# Patent

## Title
Gene therapy agent for Haemophilia B and its preparation method

## Abstract

The invention relates to site-specific integrating expression vectors for therapy Hemophilia B and to methods of preparing them. A vector of the invention contains a human Factor IX gene in a vector constructed using as a chromosome targeting sequence a polynucleotide without any important physiological function-related gene homologous to DNA on the short arms of human group D and human group G chromosomes. The vector of the invention provides high stability of Factor IX expression, high expression efficiency, no immunogenicity and safety in use.

## Background
RELATED APPLICATIONS
This application is the national phase under 35 U.S.C. § 371 of PCT International Application No. PCT/CN01/01291 which has an International filing date of Aug. 29, 2001, which designated the United States of America.
FIELD OF THE INVENTION
The invention relates to a genetic drug for treatment of hemophilia B and its preparation.
BACKGROUND OF THE INVENTION
Hemophilia B, also called second-type Hemophilia is a kind of haemorrhage. It is an X-linked, recessive hereditary disease arising due to deficiency of fibrinogen IX (FIX). Its incidence in the male is 1/30,000. Human FIX is a single-stranded glycoprotein containing 415 amino acid residues, having a molecular weight of 56 kDa. FIX can be divided into four different functional domains; in order from the N-terminus of the protein: a Gla domain (γ-carboxyl glutamic aciddomain), a growth factordomain, an activating peptide domain and a catalytic domain (or serineprotease domain). Human FIX is synthesized mainly in the liver. Its initial translation product includes a leader sequence with 46 amino acids at the N-terminus. FIX is processed into mature FIX by cleavage of the leader peptide, glycosylation and vitamin K-dependent γ-carboxylation. FIX exists in blood in as a zymogen that is activated (“FIX”) by a protease activity FIXa or by the FVII-tissue factor complex. The content of FIX in plasma in normal people is 5 μg/ml and its half-life of activity is 24 hours (refer to Chuah MKL, DesireCollen & Vanden Driessche. Gene therapy for Hemophilia. J Gene Med 2001;3:3-20).
FIX is a necessary protein factor in the processes of the endogenous blood coagulation cascade response. A complex of FIX and regulatory protein accelerates the rate of the endogenous clotting cascade response thousands of times, which makes clotting process be finished just in a few minutes. Therefore, deficiency of FIX in the human body, can lead to endless spontaneous or minutely traumatic bleeding, serious joint distortion and lameness or death due to bleeding in the bowel or skull. The human FIX gene (hFIX) was identified in 1982 at chromosome Xq27.1. hFIX is composed of 8 exons, the coding sequence is 1.383 kb, encoding 415 amino acids. (Choo K H, Goule K G, Rees D J, et al. Nature 1982;299:178-180; Kurachi K, Davie E W. Proc Natl Acad Sci USA 1982;79:6461-6464.). The normal plasma concentration of FIX protein in normal plasma is 5 μg/ml (Kaufman R J. Human Gene Therapy 1999; 10:2091-2107). Clinical treatment of Hemophilia B is confined to protein substitution treatment by blood transfusion, or by administering a replenishing FIX preparation to obtain the correct plasma concentration. However, because FIX's half-life in the body is only 24 hours, patients need repeated transfusion or administration of blood preparations toremain alive. Hemophilia B patients not only undertake heavy economic burden, but also confront a threat of infection by HIV, HBV and mad cow virus.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows FISH mapping of the 120 kb BMSF.
FIG. 2 shows construction of a gene vector-FIX recombinant of the invention (the whole length of gene vector sequence is 13928 bp); pGEM-7(11033-13928): vector reproductive component and prokaryotic screening system; TK (1-2840); negative screening gene for eukaryotic cells (TK promoter and TK polyA signal); Neo (4342-5910); positive screening gene for eukaryotic cells (SV40 promoter and SV40 polyA signal); FIX (5911-8677): FIX therapeutic gene (CMV promoter and BGH polyA signal); GLS(2841-4341 and 8678-11032): targeting sequence of the therapeutic gene; Cloning site (5910) for insertion of a therapeutic gene.
FIG. 3 shows FISH mapping of the FIX therapeutic gene in a clone of a positively transfected cell, establishes that the vector can site-direct insertion of a FIX gene into the short arms of human group D and/or G chromosomes.
FIG. 4 shows the result of Western blotting of samples from positively transformed cells. F3-F23 are 6 different positive cell strains, “−” denotes negative control.



DETAILED DESCRIPTION OF THE INVENTION 
How to introduce a normal FIX gene into a patient's body to substitute the deficient FIX gene is the key problem of gene therapy for Hemophilia B. At present, vectors used for FIX gene therapy research are mainly virus vectors, such as retrovirus vectors, adenovirus vectors and adeno-associated virus vectors.
Kay et al carried out experiments of gene therapy on a dog with Hemophilia B. (refer to Kay M A, Rothenberg S, Landen C N, et al. In vivo gene therapy of hemophilia B: sustained partial correction in factor IX deficient dogs. Science 1993; 262: 117-119). The research suggests that the retrovirus (RV) transferred gene in the liver of big animals possibly has a long expression time, but the amount of expression is low. It was also found that just 0.1%-1% of liver cells of mouse are transformed by RV inexperiments performed in mice (refer to Kay M A, Li Q T, Liu J J, et al. Hepatic Gene Therapy: Persistent expression of human a 1 antitrypsin in mice after direct gene delivery in vivo. Hum Gene Ther 1992; 3:641-647). This is mainly because retroviruses do not integrate into the genome of non-dividing cells. So it is necessary to do perform partial hepatic removal to induce the remaining hepatic cells to divide when hepatic cells are used as target cells for gene therapy. Relatively low gene transfer efficiency of RV in vivo and low retransplanting efficiency of cultured cells transformed in vitro lead to low FIX expression that cannot thoroughly correct the phenotype of Hemophilia B. (refer to Lieber A. Peters M J, Gown A, et al. A modified urokinase plasminogen activator induces liver regeneration without bleeding. Hum Gene Ther 1995; 6:1029-1037; Bowles N E, Eisensmith R C, Mohuiddin R, et al. A simple and efficient method for the concentration and purification of recombinant retrovirus for increased hepatocyte transduction in vivo. Hum Gene Ther 1996; 7:1735-1742; Bosch A, McCray P B, Jr. Chang SMW, et al. Proliferation induced by keratinocyte growth factor enhances in vivo retroviral-mediated gene transfer to mouse hepatocytes. J Clin invest 1996; 98:2683-2687). Though retroviral vectors can integrate stably into the genome of target cells, retroviruses only infectdividing cells and further have the potential danger of insertional mutagenesis.
Recombinant Adeno-associated virus (rAAV) vectors are more efficient among viral vectors used for gene therapy of Hemophilia B. rAAV vectors not only express FIX cDNA s efficiently and stably in the receiving cell, but many researchers appreciate that such vectors do not contain viral genes and so are unlikely give rise to a cytotoxic T Lymphocyte response (refer to Jooss K, Yang Y, Fishe K J, et al. Transduction of dendritic cells by DNA viral vectors directs the immune response to transgene products in muscle fibers. J Virol 1998;72:4212-4223). Kay and his colleagues carried out pre-clinical research on mice and a Hemophilia B dog and clinical experiments in some patients (refer to Kay M A, Mannno C S, Ragni M V, et al. Evidence for gene transfer and expression of factor IX in Hemophilia B patients treated with an AAV vector. Nat Genet 2000; 24:257-261). Nevertheless rAAV vectors require further research for human gene therapy because of low titer, complicated preparation and poorlong-term expression. In recent years, nonviral vectors have been developed and used such as liposomes and microcapsules (refer to Hortelano G, Xu N, Vandenberg A, et al. Persistent delivery of factor IX in mice: gene therapy for Hemophilia using implantable microcapsules. Hum Gene Ther 1999;10(8);1281-1288).
In recent ten years, many effective measures in gene therapy for Hemophilia B have been taken, but no safe and stable genetic drug with one-off therapy is available. The key problem lies in that there are no safe, non immunogenic vectors that are highly efficient in transforming the target cell and and provide long expression of the therapeutic gene in the target cell.
One objective of invention is to offer a safe genetic drug for Hemophilia B therapy that provides stable expression of the therapeutic gen in a target cell.
Another objective of invention is to offer a method for preparation of the above-mentioned genetic drug.
Gene drug for Hemophilia B therapy offered by this invention contains vector-FIX recombinant whose leading sequence of objective gene is DNA sequence without important physiological function-related gene on short arm of human group D, G chromosomes or its homologous DNA sequence.
The Inventor has found two families with normal phenotype carrying additional bisatellite microchromosome (BM) that is stably inherited among two and three generations in two families, respectively, and causes no harm to a human body. The present invention is made by dissecting the BM origins and constructing a human-originated gene vector. To date, 17 such families have been reported, both in China and elsewhere, but nobody has put forward any similar idea of using BM as a gene vector.
In this study, the Inventor confirmed using the Fluorescence In Situ Hybridization technique that the BM came from the short arms of human group D chromosomes (chromosomes 13, 14 and 15) and G chromosomes (chromosomes 21 and 22), which are include abundant ribosome DNA (rDNA) that is abundant in the nucleolus organelle and that have polymorphism in length (different contents of rDNA). Gene transcription of the rDNA section during interphase of cell division is very active.
The Inventor infers that a gene in these sites will have high, stable and harmless expression if special DNA fragments isolated from BM can be used as a leader sequence of a therapeutic gene. The Inventor further infers that the therapeutic gene can be site-directed into the nucleolus organelle if sections of the short arms of human group D, G chromosomes are used in constructing a gene vector. The examples following provide proof of principle of this invention.
The inventor at first constructed a pUC19 library of BM specific DNA fragments through micro-dissection and micro-cloning techniques, from which single copy fragments from the BM and p arms of human group D and G chromosomes were selected by Southern blotting and confirmed by the FISH technique. A 120 kb specific DNA fragment (BMSF) was acquired using single copy fragments as probes to screen a human PAC genome and DNA library. The fragments also come from the BM and short arms of human group D and G chromosomes as proved by the FISH technique (FIG. 1). Analysis of the sequence of the BMSF did not identify any important physiologic function and thus it was concluded that it is safe to use the BMSF sequence as a target site for insertion of a desired DNA fragment. The Inventor further used specific DNA fragments of 120 kb or even smaller to construct a gene vector.
The Inventor considers it within the scope of the invention to use DNA sequences lacking important physiologic function-related genes on the short arm of human group D and G chromosomes or a homologous DNA sequence as a targeting sequence of a desired gene. Preferred embodiments of the gene vector target the therapeutic gene in site-directed fashion into the short arms of human group D and/or G chromosomes and the therapeutic gene can thus be expressed with high efficiency.
A “genetic drug” or “gene drug” according to the invention can also comprise reagents for assisting introduction of the therapeutic gene vector into a host cell, and especially in a site-directed fashion, such as liposomes and proteins particular to targeting the host cell. According to the targeting sequence of the therapeutic gene, different forms of vectors can be constructed by the existing technique. The methods of constructing vectors and introducing therapeutic genes into vectors are common.
On the base of obtaining a therapeutic gene leader sequence, different vectors can be constructed. The methods for constructing vectors are routine.
Example 1 provides a vector-FIX recombinant as shown in SEQ NO.1, in which a targeting sequence of 3.8 kb is obtained from BMSF. A Neor gene for positive selection is inserted into a site at nucleotide 1500 of the leader sequence of the therapeutic gene, which is divided into two arms of 1.5 kb and 2.3 kb, respectively, using thymidine kinase (TK) as a negative screening gene. The Insertion position of the FIX therapeutic gene is at nucleotide 5910. A therapeutic gene may be inserted in either the forward or reverse direction, and the example of invention below adopts the latter. FIG. 2 is construction of vector-FIX recombinant.
The Example provides detailed description of the process of constructing an embodiment of the vector using specific DNA sequence of 3.8 kb isolated from short arms of human group D and G chromosomes as a targeting sequence of a desired gene. The vector-FIX recombinant obtained was deposited in the China Typical Culture Conservation Center (China.Wuhan Wuhan University, post code: 430072) on 29th of Sep., 2000, numbered: CCTCC M2000031. The deposit is named Escherichia coli JM109/JH/pNS FIX.
The vector carrying a therapeutic gene can be transferred into cultured human cells, such as fibroblast cells and blood stem cells, which also can be used as a gene therapy agent for treatment of hemophilia B. The Example of this invention describes an embodiment of such a delivery method using existing techniques.
In summary, to correct clinical symptoms caused by a deficient gene, cultured human cells transfected with a therapeutic gene the drug composition comprising the therapeutic gene vector can be introduced into a patient's body by means of hypodermal embed (infusion), electroporation or intravenous injection or liposome packaging and thereby the therapeutic gene can be stably expressed.
Effective Experiments of Gene Therapy:
Experiment in vitro
The recombinant human coagulatant FIX-vector was linearized and transfected into HT1080 cell by electroporation, then the positive transfected cell strain was obtained by positive and negative screening. The foreign gene integration was proved by amplifying FIX cDNA flanking an intron. The primer pair pNSNeo at the Neo gene and 876-7R at the outside of the targeting arm were used to amplify gDNA from positive transfected cells, and a 2.3 kb fragment was obtained. Sequencing analysis indicated the integration is site directed. Two positive cell strains having the FIX gene integrated into the short arms of human chromosomes 13 and 21 has fluorescence signal by FISH, which suggests site directed insertion, too. Results of assays of of FIX activity in positively transfected cultured cells reveals that activity of FIX is 3.56 μg/106 cells/24 h and the cells can express stably after passaging in vitro for 449 days. Expression of the FIX product has been proven by Western blotting.
Experiment in vivo
The targeting vector of the invention is a human-source vector. There is species diversity between human beings and animals, especially for the gene drug of the invention. Were one to carry out a targeting experiment in an animal's body, it is uncertain if there is an appropriate integration site as expected and so it is improper to evaluate efficiency and stability of the vector of the invention in an animal. It is thus unnecessary to do any animal experiment in vivo.
Toxicity Evaluation of a Gene Drug
The gene drug of the invention is administered to mice via the tail vein, at 450 μg/Kg, up to 100 times as high as the single dosage of an adult by body weight. The experiment result suggests that the drug lacks toxicity and is safe when administered by intravenous injection.
The gene drug for Hemophilia B therapy offered by the invention uses DNA sequences that lack any gene having any important physiologic function and located on the p arms of human group D and G chromosomes, or its homologous DNA sequence, as a sequence to target a desired gene to a specific site. These sequences are used to construct a gene vector. Undoubtedly, the gene vector thus constructed can a therapeutic gene it contains in a site-directed manner into a special target site of the host cell. As DNA fragments of the target site do not have any important physiological function-related gene, the introduction of the therapeutic gene is safe.
In summary, because the gene therapy drug for Hemophilia B offered by the invention adopts targeting sequence of a human-source gene to construct a vector having a therapeutic gene, it has the characteristics below:

    
    
        (1) Stability of expression of the therapeutic gene is good. Because the vector with the therapeutic gene can site-specifically insert the therapeutic gene into the short arms of human group D and G chromosomes, the therapeutic gene can be stably inherited with chromosomes.
        (2) The security is good. The target site of the therapeutic gene does not have an important physiological function-related gene, which proves the target site is safe. Moreover, the vector can site-specifically insert a therapeutic gene into a safe target site of a cell, as has been confirmed by FISH (FIG. 3), avoiding random insertion mutation and this danger of a wild-type virus vector. Therefore expression of the therapeutic gene at the target site is safe. Though the present specification does not provide clinical cases of gene therapy, cases found by the Inventor and other researchers both in China and in other countries can prove its security from another angle.
        (3) Expressive efficiency is high. First, the vector of the invention contains a targeting sequence from the short arms of human group D and/or G chromosomes, correspondingly, it has 10 target sites in a human genome with an inserting efficiency 5-10 times higher than that of other vectors. Second, the targeting sequence is from the short arms of human group D and/or G chromosomes showing active gene transcription, so the therapeutic gene introduced into the target position can be expressed with high efficiency.
        (4) It has no immunogenicity. The vector is from a human source, so it will not generate immunogenicity in a human body.
    
    


The examples of the invention are only illustrative of the invention and are not to be considered limitations of the invention.
EXAMPLE ONE
The Preparation of Gene Targeting Sequence
Obtaining a Clone of Gene Leading Sequence-PAC
1.1 BM specific pUC19 library constructed by micro-dissection, PCR and microclone methods (see, Deng H X, Yoshiura K, Dirks R W, et al. Hum Genet 1992, 89:13).
1.2 Obtaining and Identifying of BM Specific pUC19
(1) Preparation of Bacterial Colony Matrix Membrane
Draw 14×14 squares on two nylon membranes marked with A or B signal, and place the two membranes into two dishes containing solid LB medium, respectively, and pick at random 14×12 white colonies from the library dishes and put it into the relevant wells, including 100 ng single-copy DNA as a positive control in row 13, 100 ng gDNA as a negative control in row 14. Then the two dishes are incubated at 37° C. for 10-12 hrs. After taking the membrane out of the dishes, conserve B membrane at 4° C. and treat the A membrane on a filter soaked with the following solution and procedure, 10% SDS, 5 min; 0.5N NaOH/1.5M NaCl, 3 min; 1.5 M NaCl/0.5M Tris.HCl, 3 min; 2×SSC/0.2 M Tris.HCl, 10 min; vacuum dry at 80° C. for 2 hrs and then conserve it for use at 37° C.
(2) Preparation of gDNA Probe
Sample 50-75 ng of gDNA, make up in ddH2O to 11 ml and boil at 100° C. for 10 min to denature, and perform a random primer labeling reaction following the recipe below.
















2 m M d NTP (d ATP-),
3 μl,



primer mixtture,
2 μl



Klenow enzyme,
1 μl



α-32 P-d ATP,
3 μl










vortex the mixture and incubate at 37° C. for 30 min. Add 8 μl stop mixture to the system and pass it through a G-50 column to purify the probe.
(3) Hybridization
The membrane is soaked in 2×SSC solution for 10 min, then slightly wiped to remove the colony pieces on the surface of membrane. Then pre-hybridize in 5 ml hybridization buffer for 30 min. According to the value of liquid scintillation counting, sample the probe solution in the proportion of 1.2×106 cpm/ml hybridization buffer and boil at 100° C. for 10 min to denature, and then add 5 ml fresh hybridization buffer to hybridize with the colony matrix membrane at 65° C. for 12 hrs. Wash the membrane as follows: 2×SSC/0.1% SDS, at room temperature for 10 min; 2×SSC/0.1% SDS, 65° C. for 10 min; 0.1×SSC/0.1% SDS, 65° C. for 10 min, autoradiograph at −70° C. If the signal of hybridization has no or only a slight signal, it is considered as a signal of a single copy.
(4) Sequence and Identification by Southern Blotting
Pick the clone on the Membrane B without hybridization signals to amplify at small scale and then extract plasmid DNA for sequencing. Compared to data of Genbank; it is a single copy if the sequences have no similarity. Finally, digest the plasmid with EcoRI and separate the insert DNA and label it with α-32P-dATP by the random primer method, and hybridize with the gDNA digested with EcoRI enzyme on the nylon membrane using the methods described above, one or two bands of hybridization indicate the detected DNA is single copy.
1.3 Obtaining and Identifying the Specific PAC Clone of BM and Chromosomal Short Arm of Group D and/or G
(1) Obtaining of Positive Clone Number by Scanning Human PAC gDNA Library
Label the 260 bp single copy probe P8-7 by random primer method with α-32P-d ATP; purify using a G-50 column (medium size); conserve at 4° C. for use; soak 7 pieces of membranes with 2×SSC buffer for 10 min; pre-hybridize at 55° C. for 3 hrs; denature the probe at 100° C. for 10 min; hybridize with PAC membrane by adding 50 ml hybridization buffer at the proportion of 4.6×105 cpm/ml; wash membrane: 2×SSC, RT for 10 min once, 2×SSC/0.1% SDS 65° C. 10 min twice; autoradiograph at −70° C. for 12 hrs; develop X-ray film; read the positive clone number following the introduction.
(2) Pick the Positive Clone Number at Random on the 5 Different Plates and Buy PAC Clone
1.4 PAC DNA hybridized with the metaphase cells is confirmed as coming from short arm of chromosomes of Group D and/or G by FISH (see FIG. 1).
The methods for doing so can be found in J. Sambrook et al. Molecular Colony. Second Edition. Cold Spring Harbor Laboratory Press. 1989
2. Obtaining a Gene Targeting Sequence DNA
Main materials, β-agarase (Bio-Labs), Not I restriction enzyme, Agarose
(1) Digested PAC169 with Not I enzyme
(2) Separate the insert DNA (about 120 kb in size) by PFGE method
Pulse electrophoresis conditions:

    
    
        Electrode buffer: 0.5× TBE, High strength Analytical Grade Agarose (Bio-Rad, Low Melting point Agarose LMP) 1%,
        Switch Time: 2 sec - - - 15 sec.
        Electrophoresis Time: 18 hrs,
        voltage: 6 V/cm,
        Angle: 120°,
        Temperature: 14° C.
    
    


(3) Stain with ethidium bromide (EB) solution (0.2 μg/ml) for 30 min after electrophoresis and cut out the 3.8 kb (120 kb) gel band according to a molecular weight marker with a sterile knife.
(4) Digest the gel with β-agarase and precipitate the DNA with alcohol
EXAMPLE TWO 
Preparation of a recombinant gene vector-FIX gene drug for hemophilia B.
1. construction of gene vector and transduction of therapeutic gene
1.1 construction of the gene vector
1.1.1 Digest PAC DNA with Nsi I and Stu I (blunt end) enzymes, recover the 3.8 kb DNA fragment with normal agarose gel and purification by electroelution.
1.1.2 Digest pGEM-TK vector DNA with Hind III enzyme and fill-in the ends to blunt with Klenow enzyme and yield blunt ends.
1.1.3 Further digest the product of Hind III repair with NsiI enzyme.
1.1.4 Ligate the purified 3.8 kb/Nsi I+Stu I enzyme product and the product digested with HK+Nsi I at 16° C. for 17 hrs.
1.1.5 Transform E. coli JM109 with the ligation product, and culture in a petri dish on Amp+ medium at 37° C. for 18 hrs.
1.1.6 Pick the single copy clone at random and double enzyme-cut with HindIII+Nsi I enzymes and identify the positive clone.
1.1.7 Ligate Neo/Xba I+Nhe I and pGEM-TK-3.8 KB/Nhe I to construct pNS2 gene vector.
1.2 The transduction of FIX gene
1.2.1 Clone FIX gene (CDS) into pcDNA 3.1(−)
1.2.2 Design TPCF and TPCR primers and amplify FIX gene and expression component (CMV promoter and BGH poly A signal) to load the two ends with AvrIII enzyme digestion sites; the sequence of primer is

    
    
        TpcF: ATgCATCCTAggggAggTCgCTgAgTAgTg (SEQ ID NO: 2)
        
            Avr II
        
        
        TpcR; ATgCATCCTAggTACCCCTAgAgCCCAg (SEQ ID NO: 3)
        
            Avr II
        
        
    
    


1.2.3 Digest the FIX gene with Avr II enzyme and ligate it's the expression components (CMV promoter and BGH polyA signal) to the pNS2 vector digested with Nhe I enzyme.
1.2.4 The ligated product was transformed into JM109 E. coli, and the recombinant strain (Collection number is CCTCC M200031) was obtained.
Methods for the above steps may be found in J. Sambrook et al. MolecularCloning. Second Edition. Cold Spring Harbor Laboratory Press. 1989
2. Extraction of gene vector DNA
2.1 Materials:
2.1.1 QIAGE Plasmid Maxi Kit
2.1.2 Medium: liquid LB

    
    
        Tryptone 5 g
        Yeast extract 2.5 g
        NaCl 2.5 g
        ddH2O adjust the volume to 500 ml
        Autoclave
    
    


2.1.3 Ampicillin: 100 mg/ml (=1000×)
2.2 Methods
1) Pick a single positive clone into 3 ml LB medium (Amp+), incubate at 37° C. at 250 rpm for 1 hr.
2) Add 100 μl primary culture to 100 ml LB medium (Amp+), incubate at 37° C. at 250 rpm for 16 hrs.
3) Centrifuge at 600 g rotor speed for 15 min at 4° C. to obtain a pellet.
4) Resuspend the pellet with 10 ml Buffer P1.
5) Add 10 ml Buffer P2 and invert slightly 6 times for 5 min at room temperature.
6) Add 10 ml pre-cooled Buffer P3, invert slightly 6 times on ice for 20 min.
7) Centrifuge at 20000 g at 4° C. for 30 min.
8) Quickly transfer supernatant to a 40 ml of high-speed centrifugation tube and centrifuge at 20000 g at ° C. for 15 min.
9) Equilibrate a QUIAGEN Tip 500 column with 15 ml Buffer QBT.
10) Filter the supernatant through the QUIAGEN Tip 500.
11) Wash the column with 15 ml Buffer QC.
12) Elute with Buffer QF and collect the elution solution.
13) Add 10.7 ml (0.7× volume) isopropanol to elution solution and mix up.
14) Centrifuge at 15000 g at 4° C. for 30 min
15) Dispose of the supernatant and add 5 ml 70% ethanol and centrifuge at 4° C., 15000 g for 10 min to wash DNA precipitation.
16) Dispose of the ethanol and air-dry the DNA for 10 min, and then dissolve the DNA precipitate with TE buffer.
The recombinant of gene vector-FIX has been deposited in the Chinese Type culture Collection Center (Wuhan University, China, postcode: 430072) on 29th of Sep., 2000. The deposit number is CCTCC M200031. The name is Escherichia coli JM109/JH-4/PNS-FIX.
EXAMPLE THREE
The recombinant of gene vector-FIX of Example 2, comprising a FIX gene, was transduced into HT1080 host cells and expressed. The transformed HT1080 cells were preserved in the Chinese Type Culture Collection Center (Wuhan University, China, postcode: 430072) on the 18th of Aug., 2000. The deposit number is CCTCC M20005. The cell strain is named human fibrosarcoma cell strain/JH-1/FIX.
1. MATERIAL
1.1 Cell: HT1080

    
    
        Medium; high sugar DMEM+10% FBS (HT1080), EMEM+10% FBS
    
    


1.2 Electroporation device: Bio-Rad Company
2. Methods
1) Culture the cells in a 75 cm2 culture bottle and grow up to 70%-80% confluence.
2) Harvest the cells and wash twice with HeBs buffer and count the number of cells.
3) Centrifuge at 15000 rpm at 4° C. for 10 min.
4) Resuspend the cells with appropriate amount of HeBs buffer to a cell concentration of 106-107 cells/ml.
5) Add 0.8 ml cell supernatant and 10 ug DNA vector together into a 4.0 ml cuvette.
6) Electric shock at 260V voltage, 550 μF capacitance for 11-13 msec.
7) Transfer electric shocked cells into 75 cm2 culture bottle and add 14 ml culture medium with double antibiotics and culture at 37° C., 5% CO2 for 24-48 hrs.
8) Add G418 to a final concentration of 300 μg/ml to select positively transfected cells, change medium each 2-3 days and add G418 again, using normal cells as a control.
9) Count living clone numbers in the transfected cell cultures when all of the normal cells die in seven days, and change the amount of G418 to 150 ug/ml to maintain the culture.
10) Continue to screen transfected cells with final concentration 500 ng/ml G418.
11) Assay expression activities of the transferred gene when most of the cells die and add 250 μg/ml G418 to maintain the culture.
3. Result
Transfect the vector to transfer FIX gene to HT1080 cells with electroporation method and attain the positive cell strain after positive and negative screening, the site-directed insertion of gene is confirmed by FISH (see FIG. 3).
Activities of FIX gene increase from 0.1 ug/ml to 4.27 μg/ml compared to negative control. Furthermore, the amount of FIX expression is still 3.15 μg/ml after 144 days (see Table 1). The products of FIX expression are confirmed by Western Blotting (see FIG. 4).







TABLE 1







Activity detection of FIX gene (μg/106 cells/24 hr)










Days after transformation
clone F23














35
4.27



72
4.39



100
4.6



111
3.95



139
4.0



144
3.15



449
3.56










The Certification of Safety

1. The Case of Safety in Population of People
The Inventor has been engaged in research on human and medical genetics since 1973; he found and identified 732 karyotypes which were found in the world submitted by 470 clinical cytogenetists in 189 labs around China. Among these karyotypes there are 41 karyotypes which involve short arms of Group D and/or G chromosomes. No matter how the fragment translocated to short arms of Group D and/or G chromosomes originated from which chromosome of chromosome 1-22, or what different lengths of fragment from the same chromosome containing one to thousands of genes, the phenotypes of carriers themselves are normal. This finding indicates that genes translocated to chromosomal short arm in Groups D and G can be expressed normally. Therefore, it is thought safe to use the short arm of Group D, G chromosomes as a target site of gene therapy.

    1. Karyotype: 46,XX,t(1;12;22;15;11;8) (1qter→1p11::8p23→8pter;12pter→12q11::1p11→1pter;22qter→22p11::12q11→12qter;15pter→22p11→22pter; 11pter→11q21::15q15→15qter;8qter→8p23::11q21→11qter)
    
        phenotype: female, 28 years old, normal phenotype carrier
        material provider: Wu subing, Cytogenetics laboratory, Department of gynecology and obstetrics, first affiliated hospital of Zhongshan Medical University, Guangzhou
    
    
    2. Karyotype: 46,XY,t(1;13) (1pter→1q32::13p11→13qter→13p11::1p32→1qter).
    
        Phenotype: female, 24 years old, normal phenotype carrier
        Material provider: Xiao Chen, Department of biology, Harbin Medical University, Harbin 150086
    
    
    3. Karyotype: 46, XX, t(2;15) (2pter→cen→15qter;2qter→cen→15pter)
    
        phenotype: female, 26 years old, normal phenotype carrier
        material provider: Guo Yuping, et al. Cytogenetics Department, Jiangxi provincial gynecology and obstetrics hospital, Nanchang 330006, Jiangxi province
    
    
    4. Karyotype: 46,XY,t(2;21) (2pter→cen→21pter; 2qter→cen→21qter)
    
        phenotype: male, 32 years old, normal phenotype carrier
        material provider: Kang Guoqing, et al. Department of genetics, the second affiliated hospital of Shangxi Medical College, Taiyuan 030001
    
    
    5. Karyotype: 46,XY,t(3;21) (2qter→cen→22pter; 3qter→cen→22qter)
    
        phenotype: male, 26 years old, normal phenotype carrier
        material provider: Gao Yun, Department of toxicology, Bingzhou municipal Medical College, Bingzhou 256603, Shangdong province
    
    
    6. Karyotype: 46,XY,t(3;22) (3pter→cen→22pter; 3qter→cen→22qter)
    
        phenotype: male, 29 years old, normal phenotype carrier
        material provider: Shi Huajin. Department of genetics, Jingzhou Women and Baby hospital, Jingzhou 121000, Liaoning province
    
    
    7. Karyotype: 46,XX,t(4;15) (4pter→4p13::15p13→15pter;15qter→15p13::4p13→4pqter)
    
        phenotype: female, 28 years old, normal phenotype carrier
        material provider: Zhou Ling, et al. Laboratory of genetics, the Wuhan Children hospital, Wuhan 430016, Hupei province
    
    
    8. Karyotype: 46,XY,t(4;21) (4pter→4p15::21p11→21 pter;21qter→21p11::4p15→4pqter)
    
        phenotype: female, 25 years old, normal phenotype carrier
        material provider: Xu Jinfang, et al. Laboratory of genetics, the sixth people's hospital of Shanghai, Shanghai 200000
    
    
    9. Karyotype: 46,XY,t(4;14) (4qter→4-q31::14p11→14pter;14qter→14p11::4q31→4qter)
    
        phenotype: male, normal phenotype carrier
        material provider: Zhou Mingjun, et al. Xuchang Municipal Central Hospital, Xuchang 161000, Henan province
    
    
    10. Karyotype: 46,XY,t(4;14) (4qter→4q35::14p11→14pter;14qter→14p11::4q35→4qter)
    
        phenotype: male, 27 years old, normal phenotype carrier
        material provider: Zhang Xiuquan, et al. Hushan Municipal Women and Nursling Hospital, Hushan 528000, Guangdong province
    
    
    11. Karyotype: 46,XX,t(6;22) (5qter→5q13::22p11→22pter; 22qter→22p11::5q13→5qter)
    
        phenotype: female, 32 years old, normal phenotype carrier
        material provider: Zhao Jianping, Anyang Municipal Women and Nursling Hospital, Anyang 455000, Henan province
    
    
    12. Karyotype: 46,XY,t(6;22) (6pter→cen6→22qter; 6qter→cen22→22pter)
    
        phenotype: male, 25 years old, normal phenotype carrier
        material provider: Zhu Xinxia, et al. Laboratory of cytogenetics, Department of Gynecology and Obstetrics, Number 88 Hospital, Taian 271000, Shangdong province
    
    
    13. Karyotype: 46,XY,t(6;22) (6qter→6p21::22p11.2→22pter; 22qter→22p11.2::6q21→6pter)
    
        phenotype: male, 33 years old, normal phenotype carrier
        material provider: Yang Qinglan, Department of Gynecology and Obstetrics, affiliated hospital of Bingzhou Medical College, Bingzhou 256603, Shangdong province
    
    
    14. Karyotype: 45,XX,t(7;21) (7qter→7p22::21p12→21qter)
    
        phenotype: female, 23 years old, normal phenotype carrier
        material provider: Sun Qingji, et al. Laboratory of genetics, the Wuhan Children hospital, Wuhan 430016, Hubei province
    
    
    15. Karyotype: 46,XY/46XX,t(7;14) (7pter→7q11::14p11→14pter;14qter→14p11:7q11→7qter)
    
        phenotype: male, 28 years old, normal phenotype carrier
        material provider: Li Luyun, Xia Jiahui, et al. State Key Laboratory of Medical genetics (Human Medical University), Changsha 410078, Hunan province
    
    
    16. Karyotype: 46,XY,t(8;14) (8pter→8p21::14p12→14pter;14qter→14p12::8p13→8pter)
    
        phenotype: male, 27 years old, normal phenotype carrier
        material provider: Shi Huajin, et al. Department of genetics, Jingzhou Women and Baby hospital, Jingzhou 121000, Liaoning province
    
    
    17. Karyotype: 46,XY,t(9;14) (9pter→cen→14pter; 9qter→cen→14qter)
    
        phenotype: male, 28 years old, normal phenotype carrier
        material provider: Cheng Qiuyun, et al. Department of reproduction medicine, first affiliate hospital of Hengyang medical college, Hengyang 421001, Hunan province
    
    
    18. Karyotype: 46,XY,t(9;22) (9pter→9p13::22p12→22pter;22qter→22p12::9p13→9pter)mat
    
        phenotype: female, 31 years old, her mother, a young sister of her, a young brother of her and her son have the same phenotype as her, that is normal phenotype carrier
        material provider: Li Luyun, Xia Jiahui, et al. State Key Laboratory of Medical genetics (Hunan Medical University), Changsha 410078, Hunan province
    
    
    19. Karyotype: 46,XX,t(9;14) (9pter→9q12::14p12→14pter; 14qter→14p12::9q12→9qter).
    
        Phenotype: female, 32 years old, normal phenotype carrier
        Material provider: Sun Yanyang, et al, Department of biology, Harbin Medical University, Harbin 150086
    
    
    20. Karyotype: 46,XX,t(9;15) (9pter→9q21::15p12→15pter; 15qter→15p12::9q21→9qter)mat.
    
        Phenotype: female, 36 years old, normal phenotype carrier
        material provider: Zhu Guizhen, et al. Laboratory of cytogenetics, Department of Gynecology and Obstetrics, Number 88 Hospital, Taian 271000, Shangdong province
    
    
    21. Karyotype: 46,XX,t(10;13) (10pter→10q24::13p11→13pter; 13qter→13p11::10q24→10qter)
    
        Phenotype: female, 28 years old, normal phenotype carrier
        Material provider: Yan Dunqing, Department of Gynecology and Obstetrics, affiliated hospital of Qingdao Medical College, Qingdao 266003, Shangdong province
    
    
    22. Karyotype: 46,XX,t(10;13) (10pter→10q24::13p12→13pter; 13qter→13p12::10q24→10qter)
    
        Phenotype: female, 29 years old, normal phenotype carrier
        Material provider: Zhang Yinru, et al. Department of neurology First affiliated hospital of Zhongshan Medical University, Guangzhou 510080, Guangdong province
    
    
    23. Karyotype: 46,XX,t(11;14) (11pter→cen→11qter→cen→14qter)
    
        material provider: Wang Zhiyong, Department of genetics, Zhacheng County people's hospital, Zhacheng County 476200, Henan province
    
    
    24. Karyotype: 46,XX,t(11;21) (11pter→11p11::21p11→21pter; 21qter→21p11::11p11→11pter)
    
        Phenotype: female, 26 years old, normal phenotype carrier
        material provider: Zheng Jun, et al. Department of genetics, Shanxi provincial women and nursling hospital, Xian 710003 Shanxi province
    
    
    25. Karyotype: 46,XX,t(11;15) (11pter→11q13::15p12→15pter; 15qter→15p12::11q13→11qter)
    
        Phenotype: male, 23 years old, normal phenotype carrier
        material provider: Yang Ruifang, et al. Medical center of Obstetrics, affiliated hospital of Shandong Medical University, Jinan 250012, Shandong province
    
    
    26. Karyotype: 46,XX,t(12;14) (12pter→cen→14pter::12qter→cen→14qter)
    
        Phenotype: female, 28 years old, normal phenotype carrier
        material provider: Han Weitian, et al. Department of eugenics, Liaoning provincial institue of family planing, Shenyang 110031, Liaoning province
    
    
    27. Karyotype: 46,XX,t(13;16) (13pter→13p11::16p11.2→16pter;16qter→16p11.2::13p11→13pter
    
        Phenotype: female, 27 years old, normal phenotype carrier
        material provider: An Songlan. Department of genetics, Dalian municipal gynecology and obstetrics, Dalian 110078, Liaoning province
    
    
    28. Karyotype: 46,XY/46,XX,t(13;13) (13qter→13p12:;13p12→13qter)
    
        Phenotype: male, 39 years old, normal phenotype carrier
        material provider: Li Luyun, Xia Jiahui, et al. State Key Laboratory of Medical genetics (Hunan Medical University), Changsha 410078, Hunan province
    
    
    29. Karyotype: 46,XY,t(14;18) (14pter→cen→18pter;14qter→cen→18qter)
    
        Phenotype: male, 30 years old, normal phenotype carrier
        material provider: Wang Sugui, et al. Beijing Institute of family planing technology guidance, Beijing 100006
    
    
    30. Karyotype: 46,XX,t(14;15) (14pter→14q13::15p13→15pter; 15qter→15p13::14q13→14qter)
    
        Phenotype: female, 28 years old, normal phenotype carrier
        material provider: Li Luyun, Xia Jiahui, et al. State Key Laboratory of Medical genetics (Hunan Medical University), Changsha 410078, Hunan province
    
    
    31. Karyotype: 46,XX,t(15qter→cen→22qter)
    
        Phenotype: female, 27 years old, normal phenotype carrier
        material provider: Li Luyun, Xia Jiahui, et al. State Key Laboratory of Medical genetics (Hunan Medical University), Changsha 410078, Hunan province
    
    
    32. Karyotype: 46,XY,t(15;18) (15pter→cen=18pter;15qter→cen→18qter)
    
        Phenotype: male, 30 years old, normal phenotype carrier
        material provider: Ren Guoqing, et al. Beijing Institute of family planing technology guidance, Beijing 100006
    
    
    33. Karyotype: 46,XX,t(15;20) (15pter→cen→2pter; 15qter→cen→2qter)
    
        Phenotype: female, 26 years old, normal phenotype carrier
        material provider: Wang Xin, et al. Laboratory of genetics, department of obstetrics, the second affiliated hospital, Hunan Medical University, Changsha 410011, Hunan province
    
    
    34. Karyotype: 46,XX,t(15;22) (15pter→15p11::22p13→22pter;22qter→22p13::15q11→15qter)
    
        Phenotype: female, 27 years old, normal phenotype carrier
        material provider: Hu Shengdi, Department of genetics, Hainan provincial people's hospital, Haikou570011, Hainan province
    
    
    35. Karyotype: 46,XX,t(15;22) (15pter→15q22::22p11→22pter;22qter→22p11::15q22→qter)
    
        Phenotype: female, 29 years old, normal phenotype carrier
        material provider: Li Murou, Department of genetics, Xinjiang Medical College, Urumchi 830054
    
    
    36. Karyotype: 46,XY,t(16;21) (16pter→16q11::21p11→21pter;21qter→22p11::16q12→16qter)
    
        Phenotype: male, 29 years old, normal phenotype carrier
        material provider: Zhang Huifang, et al, Institute of family planing technology of Guangdong, Guangzhou510080, Guangdong province
    
    
    37. Karyotype: 46,XX,t(18;21) (18pter→cen→21pter; 18qter→cen→21qter)
    
        Phenotype: female, normal phenotype carrier
        material provider: Shi Huajin, et al. Laboratory of genetics, Jingzhou women and nursling hospital, Jingzhou 121000, Liaoning province
    
    
    38. Karyotype: 46,XX,t(18;21) (18pter→18q11::21p12→21pter;21qter→22p12::18q11→18qter)
    
        Phenotype: female, 26 years old, normal phenotype carrier
        material provider: Li Xiulin, et al, laboratory of genetics, department of pediatrics, first affiliated hospital of Chinese medical university, Shenyang 110011, Liaoning province
    
    
    39. Karyotype: 45,X,dic(Y;13) (Ypter→Yp1200::13p11→cen→13qter)
    
        Phenotype: male, 4 years old, normal phenotype carrier
        material provider: Xia Jiahui, et al. State Key Laboratory of Medical genetics (Hunan Medical University), Changsha 410078, Hunan province
    
    
    40. Karyotype: 46,XY,t(Y;15) (15pter→15p12::Yq12→Ypter)pat.
    
        Phenotype: male, 4 years old, normal phenotype carrier
        material provider: Xia Jiahui, et al. State Key Laboratory of Medical genetics (Hunan Medical University), Changsha 410078, Hunan province
    
    


Abnormal chromosome carriers above showed no abnormal syndrome, which explains that not only nucleolus tissue can receive foreign genes but also allows foreign genes to express normally.
2. Toxicity Test
Acute Toxicity Studies of Gene Drug of the Invention
The objective of this study is to investigate the acute toxicity reaction and the conditions of death upon intravenous injection of a gene drug provided by this invention.
Materials:
(1) Animals
Kunming strain mice (n=40); body weight 20.4±1.1 g, the number of female and male is equal. All of the experimental animals and feeds were provided by the Experimental Animal Department of Xiangya Medical School, Central South University. The mice are of eligible certification of medical experiment animals issued by the administrative committee of Hunan provincial medical experiment animals.
2 Drugs
Gene drugs were prepared as provided in this invention. The sterile water is made up to 11.25 μg/ml injection before experiment.
Method
Pretest: Among 10 little white mice, the number of female and male mice is equal. The gene drug was injected into the mice by the tail vein. The dose of gene drug for mice in pretest was 450 μg/kg (100 times high as that for adults). No toxicity appeared.
Formal experiment: According to the characteristics of the gene therapy drug, an experiment was conducted using the pretest dosage. The experimental animals were divided into two groups: test and control groups. The mice were given 450 μg/kg gene drug for test group (equal to 100 times of clinical dose for human being by body weight). The mice in control group were given by the tail vein the equal volume of distilled water (0.4 ml/10 g, each time). The reaction of the animal to the drug was observed after injection, continuous observation of 14 days, urine and stool situations of animals, common activity and death number were recorded. All of the animal were dissected and the conditions of the thoraxand abdominal cavity were observed by the end of day 14.
Results
The experiment on mice acute toxicity: The control groups mice (n=20) exhibited no abnormal activity or death through continuous observing over 14 days. The mice appear weary and immobile within 30 minutes after two injections, and subsequently resume normalactivity. Over 14 days continuous observation, no abnormality was observed in the animals' food uptake, urine and stool, or common activity. No animals died. There is no significant difference between the test group and control group through pathological examination. The results are shown in Table 2.







TABLE 2







human gene vector FIX acute toxicity test results















concentration
vein injection
times to clinical

general


Group
n
(μg/ml)
(ml/10 g/once)
dose
death number
condition
















control
20

0.4

0
normal


FIX
20
11.25
0.4
100
0
normal









CONCLUSION
The vein injection dosage of mice human gene vector FIX (equal to 100 times of clinical dose according to body weight calculation) caused no deaths. No obvious acute toxicity was indicated and the gene drug appears safe for intravenous injection administration and suitable for clinical application.

## Claims

1. A plasmid vector comprising:
a) a marker gene providing for selection for the vector in a mammalian host cell;
b) a polynucleotide segment comprising nucleotides 2841-4341 of SEQ ID NO: 1;
c) a polynucleotide segment comprising nucleotides 8678-11032 of SEQ ID NO: 1;
d) a polynucleotide segment providing for replication of the vector in a bacterial host cell; and
e) a polynucleotide segment providing for selection for the vector in a bacterial host cell.

2. The plasmid vector of claim 1 further comprising an expression cassette comprising a polynucleotide encoding Factor IX inserted between components b) and c).

3. The plasmid vector of claim 2, in which the expression cassette comprising a polynucleotide encoding Factor IX has the sequence of nucleotides 5911-8677 of SEQ ID NO: 1.

4. A method for site-directed insertion of a Factor IX encoding DNA segment into the short arm of human chromosome 13, 14, 15, 21 or 22 comprising transforming a human cell in vitro with the plasmid vector of claim 3.

5. A method for site-directed insertion of a Factor IX encoding DNA segment into a short arm of human chromosome 13, 14, 15, 21 or 22 comprising transforming a human cell in vitro with the plasmid vector of claim 2.

6. A method for expressing Factor IX comprising:
transforming human cells in vitro with the vector of claim 2,
selecting cells that express Factor IX.

7. The plasmid vector of claim 1 further comprising an expression cassette comprising a polynucleotide encoding Factor IX inserted between components b) and c).

8. The plasmid vector of claim 7, in which the expression cassette comprising a polynucleotide encoding Factor IX has the sequence of nucleotides 5911-8677 of SEQ ID NO: 1.

9. A method for site-directed insertion of a Factor IX encoding DNA segment into the short arm of human chromosome 13, 14, 15, 21 or 22 comprising transforming a human cell in vitro with the plasmid vector of claim 8.

10. A method for site-directed isertion of a Factor IX encoding DNA segment into the short arm of human chromosome 13, 14, 15, 21 or 22 comprising transforming a human cell in vitro with the plasmid vector of claim 7.

11. A method for site-directed insertion of a desired DNA segment into the short arm of human chromosome 13, 14, 15, 21 or 22 comprising transforming a cell comprising said human chromosome 13, 14, 15, 21 or 22 in vitro with the plasmid vector of claim 1.

12. The vector deposited as CCTCC M2000031.

13. A method for making a vector comprising:
i) isolating a DNA fragment of human genomic DNA from a short arm of a group D,G chromosome comprising nucleotides 2841-4341 of SEQ ID NO: 1;
ii) isolating a DNA fragment of human genomic DNA from a short arm of a group D or group G chromosome comprising nucleotides 8678-11032 of SEQ ID NO:1; and
iii) inserting the DNA fragments into a vector comprising a gene encoding a selectable marker effective in a mammalian cell.

14. The method of claim 13, in which the vector comprising a gene encoding a selectable marker effective in a mammalian cell further comprises a polynucleotide segment providing for replication of the vector in a bacterial host cell and a polynucleotide segment providing for selection for the vector in a bacterial host cell.