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Katsushi Tokunaga

Publications and source records attributed to Katsushi Tokunaga.

At least 19 recordsLinked to original sources
PubMed2025

DNA methylation and multi-omics profiling of T cells uncovers chemotactic pathways and proliferation-linked hypomethylation in narcolepsy type 1.

Narcolepsy type 1 (NT1) is a chronic sleep disorder caused by a loss of orexin-producing cells in the brain and involves autoimmune mechanisms, including the presence of autoreactive T cells. In this study, we performed genome-wide DNA methylation analysis using both CD4+/CD8+ T cells from 42 NT1 patients and 42 controls across discovery and replication cohorts. To identify methylation changes more robustly associated with the disease, we prioritized differentially methylated regions (DMRs) over single-site differentially methylated positions (DMPs). Furthermore, to validate and interpret DMP-level associations, we integrated genome-wide genotype and gene expression data obtained from the same individuals. As a result, the DMR analysis identified 15 reproducible DMRs in CD4+ T cells and 5 in CD8+ T cells, with most DMRs shared between the two cell types. Shared DMRs included regions associated with CCL5 (p = 2.1E-02) and CCR4 (p = 8.3E-03). Integrative analysis with genotype and gene expression data also showed that the DMP related to S100A4, which promotes lymphocyte migration through CCR5 and CXCR3 receptors, was associated with the disease in CD4+ T cells. Pathway analysis of genes identified through both the DMR and integrative analyses indicated enrichment in cell chemotaxis-related pathways, suggesting that aberrant chemokine-mediated cell migration plays a central role in NT1 pathogenesis. Further, NT1-associated methylation changes were predominantly hypomethylation events, significantly enriched in non-promoter, non-CpG island regions (p = 1.74E-102). We further observed that global hypomethylation levels were correlated with hypoSC, a mitotic index estimated from methylation data, highlighting increased T cell proliferation in NT1.

Humans↗
PubMed2007

Association study between the TNXB locus and schizophrenia in a Japanese population.

The chromosome 6p21-24 region, which contains the human leukocyte antigen (HLA) region, has been suggested as an important locus for a susceptibility gene for schizophrenia. Recently, a significant association between schizophrenia and the TNXB locus, located immediately telomeric of the NOTCH4 locus in the HLA region, was observed. Few studies have further investigated the region in schizophrenia. In the present study, we investigated the region in a Japanese population. Subjects included 241 patients with schizophrenia and 290 controls. Twenty-six single nucleotide polymorphisms (SNPs) and the corresponding haplotypes were analyzed. As a result, exactly the same SNPs in the TNXB locus (rs1009382 and rs204887) as in the previous study were associated with schizophrenia (P = 0.034 and 0.034, respectively, uncorrected). A SNP (rs2071287) in the NOTCH4 locus and haplotype around it were also suggested to associate with the disease, consistent with another previous study (P = 0.041 and permutation P = 0.024, respectively, uncorrected). Although these associations became insignificant after Bonferroni correction, the findings might provide support for the association of the TNXB locus or its adjacent region of the NOTCH4 locus with schizophrenia.

Adult↗
PubMed2006

Human leukocyte antigen matching estimations in a hypothetical bank of human embryonic stem cell lines in the Japanese population for use in cell transplantation therapy.

Human embryonic stem (hES) cell lines are of great potential in cell transplantation therapy. However, recipients of such allogeneic transplants probably need treatment with immunosuppressants. Recently, Taylor et al. [Lancet 2005;366:2019-2025] proposed banking of hES cell lines and estimated the required number of hES cell lines for beneficial human leukocyte antigen (HLA) matching in the U.K. population. Here, we carried out such an estimation in the Japanese population. We calculated the proportion of patients who can find at least one HLA-matched donor at three loci of HLA-A, -B, and -DR. With a bank of hES cell lines from 170 randomly selected donated embryos, 80% of patients were expected to find at least one hES cell line with a single mismatch at one HLA locus or a better match. Furthermore, 80% of patients are expected to find at least one donor with complete matching at the three HLA loci if parthenogenetic homozygous hES cell lines are established from 55 randomly selected donated oocytes. The relatively low ethnic diversity of the Japanese population may have resulted in a high success rate in beneficial matching. Moreover, parthenogenetic hES cell lines can greatly reduce the number required for a higher degree of HLA matching.

Cell Line↗
PubMed2006

Role of B cell inhibitory receptor polymorphisms in systemic lupus erythematosus: a negative times a negative makes a positive.

B lymphocytes play a pivotal role in the pathogenesis of systemic lupus erythematosus (SLE). Here, we will review our studies on the role of polymorphisms of two genes coding for B cell inhibitory receptors, FCGR2B and CD72. In FCGR2B, a single nucleotide polymorphism leading to a nonsynonymous substitution, Ile232Thr, within the transmembrane domain was identified, and a significant association of the 232Thr/Thr genotype with SLE was observed in Japanese, Thai and Chinese populations, while this allele was found to be rare in Caucasians. On the other hand, the association of FCGR2B promoter polymorphism with SLE in Caucasians has been reported by two independent groups, but this allele was not found to be present in Japanese. These observations demonstrate that the association of FCGR2B polymorphisms with SLE is common to multiple populations, but the alleles associated with SLE depend upon the genetic background of each population. Functional analyses using a human B cell line lacking endogenous FcgammaRIIb revealed that SLE-associated 232Thr allele product was partially excluded from membrane lipid rafts under resting conditions and after coligation with B cell receptor, and was significantly less potent at inhibiting B cell activation. Two haplotypes were identified in CD72, one of which was associated with increased production of an alternative splicing isoform that substantially alters the extracellular region of CD72. Interestingly, the presence of the haplotype significantly decreased the risk of SLE conferred by FCGR2B-232Thr in an epistatic manner. These observations emphasize the need to understand human immune system diversity if we are to improve our understanding of the pathogenesis of autoimmune diseases.

Alternative Splicing↗
PubMed2006

Association study of the dysbindin (DTNBP1) gene in schizophrenia from the Japanese population.

Dysbindin (DTNBP1: dystrobrevin binding protein 1), located on 6p22.3, is a candidate susceptibility gene for schizophrenia. Several studies, mostly in Caucasians, have provided evidence for an association between schizophrenia and the gene, although no common polymorphism or haploytpe has been established. In Asian populations, two studies investigated a limited number of single nucleotide polymorphisms (SNPs) of dysbindin and observed support for the association. In the present study, we investigated 12 SNPs of dysbindin, including those examined in previous Asian studies, and the corresponding haplotypes in a Japanese people with schizophrenia. As a result, no significant difference was observed between patients and controls in allelic frequencies or genotypic distributions of the 12 SNPs. Permutation test however showed significant differences in frequencies of the estimated 10-marker haplotypes between patients and controls (global p = 0.006). The present study may provide further support for an association between dysbindin and schizophrenia in Asian populations. The results might be similar to a previous Asian study, but specific haplotypes suggested for the association differed between the studies. Studies with more markers and subjects may be required before firm conclusions can be reached.

Adult↗
PubMed2006

Unique secondary chromosomal abnormalities are frequently found in the chronic phase of chronic myeloid leukemia in southern Vietnam.

During the Vietnam War, southern Vietnam was exposed to a large amount of dioxin, a strong human carcinogen. Although we have observed much shorter survival in southern Vietnamese chronic myeloid leukemia (CML) patients, the cause remains to be clarified. Here, we report cytogenetic and molecular findings for 47 CML patients. Cytogenetically, the Philadelphia (Ph) chromosome was found in 44 patients (93.6%); of the remaining 3 patients with Ph-negative CML, 2 exhibited BCR/ABL transcripts but no BCR/ABL FISH fusion signals, suggesting the existence of two clones, with and without the BCR/ABL fusion gene. Surprisingly, in 17 patients (36.2%) (4 at diagnosis, 11 during chronic phase, and 2 in accelerated phase), we found several unique secondary chromosome abnormalities including trisomy 13, partial trisomy 13, and abnormalities of 1p, 3p, 6p, 7p, 10p, and 11p, which are different from the so-called additional chromosome abnormalities (extra Ph, +8, i(17q), +19, and +21) observed in blastic phase CML. FISH analysis revealed the Ph translocation with der(9) deletion in 11 patients (23.4%). Of these, 2 had two clones, with and without der(9) deletion, suggesting that der(9) deletion would occur in a subset of patients during disease progression. These observations point to preexisting genetic instability that induces various secondary chromosome abnormalities and multiple clones, resulting in shorter survival.

Adolescent↗
PubMed2006

Genomewide association analysis of human narcolepsy and a new resistance gene.

Human narcolepsy is a hypersomnia that is affected by multiple genetic and environmental factors. One genetic factor strongly associated with narcolepsy is the HLA-DRB1*1501-DQB1*0602 haplotype in the human leukocyte antigen region on chromosome 6, whereas the other genetic factors are not clear. To discover additional candidate regions for susceptibility or resistance to human narcolepsy, we performed a genomewide association study, using 23,244 microsatellite markers. Two rounds of screening with the use of pooled DNAs yielded 96 microsatellite markers (including 16 markers on chromosome 6) with significantly different estimated frequencies in case and control pools. Markers not located on chromosome 6 were evaluated by the individual typing of 95 cases and 95 controls; 30 markers still showed significant associations. A strong association was displayed by a marker on chromosome 21 (21q22.3). The surrounding region was subjected to high-density association mapping with 14 additional microsatellite markers and 74 SNPs. One microsatellite marker (D21S0012m) and two SNPs (rs13048981 and rs13046884) showed strong associations (P < .0005; odds ratios 0.19-0.33). These polymorphisms were in a strong linkage disequilibrium, and no other polymorphism in the region showed a stronger association with narcolepsy. The region contains three predicted genes--NLC1-A, NLC1-B, and NLC1-C--tentatively named "narcolepsy candidate-region 1 genes," and NLC1-A and NLC1-C were expressed in human hypothalamus. Reporter-gene assays showed that the marker D21S0012m in the promoter region and the SNP rs13046884 in the intron of NLC1-A significantly affected expression levels. Therefore, NLC1-A is considered to be a new resistance gene for human narcolepsy.

Genetic Markers↗
PubMed2006

Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity.

A plausible explanation for many MHC-linked diseases is lacking. Sequencing of the MHC class I region (coding units or full contigs) in several human and nonhuman primate haplotypes allowed an analysis of single nucleotide variations (SNV) across this entire segment. This diversity was not evenly distributed. It was rather concentrated within two gene-rich clusters. These were each centered, but importantly not limited to, the antigen-presenting HLA-A and HLA-B/-C loci. Rapid evolution of MHC-I alleles, as evidenced by an unusually high number of haplotype-specific (hs) and hypervariable (hv) (which could not be traced to a single species or haplotype) SNVs within the classical MHC-I, seems to have not only hitchhiked alleles within nearby genes, but also hitchhiked deleterious mutations in these same unrelated loci. The overrepresentation of a fraction of these hvSNV (hv1SNV) along with hsSNV, as compared to those that appear to have been maintained throughout primate evolution (trans-species diversity; tsSNV; included within hv2SNV) tends to establish that the majority of the MHC polymorphism is de novo (species specific). This is most likely reminiscent of the fact that these hsSNV and hv1SNV have been selected in adaptation to the constantly evolving microbial antigenic repertoire.

Alleles↗
PubMed2006

Polymorphisms in the ABO blood group gene in three populations in the New Georgia group of the Solomon Islands.

To examine genetic affinity among Oceanian populations, polymorphisms of exons six and seven of the ABO blood group gene (ABO) were investigated in three populations--Munda town, Paradise village, and Rawaki village--in the New Georgia group of the Solomon Islands. The Munda and Paradise populations consist of Austronesian (AN)-speaking Melanesians; the Rawaki population consists of AN-speaking Micronesians who migrated from the Gilbert Islands to the New Georgia Islands approximately 30 years ago. We recently described the polymorphisms of ABO in three other Oceanian populations--Balopa Islanders (AN-speaking Melanesians), Gidra (non-AN-speaking Melanesians), and Tongans (AN-speaking Polynesians). The results from these six Oceanian populations suggest: (1) the main alleles in Oceanian populations are ABO*A101, ABO*A102, ABO*B101, ABO*O01, and ABO*O02, among which the most predominant is ABO*O01, and (2) there are marked differences in the ABO allele frequency spectrum among Oceanian populations. The different geographical distribution of ABO alleles provides insight into the migration history of AN-speaking populations in Oceania.

ABO Blood-Group System↗
PubMed2006

Long-term persistence of both functional and non-functional alleles at the leukocyte immunoglobulin-like receptor A3 (LILRA3) locus suggests balancing selection.

The leukocyte immunoglobulin-like receptor (LILR) family consists of 13 loci, and a number of variations have been identified in these genes. Some polymorphisms of the LILR genes are reported to be associated with susceptibility to diseases such as rheumatoid arthritis and multiple sclerosis. LILRA3, one of the LILR genes, exhibits a presence or absence variation due to a 6.7-kb deletion in various populations. In this study, variation screening of the LILRA3 gene revealed high allele frequency of the 6.7-kb LILRA3 deletion (71%) in Japanese, in contrast to the frequency reported for the other populations. In addition, we identified a splice acceptor mutation in intron 1 with allele frequency of 19%, resulting in three alternatively spliced isoforms. Surprisingly, all of these isoforms were found to contain premature termination codons (PTCs) in the exon 3. Taken together, approximately 80% of Japanese lack functional LILRA3 alleles. The maximum likelihood coalescent analysis suggested that two major lineages, functional alleles and PTC-containing alleles, have been maintained for 2.75 million years in humans. These results prompted us to hypothesize that balancing selection had maintained both the functional and non-functional alleles at the LILRA3 locus. This hypothesis is consistent with the observation that the 6.7-kb LILRA3 deletion is detected worldwide in the presence of functional LILRA3 alleles.

Alleles↗
PubMed2006

A SNP in the ABCC11 gene is the determinant of human earwax type.

Human earwax consists of wet and dry types. Dry earwax is frequent in East Asians, whereas wet earwax is common in other populations. Here we show that a SNP, 538G --> A (rs17822931), in the ABCC11 gene is responsible for determination of earwax type. The AA genotype corresponds to dry earwax, and GA and GG to wet type. A 27-bp deletion in ABCC11 exon 29 was also found in a few individuals of Asian ancestry. A functional assay demonstrated that cells with allele A show a lower excretory activity for cGMP than those with allele G. The allele A frequency shows a north-south and east-west downward geographical gradient; worldwide, it is highest in Chinese and Koreans, and a common dry-type haplotype is retained among various ethnic populations. These suggest that the allele A arose in northeast Asia and thereafter spread through the world. The 538G --> A SNP is the first example of DNA polymorphism determining a visible genetic trait.

ATP-Binding Cassette Transporters↗
PubMed2006

Effects of down-regulating the Id genes in human colorectal cancer cells on early steps of haematogenous metastasis.

Id genes (inhibitor of DNA binding/differentiation) play important roles in tumour growth. We have previously described crucial roles of Id gene over-expression in endothelial cells for tumour angiogenesis. Here, we have evaluated direct effects of Id gene down-regulation on tumour cells, namely on cell proliferation, motility, and adhesion to lung microvasculature during haematogenous metastasis. For this purpose, Id genes were stably down-regulated by RNA interference in human colorectal cancer cells. These cells showed delayed proliferation, inhibited motility and decreased expression of integrin alpha6 and consequently reduced adhesion to lung microvasculature in mice. Static adhesion assays and laminar flow assays revealed decreased laminin binding capacity of these cells, and blocking experiments confirmed that it could be attributed to decreased expression of integrin alpha6. The present results indicate important roles of Id genes in tumour cells during early steps of haematogenous metastasis and suggest dual effects from their therapeutic inhibition.

Animals↗
PubMed2006

Functional polymorphisms in the vascular endothelial growth factor gene are associated with development of end-stage renal disease in males.

This study elucidates the genetic role of vascular endothelial growth factor (VEGF) as a predisposing factor for progression of chronic kidney disease. Single-nucleotide polymorphisms were genotyped and haplotype structures were determined in the 3' untranslated region (UTR) of VEGF gene, and the distribution of each haplotype in male patients with ESRD (n=101) and healthy male control subjects (n=189) was examined. The 936C/T and 1451C/T polymorphisms in the 3' UTR were in nearly absolute linkage disequilibrium, and haplotype analysis demonstrated that they were the primary responsible single-nucleotide polymorphisms. The distribution of the 936CC-1451CC genotype was significantly more frequent among patients with ESRD than among the age-matched healthy control subjects. In addition to case-control association study, the 936CC-1451CC genotype was also associated with significantly higher plasma VEGF levels in healthy individuals, but a significant association was found only in males, not in females. We also examined the effect of the 936C-1451C haplotype on mRNA stability. Consistent with the results of plasma VEGF levels, mRNA carrying 936C-1451C haplotype showed higher stability. The 936CC-1451CC genotype in the 3' UTR showed not only susceptibility for ESRD but also higher plasma VEGF levels and mRNA stability, indicating the contribution of VEGF to chronic kidney disease progression, especially in males.

Adult↗
PubMed2006

Coexistence of Philadelphia chromosome positive cells with and without der(9) deletion in a patient with chronic myelogenous leukemia.

Recently, large deletions adjacent to the Philadelphia (Ph) translocation breakpoint on the derivative chromosome 9 have been reported to be found in a substantial number of patients with chronic myelogenous leukemia (CML). The existence of der(9) deletion is reported as a powerful indicator of a poor prognosis. So far, der(9) deletion is considered to be generated when the Ph translocation occurs, because when der(9) deletion is found, it is detected in all the Ph-positive (Ph+) cells of a particular CML patient. On FISH examination of 47 Vietnamese CML patients, we found 11 patients carrying der(9) deletion. Among these, two patients harbored Ph+ metaphase cells with der(9) deletion and also Ph+ cells without it. In CML patients with der(9) deletion, reportedly no ABL/BCR transcript is detected. In these two patients, the proportion of Ph+ cells without der(9) deletion was much smaller than that of the cells with der(9) deletion. Nevertheless, we detected a ABL/BCR (1b-b4) transcript in the two patients. This is further evidence for the existence of Ph+ cells without der(9) deletion. It is possible that in some CML patients, der(9) deletion is generated in the progression of the disease.

Adult↗
PubMed2006

Brief communication: mitochondrial DNA variation suggests extensive gene flow from Polynesian ancestors to indigenous Melanesians in the northwestern Bismarck Archipelago.

Archaeological, linguistic, and genetic studies show that Austronesian (AN)-speaking Polynesian ancestors came from Asia/Taiwan to the Bismarck Archipelago in Near Oceania more than 3,600 years ago, and then expanded into Remote Oceania. However, it remains unclear whether they extensively mixed with indigenous Melanesians who had populated the Bismarck Archipelago before their arrival. To examine the extent of admixture between Polynesian ancestors and indigenous Melanesians, mitochondrial DNA (mtDNA) variations in the D-loop region and the cytochrome oxidase and lysine transfer RNA (COII/tRNA(Lys)) intergenic 9-bp deletion were analyzed in the following three Oceanian populations: 1) Balopa Islanders as AN-speaking Melanesians living in the northwestern end of the Bismarck Archipelago, 2) Tongans as AN-speaking Polynesians, and 3) Gidra as non-Austronesian-speaking Melanesians in the southwestern lowlands of Papua New Guinea. Phylogenetic analysis of mtDNA sequences revealed that more than 60% of mtDNA sequences in the Balopa Islanders were very similar to those in Tongans, suggesting an extensive gene flow from Polynesian ancestors to indigenous Melanesians. Furthermore, analysis of pairwise difference distributions for the D-loop sequences with the 9-bp deletion and the Polynesian motif (i.e., T16217C, A16247G, and C16261T) suggested that the expansion of Polynesian ancestors possessing these variations occurred approximately 7,000 years ago.

Base Pairing↗
PubMed2006

Association of killer cell immunoglobulin-like receptor genotypes with microscopic polyangiitis.

OBJECTIVE: Genetic background and infection have been implicated in the etiology of microscopic polyangiitis (MPA). Killer cell immunoglobulin-like receptors (KIRs) are a diverse family of activating and inhibitory receptors expressed on natural killer (NK) cells and T cells, the genes of which show extreme polymorphism. Some KIRs bind to HLA class I subgroups, and genetic interactions between KIR genes and their ligand HLA have been shown to be associated with several autoimmune and viral diseases. In this study, we examined possible associations of the presence or absence of KIR loci with a genetic predisposition to MPA. METHODS: The presence or absence of 14 KIR loci was determined in 57 myeloperoxidase antineutrophil cytoplasmic antibody-positive Japanese subjects (43 patients with MPA and 239 healthy controls). RESULTS: The carrier frequency of activating KIR2DS3 was significantly decreased among patients with MPA compared with healthy controls (4.7% versus 16.7%; P = 0.038, odds ratio [OR] 0.24, 95% confidence interval [95% CI] 0.06-0.94). When KIRs were analyzed in combination with their HLA ligands, the proportion of individuals carrying inhibitory KIR3DL1 and HLA-Bw4 but not activating receptor KIR3DS1, a combination presumed to be the most inhibitory of all KIR3DS1/3DL1/HLA-B combinations, was significantly increased in the MPA group compared with the control group (46.5% versus 27.0%; P = 0.014, OR 2.35, 95% CI 1.18-4.70). Furthermore, when subjects were classified according to KIR3DL1/3DS1/HLA-B and KIR2DL1/ HLA-C combinations, an increasing trend toward susceptibility was observed as combinations became more inhibitory. CONCLUSION: The decreased activation potential of NK and/or T cells associated with KIR/HLA genotypes may predispose to MPA, possibly through insufficient resistance against infections.

Aged↗
PubMed2006

Major histocompatibility complex haplotype is associated with postherpetic pain in mice.

BACKGROUND: Postherpetic neuralgia is one of the major complications of herpes zoster caused by the reactivation of varicella-zoster virus and is characterized by severe pain. The authors previously showed the association of a human major histocompatibility complex (MHC) haplotype with postherpetic neuralgia. This study was performed to experimentally confirm the role of MHC haplotype in the development of postherpetic pain using a mouse model of postherpetic pain, which corresponds to postherpetic neuralgia. METHODS: BALB/c mice (MHC haplotype: H-2), C57BL/6 mice (MHC haplotype: H-2), and BALB/b mice, a congenic BALB/c strain with H-2, were used. Herpes simplex virus type I was transdermally inoculated on the hind paw. Unilaterally zosteriform skin lesion and pain-related responses (acute herpetic pain) were caused, and some mice showed pain-related responses (postherpetic pain) after the cure of skin lesions. Herpes simplex virus type I antigen and CD3-positive cells were immunostained in the dorsal root ganglion in the acute phase. RESULTS: The incidence (78%) of postherpetic pain in C57BL/6 mice was significantly higher than that (35%) in BALB/c mice (P = 0.004, odds ratio = 6.7). Furthermore, the incidence of postherpetic pain in BALB/b (H-2) was similar to that in C57BL/6. Herpes simplex virus type I antigen-positive cells were less in the dorsal root ganglion of C57BL/6 mice than that of BALB/c mice. CD3-positive T cells were more in the dorsal root ganglion of C57BL/6 mice than BALB/c mice. CONCLUSIONS: These results suggest that the MHC haplotype (H-2) is involved in the incidence of postherpetic pain, and CD3-positive T cells may play a role in its pathogenesis.

Animals↗