Title:  Carrier for gene detection and its use for detecting validity of interferon therapy

United States Patent:  6,667,155

Issued:  December 23, 2003

Inventors:  Hijikata; Minako (Tokyo, JP); Mishiro; Shunji (Tokyo, JP); Oota; Yasuhiko (Tokyo, JP); Hashimoto; Koji (Sagamihara, JP)

Assignee:  Kabushiki Kaisha Toshiba (Kawasaki, JP)

Appl. No.:  813031

Filed:  March 21, 2001

Abstract

A carrier for gene detection as a means for prediction before treatment whether interferon therapy is valid or not for a patient, a method for detection of interferon therapy for an individual, an apparatus for gene detection, and a kit for detection of validity of interferon therapy.

BRIEF SUMMARY OF THE INVENTION

An object of the invention is to provide a method for predicting whether interferon therapy is effective to a patient, before the treatment is effected.

According to the first aspect of the present invention, there is provided a carrier for gene detection, which comprises:

a base body; and

a polynucleotide immobilized on the base body, the polynucleotide comprising a polynucleotide selected from the group consisting of:

(at) the polynucleotide of Sequence ID No. 1 in the sequence listing;

(bt) a modified polynucleotide derived from the polynucleotide (at) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(ct) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 1;

(dt) a polynucleotide containing the sequence which spans from 449the to 459th position of Sequence ID No. 1; and

(et) a complementary strand of the polynucleotide selected from the group consisting of (at), (bt), (ct) and (dt) mentioned above.

According to the second aspect of the present invention, there is provided a carrier for gene detection which comprises:

a base body; and

a polynucleotide immobilized on the base body, the polynucleotide comprising a polynucleotide selected from the group consisting of:

(ag) the polynucleotide of Sequence ID No. 2 in the sequence listing;

(bg) a modified polynucleotide derived from the polynucleotide (ag) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(cg) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 2;

(dg) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 2; and

(eg) a complementary strand of the polynucleotide selected from the group consisting of (ag), (bg), (cg) and (dg) mentioned above.

According to the third aspect of the present invention, there is provided a carrier for gene detection which comprises:

a base body; and

a polynucleotide immobilized on the base body, the polynucleotide comprising a polynucleotide selected from the group consisting of:

(aa) the polynucleotide of Sequence ID No. 3 in the sequence listing;

(ba) a modified polynucleotide derived from the polynucleotide (aa) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(ca) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 3;

(da) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 3; and

(ea) a complementary strand of the polynucleotide selected from the group consisting of (aa), (ba), (ca) and (da) mentioned above.

According to the fourth aspect of the present invention, there is provided a carrier for gene detection which comprises:

a base body; and

a polynucleotide immobilized on the base body, the polynucleotide comprising a polynucleotide selected from the group consisting of:

(ac) the polynucleotide of Sequence ID No. 4 in the sequence listing;

(bc) a modified polynucleotide derived from the polynucleotide (ac) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(cc) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 4;

(dc) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 4; and

(ec) a complementary strand of the polynucleotide selected from the group consisting of (ac), (bc), (cc) and (dc) mentioned above.

According to the fifth aspect of the present invention, there is provided a DNA chip, which comprises:

a base body; and

a first and a second electrodes formed on the base body,

the first electrode comprising a conductive body and at least one polynucleotide immobilized on the conductive body, the polynucleotide being selected from the group consisting of (at) to (et) shown below;

(at) the polynucleotide of Sequence ID No. 1 in the sequence listing;

(bt) a modified polynucleotide derived from the polynucleotide (at) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(ct) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 1;

(dt) a polynucleotide containing the sequence which spans from 449the to 459th position of Sequence ID No. 1; and

(et) a complementary strand of the polynucleotide selected from the group consisting of (at), (bt), (ct) and (dt) mentioned above, the second electrode comprising a conductive body, and at least one polynucleotide immobilized on the conductive body, the polynucleotide being selected from the group consisting of (ag) to (eg), (aa) to (ea), and (ac) to (ec) shown below;

(ag) the polynucleotide of Sequence ID No. 2 in the sequence listing;

(bg) a modified polynucleotide derived from the polynucleotide (ag) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(cg) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 2;

(dg) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 2;

(eg) a complementary strand of the polynucleotide selected from the group consisting of (ag), (bg), (cg) and (dg) mentioned above;

(aa) the polynucleotide of Sequence ID No. 3 in the sequence listing;

(ba) a modified polynucleotide derived from the polynucleotide (aa) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(ca) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 3;

(da) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 3;

(ea) a complementary strand of the polynucleotide selected from the group consisting of (aa), (ba), (ca) and (da) mentioned above;

(ac) the polynucleotide of Sequence ID No. 4 in the sequence listing;

(bc) a modified polynucleotide derived from the polynucleotide (ac) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(cc) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 4;

(dc) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 4; and

(ec) a complementary strand of the polynucleotide selected from the group consisting of (ac), (bc), (cc) and (dc) mentioned above.

According to the sixth aspect of the present invention, there is provided a method for detecting validity of interferon therapy for an individual, the method comprises:

1) contacting a polynucleotide sample taken from the individual with the carrier for gene detection according to the present invention; and

2) determining the nucleotide sequence of the polynucleotide in the sample, by detecting the hybridization reaction between the polynucleotide sample and the polynucleotide immobilized on the carrier for gene detection.

Further, according to the seventh aspect of the present invention, there is provided a method for detecting validity of interferon therapy for an individual, the method comprises:

1) contacting the probe polynucleotide to a carrier for gene detection which has a polynucleotide sample taken from the individual immobilized on a substrate; and

2) determining the nucleotide sequence of the polynucleotide sample by detecting the hybridization reaction between the polynucleotide sample immobilized on the substrate and the probe polynucleotide;

The probe polynucleotide comprises a polynucleotide selected from the group consisting of:

(at) the polynucleotide of Sequence ID No. 1 in the sequence listing;

(bt) a modified polynucleotide derived from the polynucleotide (at) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(ct) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 1;

(dt) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 1;

(et) a complementary strand of the polynucleotide selected from the group consisting of (at), (bt), (ct) and (dt) mentioned above;

(ag) the polynucleotide of Sequence ID No. 2 in the sequence listing;

(bg) a modified polynucleotide derived from the polynucleotide (ag) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(cg) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 2;

(dg) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 2;

(eg) a complementary strand of the polynucleotide selected from the group consisting of (ag), (bg), (cg) and (dg) mentioned above;

(aa) the polynucleotide of Sequence ID No. 3 in the sequence listing;

(ba) a modified polynucleotide derived from the polynucleotide (aa) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(ca) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 3;

(da) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 3;

(ea) a complementary strand of the polynucleotide selected from the group consisting of (aa), (ba), (ca) and (da) mentioned above;

(ac) the polynucleotide of Sequence ID No. 4 in the sequence listing;

(bc) a modified polynucleotide derived from the polynucleotide (ac) by including one or several deletions, substitutions or additions at any positions except for 455th position;

(cc) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 4;

(dc) a polynucleotide containing the sequence which spans from 449th to 459th position of Sequence ID No. 4; and

(ec) a complementary strand of the polynucleotide selected from the group consisting of (ac), (bc), (cc) and (dc) mentioned above.

According to the eighth aspect of the present invention, there is provided a gene detecting apparatus for detecting validity of interferon therapy, the apparatus comprising:

the carrier for gene detection of the present invention described above;

a reaction section for contacting a first polynucleotide immobilized on a base body of the carrier with a sample which contains a second polynucleotide labeled with a marker, and putting the first and the second polynucleotides under hybridization reaction condition; and

a marker-detecting apparatus for detecting the marker attached to the second polynucleotide.

According to the ninth aspect of the present invention, there is provided a gene detection apparatus for detecting validity of interferon therapy, the apparatus comprising:

a carrier for gene detection of the present invention described above, which is used as an electrode;

a counter electrode;

a voltage application means for applying voltage between the carrier for gene detection and the counter electrode,

a reaction section for contacting a first polynucleotide immobilized on a base body of the carrier with a sample which contains a second polynucleotide, and putting the first and the second polynucleotides under hybridization reaction condition; and

a measurement section for measuring an electric signal generated between the carrier for gene detection and the counter electrode when voltage is applied by the voltage applying means after the hybridization reaction.

According to the tenth aspect of the present invention, there is provided a kit for determining validity of interferon therapy, which comprises the carrier for gene detection described above and a buffer solution.

According to the eleventh aspect of the present invention, there is provided a kit for detecting validity of interferon therapy for an individual, which comprises the carrier for gene detection described above, a double-strand recognizer, and a buffer solution.

DETAILED DESCRIPTION OF THE INVENTION

Polynucleotides of Sequence ID Nos. 1, 2, 3 and 4 are those containing promoter regions of human MxA genes, and it was found for the first time by the present inventors that the single nucleotide polymorphism (to be called SNP hereafter) existing at 455th position of these polynucleotides contributes to responsibility to the effect of interferon therapy.

The interferon-stimulated response element (to be called ISRE hereafter) exists from 441st to 456th position of each polynucleotide.

The nucleotide sequence of ISRE from 441st to 456th position of Sequence ID No. 1 is [GGTTTCGTTTCTGCTC] (Sequence ID No. 5). The 15th position of ISRE (corresponding to 455th position of Sequence ID No. 1) is thymine. Note that according to the ordinary representation in which the transcription initiation site is referred to as +1st position, 455th position in Sequence ID No. 1 is designated as -88th position.

The nucleotide sequence of ISRE from 441st to 456th position of Sequence ID No. 2 is [GGTTTCGTTTCTGCTC] (Sequence ID No. 6). The 15th position of ISRE (corresponding to 455th position of Sequence ID No. 1) is guanine. Note that according to the ordinary representation in which the transcription initiation site is referred to as +1st position, 455th position in Sequence ID No. 1 is designated as -88th position.

The nucleotide sequence of ISRE from 441st to 456th position of Sequence ID No. 3 is [GGTTTCGTTTCTGCGC] (Sequence ID No. 7) and the 15th position of ISRE (corresponding to 455th position of Sequence ID No. 3) is adenine. Note that according to the ordinary representation in which the transcription initiation site is referred to as +1st position, 455th position in Sequence ID No. 3 is designated as -88th position.

The nucleotide sequence of ISRE from 441st to 456th position of Sequence ID No. 4 is [GGTTTCGTTTCTGCCC] (Sequence ID No. 8) and the 15th position of ISRE (corresponding to 455th position of Sequence ID No. 4) is cytosine. Note that according to the ordinary representation in which the transcription initiation site is referred to as +1st position, 455th position in Sequence ID No. 4 is designated as -88th position.

Hereinafter throughout the present specification, 455th position of Sequence ID Nos. 1, 2, 3, and 4 are called the SNP site.

The regions of these ISRE except for said SNP sites are common for each sequence. It was epidemiologically proved that while interferon therapy is effective for HCV-infected patients having ISRE (Sequence ID No. 5) in which the 15th nucleotide is thymine, interferon therapy is not effective for HCV-infected patients not having ISRE (Sequence ID No. 5) in which the 15th nucleotide is thymine.

In other words, as described in detail in examples described later, it was proved that interferon therapy is less effective for HCV-infected patients possessing homozygous promoter region comprising the polynucleotide of Sequence ID No. 2 which has guanine at 455th position (to be referred to G/G homo hereinafter), in comparison with those possessing heterozygous promoter regions comprising the polynucleotide of Sequence ID No. 1 which has thymine at the 455th position and the polynucleotide of Sequence ID No. 2 which has guanine at the 455th position (to be referred to G/T hetero hereinafter), or those having homozygous promoter region comprising the polynucleotide of Sequence ID No. 1 (to be referred to T/T homo hereinafter).

Alternatively, the interferon therapy was shown to be less effective for HCV-infected patients having homozygous promoter regions of MxA genes which has not thymine at the 455th position (to be referred to non-T/non-T homo hereinafter), in comparison with those with T/non-T hetero or T/T homo. There are G/G, G/A, G/C, A/A, A/C, and C/C as combinations of non-T/non-T homo. Combinations of T/non-T include T/G, T/A, and T/C.

Therefore, validity of interferon therapy for an HCV-infected patient can be detected prior to implementation of interferon therapy, for example by determining the nucleotide of the SNP site in ISRE of the polynucleotide which contains promoter regions of human MxA gene possessed by HCV-infected patients.

In the carrier for gene detection according to the present invention, the polynucleotide of Sequence ID No. 1 having thymine at the SNP site, a fragment or a complementary strand thereof is used as a probe for detecting sequence of nucleic acid strand of the polynucleotide extracted from a subject.

Use of the carriers for gene detection, etc. of the present invention allows examination whether said SNP site in the promoter region of human MxA gene from the subject is thymine or not, thereby enabling prediction of validity of interferon therapy for the subject.

Also, in the carriers for gene detection of the present invention, the polynucleotide of Sequence ID No. 2 having guanine at the SNP site, a fragments or a complementary strand thereof; the polynucleotide of Sequence ID No. 3 having adenine at the SNP sites, a fragments or a complementary strand thereof; and the polynucleotide of Sequence ID No. 4 having cytosine at the SNP sites, a fragment or a complementary strand thereof are used as probes for detecting the nucleic acid sequence of polynucleotides extracted from the subject.

Use of the carrier for gene detection according to an embodiment of the present invention allows identification of the nucleotide at the SNP site of the promoter regions of human MxA gene from the subject, thereby enabling prediction of validity of interferon therapy on the subject.

Besides hepatitis C, examples of diseases possibly requiring interferon therapy include glioblastoma, medulloblastoma, astrocytoma, malignant melanoma of the skin, hepatitis B, renal carcinoma, multiple myeloma, hairy cell leukemia, chronic myeloid leukemia, subacute screlosing panencephalitis, viral encephalitis, systemic herpes zoster and varicella of immunologic inhibition patients, undifferentiated epiphoryngeal carcinoma, viral internal ear infection disease accompanying hearing ability degradation, herpetic keratitis, flat condyloma, conjunctivitis due to adenovirus and herpesvirus, herpes progenitalis, herpes labialis, carcinoma uterine cervix, hepatic hydrothorax, keratoacanthoma, basal cell carcinoma, and delta chronic active hepatitis are included in diseases. Interferons used in the interferon therapy include interferon .alpha., .beta., and .omega., and so on.

The carrier for gene detection of the present invention can be used to detect the validity of interferon therapy prior to applying the therapy to the patients suffered from these diseases mentioned above.

Next, the aspects of the present invention are described in more detail.

First, the present invention provides a carrier for gene detection, which can be used to detect validity of interferon therapy for the patient suffered from the disease indicated for interferon therapy, prior to implementation of the therapy.

Outline of a Carrier for Gene Detection

The carrier for gene detection according to the embodiment of the present invention can be prepared by immobilizing the predetermined polynucleotide on a base body such as a substrate board, porous body, a microtiter plate, a particle and beads etc.

Materials, size, and shape of the base body on which the polynucleotide is immobilized are not limited, and any base body capable of being immobilized with the polynucleotide can be used.

Examples of the material for the base body include, for example, inorganic materials such as silicone, glass, crystal glass, alumina, sapphire, forsterite, silicon carbide, silicon oxide, silicon nitride, and magnetic materials, and organic materials such as polyethylene, polypropylene, polyisobutylene, polyethylene terephthalate, unsaturated polyester, fluorine-containing resins, polyvinyl chloride, polyvinylydene chloride, polyvinyl acetate, polyvinyl alcohol, polyvinyl acetate, acrylic resin, polyacrylonitrile, polystyrene, acetal resin, polycarbonate, polyamide, phenolic resin, urea resin, epoxy resin, melamine resin, styrene-acrylonitrile copolymer, acrylonitrile-butadiene-styrene copolymer, silicone resin, polyphenylene oxide, polysulfone, nitrocellulose, nylon, polymethyl methacrylate, polyphenylenesulphone, polyethersulphone, polyether ketone, fluoroethylene copolymer, polymethylpentene. Further, composites of above mentioned inorganic and organic materials can be used.

As a method for immobilizing the polynucleotide on the base body, the method disclosed in Science 251:767773(1991) can be used. In addition to this method, an improved method for immobilizing the polynucleotide on the base body is known, and can also be used for immobilizing the polynucleotide on the base body.

When the base body made of organic material or glass is used, stable immobilization of the polynucleotides can be attained by coating the surface of the base body with polylysine or aminosilane.

In the present specification, "polynucleotide" means chemical substances formed by coupling two or more nucleosides through phosphate bonds. "Nucleosides" include, but not limited to, deoxyribonucleoside and ribonucleosides.

Furthermore, examples of the polynucleotide to be immobilized on the base body of the present invention include RNA, DNA, PNA, methyl phosphonate nucleic acids, oligonucleotide such as S-oligo, and polynucleotides such as cDNA, and cRNA.

In the present specification, "promoter region" indicates not only the region directly involved in transcription initiation reaction such as TATA box, but also sequences including control sequences that exist in close proximity of or distant from said region to influence the efficiency of the transcription initiation reaction. Therefore, it should be noted that the term "promoter region" includes a sequence involved in transcription initiation reaction alone, a control sequence alone, and a conjugated sequence between the both sequences.

Incidentally, "ISRE" means a nucleotide sequence consisting of about 12 to 15 nucleotides which exist in the transcription control region of the gene induced by the stimulus of interferon .alpha., .beta., .gamma., or .omega..

Examples of the polynucleotide, which can be immobilized on the base body according to the present invention, include the polynucleotide selected from the group consisting of the following (a) to (e).

(a) Polynucleotide indicated by any one of Sequence ID Nos. 1, 2, 3, or 4.

(b) A modified polynucleotide derived from the polynucleotide listed in (a) by including one or several deletions, substitutions or additions at any positions except for 455th position.

Examples of the deletion, substitution and addition include deletion at 128th, 133rd, 152nd, 508th, and 543rd position, substitution at 330th position (GET), and addition at 501st position.

Furthermore, it is possible to use a combined polynucleotide in which the polynucleotide of the Sequence ID Nos. 1, 2, 3, or 4 or fragments thereof is conjugated with at least one functional polynucleotide selected from the group consisting of promoters, enhancers, upstream activation sequence, silencers, upstream suppression sequence, attenuators, poly A tail, nucleus transition signals, Kozak sequence, ISRE, drug resistance factors, genes of signal peptide, genes of transmembrane domeins, luciferin gene, green fluorescent protein gene, phycocianin gene, genes of marker protein containing horseradish peroxidase, genes of interferon-responding protein, and genes of interferon-non-responding protein.

Further, in the nucleotide sequences of said polynucleotides of Sequence ID Nos. 1, 2, 3, and 4, only one nucleotide at the SNP site (located at 455th position) is involved in the validity of interferon therapy. Therefore, the polynucleotide to be immobilized on the base body can be a fragment of said polynucleotide containing the SNP site at the 455th position.

When said fragment is used as the polynucleotide to be immobilized on the base body, it is preferably of length not shorter than 11 nucleotides and no longer than 30 nucleotides. More preferably, it is of length not shorter than 15 nucleotides. When the polynucleotide to be immobilized on the base body is too long, it is difficult to identify difference of one nucleotide. On the other hand, when the polynucleotide to be immobilized on the base body is too short, it is difficult to hybridize with and determine the nucleotide sequence of the polynucleotide included in the sample.

Particularly preferable polynucleotides to be immobilized on the base body are:

(c) A fragment of polynucleotide of Sequence ID Nos. 1, 2, 3, or 4 including the SNP site at the 455th position, a fragment containing the polynucleotide of Sequence ID Nos. 5, 6, 7, or 8 (namely said ISRE) corresponding to the sequence from 441st to 456th position of Sequence ID Nos. 1, 2, 3, or 4.

(d) A fragment of polynucleotides of Sequence ID NOS. 1, 2, 3, or 4 including said 455th SNP site, a fragment containing the polynucleotide of Sequence ID Nos. 9, 10, 11, or 12 corresponding to the sequence from 449th to 459th position of Sequence ID Nos. 1, 2, 3, or 4. Particularly, since the fragment (d) has said SNP site roughly at the center thereof and contains nucleotide sequences of equal length on both sides, high-precision determination of nucleotide sequence can be achieved. In order to carry out detection of still higher precision, a fragment including the polynucleotide corresponding to the sequence from 447th to 461st position of Sequence ID Nos. 1 to 4 are preferable.

Furthermore, a polynucleotide to be immobilized on the base body can be:

(e) A complementary strands of polynucleotide selected from the group consisting of (a), (b), (c) and (d) described above.

Note that complementary strands of the polynucleotides indicated by Sequence ID Nos. 5, 6, 7, and 8 (i.e., the ISRE) are the polynucleotide strands of Sequence ID Nos. 13, 14, 15, and 16, respectively.

Note that complementary strands of the polynucleotide indicated by Sequence ID Nos. 9, 10, 11, and 12 are the polynucleotide strands of Sequence ID Nos. 17, 18, 19, and 20, respectively.

The carriers for gene detection according to the embodiment of the present invention are used in order to detect hybridization reaction of the polynucleotide extracted from the subject with a probe using the predetermined polynucleotide immobilized on the base body as the probe, to determine the polynucleotide sequence containing promoter region of human MxA gene of the subject, and to examine what type of nucleotide is exist at the SNP site.

Method for Using Carriers for Gene Detection

The method for determining sequences of polynucleotides extracted from a subject by using said carrier for gene detection is particularly explained.

In order to perform sequencing of polynucleotides extracted from a subject by using said carrier for gene detection, there can be two kinds of methods: (1) the method using a marker substance and (2) the electrochemical method.

First, (1) the method using a marker substance is specifically explained.

Samples containing polynucleotides (body fluid such as blood, blood cells, biopsy tissue, or cultured cells) are taken from a subject of an individual, which is a mammal including humans, for example. They can be arbitrary samples taken from an individual since polynucleotides are widely distributed in the body. A preferable sample is blood.

Then, if necessary, extraction and separation processes such as phenol extraction and ethanol precipitation is performed. Subsequently, amplifying processes such as PCR are carried out, and then, the sample polynucleotides contained in said sample are extracted. For extracting the sample polynucleotides, optional extraction methods can be used other than phenol extraction and ethanol precipitation, for example. When m RNA is extracted, oligo dT column can be used. When the amount of sample polynucleotide is small, optional amplification of the sample polynucleotides may be carried out, if necessary.

Then, labeling procedure is carried out to provide the sample polynucleotide labeled with the marker. Alternatively, secondary probe containing polynucleotides labeled with the marker substances can be mixed instead of labeling the sample polynucleotide.

As detectable markers, use can be made of, but not limited to, light emitting substances such as fluorescent substances, hapten, enzymes, radio isotopes, and electrode active substances. Labeling of sample polynucleotides is preferably performed for labeling the promoter region. Various known methods can be used to label the promoter region. In particular, PCR reaction using labeled primers may be useful since amplification and labeling can be carried out simultaneously.

Then, the sample polynucleotides are subjected to the hybridization reaction with the polynucleotide-immobilized base body of the gene detection carrier. In other words, after said labeled sample polynucleotide is first added to the reaction solution for hybridization, said reaction solution is contacted with the gene detection carrier. When the sample contains a certain polynucleotide complementary to the polynucleotide strand immobilized on the base body, the sample polynucleotide is hybridized with the polynucleotide on the base body and immobilized thereon.

Regarding the condition of the hybridization reaction, reaction temperature may range from 10 to 90^oC. and reaction time may range from 1 minute or longer to overnight. During the reaction, the reaction rate can be accelerated by operations such as agitation and shaking. The reaction solution for the hybridization can be buffer solutions with ionic intensity in the range of 0.01-5, and pH in the range of 5-10. Hybridization promoters such as dextran sulfate, salmon sperm DNA, bovine pectus DNA, EDTA, and surfactants can be added to the reaction solution.

Afterwards appropriate washing is carried out.

Then, in order to determine what type of nucleotide the subject possesses at said SNP site, detection is made for finding if the hybridization reaction between the sample polynucleotide and the polynucleotide on the base body has took place or not.

If the sample polynucleotide is detected to have been hybridized to a polynucleotide which has thymine at the SNP site or its complementary strand among the polynucleotides (a) to (e) immobilized on the base body, the SNP site of the polynucleotide which contains the promoter region of the subject's human MxA gene is thymine. On the other hand, if the sample polynucleotide is detected to have been hybridized to a polynucleotide which has guanine at the SNP site or its complementary strand, the SNP site of the polynucleotide which contains the promoter region of the subject's human MxA gene is guanine. The same is held true for the cases of adenine and cytosine.

This detection is carried out by detecting the marker in the labeled polynucleotide or the labeled secondary probe in the sample, using an appropriate detection apparatus depending on the kind of labeling markers. For example, when the marker is a fluorescent substance, the marker can be detected using a fluorescence detector. The carrier for gene detection may comprise any polynucleotide selected from the group consisting of the polynucleotide (a) to (e) described above immobilized on the base body. Specifically, the polynucleotide can be at least one polynucleotide selected from the group consisting of the polynucleotide having thymine at the SNP site or its complementary strand, the polynucleotide having guanine at the SNP site or its complementary strand, the nucleotide having adenine at the SNP site or its complementary strand, and the polynucleotide having cytosine at the SNP site or its complementary strand. In this case, however, it is required that the SNP type of the polynucleotide immobilized on the base body, as well as at least one of the address of each polynucleotide on the base body surface and type of marker should be determined in advance. At least one of the address and the type of the detectable marker enables to determine which polynucleotide on the base body has hybridized with the polynucleotide of the sample.

In the method (1) using the marker substance, the sequence of the sample polynucleotide can be determined even when the sample polynucleotide taken from the subject is immobilized on the base body of the carrier for gene detection. Namely, the sample polynucleotide immobilized on the base body are contacted with solutions of polynucleotides selected from (a) to (e) described above which has known sequences and labeled in advance with different markers based on the difference of said SNPs, in order to put the both polynucleotides under the hybridization reaction condition. If a polynucleotide strand complementary to the sample polynucleotide immobilized on the base body is contained in the solution, the complementary polynucleotide strand is hybridized with the sample polynucleotide on the base body and is immobilized on the base body. Thereafter, by detecting the type of marker substance immobilized on the base body, it is possible to detect which polynucleotide has been hybridized with the sample polynucleotide, and further, to know the sequence of the sample polynucleotide based on the known sequence of the labeled polynucleotide.

In the method mentioned above, when the sample polynucleotide hybridized with the labeled polynucleotide having thymine at SNP site or its complementary strand, the subject has thymine at said SNP site, and therefore, it can be predicted that the interferon therapy is valid in the subject. On the other hand, when the sample polynucleotide hybridized with the labeled polynucleotide having thymine at SNP site or its complementary strand, and did not hybridize with the labeled nucleotide having thymine at SNP site, the subject does not have thymine at said SNP site, and therefore, interferon therapy can be predicted to be invalid.

Next, the electrochemical method (2) is particularly explained.

In contrast to the method (1) in which hybridization reaction between the sample polynucleotide and the probe polynucleotide is determined by detection of marker substances as described above, the electrochemical method (2) electrochemically detects the hybridization reaction.

In the electrochemical method, a polunucleotide-immobilized electrode is used as the carrier for gene detection. The polynucleotide-immobilized electrode (to be referred as the electrode of the present invention hereafter) comprises a base body made of conductive material, and at least any one of the polynucleotides (a) to (e) described above immobilized on the base body.

Although preferable conductive material for the base body is gold, other materials can be used. For example, gold alloy, elemental metals and their alloys such as silver, platinum, palladium, silicon, germanium, gallium, tungsten, and carbons such as graphite and glassy carbon, as well as their oxides and compounds can be used. These conductive materials can be formed on a separate substrates as a film by plating, printing, sputtering and vapor deposition.

The method of immobilizing polynucleotide on the base body made of conductive material is not especially limited. For example, the immobilization can be easily carried out by utilizing the affinity bond between thiol groups introduced in the polynucleotides and gold surface of the base body. In addition, the immobilization may be possible by physical adsorption, chemical adsorption, hydrophobic bonding, embedding, and covalent bonding. Further, biotin-avidin bonding and use of condensation agents such as carbodiimides can be employed. In these cases, the immobilization can be facilitated when the conductive surface of the base body is modified with molecules having functional groups. Further, in order to suppress non-specific adsorption of polynucleotides on the surface of the base body, the surface is desirably coated with mercaptans such as mercaptoethenol or lipids such as stearylamine.

As an example, a method for immobilizing polynucleotide on a gold base body is described below. First the gold base body is subjected to activation treatment after it was rinsed with deionized water. A sulfuric acid solution of 0.1 to 10 mmol/L is used for the activation. In this solution, voltage is scanned in the ranges of -0.5 to 2 V (vs Ag/AgCl) and 1 v/s to 100000 v/s. This treatment activates the surface of the gold substrate to the condition under which polynucleotides can be immobilized thereon.

On the other hand, thiol groups are introduced at the 5' and the 3' ends of the probe polynucleotides to be immobilized. The thiolated polynucleotides are kept dissolved in a solution of a reducing agent such as DTT, and the DTT is removed just before use by gel filtration or ethyl acetate extraction. For immobilization, a probe is dissolved in the range of 1 ng/mL to 1 mg/mL in a buffer solution of ionic intensity of 0.011 to 5 and pH of 5 to 10, and the substrate just after activation is immersed in the solution. The immobilization reaction is carried out at 4 to 100^oC. for 10 minutes to overnight. The base body after polynucleotide immobilization is desirably kept under the condition that nucleic acid decomposing enzymes (nuclease) are absent, and possibly in the dark.

When immobilizing polynucleotides on a base body, immobilizing apparatuses such as the DNA spotter and the DNA arrayer can be used to immobilize polynucleotides relatively easily. A spotter of ink-jet type or static electricity type is desirably used to avoid damaging the surface of the substrate. Further, it is possible to synthesize the polynucleotides directly on the substrate.

It is desirable that the electrode of the present invention is constructed as so called DNA chip in which the conductor and the electrode electrically connected, and are arranged on a same base body. The DNA chip is manufactured by arranging the conductors such as metal wirings appropriately coated with insulating materials on the base body (desirably an insulating base body), followed by electrically connecting the electrode (on which the predetermined polynucleotides are previously immobilized) to the conductors.

Polynucleotides of different sequences need to be immobilized on plurality of different electrodes that are insulated with each other. In arranging plurality of electrodes on a base body, the number of electrodes to be arranged on a substrate can practically be 10¹ to 10⁵.

When plurality of electrodes of the present invention are arranged on a same base body, scanning lines can be further arranged to locate switching elements on each crossings of said conductors and the scanning lines. This enables quick determination of whether hybridization reaction occurred or not for each electrode, by applying voltage on one electrode after another. In detection of occurrence of hybridization reaction using the electrode, at least a counter electrode, and a reference electrode, if necessary, is provided in the same manner as in other ordinary electrochemical detection methods. When the reference electrode is employed, ordinary reference electrode such as silver/silver chloride electrode, and mercury/mercury chloride electrode can be used. These electrodes are desirably arranged on the same base body as the electrode of embodiment of the present invention is arranged.

In order to determine the sequence of the polynucleotides sampled from subjects using the electrode of the present invention, following operations are carried out.

First, a sample polynucleotide is taken from a subject such a mammal including humans, for example, to which above mentioned extraction, amplification and labeling with a marker are optionally carried out. These procedures are same as in the method (1). However, labeling is not necessarily required.

Next, the solution containing said sample is put in contact with the electrode to place the sample polynucleotide and the polynucleotide immobilized on the base body under the condition of hybridization reaction. In case that the complementary strand of the polynucleotide on the base body is contained in the sample polynucleotide, the complementary sample polynucleotide is hybridized with the polynucleotide immobilized on the base. The procedure and the condition are same as the method (1). Then the electrode is rinsed.

Subsequently, a solution of electro-active double strand recognizer is added in the hybridization reaction system, thereby intercalating the double strand recognizer into the double strand polynucleotide formed by hybridization of the polynucleotide immobilized on the electrode and the sample polynucleotide. Occurrence of hybridization between the sample polynucleotide and the polynucleotide immobilized on the base body can be detected by applying voltage to the electrode and the counter electrode. When the voltage is applied, the electric signal is generated from the double strand recognizer intercalated to the double strand polynucleotide which has been formed by the hybridization. Therefore, the electric signal indicate the occurrence of the hybridization.

The electro-active double strand recognizer used here is not especially limited, and for example, Hoechst 33258, acridine orange, quinacrine, daunomycin, metallo-intercalator, bisintercalators such as bisacridine, trisintercalator, polyintercalator, and so on can be used. Complexes of metals such as ruthenium, cobalt and iron called metallo-intercalators, as well as organic compounds such as ethylene dibromide can be used. Further, groove binders such as Hoechst 33258 and cyanine dyes, and high molecular bio-substances such as antibodies and enzymes can also be used.

The concentration of the double strand recognizer varies depending upon the types, but generally used in the range of 1 ng/mL to 1 mg/mL. Here, a buffer solution having ionic intensity in the range of 0.001 to 5 and pH in the range of 5 to 10 is used.

After the electrode is reacted with the double strand recognizer, the electrode is optionally rinsed further. Subsequently, the electrode of the present invention is used as a working electrode, and voltage is applied between the working electrode and a separately provided counter electrode to detect the electrochemical signal by determining the electric current between the two electrodes. While an electrochemical signal can be detected with such two electrodes (working and counter electrodes), the detection can also be carried out using three electrodes, i.e., working, counter and reference electrodes. In detecting the electrochemical signal, the voltage can be scanned at constant speed, or applied by pulses, or constant voltage can be applied. For measurement, electric current and voltage are controlled using such apparatuses as potentiostats, digital multimeters, and function generators. The concentration of target genes may calculated from calibration curve based upon the current values obtained.

Among the polynucleotides (a) to (e) described above, the polynucleotide having thymine at the SNP site and its complementary strand, the polynucleotide having guanine at the SNP site and its complementary strand, the polynucleotide having adenine at the SNP site and its complementary strand, and the polynucleotide having cytosine at the SNP site and its complementary strand are desirably immobilized on separate electrodes which are insulated from each other and provided on the same substrate to form a DNA chip in order to carry out high-precision determination. In this case, electrochemical signal corresponding to each polynucleotide is detected from each electrode.

The sequence of the sample polynucleotide can also be determined by the electrochemical method (2) using an electrode on which the sample polynucleotide taken from a subject is immobilized. Thus, the polynucleotide in the solution and the sample polynucleotide on the electrode are put under hybridization reaction condition by contacting a solution of any one of the polynucleotides (a) to (e) in which the sequences thereof are previously known. If the complementary strand of the sample polynucleotide is contained in the solution, the complementary polynucleotide is immobilized on the base body through hybridization with the sample polynucleotide previously immobilized on the base body. The sequence of the sample polynucleotide can be known by detecting the hybridization reaction.

When the hybridization reaction of the sample polynucleotide with the polynucleotide having thymine at SNP site or its complementary strand is detected by the above mentioned method, the subject possesses thymine at SNP site, and therefore, interferon therapy can be predicted to be valid. On the other hand, when the hybridization reaction of the polynucleotide of the sample with the polynucleotide having other bases than thymine at SNP site or its complementary strand is detected, and the hybridization reaction with the polynucleotide having thymine at said SNP site or its complementary strand is not detected, the subject does not have thymine at said SNP site, and therefore, interferon therapy is detected to be invalid.

Claim 1 of 12 Claims

What is claimed is:

1. A method for predicting the efficacy of interferon therapy using interferon-.alpha. and/or interferon-.beta. for treating an individual who suffers from hepatitis C virus, comprising:

(1) contacting a polynucleotide sample obtained from said individual with a carrier for gene detection comprising

a base body; and

a polynucleotide immobilized on said base body,

wherein said polynucleotide comprises a polynucleotide selected from the group consisting of:

(at) the polynucleotide of Sequence ID No. 1 in the sequence listing;

(bt) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 1;

(ct) a polynucleotide containing the sequence which spans from 449the to 459th position of Sequence ID No. 1; and

(dt) a complementary strand of the polynucleotide selected from the group consisting of (at), (bt), and (ct), mentioned above;

(2) determining the nucleotide sequence of the polynucleotide in said sample by detecting the hybridization reaction between said polynucleotide sample and the polynucleotide immobilized on said carrier for gene detection; and either

(3a) predicting that the interferon therapy will be successful for said individual if the nucleotide sequence of said sample polynucleotide determined by the determination step is that of the polynucleotide selected from the group consisting of:

(at) the polynucleotide of Sequence ID No. 1;

(bt) a polynucleotide containing the sequence which spans from 441st to 455th position of Sequence ID No. 1;

(ct) a polynucleotide containing the sequence which spans from 449the to 459th position of Sequence ID No. 1; and

(dt) a complementary strand of the polynucleotide selected from the group consisting of (at), (bt), and (ct), mentioned above, or

(3b) predicting the interferon therapy will not be successful for said individual if the nucleotide sequence of said sample polynucleotide determined by the determination step is not that of the polynucleotide recited in (3a) above.

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