Patent Application: US-79874301-A

Abstract:
the gene responsible for systemic carnitine deficiency was found to be the octn2 gene involved in the transportation of organic cations . this invention enables tests for this disease by detecting whether or not the octn2 gene has a mutation . furthermore , systemic carnitine deficiency can be treated using the normal octn2 gene and its protein .

Description:
the invention shall be described in detail below , but it is not to be construed as being limited thereto . proof in mouse and human showing that the gene responsible for systemic carnitine deficiency ( scd ) is octn2 the inventors have previously isolated human cdna encoding a protein having an activity to transport carnitine in a sodium - ion dependent manner , and also the corresponding mouse cdna ( japanese patent application no . hei 9 - 260972 , japanese patent application no . hei 10 - 156660 ). the nucleotide sequences of the human and mouse octn2 cdna isolated by the inventors are shown in seq id no : 2 and 4 , respectively , and the amino acid sequences of the proteins encoded by these cdnas are shown in seq id no : 1 and 3 , respectively . the inventors drew up a working hypothesis that octn2 might be the gene responsible for systemic carnitine deficiency , and conducted experiments to prove this . the juvenile visceral steatosis ( jvs ) mouse was generated due to a mutation in the c3h . oh mouse . this jvs mouse shows symptoms similar to systemic carnitine deficiency patients , and shows an extremely low carnitine concentration within its blood and tissues . this phenotype is inherited by autosomal inheritance . from the above facts , the jvs mouse is considered to be a mouse model for systemic carnitine deficiency ( hashimoto , n . et al ., gene - dose effect on carnitine transport activity in embryonic fibroblasts of jvs mice as a model of human carnitine transporter deficiency , biochem pharmacol , 1998 , 55 : 1729 - 1732 ). the inventors examined the octn2 gene arrangement of the jvs mouse . specifically , whole rna was extracted from the kidney of a jvs homologous mouse , cdna was synthesized , jvs mouse octn2 cdna was amplified using this synthesized cdna as the template by rt - pcr , and the sequence was examined by direct sequencing . the amplification reaction by pcr was conducted as follows . for the 5 ′ side fragment , the primers monb 31 ( 5 ′- gataagcttacggtgtccccttattcccatacg - 3 ′/ seq id no : 22 ) and monb 20 ( 5 ′- cccatgccaacaaggacaaaaagc - 3 ′/ seq id no : 23 ) were prepared . then , amplification was done within a reaction solution ( 50 μl ) containing , cdna , 5 μl of 10 × kod buffer ( toyobo ), 5 μl of 2 mm dntps , 2 μl of 25 mm mgcl 2 , 0 . 5 μl of kod dna polymerase ( toyobo ), 1 μl of 20 μm monb 31 primer , and 1 μl of 20 μm monb 20 primer at 94 ° c . for 3 min , 30 cycles of “ 94 ° c . for 30 sec , 50 ° c . for 30 sec , and 74 ° c . for 1 min ”, and 72 ° c . for 10 min . as for the 3 ′ side fragment , the primers monb 6 ( 5 ′- tgtttttcgtgggtgtgctgatgg - 3 ′/ seq id no : 24 ) and monb 26 ( 5 ′- acagaacagaaaagccctcagtca - 3 ′/ seq id no : 25 ) were prepared , and amplification was done within a reaction solution ( 50 μl ) containing cdna , 5 μl of 10 × extaq buffer ( takara ), 4 μl of 2 . 5 mm dntps , 1 μl of a mixture of extaq dna polymerase ( takara ) and anti taq antibody ( taqstart antibody ™, clontech ), 1 μl of 20 μm monb 6 primer , and 1 μl of 20 μm monb 26 primer , at 94 ° c . for 2 min , 30 cycles of “ 94 ° c . for 30 sec , 60 ° c . for 30 sec , and 74 ° c . for 2 min ”, and 72 ° c . for 10 min . sequencing revealed that the codon encoding the 352 nd leucine ( ctg ) was mutated to a codon encoding arginine ( cgg ) ( fig1 ). this mutation can be detected by restriction fragment length polymorphism ( pcr - rflp ) due to the presence of the cfr13i restriction enzyme site . this method revealed that the jvs homologous mouse ( jvs / jvs ) had this mutation in both alleles , and that the heterologous mouse ( wt / jvs ) has both the mutated and wild type alleles ( fig2 left ). this mutation was also found in the c57bl jvs mouse in which the genetic background has been replaced with that of the c57bl / 6 mouse by backcrossing 12 times or more ( fig2 right ). since the c57bl jvs mouse was constructed after a series of selections using the jvs phenotype as an index , the jvs phenotype and octn2 mutations are considered to be very closely associated . next , the effect this mutation has on the carnitine transporting activity was examined . plasmid dna expressing wild - type mouse octn2 , and those expressing mutated octn2 were separately introduced into hek293 cells , and then , carnitine transporting ability was measured similar to the assay of human octn2 described in japanese patent application hei 10 - 156660 ( fig3 ). this revealed that although wild - type mouse octn2 shows a carnitine transporting activity similar to human octn2 , the mutated octn2 has absolutely no activity . however , both proteins were confirmed to be expressed at a similar amount by a western blotting using an antibody against the c - myc epitope sequence ( nh 2 — eqkliseedl — cooh ) added to the c terminus ( fig4 ). thus , the jvs mouse is thought to have developed the disease due to a functional deletion mutation of the octn2 gene . a database search using human octn2 cdna sequence revealed that the human octn2 genomic dna sequence has been decoded by lawrence berkeley national laboratory ( lbnl ) of the united states as a part of the human genome project . however , it was only recorded as several cosmid clone sequences , therefore , the inventors determined a complete human octn2 genomic dna sequence ( seq id no : 5 ) by comparing with human octn2 cdna sequence and suitably combining the clone sequences . the human octn2 gene is an about 26 kb gene comprising ten exons and nine introns . the eight pairs of primers shown below , which can amplify all the exons as eight fragments , were prepared from this gene arrangement . specifically , ocn2 43 ( 5 ′- gcaggaccaaggcggcggtgtcag - 3 ′, seq id no : 6 ) and ocn2 44 ( 5 ′- agactagaggaaaaacgggatagc - 3 ′, seq id no : 7 ) for exon one ; ocn2 25 ( 5 ′- agatttttaggagcaagcgttaga - 3 ′ seq id no : 8 ) and ocn2 26 ( 5 ′- gaggcagacaccgtggcactacta - 3 ′, seq id no : 9 ) for exon two ; ocn2 27 ( 5 ′- ttcacacccacttactggatggat - 3 ′ seq id no : 10 ) and ocn2 50 ( 5 ′- attctgttttgttttggctctttt - 3 ′, seq id no : 11 ) for exons three and four ; ocn2 31 ( 5 ′- agcagggcctgggctgacatagac - 3 ′, seq id no : 12 ) and ocn2 32 ( 5 ′- aaaggacctgactccaagatgata - 3 ′, seq id no : 13 ) for exon five ; ocn2 33 ( 5 ′- tctgaccacctcttcttcccatac - 3 ′, seq id no : 14 ) and ocn2 34 ( 5 ′- gcctcctcagccactgtcggtaac - 3 ′, seq id no : 15 ) for exon six ; ocn2 35 ( 5 ′- atgttgttccttttgttatcttat - 3 ′, seq id no : 16 ) and ocn2 36 ( 5 ′- cttgttttcttgtgtatcgttatc - 3 ′, seq id no : 17 ) for exon seven ; ocn2 37 ( 5 ′- tatgtttgttttgctctcaatagc - 3 ′, seq id no : 18 ) and ocn2 40 ( 5 ′- tctgtgagagggagtttgcgagta - 3 ′, seq id no : 19 ) for exon eight and nine ; and , ocn2 41 ( 5 ′- tacgaccgcttcctgccctacatt - 3 ′, seq id no : 20 ) and ocn2 42 ( 5 ′- tcattctgctccatcttcattacc - 3 ′, seq id no : 21 ) for exon 10 . next , human octn2 gene mutations in three families that have systemic carnitine deficiency patients , but no blood relationships were examined . the analysis is done by amplifying all the exons using the above primers and genomic dna prepared from blood cells as the template , and subjecting the amplified products into direct sequencing . the amplification reaction by pcr was done within a reaction solution ( 50 μl ) containing 100 ng of genomic dna , 5 μl of 10 × extaq buffer ( takara ), 4 μl of 2 . 5 mm dntps , 1 μl of a mixture of extaq dna polymerase ( takara ) and anti taq antibody ( taqstart antibody ™, clontech ), and 1 μl of each of the 20 μm primers . the reaction conditions were , 94 ° c . for 2 min , 36 cycles of “ 94 ° c . for 30 sec , 60 ° c . for 30 sec , and 74 ° c . for 2 min ”, and 72 ° c . for 10 min . however , in the case of exon one and exon five amplification , a reaction solution ( 50 μl ) containing 100 ng genomic dna , 25 μl of 2 × gc buffer 1 ( takara ), 8 μl of 2 . 5 mm dntps , 0 . 5 μl of la taq dna polymerase ( takara ), and 1 μl of each of the 20 μm primers , was used . in the first family ( kr family ), a 113 bp deletion was found in first exon of the octn2 gene of a systemic carnitine deficiency patient ( fig5 ). this deletion affects the initiation codon and thus , a complete protein will not be produced . the next usable atg codon present in the correct frame is at nucleotide no . 177 , and in this case , it is thought that at least two transmembrane regions will be deleted . the two systemic carnitine deficiency patients in this family were found to contain this mutated octn2 gene in both alleles . on the other hand , the parents and the two brothers of the patient , who have not developed the disease , carry the mutation on just one allele . in the second family ( ak family ), the systemic carnitine patients were found to contain two types of mutated octn2 genes . one mutation was a cytosine insertion just after the initiation codon , which is thought to cause a frame shift and prevent the proper protein from being produced ( fig6 ). the other mutation is a single base substitution ( g to a ) in the codon encoding the 132 nd tryptophan ( tgg ). this mutation had altered the codon into a stop codon ( tga ) ( fig7 ). these mutations are thought to prevent the production of active octn2 proteins in patients . these mutations can be detected by pcr - rflp analysis using bcni , nlaiv restriction enzymes , respectively , which revealed that the patient &# 39 ; s parents who have not developed the disease , had one of each of the mutations , and the patient &# 39 ; s sisters who have not developed the disease , do not have any mutated genes ( fig8 ). in the third family ( th family ), a mutation ( ag to aa ) was found in the splicing site in the 3 ′ end of the intron eight of the octn2 gene ( fig9 ). this mutation prevents the gene from undergoing normal splicing , and thus , it is expected that the normal protein would not be produced . sequencing analysis showed that the systemic carnitine deficiency patient belonging to this family had this mutation in both alleles . on the other hand , the patient &# 39 ; s parents and one of the brothers who have not developed the disease had one mutated allele . the above results revealed that systemic carnitine deficiency is a genetic disease caused by mutations in the octn2 gene . thus , the present invention enables definitive diagnosis , prenatal diagnosis and such , of systemic carnitine deficiency by examining mutations in the octn2 gene using analyses described herein , as well as other methods . the present invention also enables treatment of systemic carnitine deficiency by treatments such as gene therapy using the octn2 gene . the present invention revealed that the octn2 gene is the gene responsible for systemic carnitine deficiency , thus enabling tests for the disease by detecting mutations in the octn2 gene and its protein . moreover , the present invention facilitates treatment of systemic carnitine deficiency by utilizing the octn2 gene and its protein . met arg asp tyr 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val lys gly gln glu arg pro thr ile leu lys ser thr ala phe ggc atg cgg gac tac gac gag gtg acc gcc ttc ctg ggc gag tgg ggg 168 met arg asp tyr asp glu val thr ala phe leu gly glu trp gly ccc ttc cag cgc ctc atc ttc ttc ctg ctc agc gcc agc atc atc ccc 216 aat ggc ttc acc ggc ctg tcc tcc gtg ttc ctg ata gcg acc ccg gag 264 asn gly phe thr gly leu ser ser val phe leu ile ala thr pro glu cac cgc tgc cgg gtg ccg gac gcc gcg aac ctg agc agc gcc tgg cgc 312 his arg cys arg val pro asp ala ala asn leu ser ser ala trp arg aac cac act gtc cca ctg cgg ctg cgg gac ggc cgc gag gtg ccc cac 360 agc tgc cgc cgc tac cgg ctc gcc acc atc gcc aac ttc tcg gcg ctc 408 agc tgt ctg gat ggc tgg gag ttc agt cag gac gtc tac ctg tcc acc 504 ser cys leu asp gly trp glu phe ser gln asp val tyr leu ser thr att gtg acc gag tgg aac ctg gtg tgt gag gac gac tgg aag gcc cca 552 ile val thr glu trp asn leu val cys glu asp asp trp lys ala pro ctc aca atc tcc ttg ttc ttc gtg ggt gtg ctg ttg ggc tcc ttc att 600 tca ggg cag ctg tca gac agg ttt ggc cgg aag aat gtg ctg ttc gtg 648 acc atg ggc atg cag aca ggc ttc agc ttc ctg cag atc ttc tcg aag 696 aat ttt gag atg ttt gtc gtg ctg ttt gtc ctt gta ggc atg ggc cag 744 atc tcc aac tat gtg gca gca ttt gtc ctg ggg aca gaa att ctt ggc 792 ile ser asn tyr val ala ala phe val leu gly thr glu ile leu gly aag tca gtt cgt ata ata ttc tct acg tta gga gtg tgc ata ttt tat 840 lys ser val arg ile ile phe ser thr leu gly val cys ile phe tyr gca ttt ggc tac atg gtg ctg cca ctg ttt gct tac ttc atc cga gac 888 ala phe gly tyr met val leu pro leu phe ala tyr phe ile arg asp tgg cgg atg ctg ctg gtg gcg ctg acg atg ccg ggg gtg ctg tgc gtg 936 gca ctc tgg tgg ttc atc cct gag tcc ccc cga tgg ctc atc tct cag 984 gga cga ttt gaa gag gca gag gtg atc atc cgc aag gct gcc aaa gcc 1032 aat ggg att gtt gtg cct tcc act atc ttt gac ccg agt gag tta caa 1080 asn gly ile val val pro ser thr ile phe asp pro ser glu leu gln gac cta agt tcc aag aag cag cag tcc cac aac att ctg gat ctg ctt 1128 cga acc tgg aat atc cgg atg gtc acc atc atg tcc ata atg ctg tgg 1176 atg acc ata tca gtg ggc tat ttt ggg ctt tcg ctt gat act cct aac 1224 met thr ile ser val gly tyr phe gly leu ser leu asp thr pro asn ttg cat ggg gac atc ttt gtg aac tgc ttc ctt tca gcg atg gtt gaa 1272 leu his gly asp ile phe val asn cys phe leu ser ala met val glu gtc cca gca tat gtg ttg gcc tgg ctg ctg ctg caa tat ttg ccc cgg 1320 cgc tat tcc atg gcc act gcc ctc ttc ctg ggt ggc agt gtc ctt ctc 1368 ttc atg cag ctg gta ccc cca gac ttg tat tat ttg gct aca gtc ctg 1416 gtg atg gtg ggc aag ttt gga gtc acg gct gcc ttt tcc atg gtc tac 1464 gtg tac aca gcc gag ctg tat ccc aca gtg gtg aga aac atg ggt gtg 1512 val tyr thr ala glu leu tyr pro thr val val arg asn met gly val gga gtc agc tcc aca gca tcc cgc ctg ggc agc atc ctg tct ccc tac 1560 ttc gtt tac ctt ggt gcc tac gac cgc ttc ctg ccc tac att ctc atg 1608 phe val tyr leu gly ala tyr asp arg phe leu pro tyr ile leu met gga agt ctg acc atc ctg aca gcc atc ctc acc ttg ttt ctc cca gag 1656 agc ttc ggt acc cca ctc cca gac acc att gac cag atg cta aga gtc 1704 ser phe gly thr pro leu pro asp thr ile asp gln met leu arg val aaa gga atg aaa cac aga aaa act cca agt cac aca agg atg tta aaa 1752 gat ggt caa gaa agg ccc aca atc ctt aaa agc aca gcc ttc 1794 asp gly gln glu arg pro thr ile leu lys ser thr ala phe met arg asp tyr asp glu val thr ala phe leu gly glu trp gly pro gly phe asn gly met ser ile val phe leu ala gly thr pro glu his arg cys leu val pro his thr val asn leu ser ser ala trp arg asn his ser ile pro leu glu thr lys asp gly arg gln val pro gln lys cys arg arg tyr arg leu ala thr ile ala asn phe ser glu leu gly cys leu asp gly trp glu tyr asp lys asp val phe leu ser thr ile gly gln leu ser asp arg phe gly arg lys asn val leu phe leu thr ser asn tyr val ala ala phe val leu gly thr glu ile leu ser lys ser ile arg ile ile phe ala thr leu gly val cys ile phe tyr ala phe gly phe met val leu pro leu phe ala tyr phe ile arg asp trp gly ile val ala pro ser thr ile phe asp pro ser glu leu gln asp leu asn ser thr lys pro gln leu his his ile tyr asp leu ile arg thr ile ser val gly tyr phe gly leu ser leu asp thr pro asn leu his gly asp ile tyr val asn cys phe leu leu ala ala val glu val met gln leu val pro ser glu leu phe tyr leu ser thr ala leu val tyr thr ala glu leu tyr pro thr val val arg asn met gly val gly val ser ser thr ala ser arg leu gly ser ile leu ser pro tyr phe val tyr leu gly ala tyr asp arg phe leu pro tyr ile leu met gly phe gly val pro leu pro asp thr ile asp gln met leu arg val lys atg cgg gac tac gac gag gtg acc gcc ttc cta ggc gag tgg ggg ccc 107 met arg asp tyr asp glu val thr ala phe leu gly glu trp gly pro ttc cag cgc ctc atc ttc ttc ctg ctc agc gcc agc atc atc ccc aat 155 ggc ttc aat ggt atg tcc atc gtg ttc ctg gcg ggg acc ccg gag cac 203 gly phe asn gly met ser ile val phe leu ala gly thr pro glu his cgt tgc ctt gtg cct cac acc gtg aac ctg agc agc gcg tgg cgc aac 251 arg cys leu val pro his thr val asn leu ser ser ala trp arg asn cac agt atc ccg ttg gag acg aag gac gga cga cag gtg cct cag aaa 299 his ser ile pro leu glu thr lys asp gly arg gln val pro gln lys tgc cgc cgc tac cga ctg gcc acc atc gcc aac ttc tct gag cta ggg 347 cys arg arg tyr arg leu ala thr ile ala asn phe ser glu leu gly ctg gag ccg ggg cgg gac gtg gac ctg gag cag ctg gag cag gag agc 395 tgc ctg gat ggc tgg gag tac gac aag gac gtc ttc ctg tcc acc atc 443 cys leu asp gly trp glu tyr asp lys asp val phe leu ser thr ile gtg aca gag tgg gac ctg gtg tgt aag gat gac tgg aaa gcc cca ctc 491 acc acc tcc ttg ttt ttc gtg ggt gtg ctg atg ggc tcc ttc att tca 539 gga cag ctc tca gac agg ttt ggt cgc aag aat gtg ctg ttt ttg acc 587 gly gln leu ser asp arg phe gly arg lys asn val leu phe leu thr atg ggc atg cag act ggc ttc agc ttc ctg cag gtc ttc tct gtg aac 635 ttc gag atg ttt aca gtg ctt ttt gtc ctt gtt ggc atg ggt cag atc 683 tcc aac tac gtg gca gca ttt gtc ctg gga aca gaa att ctt tcc aag 731 ser asn tyr val ala ala phe val leu gly thr glu ile leu ser lys tca att cga att ata ttc gcc acc tta gga gtt tgc ata ttt tat gcg 779 ser ile arg ile ile phe ala thr leu gly val cys ile phe tyr ala ttt ggc ttc atg gtg ctg cca ctg ttt gca tac ttc atc aga gac tgg 827 phe gly phe met val leu pro leu phe ala tyr phe ile arg asp trp agg atg ctg ctg ctg gcg ctc act gtg cca ggg gtg cta tgt ggg gct 875 ctc tgg tgg ttc atc cct gag tcc cca cga tgg ctc atc tct caa ggc 923 cga att aaa gag gca gag gtg atc atc cgc aaa gct gcc aaa atc aat 971 ggg att gtt gca cct tcc act atc ttc gat cca agt gag tta caa gac 1019 gly ile val ala pro ser thr ile phe asp pro ser glu leu gln asp tta aat tct acg aag cct cag ttg cac cac att tat gat ctg atc cga 1067 leu asn ser thr lys pro gln leu his his ile tyr asp leu ile arg aca cgg aat atc agg gtc atc acc atc atg tct ata atc ctg tgg ctg 1115 acc ata tca gtg ggc tat ttt gga cta tct ctt gac act cct aac ttg 1163 thr ile ser val gly tyr phe gly leu ser leu asp thr pro asn leu cat ggg gac atc tat gtg aac tgc ttc cta ctg gcg gct gtt gaa gtc 1211 his gly asp ile tyr val asn cys phe leu leu ala ala val glu val cca gcc tat gtg ctg gcc tgg ctg ttg ttg cag tac ttg ccc cgg cga 1259 tat tct atc tcg gct gcc ctt ttc ctg ggt ggc agt gtc ctt ctc ttc 1307 atg cag ctg gtg cct tca gaa ttg ttt tac ttg tcc act gcc ctg gtg 1355 met gln leu val pro ser glu leu phe tyr leu ser thr ala leu val atg gtg ggg aag ttt gga atc acc tct gcc tac tcc atg gtc tat gtg 1403 tac aca gct gag ctg tac ccc act gtg gtc aga aac atg ggt gtg ggg 1451 tyr thr ala glu leu tyr pro thr val val arg asn met gly val gly gtc agc tcc aca gca tcc cgc ctt ggc agc atc ctg tct ccc tac ttt 1499 val ser ser thr ala ser arg leu gly ser ile leu ser pro tyr phe gtt tac cta ggt gcc tat gat cgc ttc ctg cct tat att ctc atg gga 1547 val tyr leu gly ala tyr asp arg phe leu pro tyr ile leu met gly agt ctg acc atc ctg aca gct atc ctc acc ttg ttc ttc cct gag agc 1595 ttt ggt gtc cct ctc cca gat acc att gac cag atg cta agg gtc aaa 1643 phe gly val pro leu pro asp thr ile asp gln met leu arg val lys gga ata aaa cag tgg caa atc caa agc cag aca aga atg caa aaa gat 1691 ggt gaa gaa agc cca aca gtc cta aag agc aca gcc ttc taacaccctg 1740