






ILD +






Tarceva




Chinese

ILD”



Caucasians
Hans
Japanese
patients



Ref/
Ref/
Ref/
Ref/



RefRef/
RefRef/
RefRef/
RefRef/



AltAlt/
AltAlt/
AltAlt/
AltAlt/



Alt
Alt
Alt
Alt




























rs6805660
51
0
2
68
0
0
65
0
5
0
0
36


rs62282486
53
0
0
68
0
0
67
0
3
2
0
34









Surprisingly, as is evident from Table 1, all “Iressa ILD+Tarceva ILD” patients (that is, patients who developed diffuse alveolar damage, as described in Example 1) had the mutant sequence of rs6805660 as a homozygote, and all of these patients except 2 cases had the mutant sequence of rs62282486 as a homozygote. That is, among the patients with diffuse alveolar damage caused by these drugs, 100% (36/36) had the mutant sequence of rs6805660, and about 95% (34/36) had the mutant sequence of rs62282486. It is very surprising that such extremely strong associations were found.
Among the 70 normal Japanese, only 5 individuals had the mutant sequence of rs6805660 as a homozygote, and only 3 individuals had the mutant sequence of rs62282486 as a homozygote. Either of these mutations is present in only about 4% to about 7% of normal Japanese.
It should be noted that exon 2 is the variable number of tandem repeat (VNTR) region of MUC4. Although rs6805660 and rs62282486 cause amino acid mutations, there is also a possibility that these are associated with the number of VNTRs.
(Example 3) <IPF Acute Exacerbation Patients>
By the same method as in <Association Analysis> in Example 2-1, association analysis was carried out between the 45 IPF acute exacerbation patients and the 70 normal Japanese. The results are shown in FIG. 4.
In addition, by the same method as in <Identification of Gene Polymorphisms in MUC4> in Example 2-3, association analysis was carried out between the 45 IPF acute exacerbation patients and the 70 normal Japanese. The results are shown in FIG. 5. Since MUC4 is present in the reverse strand, the right side corresponds to the 5′ side in FIG. 5. The part corresponding to exon 2 (nucleotide positions 195,505,661-195,518,368) contained an especially large number of mutations.
In exon 2, the following positions showed extremely strong associations: rs6805660 (nucleotide position 195,512,042) and rs62282486 (nucleotide position 195,512,245).
In addition, by the same method as in <Relationship between Gene Polymorphisms and Diseases> in Example 2-4, the frequencies of polymorphisms of rs6805660 and rs62282486, which showed the strongest associations, were studied. The results are shown in Table 2. In Table 2, Ref/Ref represents the homozygote of the human genome reference sequence; Alt/Alt represents the homozygote of the mutant sequence; and Ref/Alt represents the heterozygote.












TABLE 2










IPF acute




Chinese
Chinese
exacerbation



Caucasians
Hans
Hans
patients



Ref/
Ref/
Ref/
Ref/



RefRef/
RefRef/
RefRef/
RefRef/



AltAlt/
AltAlt/
AltAlt/
AltAlt/



Alt
Alt
Alt
Alt




























rs6805660
51
0
2
68
0
0
65
0
5
0
0
45


rs62282486
53
0
0
68
0
0
67
0
3
5
0
40









Surprisingly, as is evident from Table 2, all “IPF acute exacerbation” patients (that is, patients who developed diffuse alveolar damage, as described in Example 1) had the mutant sequence of rs6805660 as a homozygote, and all of these patients except 5 cases had the mutant sequence of rs62282486 as a homozygote. That is, among the patients with diffuse alveolar damage caused by these drugs, 100% (45/45) had the mutant sequence of rs6805660, and about 89% (40/45) had the mutant sequence of rs62282486. It is very surprising that such extremely strong associations were found.
As described above, among the 70 normal Japanese, only 5 individuals had the mutant sequence of rs6805660 as a homozygote, and only 3 individuals had the mutant sequence of rs62282486 as a homozygote. Either of these mutations is present in only about 4% to about 7% of normal Japanese.
(Example 4) <Taxotere ILD Patients and Xalkori ILD Patients>
By the same method as in <Relationship between Gene Polymorphisms and Diseases> in Example 2-4, the frequencies of polymorphisms of rs6805660 and rs62282486 were studied also for the 15 Taxotere ILD patients and the 2 Xalkori ILD patients. The results are shown in Table 3.











TABLE 3








Taxotere
Xalkori



Japanese
ILD patients
ILD patients



Ref/RefRef/
Ref/RefRef/
Ref/RefRef/



AltAlt/Alt
AltAlt/Alt
AltAlt/Alt

























rs6805660
65
0
5
0
0
15
0
0
2


rs62282486
67
0
3
1
0
14
0
0
2









Surprisingly, as is evident from Table 3, all Taxotere ILD patients (that is, patients who developed diffuse alveolar damage, as described in Example 1) had the mutant sequence of rs6805660 as a homozygote, and all of these patients except 1 case had the mutant sequence of rs62282486 as a homozygote. That is, among the patients with diffuse alveolar damage caused by the drug, 100% (15/15) had the mutant sequence of rs6805660, and about 93% (14/15) had the mutant sequence of rs62282486. It is very surprising that such extremely strong associations were found.
Further, surprisingly, as is evident from Table 3, all Xalkori ILD patients (that is, patients who developed diffuse alveolar damage, as described in Example 1) had the mutant sequences of rs6805660 and rs62282486 as homozygotes. It is very surprising that such extremely strong associations were found.
CONCLUSION
As described above, as a result of intensive study, the present inventors discovered that “Iressa ILD+Tarceva ILD” patients, Taxotere ILD patients, Xalkori ILD patients, and IPF acute exacerbation patients who are suffering from diffuse alveolar damage carry specific gene polymorphisms in the MUC4 gene with extremely high probability unlike other populations.
In spite of the past efforts by research institutes around the world, gene polymorphisms associated with diffuse alveolar damage have not been discovered. Therefore, needless to say, no gene polymorphism has been reported to have very strong association with diffuse alveolar damage so far.
The fact that totally the same results could be obtained not only for anticancer drugs belonging to tyrosine kinase inhibitors such as Iressa, Tarceva, and Xalkori, but also for anticancer drugs belonging to microtubule depolymerization inhibitors such as Taxotere, indicates that diffuse alveolar damage has very strong associations with specific gene polymorphisms independent of the action mechanisms of the drugs. Thus, the method of the present invention can be very useful means for determining the risk of development of diffuse alveolar damage due to any anticancer drug or generic drug. This is because the method enables prevention of death of a cancer patient due to an anticancer drug, which should originally be administered for the purpose of saving the life of the patient.

## Claims

1. A method for treating diffuse alveolar damage caused by a drug, the method comprising:
administering a lower dosage of the drug to a patient in whom a gene polymorphism in MUC4 gene has been detected than a dosage of the drug that would be administered to the same patient if the polymorphism had not been detected;
wherein the gene polymorphism is a gene polymorphism in exon 2 of MUC4 gene selected from the group consisting of:
(1) rs150551454 (C/T polymorphism at nucleotide position 195,507,491 in chromosome 3 of NCBI b37.3);
(2) rs62282480 (C/A polymorphism at nucleotide position 195,510,749 in chromosome 3 of NCBI b37.3);
(3) rs2911272 (A/G polymorphism at nucleotide position 195,510,773 in chromosome 3 of NCBI b37.3);
(4) rs413807 (C/T polymorphism at nucleotide position 195,510,827 in chromosome 3 of NCBI b37.3);
(5) rs6805660 (T/C polymorphism at nucleotide position 195,512,042 in chromosome 3 of NCBI b37.3); and
(6) rs62282486 (T/C polymorphism at nucleotide position 195,512,245 in chromosome 3 of NCBI b37.3).

2. The method according to claim 1, wherein the gene polymorphism is rs6805660 or rs62282486.

3. The method according to claim 1, wherein the lower dose is 0 mg/kg.

4. The method according to claim 1, wherein the drug is an anticancer drug.

5. The method according to claim 4, wherein the anticancer drug is selected from the group consisting of molecular-targeted agents, antimetabolites, and microtubule depolymerization inhibitors.

6. The method according to claim 4, wherein the anticancer drugs is selected from the group consisting of gefitinib, erlotinib, crizotinib, gemcitabine, irinotecan, pemetrexed, and docetaxel.

7. The method according to claim 1, wherein the diffuse alveolar damage is caused by acute exacerbation of idiopathic pulmonary fibrosis.

8. The method of claim 1, wherein at least one single nucleotide polymorphism selected from the group consisting of the gene polymorphisms (1), (2), (3), (4), (5), and (6) is detected by using at least one agent selected from the group consisting of:
a) a set of forward primer and reverse primer designed to amplify a sequence that includes at least one of the single nucleotide polymorphisms (1), (2), (3), (4), (5), and (6);
b) a set of forward primer and reverse primer at least one of which is designed to anneal to a position that includes at least one of the single nucleotide polymorphisms (1), (2), (3), (4), (5), and (6), such that amplification occurs only in cases where the polymorphism is present; and
c) a labeled probe that hybridizes to at least one of the single nucleotide polymorphisms (1), (2), (3), (4), (5), and (6).