Disease-causing allele-specific silencing against the ALK2 mutants, R206H and G356D, in fibrodysplasia ossificans progressiva.

Fibrodysplasia ossificans progressiva (FOP) is an autosomal dominant congenital disorder characterized by progressive heterotopic bone formation. Currently, no definitive treatment exists for FOP. The activin receptor type IA / activin-like kinase 2 (ACVR1/ALK2) gene has been identified as the responsible gene for FOP, and disease-associated ALK2 mutations have been found. Chemical inhibitors to the pathogenic ALK2 receptors are considered possible medical agents for FOP, but their adverse effects on normal ALK2 and other receptors cannot be excluded. Here we describe another treatment strategy for FOP using allele-specific RNA interference (ASP-RNAi), and show modified small interfering RNAs (siRNAs) conferring allele-specific silencing against disease-causing ALK2 mutants found in FOP, without affecting normal ALK2 allele. Thus, the siRNAs presented here may become novel therapeutic agents for FOP, and their induced ASP-RNAi may pave the way for the achievement of radical treatment of FOP and/or for the relief of its severe symptoms.

Epigenetic aberration of the human REELIN gene in psychiatric disorders.

Epigenetic genome modifications such as DNA methylation appear to be involved in various diseases. Here, we suggest that the levels of DNA methylation at the BssHII methylation-sensitive restriction enzyme sites in the human REELIN (RELN) gene in the forebrain vary among individuals. Interestingly, although a statistically significant correlation between the levels of DNA methylation in RELN and age was detected in healthy individuals, no such correlations were seen in either schizophrenic or bipolar patients. In addition, reverse correlations between DNA methylation levels and RELN expression were also detected in postmortem brain RNA and on in vitro assay. These data suggest the possibility that epigenetic aberration from the normal DNA methylation status of RELN may confer susceptibility to psychiatric disorders.

Estimation of the species-specific mutation rates at the DRB1 locus in humans and chimpanzee.

To estimate the species-specific mutation rates at the DRB1 locus in humans and chimpanzee, we analyzed the nucleotide sequence of a 37.6-kb chimpanzee chromosomal segment containing the entire Patr-DRB1*0701 allele and the flanking nongenic region and we compared it with two corresponding human sequences containing the HLA-DRB1*070101 allele using the sequence of HLA-DRB1*04011 as an outgroup. Because the allelic pair of HLA-DRB1*070101 and Patr-DRB1*0701 shows the lowest number of substitutions between the two species, it appears that these sequences diverged close to the time of the humans-chimpanzee divergence (6 million years ago). Alignment of the nucleotide sequences for HLA-DRB1*070101 and Patr-DRB1*0701 alleles showed that they share a high degree of similarity, suggesting that the studied chromosomal segments with these sequences have not been subjected to recombination since the humans-chimpanzee divergence. Comparison of the flanking 10.6 kb of nongenic sequences revealed an average of 41.5 and 83 single nucleotide substitutions in humans and chimpanzee, respectively. Thus, the species-specific nucleotide substitution rates in the flanking nongenic region were estimated to be 6.53 x 10(-10) and 1.31 x 10(-9) per site per year in humans and chimpanzee, respectively. Unexpectedly, the estimated rate in humans was twofold lower than in chimpanzee (P < 10(-3), Tajima's relative rate test) and lower than the average substitution rate in the human genome. Because the nucleotide substitution rate in nongenic regions free from selection is expected to be equal to the mutation rate, the estimated substitution rate should correspond to the species-specific mutation rate at the DRB1 locus. Our results strongly suggest that the mutation rate at DRB1 locus differs among species.

Profiling of genes expressed in human monocytes and monocyte-derived dendritic cells using cDNA expression array.

Using a human cDNA expression array, we obtained expression profiles of 588 genes in CD14+ monocytes and monocyte-derived dendritic cells (DCs). Overall, 22 genes were upregulated, and nine genes were downregulated in DCs of both samples from two different individuals. Many of the genes that were upregulated in DCs encode proteins that are related to differentiation, cell structure, migration, termination of cell cycle as well as proliferation, e.g. tumour necrosis factor-alpha (TNF-alpha), tumour necrosis factor receptor II (TNFRII), thymosin beta-10, epithelial discoidin domain receptor 1, replication factor C, putative transcription factor DB1, alpha catenin, transforming growth factor-beta 1, prohibitin, p53-regulating protein and neu differentiation factor. Among the downregulated genes in DCs were genes that encode proteins of cell cycle regulation: mitotic growth and transcription activator, platelet-derived growth factor receptor-beta subunit, interleukin 2 receptor (IL-2R)-gamma subunit, IL-7R-alpha subunit, leucocyte interferon-gamma (IFN-gamma) and granulocyte-macrophage colony-stimulating factor receptor (GM-CSFR). Semi-quantitative reverse transcription-polymerase chain reaction method confirmed the upregulated expression levels in DCs for TNFRII, TNF-alpha, alpha catenin and downregulation of IFN-gamma, GM-CSFR on four different donor samples of DCs and monocytes. Moreover, our data show the presence of a 'switch-on' step for the TNF-alpha and TNFRII gene expression in immature DCs for further differentiation into mature DCs.

Allele-specific binding of the ubiquitous transcription factor OCT-1 to the functional single nucleotide polymorphism (SNP) sites in the tumor necrosis factor-alpha gene (TNFA) promoter.

The tumor necrosis factor-alpha (TNFA) is characterized by several single nucleotide polymorphisms (SNPs) in its promoter region. Interestingly some of these SNPs appear to influence TNFA expression and susceptibility to various human diseases, but the molecular mechanisms by which such possibly functional SNPs modulate TNFA expression are poorly understood. In this study we show allele-specific binding of the ubiquitous transcription factor OCT-1 to the SNP sites at positions -863 and -857 in the promoter, which appear to affect TNFA expression: the protein was associated with variant allele possessing either -863A or -857T, but rarely with the common allele (-863C and -857C). The evidence presented here, therefore, suggests the possibility that OCT-1 could contribute to the modulation of TNFA expression by means of its allele-specific binding manner.

Case-control study with narcoleptic patients and healthy controls who, like the patients, possess both HLA-DRB1*1501 and -DQB1*0602.

In previous studies, we suggested that the tumor necrosis factor (TNF-alpha and its receptor 2 (TNFR2) genes could be associated with the susceptibility to human narcolepsy, and that haplotype carrying DRB1*1502 had a negative association with the disorder. To further evaluate these associations, we herein compared narcoleptic patients with healthy individuals who, like the patients, possessed both DRB1*1501 and DQB1*0602. Results agreed with the negative association of DRB1*1502 and positive association of the TNF-alpha(-857T) and TNFR2-196R combination with the disorder. In addition, a significant association of the TNF-alpha(-857T) homozygote with the disorder and an increase in a rare haplotype carrying DRB1*1501 and TNF-alpha(-857T) in the patients were also observed in the present study.

Haplotype analyses with the human leucocyte antigen and tumour necrosis factor-alpha genes in narcolepsy families.

Our previous study suggested that the tumour necrosis factor-alpha gene with thymine residue at position -857 in its promoter region [TNF-alpha(-857T)] could be associated with human narcolepsy independently of a strong association of the human leucocyte antigen (HLA)-DRB1*1501 with the disorder. To understand the relationship of DRB1*1501 with TNF-alpha(-857T) in narcoleptic patients, we investigated 28 members of four Japanese narcolepsy families and determined the haplotypes with the HLA-B, TNF-alpha(-857C/T) and HLA-DRB1 in the members. The resultant haplotypes indicated that not only the DRB1*1501-TNF-alpha(-857C) haplotype but also the DRB1*1501-TNF-alpha(-857T) haplotype, which is rare in healthy individuals and may have a strong predisposition to the disorder, were present in the affected members. From the chromosomal recombination observed in a few members, it is possible that chromosomal recombination could play a role in the generation of the rare DRB1*1501-TNF-alpha(-857T) haplotype.

Complex HLA-DR and -DQ interactions confer risk of narcolepsy-cataplexy in three ethnic groups.

Human narcolepsy-cataplexy, a sleep disorder associated with a centrally mediated hypocretin (orexin) deficiency, is tightly associated with HLA-DQB1*0602. Few studies have investigated the influence that additional HLA class II alleles have on susceptibility to this disease. In this work, 1,087 control subjects and 420 narcoleptic subjects with cataplexy, from three ethnic groups, were HLA typed, and the effects of HLA-DRB1, -DQA1, and -DQB1 were analyzed. As reported elsewhere, almost all narcoleptic subjects were positive for both HLA-DQA1*0102 and -DQB1*0602. A strong predisposing effect was observed in DQB1*0602 homozygotes, across all ethnic groups. Relative risks for narcolepsy were next calculated for heterozygous DQB1*0602/other HLA class II allelic combinations. Nine HLA class II alleles carried in trans with DQB1*0602 were found to influence disease predisposition. Significantly higher relative risks were observed for heterozygote combinations including DQB1*0301, DQA1*06, DRB1*04, DRB1*08, DRB1*11, and DRB1*12. Three alleles-DQB1*0601, DQB1*0501, and DQA1*01 (non-DQA1*0102)-were found to be protective. The genetic contribution of HLA-DQ to narcolepsy susceptibility was also estimated by use of lambda statistics. Results indicate that complex HLA-DR and -DQ interactions contribute to the genetic predisposition to human narcolepsy but that additional susceptibility loci are also most likely involved. Together with the recent hypocretin discoveries, these findings are consistent with an immunologically mediated destruction of hypocretin-containing cells in human narcolepsy-cataplexy.

Haplotype-specific sequence encoding the protein kinase, interferon-inducible double-stranded RNA-dependent activator in the human leukocyte antigen class II region.

The protein kinase, interferon-inducible double-stranded (ds)RNA-dependent activator (PRKRA) is a dsRNA-binding protein which activates a protein kinase participating in the antiviral activity of interferon. Our previous studies indicated that the nucleotide sequence encoding PRKRA, which appeared to be an intronless gene, was present in PAC HS265J14 containing the human leukocyte antigen (HLA) DR subregion. In this study, we further investigated and characterized the PRKRA gene on the human genome by means of Southern blotting and polymerase chain reaction with homozygous typing cell lines for HLA genes. Results indicated that the presence of PRKRA in the DR subregion was dependent on the DR53 group. Consistently, fluorescence in situ hybridization profiles with PRKRA as a probe showed that the hybridization signal on Chromosome (Chr) 6p21.3 was seen only in the samples carrying the DR haplotypes that belonged to the DR53 group. Interestingly, another hybridization signal, which was mapped on Chr 2q31.2-q32.1, was always detected in the samples examined, i.e., even in the samples negative for the DR53 group. The outcome of a sequence-database homology search further indicated that the PRKRA gene with introns appeared to be present in a recently opened draft-sequence, RP11-65L3 (GenBank accession number AC009948), which is located between D2S335 and D2S2257. Together, the data presented here indicate that the PRKRA gene in the DR subregion is a processed pseudogene (PRKRApsi), which could have been generated only on the DR53 common ancestor's genome, and that the master copy of PRKRApsi is most probably present on Chr 2q31.2-q32.1.

Identification of a telomeric boundary of the HLA region with potential for predisposition to human narcolepsy.

We report on a study performed to determine a boundary of the region with the potential to contribute to the predisposition to human narcolepsy (the susceptibility region) in the human leukocyte antigen (HLA) region. We investigated a Japanese narcolepsy family, in which a de novo chromosomal recombination occurred between the HLA-DRB1 and HLA-B genes in the proband. The recombinant chromosome carrying HLA-DRB1*1501 was transmitted to the affected child and grandchild, suggesting that a strong genetic factor(s) predisposing to the disorder was (were) present on the chromosome, and that the recombination breakpoint could be regarded as a boundary to the susceptibility region. To search for the breakpoint, we carried out allele typing at various polymorphic sites, e.g., microsatellite repeat polymorphisms, restriction fragment length polymorphisms, and single-nucleotide polymorphisms in the HLA region, and examined haplotypes with the polymorphic sites in the family members. Haplotype analyses revealed that the recombination breakpoint was present approximately 50 kb to the telomeric side of the palmitoyl-protein thioesterase-2 (PPT2) gene in the HLA class III region. From the gene map of the HLA region, the cyclic AMP response element-binding protein-related protein gene (CREB-RP) appeared to be located at the telomeric end in the 50-kb region. Therefore, the data presented here suggest that the susceptibility region for the disorder in the family is present on the centromeric side of the CREB-RP gene in the recombinant Chromosome 6 carrying HLA-DRB1*1501.

Support for an association between HLA-DR1 and schizophrenia in the Japanese population.

An increase of HLA-DR1 has been observed in schizophrenia patients from the Japanese population. A decrease of DR4, which was reported in Caucasian patients, has also been found in some of the Japanese studies. This small study further investigated frequencies of HLA-DR1 and DR4 in unrelated Japanese patients with schizophrenia (n = 45) and healthy comparison subjects (n = 117). The number of patients possessing DR1 was higher (10 of 45, 22%) compared with the comparison group (11 of 117, 9.4%, P = 0.03). This may support the previous observation of an increased DR1 frequency in the Japanese patients. When the present data is combined with three previous studies, proportions of the Japanese subjects with DR1 were 98 of 588 schizophrenia patients (16.7%) vs. 93 of 942 comparison subjects (9.9%). However, no difference was observed in DR4 frequencies between the patients (51%) and comparison subjects (44%). Am. J. Med. Genet. (Neuropsychiatr. Genet.) 96:725-727, 2000.

MHC (major histocompatibility complex)-DRB genes and polymorphisms in common marmoset.

A New World monkey, the common marmoset (Callithrix jacchus), will be used as a preclinical animal model to study the feasibility of cell and gene therapy targeting immunological and hematological disorders. For elucidating the immunogenetic background of common marmoset to further studies, in the present study, polymorphisms of MHC-DRB genes in this species were examined. Twenty-one Caja-DRB exon 2 alleles, including seven new ones, were detected by means of subcloning and the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) methods followed by nucleotide sequencing. Based on the alignment of these allele sequences, we designed two pairs of specific primers and established a PCR-SSCP method for DNA-based histocompatibility typing of the common marmoset. According to the family segregation data and phylogenetic analyses, we presumed that Caja-DRB alleles could be classified into five different loci. Southern blotting analysis also supported the existence of multiple DRB loci. The patterns of nucleotide substitutions suggests that positive selection operates in the antigen-recognition sites of Caja-DRB genes.

Novel allele containing a 190C>T nonsynonymous substitution in the N-acetyltransferase (NAT2) gene.

N-acetyltransferase (NAT2) is an enzyme involved in detoxification of various carcinogens. The gene is highly polymorphic with a number of alleles, and is also known as acetylator phenotypes: the fast, intermediate and slow acetylators. In this report, we describe a novel NAT2 allele, which was found in the allele typing with 109 Japanese individuals using conventional restriction fragment length polymorphism (RFLP) method. The sequence analyses of the entire amino acid coding region of the novel allele showed that it possessed a 190C>T variation leading to an amino acid substitution from arginine to tryptophan at position 64 (R64W). Consequently, the novel allele we found has been given the name of NAT2*19 by the arylamine N-acetyltransferase nomenclature committee.

Human leukocyte antigen and season of birth in Japanese patients with schizophrenia.

OBJECTIVE: Five Japanese studies, to the authors' knowledge, without exception, have consistently shown an increased frequency of human leukocyte antigen (HLA)-DR1 in patients with schizophrenia. This suggests an association between HLA-DR1 and schizophrenia in the Japanese population. The mechanism of the association is unknown; however, prenatal infections may be involved. The present study explored factors, including winter birth, that might correlate with this mechanism. Age at onset and gender were also studied. METHOD: Factors were compared between Japanese patients with schizophrenia with and in those without HLA-DR1 (N=60 and N=307, respectively). RESULTS: A significantly higher incidence of births in February and March was observed in patients with (31.7%) than those without (15. 6%) HLA-DR1. No association was found between the presence of HLA-DR1 and other variables. CONCLUSIONS: Although this result is preliminary, it may suggest an interaction between HLA and winter birth in the development of schizophrenia in the Japanese population.

Significant association of the tumor necrosis factor receptor 2 (TNFR2) gene with human narcolepsy.

We report on the association study of the tumor necrosis factor receptor 2 (TNFR2) gene with human narcolepsy. A single-nucleotide polymorphism in TNFR2, which is involved in an amino acid substitution [methionine(M)/arginine(R)] at position 196, was investigated in 149 Japanese narcoleptic patients and 204 healthy individuals as controls. Results reveal that the frequency of the TNFR2-196R allele significantly increased in the patients as compared with that in the controls (P=0.029), suggesting that TNFR2 is likely associated with the susceptibility to narcolepsy. In addition, the analyses of the relationship of TNFR2 and TNF-alpha with the susceptibility to narcolepsy indicate the possibility that an additive effect on the susceptibility to the disorder lies between TNFR2-196R and TNF-alpha(-857T) alleles.

Predisposing factors in delayed sleep phase syndrome.

We classified 64 patients with chronic delayed sleep phase syndrome (DSPS) into the primary (n = 53) and secondary (n = 11) group according to presence or absence of such signs as difficulty in waking up which appeared much earlier than the onset of DSPS. The age at the onset of the early signs concentrated in adolescence. The familial occurrence of DSPS was noted in 11 patients of the primary group. In human leukocyte antigen (HLA) typing, the incidence of DR1 positivity alone was significantly higher in DSPS patients than in healthy subjects. Minnesota Multiphasic Personality Inventory revealed high scores on depression, psychoasthenia and hypochondriasis. We suggest that a predisposition to DSPS includes biological, genetic, social and psychological factors, various combinations of which may lead to DSPS.

Molecular analyses of the possible RNA-binding protein gene located in the human leukocyte antigen (HLA)--DR subregion.

We have previously found the sequence having potential for encoding a new protein in the human leukocyte antigen (HLA) class II region. The predicted amino acid sequence showed a significant sequence homology to the Xenopus double-stranded RNA-binding protein (Xlrbp) and the human cellular protein bound to the transactivation response (TAR) of human immunodeficiency virus type-1 (HIV-1) RNA (TRBP). Reverse transcription-polymerase chain reaction (RT-PCR) with poly(A)(+) RNA prepared from human peripheral lymphocytes and direct sequencing analyses in this study showed that the transcripts of the gene encoding the putative RNA-binding protein occurred in human cells: the gene was provisionally named Homo sapiens RNA-binding protein (hsRBP). From the result of Southern blot analyses, it appears that multiple copies of hsRBP are present in the human genome. Together with the known cDNAs having a high sequence homology to hsRBP, the data presented here suggest that the multigene family of the double-stranded RNA-binding protein exists in the human genome.

Significant association of a single nucleotide polymorphism in the tumor necrosis factor-alpha (TNF-alpha) gene promoter with human narcolepsy.

Narcolepsy is a sleep disorder in which multiple factors, including environmental and genetic factors, are involved. A genetic factor strongly associated with the disorder has been found in the human leukocyte antigen (HLA) class II region: the haplotype, DRB1*1501-DQB1*0602, predisposes to narcolepsy. No susceptibility genes other than the HLA-haplotype have been found. In this paper, we performed an association study of the tumor necrosis factor-alpha (TNF-alpha) gene located in the HLA class III region with human narcolepsy, in which we examined the known single-nucleotide polymorphisms (SNPs) in the promoter region in 49 narcoleptic patients, who were all positive for DRBI*1501, and 111 healthy control individuals. The results indicated that the frequency of the genotype at position -857 (-857SNP) was significantly different between the patients and controls, and the allele frequencies of 857SNP revealed that the frequency of -857T was significantly increased in the patients as compared with that in the controls (P=0.0068). In addition, haplotypes presumed from HLA-DRB1, -857SNP and HLA-B loci suggested that -857T was mainly associated with DRB1 alleles other than DRB1*1501: the significant increase in frequency of -857T in the patients was not caused by allelic association with DRB1*1501. Therefore, it is conceivable that the TNF-alpha with 857T was associated with narcolepsy independently of the strong association of DRB1*1501 with the disorder. Altogether, the data presented here lead us to propose that TNF-alpha could be a new susceptibility gene in human narcolepsy.