論文 - 木村　亮介

A new anatomical classification of the bronchial arteries based on the spatial relationships to the esophagus and the tracheobronchus.

Hayasaka K, Ishida H, Kimura R, Nishimaki T

Surgery today ( Surgery Today )  47 ( 7 ) 883 - 890   2017年07月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Purpose To reveal the patterns of the mediastinal course of the bronchial arteries (BAs). Methods The BAs were dissected to determine the positional relationships of their mediastinal courses with the tracheobronchus and the esophagus in 72 adult cadavers. Results The mediastinal courses of the 227 BAs found in this study were classified into 4 types. There were 61 and 163 BAs passing the right side (Type I) and the left side (Type II reaching dorsal surface (n = 98), or Type III reaching ventral surface (n = 65) of the tracheobronchus) of the esophagus, respectively. Three BAs originated from the subclavian artery (Type IV). All Type I BAs were right BAs, whereas 91.8% of the Type II BAs were left BAs. However, 43.1 and 56.9% of the Type III BAs were the right and left BAs, respectively. Conclusion The classification of the mediastinal course of the BAs determined by the spatial relationships to the tracheobronchus and the esophagus may be clinically useful, because each category of this classification can be determined during esophagectomy and indicates whether the BA is a right or left BA.

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Characterising private and shared signatures of positive selection in 37 Asian populations.

Liu X, Lu D, Saw WY, Shaw PJ, Wangkumhang P, Ngamphiw C, Fucharoen S, Lert-Itthiporn W, Chin-Inmanu K, Chau TN, Anders K, Kasturiratne A, de Silva HJ, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Takeuchi F, Yamamoto K, Yokota M, Mamatyusupu D, Yang W, Chung YJ, Jin L, Hoh BP, Wickremasinghe AR, Ong RH, Khor CC, Dunstan SJ, Simmons C, Tongsima S, Suriyaphol P, Kato N, Xu S, Teo YY

European journal of human genetics : EJHG ( European Journal of Human Genetics )  25 ( 4 ) 499 - 508   2017年04月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.

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Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands.

Nakagome S, Chinen H, Iraha A, Hokama A, Takeyama Y, Sakisaka S, Matsui T, Kidd JR, Kidd KK, Said HS, Suda W, Morita H, Hattori M, Hanihara T, Kimura R, Ishida H, Fujita J, Kinjo F, Mano S, Oota H

Human genetics ( Human Genetics )  136 ( 4 ) 387 - 397   2017年04月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Growth hormone receptor gene variant and three-dimensional mandibular morphology.

Nakawaki T, Yamaguchi T, Isa M, Kawaguchi A, Tomita D, Hikita Y, Suzuki-Tomoyasu Y, Adel M, Ishida H, Maki K, Kimura R

The Angle orthodontist ( Angle Orthodontist )  87 ( 1 ) 68 - 73   2017年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Objective: To examine the relationship between three-dimensional mandibular morphology and growth hormone receptor (GHR) gene variants in a healthy Japanese population. Materials and Methods: The subjects, who were unrelated Japanese orthodontic patients, consisted of 64 men and 114 women. Using the Taqman genotyping assay, GHR gene rs6184 and rs6180 variants were detected in genomic DNA extracted from saliva. Mandibular volume and length were measured from cone-beam computed tomography images that were analyzed using Analyze image-processing software. The relationship between GHR gene variants and three-dimensional mandibular morphology was statistically examined. Results: Statistical significance for the relationship between the distance between the left and right coronoid processes and rs6180 was noted (P < .05). Conclusion: Our results indicate that the GHR variant rs6180 is associated with the distance between the left and right coronoid process in the Japanese subjects.

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The fine-scale genetic structure and evolution of the Japanese population.

Takeuchi F, Katsuya T, Kimura R, Nabika T, Isomura M, Ohkubo T, Tabara Y, Yamamoto K, Yokota M, Liu X, Saw WY, Mamatyusupu D, Yang W, Xu S, Japanese Genome Variation Consortium., Teo YY, Kato N

PloS one ( PLoS ONE )  12 ( 11 ) e0185487   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The contemporary Japanese populations largely consist of three genetically distinct groups Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

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Polymorphisms associated with a tropical climate and root crop diet induce susceptibility to metabolic and cardiovascular diseases in Solomon Islands.

Furusawa T, Naka I, Yamauchi T, Natsuhara K, Eddie R, Kimura R, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J

PloS one ( PLoS ONE )  12 ( 3 ) e0172676   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The people of the Solomon Islands represent an Austronesian (AN)-speaking population's adaptation to a humid tropical environment and subsistence of tuberous crops. Genome-wide association studies (GWASs) of other populations (e.g. the Human Genome Diversity Project [HGDP]) have suggested the existence of genotypes adaptive to ecoregion, diet, and subsistence, and that those genotypes are also associated with metabolic and cardiovascular diseases. Recently, the incidence of non-communicable diseases has been increasing in the Solomon Islands. In the present study, we explored the association of genotypes adaptive to a tropical environment and tuberous crop diet with metabolic and cardiovascular conditions in rural and urban AN-speaking Melanesian and Micronesian populations of the Solomon Islands. A total of 561 participants were genotyped for single nucleotide polymorphisms (SNPs) potentially associated with a tropical environment (rs174570 and rs2237892) and a tuberous crop diet (rs162036, rs185819, and rs2722425). The results showed that the allele frequencies of the Solomon Islands populations adopted patterns similar to those in populations from other hot, tropical areas with a tuberous crop diet in previous studies. Furthermore, rs162036, rs185819, rs2237892, and rs2722425 were all strongly associated with one or more metabolic and cardiovascular conditions. The derived allele of rs2722425 (i.e. rs2722425-G) was significantly associated with an elevated LDL level (P = 0.000264) even after the significance level was adjusted for multiple testing (i.e., alpha = 0.0005). Our results suggest that the inhabitants of the Solomon Islands exhibit the effects of the tropical environment and tuberous crop diet on their allele frequencies, and that their susceptibility to metabolic and cardiovascular diseases is therefore considered to be associated with their environment and diet.

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Contribution of FGFR1 Variants to Craniofacial Variations in East Asians.

Adel M, Yamaguchi T, Tomita D, Nakawaki T, Kim YI, Hikita Y, Haga S, Takahashi M, Nadim MA, Kawaguchi A, Isa M, El-Kenany WH, El-Kadi AA, Park SB, Ishida H, Maki K, Kimura R

PloS one ( PLoS ONE )  12 ( 1 ) e0170645   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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FGFR1 plays an important role in the development of the nervous system as well as the regulation of the skeletal development and bone homeostasis. Mutations in FGFR1 genes affect skull development, specifically suture and synchondrosis, resulting in craniosynostosis and facial abnormalities. We examined subjects with normal skull morphology for genetic polymorphisms that might be associated with normal craniofacial variations. Genomic DNA was obtained from 216 Japanese and 227 Korean subjects. Four FGFR1 SNPs, namely, rs881301, rs6996321, rs4647905, and rs13317, were genotyped. These SNPs were tested for association with craniofacial measurements obtained from lateral and posteroanterior cephalometries, in which principle component analysis was performed to compress the data of the craniofacial measurements. We observed that SNPs rs13317 and rs6996321 were correlated with the overall head size and midfacial development, indicating that FGFR1 SNPs played crucial roles in the normal variation of human craniofacial morphology. Subjects with the derived alleles of SNPs rs13317 and rs6996321 had a small face and a facial pattern associated with a retruded midface and relatively wide-set eyes. These facial features were similar to but were milder than those of individuals with Pfeiffer syndrome, which is caused by a dysfunctional mutation in FGFR1.

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Comprehensive genetic exploration of selective tooth agenesis of mandibular incisors by exome sequencing.

Yamaguchi T, Hosomichi K, Yano K, Kim YI, Nakaoka H, Kimura R, Otsuka H, Nonaka N, Haga S, Takahashi M, Shirota T, Kikkawa Y, Yamada A, Kamijo R, Park SB, Nakamura M, Maki K, Inoue I

Human genome variation ( Human Genome Variation )  4   17005 - 17005   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Tooth agenesis is described as the absence of one or more teeth. It is caused by a failure in tooth development and is one of the most common human developmental anomalies. We herein report genomic analyses of selective mandibular incisor agenesis (SMIA) using exome sequencing. Two Japanese families with SMIA were subjected to exome sequencing, and family with sequence similarity 65 member A (FAM65), nuclear factor of activated T-cells 3 (NFATC3) and cadherin-related 23 gene (CDH23) were detected. In the follow-up study, 51 Japanese and 32 Korean sporadic patients with SMIA were subjected to exome analyses, and 18 reported variants in PAX9, AXIN2, EDA, EDAR, WNT10A, BMP2 and GREM2 and 27 variants of FAM65, NFATC3 and CDH23 were found in 38 patients. Our comprehensive genetic study of SMIA will pave the way for a full understanding of the genetic etiology of SMIA and provide targets for treatment.

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An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression.

Akiyama T, Katsumura T, Nakagome S, Lee SI, Joh K, Soejima H, Fujimoto K, Kimura R, Ishida H, Hanihara T, Yasukouchi A, Satta Y, Higuchi S, Oota H

PloS one ( PUBLIC LIBRARY SCIENCE )  12 ( 6 ) e0178373   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Humans show various responses to the environmental stimulus in individual levels as "physiological variations." However, it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological data from 43 subjects, including light-induced melatonin suppression, and performed haplotype analyses on the clock genes, PER2 and PER3, exhibiting geographical differentiation of allele frequencies. Among the haplotypes of PER3, no significant difference in light sensitivity was found. However, three common haplotypes of PER2 accounted for more than 96% of the chromosomes in subjects, and 1 of those 3 had a significantly low-sensitive response to light-stimulus (P < 0.05). The homozygote of the low-sensitive PER2 haplotype showed significantly lower percentages of melatonin suppression (P 0.05), and the heterozygotes of the haplotypes varied their ratios, indicating that the physiological variation for light-sensitivity is evidently related to the PER2 polymorphism. Compared with global haplotype frequencies, the haplotype with a low-sensitive response was more frequent in Africans than in non-Africans, and came to the root in the phylogenetic tree, suggesting that the low light-sensitive haplotype is the ancestral type, whereas the other haplotypes with high sensitivity to light are the derived types. Hence, we speculate that the high light-sensitive haplotypes have spread throughout the world after the Out-of-Africa migration of modern humans.

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Whole-body patterns of the range of joint motion in young adults: masculine type and feminine type.

Moromizato K, Kimura R, Fukase H, Yamaguchi K, Ishida H

Journal of physiological anthropology ( Journal of Physiological Anthropology )  35 ( 1 ) 23   2016年10月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Degenerative changes in the appendicular joints of ancient human populations from the Japan Islands

Suzuki S.

Quaternary International ( Quaternary International )  405   147 - 159   2016年06月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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An Okhotsk adult female human skeleton (11th/12th century AD) with possible SAPHO syndrome from Hamanaka 2 site, Rebun Island, northern Japan

OKAMOTO Yuka, ISHIDA Hajime, KIMURA Ryosuke, SATO Takehiro, TSUCHIYA Nanae, MURAYAMA Sadayuki, FUKASE Hitoshi, NAGAOKA Tomohito, ADACHI Noboru, YONEDA Minoru, WEBER Andrzej, KATO Hirofumi

Ａｎｔｈｒｏｐｏｌｏｇｉｃａｌ　Ｓｃｉｅｎｃｅ ( 日本人類学会 )  124 ( 2 ) 107 - 115   2016年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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<p>We present the oldest human skeletal case yet identified with possible SAPHO syndrome (synovitis, acne, pustulosis, hyperostosis, osteitis), a chronic disease involving the skin, bone, and joints. A human skeleton with a severe pathological condition was recovered from a shell mound of the prehistoric Okhotsk culture at the Hamanaka 2 site, Rebun Island, Hokkaido, Japan in 2013. Morphological and <i>Amelogenin</i> gene analyses determined the sex as female, and the age at time of death was estimated to be in the forties using analysis of the auricular surface of the ilium. The stable isotope ratios of this individual (NAT002) and other Hamanaka 2 samples indicated a heavy dependence on marine mammals and fish for dietary protein intake. Radiocarbon age on collagen from the bone of NAT002 was 1689 ± 20 BP, or 1060–1155 (68.2%) calAD. Macroscopic and computed tomography (CT) findings indicated diffuse hyperostosis in the axial and appendicular skeleton, including the mandible, vertebrae, clavicles, sternum, scapulae, humeri, radii, ulnae, and ilium, caused by osteitis and synovitis. The bilateral clavicles were most affected, in which CT imaging revealed irregular cortical thickening, termed 'grotesque periostitis.' The case was diagnosed as most likely having SAPHO syndrome, although dermatological findings could not be detected. Although SAPHO syndrome is a fairly new concept in autoimmune diseases, this case suggests the syndrome originated much earlier in human history.</p>

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A comparative study of craniofacial measurements between Ryukyuan and mainland Japanese females using lateral cephalometric images

YAMAUCHI Tadashi, KIMURA Ryosuke, KAWAGUCHI Akira, SATO Takehiro, YAMAGUCHI Kyoko, TOMA Takashi, MIYAMOTO Kiyoto, FUKASE Hitoshi, YAMAGUCHI Tetsutaro, ISHIDA Hajime

Ａｎｔｈｒｏｐｏｌｏｇｉｃａｌ　Ｓｃｉｅｎｃｅ ( 日本人類学会 )  124 ( 1 ) 45 - 62   2016年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Using lateral cephalometric images, we compared the skeletal and soft tissue configurations of Ryukyuan and mainland Japanese females. We collected lateral cephalometric images of 30 females each from Okinawa Island and mainland Japan. Sixty landmarks were plotted on each image. Then, based on the coordinates of the landmarks, 68 distances and 34 angles were calculated according to orthodontic and anthropometric methods. We confirmed that the Ryukyuans have a smaller height in the upper and midfacial region than the mainland Japanese. Moreover, our findings indicate that, compared with the mainland Japanese females, the Ryukyuan females clearly have the following features: (1) a shallower mandibular notch, (2) an anterior-inclined symphysis of mandible, and (3) a smaller depth from upper lip to incisors. We also found that an anterior-inclined mandibular corpus and incisors are associated with a smaller distance between the surfaces of the upper lip and teeth and with a more protruded lip shape.

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Mapping the genetic diversity of HLA haplotypes in the Japanese populations.

Saw WY, Liu X, Khor CC, Takeuchi F, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Yamamoto K, Yokota M, Japanese Genome Variation Consortium., Teo YY, Kato N

Scientific reports ( Scientific Reports )  5   17855   2015年12月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Japan has often been viewed as an Asian country that possesses a genetically homogenous community. The basis for partitioning the country into prefectures has largely been geographical, although cultural and linguistic differences still exist between some of the districts/prefectures, especially between Okinawa and the mainland prefectures. The Major Histocompatibility Complex (MHC) region has consistently emerged as the most polymorphic region in the human genome, harbouring numerous biologically important variants; nevertheless the presence of population-specific long haplotypes hinders the imputation of SNPs and classical HLA alleles. Here, we examined the extent of genetic variation at the MHC between eight Japanese populations sampled from Okinawa, and six other prefectures located in or close to the mainland of Japan, specifically focusing at the haplotypes observed within each population, and what the impact of any variation has on imputation. Our results indicated that Okinawa was genetically farther to the mainland Japanese than were Gujarati Indians from Tamil Indians, while the mainland Japanese from six prefectures were more homogeneous than between northern and southern Han Chinese. The distribution of haplotypes across Japan was similar, although imputation was most accurate for Okinawa and several mainland prefectures when population-specific panels were used as reference.

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Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data.

Nakagome S, Sato T, Ishida H, Hanihara T, Yamaguchi T, Kimura R, Mano S, Oota H, Asian DNA Repository Consortium.

Molecular biology and evolution ( Molecular Biology and Evolution )  32 ( 6 ) 1533 - 43   2015年06月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are assumed to have originated in southeast Asia and lived in the Japanese archipelago greater than 10,000 years ago, admixed with an agricultural people known as Yayoi, whom were migrants from the East Asian continent 2,000-3,000 years ago. Meanwhile, some anthropologists propose that rather, morphological differences between the Jomon and Yayoi people can be explained by microevolution following the lifestyle change. To resolve this controversy, we compared three demographic models by approximate Bayesian computation using genome-wide single nucleotide polymorphism (gwSNP) data from the Ainu people who are thought to be direct descendants of indigenous Jomon. If we assume Chinese people sampled in Beijing from HapMap have the same ancestry as Yayoi, then the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively. Furthermore, our data provide strong support for a model in which the Jomon lineages had population structure diversified in local areas before the admixture event. Initial divergence between the Jomon and Yayoi ancestries was dated to late Pleistocene, followed by the divergence of Jomon lineages at early Holocene. These results suggest gwSNP data provides a detailed picture of the complex hybridization model for Japanese population history.

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Common polymorphisms in WNT10A affect tooth morphology as well as hair shape.

Kimura R, Watanabe C, Kawaguchi A, Kim YI, Park SB, Maki K, Ishida H, Yamaguchi T

Human molecular genetics ( Human Molecular Genetics )  24 ( 9 ) 2673 - 80   2015年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Hair and teeth are appendages of ectodermal origin, and there are common molecular backgrounds involved in their formation. To date, it has been revealed that a non-synonymous polymorphismin EDAR has effects on the morphological variation in both hair and teeth. Previous association studies have confirmed that single-nucleotide polymorphisms (SNPs) in/near THADA, FRAS1, WNT10A, NAF1 and FGFR2 are associated with hair morphology. In this study, we thus examined whether these SNPs are also associated with dental characteristics. We measured metric dental traits including crown size and also evaluated non-metric dental traits using plaster casts obtained from subjects (272 Japanese and 226 Koreans). DNA samples were prepared from the subjects and genotyped for the hair morphology-associated SNPs. We observed a significant association of crown size with an SNP in WNT10A (rs7349332), but not with SNPs in other genes. Therefore, we further examined four SNPs within and around WNT10A, among which rs10177996 had the strongest association with dental traits. World distribution of the derived allele in rs10177996, which is associated with larger teeth, showed that Eurasians have a higher allele frequency than Africans. Together with previous studies on hair morphology, this study demonstrated that common variations in WNT10A have pleiotropic effects on the morphology of ectodermal appendages.

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D-12-19 3次元顔面形態の局所的統計解析(D-12.パターン認識・メディア理解A(パターンメディアの認識・理解・生成),一般セッション)

中津 美冴, 韓 先花, 木村 亮介, 陳 延偉

電子情報通信学会総合大会講演論文集 ( 一般社団法人電子情報通信学会 )  2015 ( 2 )   2015年02月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Common polymorphisms in WNT10A affect tooth morphology as well as hair shape.

Kimura R, Watanabe C, Kawaguchi A, Kim YI, Park SB, Maki K, Ishida H, Yamaguchi T

Hum Mol Genet ( その他の出版社 )  24   2673 - 2680   2015年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Model-Based Verification of Hypotheses on the Origin of Modern Japanese Revisited by Bayesian Inference Based on Genome-Wide SNP Data.

Nakagome S, Sato T, Ishida H, Hanihara T, Yamaguchi T, Kimura R, Mano S, Oota H, Consortium ADR

Molecular Biology and Evolution ( その他の出版社 )  32   1533 - 1543   2015年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

ゲノム情報から古代人の姿を探る

木村 亮介

細胞工学   34   1172 - 1176   2015年

掲載種別: 研究論文（学術雑誌）

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