Dr. Shigeki Nakagome

Dr. Shigeki Nakagome

Assistant Professor, Psychiatry

3531896 2241https://shigekinakagomelab.com/

Biography

Shigeki Nakagome is Ussher Assistant Professor in Genomic Medicine at School of Medicine. Dr. Nakagome received his Ph.D. at The University of Tokyo in 2010 with the focus on the evolutionary model in which high risk variants associated with Crohn's disease at the NOD2 locus may have exclusively spread into European populations by natural selection. As a postdoctoral researcher, Dr. Nakagome first joined The Institute of Statistical Mathematics from 2011 to 2014 where he was awarded a competitive Research Fellowship of the Japan Society for the Promotion of Science (JSPS) for Young Scientists and developed a new statistical method that incorporates kernel methods into Approximate Bayesian Computation (kernel ABC). Dr. Nakagome obtained further postdoctoral training on experimental aspects of functional genomics at The University of Chicago from 2013 to 2016 as JSPS Overseas Research Fellow. During this training, Dr. Nakagome has acquired expertise in population and functional genomics to develop statistical approaches for understanding selective pressures on immunity genes and to connect genetic polymorphisms to their functional consequences in the immune system.

Publications and Further Research Outputs

  • Nakagome S, Alkorta-Aranburu G, Amato R, Howie B, Peter BM, Hudson RR, Di Rienzo A, Estimating the Ages of Selection Signals from Different Epochs in Human History., Molecular biology and evolution, 33, (3), 2016, p657-69Journal Article, 2016, DOI
  • Jeong C, Nakagome S, Di Rienzo A, Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu., Genetics, 202, (1), 2016, p261-72Journal Article, 2016, DOI
  • Kariuki SN, Maranville JC, Baxter SS, Jeong C, Nakagome S, Hrusch CL, Witonsky DB, Sperling AI, Di Rienzo A, Mapping Variation in Cellular and Transcriptional Response to 1,25-Dihydroxyvitamin D3 in Peripheral Blood Mononuclear Cells., PloS one, 11, (7), 2016, pe0159779Journal Article, 2016, DOI , TARA - Full Text
  • Kariuki SN, Blischak JD, Nakagome S, Witonsky DB, Di Rienzo A, Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes., G3 (Bethesda, Md.), 6, (5), 2016, p1345-55Journal Article, 2016, DOI , TARA - Full Text
  • Nakagome S, Sato T, Ishida H, Hanihara T, Yamaguchi T, Kimura R, Mano S, Oota H, Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data., Molecular biology and evolution, 32, (6), 2015, p1533-43Journal Article, 2015, DOI
  • Katsumura T, Oda S, Nakagome S, Hanihara T, Kataoka H, Mitani H, Kawamura S, Oota H, Natural allelic variations of xenobiotic-metabolizing enzymes affect sexual dimorphism in Oryzias latipes., Proceedings. Biological sciences / The Royal Society, 281, (1797), 2014Journal Article, 2014, DOI
  • Sato T, Nakagome S, Watanabe C, Yamaguchi K, Kawaguchi A, Koganebuchi K, Haneji K, Yamaguchi T, Hanihara T, Yamamoto K, Ishida H, Mano S, Kimura R, Oota H, Genome-wide SNP analysis reveals population structure and demographic history of the ryukyu islanders in the southern part of the Japanese archipelago., Molecular biology and evolution, 31, (11), 2014, p2929-40Journal Article, 2014, DOI
  • Said HS, Suda W, Nakagome S, Chinen H, Oshima K, Kim S, Kimura R, Iraha A, Ishida H, Fujita J, Mano S, Morita H, Dohi T, Oota H, Hattori M, Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers., DNA research : an international journal for rapid publication of reports on genes and genomes, 21, (1), 2014, p15-25Journal Article, 2014, DOI , TARA - Full Text
  • Nakagome S, Fukumizu K, Mano S, Kernel approximate Bayesian computation in population genetic inferences., Statistical applications in genetics and molecular biology, 12, (6), 2013, p667-78Journal Article, 2013, DOI
  • Osada N, Nakagome S, Mano S, Kameoka Y, Takahashi I, Terao K, Finding the factors of reduced genetic diversity on X chromosomes of Macaca fascicularis: male-driven evolution, demography, and natural selection., Genetics, 195, (3), 2013, p1027-35Journal Article, 2013, DOI
  • Nakagome S, Nakajima Y, Mano S, Biogeography revealed by mariner-like transposable element sequences via a Bayesian coalescent approach., Journal of molecular evolution, 77, (3), 2013, p64-9Journal Article, 2013, DOI
  • Nakagome S, Mano S, Hasegawa M, Comment on "Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage"., Science, 339, (6127), 2013, p1522Journal Article, 2013, DOI , TARA - Full Text
  • Nakagome S, Mano S, Hasegawa M, Ancestral polymorphisms and sex-biased migration shaped the demographic history of brown bears and polar bears., PloS one, 8, (11), 2013, pe78813Journal Article, 2013, DOI , TARA - Full Text
  • Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H, Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation., Molecular biology and evolution, 29, (6), 2012, p1569-85Journal Article, 2012, DOI , TARA - Full Text
  • Evolutionary Insights into the "Population-Specificity" of the Genetic Factors Associated with Inflammatory Bowel Diseases in, editor(s)Mustafa M. Shennak , Ulcerative Colitis from Genetics to Complications, 2012, [Shigeki Nakagome, Hiroki Oot]Book Chapter, 2012, DOI , TARA - Full Text
  • Koganebuchi K., Katsumura T., Nakagome S., Ishida H., Kawamura S., Oota H., The Asian Archival DNA Repository Consortium, Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders, Anthropological Science, 120, (3), 2012, p199--208Journal Article, 2012
  • Nakagome S, Takeyama Y, Mano S, Sakisaka S, Matsui T, Kawamura S, Oota H, Population-specific susceptibility to Crohn's disease and ulcerative colitis; dominant and recessive relative risks in the Japanese population., Annals of human genetics, 74, (2), 2010, p126-36Journal Article, 2010, DOI
  • Nakagome S, Pecon-Slattery J, Masuda R, Unequal rates of Y chromosome gene divergence during speciation of the family Ursidae., Molecular biology and evolution, 25, (7), 2008, p1344-56Journal Article, 2008, DOI , TARA - Full Text
  • Nakagome S, On the use of kernel approximate Bayesian computation to infer population history., Genes & genetic systems, 90, (3), 2015, p153-62Journal Article, 2015, DOI
  • Lindo, J., Huerta-Sánchez, E., Nakagome, S., Rasmussen M., Petzelt B., Mitchell J., Cybulski J.S., Willerslev E., Degiorgio, M., Malhi, R.S., A time transect of exomes from a Native American population before and after European contact, Nature Communications, 7, 2016, p13175Journal Article, 2016, DOI , TARA - Full Text
  • Nakagome S., Oota H., Population Genetics Analysis of the Origin of Modern Japanese, eLS , 2016Journal Article, 2016
  • Alleyne D, Witonsky DB, Mapes B, Nakagome S, Sommars M, Hong E, Muckala KA, Di Rienzo A, Kupfer SS, Colonic transcriptional response to 1alpha,25(OH)2 vitamin D3 in African- and European-Americans., The Journal of Steroid Biochemistry and Molecular Biology, 168, 2017, p49 - 59Journal Article, 2017
  • 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, Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands., Human Genetics, 2017Journal Article, 2017
  • Foley C, Corvin A, Nakagome S, Genetics of Schizophrenia: Ready to Translate?, Current Psychiatry Reports, 19, (9), 2017, p61-Journal Article, 2017, DOI , URL
  • Akiyama T., Katsumura T., Nakagome S., Lee S., Joh K., Soejima H., Fujimoto K., Kimura R., Ishida H., Hanihara T., Yasukouchi A., Satta Y., Higuchi S., Oota H., An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression, PLOS ONE, 12, (6), 2017, e0178373Journal Article, 2017, DOI , URL
  • McColl H., Racimo F., Vinner L., Demeter F., Gakuhari T., Moreno-Mayar J., van Driem G., Gram Wilken U., Seguin-Orlando A., de la Fuente C., Wasef S., Shoocongdej R., Souksavatdy V., Sayavongkhamdy T., Saidin M., Allentoft M., Sato T., Korneliussen T., Prohaska A., Margarayan A., de Barros Damgaard P., Kaewsutthi S., Lertrit P., Nguyen T., Hung H., Minh Tran T., Nghia Truong H., Nguyen G., Shahidan S., Wiradnyana K., Matsumae H., Shigehara N., Yoneda M., Ishida H., Masuda Y., Yamada Y., Tajima A., Shibata H., Toyoda A., Hanihara T., Nakagome S., Deviese T., Bacon A., Duringer P., Ponche J., Shackelford L., Patole-Edoumba E., Nguyen T., Bellina-Pryce B., Galipaud J., Kinaston R., Buckley H., Pottier C., Rasmussen S., Higham T., Foley R.A., Mirazón Lahr M., Orlando L., Sikora M., Oota H., Higham C., Lambert D.M., Willerslev E., The prehistoric peopling of Southeast Asia, Science, 361, 2018, p88 - 92Journal Article, 2018, DOI , URL
  • Cooke N.P., Nakagome S., Fine-tuning of Approximate Bayesian Computation for human population genomics, Current Opinion in Genetics & Development, 53, 2018, p60 - 69Journal Article, 2018, DOI , URL
  • Lin M., Siford R.L., Martin A.R., Nakagome S., Möller M., Hoal E.G., Bustamante C.D., Gignoux C.R., Henn B.M., Rapid evolution of a skin-lightening allele in southern African KhoeSan, Proceedings of the National Academy of Sciences of the United States of America, 115, (52), 2018, p13324 - 13329Journal Article, 2018, DOI , URL
  • Nakagome S., Hudson R.R., Di Rienzo A., Inferring the model and onset of natural selection under varying population size from the site frequency spectrum and haplotype structure, Proceedings of the Royal Society B: Biological Sciences, 286, 2019, p20182541-Journal Article, 2019, DOI , URL , TARA - Full Text
  • Nakagome S., Hudson R.R., Di Rienzo A., Estimating the onsets of selection on new mutations and standing variation in human populations, European Mathematical Genetics Meeting 2017, Tartu, Estonia, April 4-7, 2017Oral Presentation, 2017, URL
  • Nakagome S. and Mano S., Application of kernel approximate Bayesian computation to demographic inferences, Annual Meeting of the Society for Molecular Biology and Evolution 2014, San Juan, Puerto Rico, June 9-12, 2014Oral Presentation, 2014, URL
  • CookeN., Bradley D.G., Nakagome S., A simulation study on the origin of natural selection in an admixed population, Irish Society of Human Genetics 2018, Dublin, Ireland, September 21st, 2018Poster, 2018, URL
  • Nakagome S., Chinen H., Iraha A., Hokama A., Takeyama Y., Sakisaka S., Matsui T., Kidd J.R., Kidd K.K., Said H.S., Suda W., Morita H., Hattori M., Hanihara T., Kimura R., Ishida H., Fujita J., Kinjo F., Mano S., Oota H. , Testing a host-microbiome interaction in the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands, Immunogenomics of disease: accelerating to patient benefit, Cambridge, UK, February 6th-8th, 2017Poster, 2017
  • Nakagome S., Mano S., Kozlowski L., Bujnicki J. M., Shibata H., Fukumaki Y., Kidd J. R., Kidd. K. K., Kawamura S., Oota H., Population specific distribution of Crohn's disease risk alleles on the NOD2 locus and natural selection on standing variation, Annual Meeting of the Society for Molecular Biology and Evolution 2011, Kyoto, Japan, July 26-30, 2011Oral Presentation, 2011, URL
  • Nakagome S., Fukumizu K., Mano S., Kernel Bayesian computation, Population Genetics Group Meeting 45, Nottingham, UK, January 4-7, 2012Oral Presentation, 2012, URL
  • Nakagome S., Fukumizu K., Mano S., Kernel Bayesian computation, XXVIth International Biometric Conference, Kobe, Japan, August 26-31, 2012Oral Presentation, 2012, URL
  • Nakagome S., Chinen H., Iraha A., Hokama A., Takeyama Y., Sakisaka S., Matsui T., Kidd J.R., Kidd K.K., Said H.S., Suda W., Morita H., Hattori M., Hanihara T., Kimura R., Ishida H., Fujita J., Kinjo F., Mano S., Oota H., Evolutionary insights into genetic and environmental factors for Crohn's disease in Ryuku and Northern Kyushu, American Society of Human Genetics 2013 Annual Meeting, Boston, USA, October 22-26, 2013Poster, 2013, URL
  • Nakagome S., Takeyama Y., Mano S., Sakisaka S., Matsui T., Kawamura S., and Oota H., A population specific susceptibility and genotype risk to Crohn's disease and ulcerative colitis, American Society of Human Genetics 2009 Annual Meeting, Honolulu, USA, October 20-24, 2009Poster, 2009
  • Nakagome S., Mano S., Kidd J. R., Kidd K. K., Kawamura S., and Oota H., An evolutionary analysis of the NOD2 gene associated with Crohn's disease, Annual Meeting of the Society for Molecular Biology and Evolution 2010, Lyon, France, July 4-8, 2010Poster, 2010
  • Nakagome S., Mano S., Kozlowski L., Bujnicki J. M., Shibata H., Fukumaki Y., Kidd J. R., Kidd. K. K., Kawamura S., Oota H., Population specific susceptibility to Crohn's disease and signals of natural selection on standing variation, American Society of Human Genetics 2011 Annual Meeting, Montreal, Canada, October 11-15, 2011Poster, 2011
  • Saravanarajan K, Douglas AR, Ismail MS, Omorogbe J, Semenov S, Muphy G, O'Riordan F, McNamara D, Nakagome S, Genomic profiling of intestinal T-cell receptor repertoires in inflammatory bowel disease. , Genes and Immunity, 2020, pEpub Ahead of Print Feb 2020Journal Article, 2020, DOI
  • Hudson M.J., Nakagome S., Whitman J.B., The evolving Japanese: the dual structure hypothesis at 30, Evolutionary Human Sciences, 2, 2020, p1 - 13Journal Article, 2020, DOI
  • Shigeki Nakagome, The origins of Jomon and its contribution to modern Japanese, World Archaeological Congress 9, Prague, Czech Republic, July 4-9, 2021Invited Talk, 2021, URL
  • Saitou, M. and Resendez, S. and Pradhan, A.J. and Wu, F. and Lie, N.C. and Hall, N.J. and Zhu, Q. and Reinholdt, L. and Satta, Y. and Speidel, L. and Nakagome, S. and Hanchard, N.A. and Churchill, G. and Lee, C. and Atilla-Gokcumen, G.E. and Mu, X. and Gokcumen, O., Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor, Science Advances, 7, (39), 2021Journal Article, 2021, DOI , URL
  • Cooke, N.P. and Mattiangeli, V. and Cassidy, L.M. and Okazaki, K. and Stokes, C.A. and Onbe, S. and Hatakeyama, S. and Machida, K. and Kasai, K. and Tomioka, N. and Matsumoto, A. and Ito, M. and Kojima, Y. and Bradley, D.G. and Gakuhari, T. and Nakagome, S., Ancient genomics reveals tripartite origins of Japanese populations, Science Advances, 7, (38), 2021Journal Article, 2021, DOI , URL
  • Gakuhari, T. and Nakagome, S. and Rasmussen, S. and Allentoft, M.E. and Sato, T. and Korneliussen, T. and Chuinneagáin, B.N. and Matsumae, H. and Koganebuchi, K. and Schmidt, R. and Mizushima, S. and Kondo, O. and Shigehara, N. and Yoneda, M. and Kimura, R. and Ishida, H. and Masuyama, T. and Yamada, Y. and Tajima, A. and Shibata, H. and Toyoda, A. and Tsurumoto, T. and Wakebe, T. and Shitara, H. and Hanihara, T. and Willerslev, E. and Sikora, M. and Oota, H., Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations, Communications Biology, 3, (1), 2020Journal Article, 2020, DOI , URL
  • Gakuhari T., Nakagome S., Rasumussen S., Allentoft M., Sato T., Korneliussen T., Ni Chuinneagain B., Matsumae H., Koganebuchi K., Schmidt R., Mizushima S., Kondo O., Shigehara N., Yoneda M., Kimura R., Ishida H., Masuyama Y., Yamada Y., Tajima A., Shibata H., Toyoda A., Tsurumoto T., Wakebe T., Shitara H., Hanihara T., Willerslev E., Sikora M., Oota H., Jomon genome sheds light on East Asian population history, 2019Journal Article, URL
  • Evolutionary consequence of the human Out-of-Africa in, editor(s)Hiroki Oota and Mariko Hasegawa , Human disease and evolution, Keiso-shobo, 2013, pp87 - 124, [Nakagome S. and Oota H.]Book Chapter, URL
  • Nakagome S., Japanese Origins 2019: The Dual Structure Hypothesis at 30, Interdisciplinary TransEurasian Conference, Jena, Germany, January 9-10, 2019, Martine RobbeetsInvited Talk, URL
  • Nakagome S., Identifying the Origin of Natural Selection in Modern Japanese, Future Perspective on Ancient Genomics in East Asia, Tokyo, Japan, October 21, 2018, Takashi GakuhariInvited Talk, URL
  • Nakagome S., Mano S., Kozlowski L., Bujnicki J. M., Kidd J. R., Kidd. K. K., Kawamura S., Oota H., An evolutionary study of human complex diseases, Workshop on Evolutionary Analyses and Applications, Xi'an and Lhasa, China, June 9, 2011Invited Talk
  • Nakagome S., Evolutionary study of Crohn's disease gene, Invited seminar at National Institute of Biomedical Genomics, West-Bengal, India, March 5, 2013, Partha P. MajumderInvited Talk
  • Nakagome S., Applying population genetics to human complex disease, The 1739th Biological Symposium, National Institute of Genetics, Mishima, Japan, February 28, 2014Invited Talk, URL
  • Resendez S., Saitou M., Parisi L.R., Wu F., Nakagome S., Satta Y., Atilla-Gokcumen G.E., Mu X., Gokcumen O., Sex-specific phenotypic effects and evolutionary history of an ancient deletion polymorphism of the human growth hormone receptor, bioRxiv, 2019, p35Journal Article, DOI
  • O'Connor C., McNamara D., Nakagome S., A statistical modelling reveals bi-directional chromatin scanning by RAG in the human TCR-alpha locus, bioRxiv, 2020, p14Journal Article, DOI
  • Nakagome S., Systematic profiling of the T cell receptor repertoire in intestinal inflammation, ASHBi Seminar, Kyoto University Institute for the Advanced Study of Human Biology, 2020Invited Talk
  • Nakagome S., Population genetics inference on the mode, tempo, and origins of natural selection, 21st Annual Meeting of the Society of Evolutionary Studies, Japan, Hokkaido University, Sapporo, Japan, 2019Invited Talk
  • Evolutionary perspective on human disease - targets of natural selection and its by-products in, editor(s)Akihiro Fujimoto , Understanding human disease in the context of molecular evolution, Igaku-no Ayumi, Ishiyaku Shuppan, 2020, [Shigeki Nakagome]Book Chapter

Research Expertise

Symbiosis between human host and gut microbiota is essential for our health, a disruption of which leads to autoimmune conditions, as is the case in inflammatory bowel disease (IBD). A critical challenge for the host under the intestinal environment is to mount an efficient and appropriate immune response to pathogens while maintaining tolerance to symbiotic bacteria. However, we still do not know the underlying molecular mechanisms whereby humans acquire tolerance to host trillions of microorganisms in their intestine. Our research team aims to understand the nature and function of host immune repertoires that provide the ability to discriminate pathogenic from symbiotic bacteria. Outcomes from our research will not only yield deeper insights into the host-microbiota crosstalk in IBD, but also pioneer personalized and targeted interventions to control this interaction for prevention and treatment of IBD. Taking advantage of our expertise in quantitative genetics and its application to high-throughput sequencing, we develop statistical and computational approaches to immunogenomics profiling on patients affected by IBD. Our research aims to describe (i) the patterns of inter-individual variation in the host immunity and bacterial activity, (ii) the processes of immune development that ends up with the breakdown of host tolerance to gut bacteria, and (iii) the impacts of past selective pressures during human evolution on an individual's ability to adapt to its own intestinal environments.

Immunity and Infection (including Rheumatology & Inflammatory disease), Immunity and Infection (including Rheumatology & Inflammatory disease), Genetics and Genomics, Mathematical and Computational Biology including Bioinformatics and Systems Biology, Genetics and Genomics, Mathematical and Computational Biology including Bioinformatics and Systems Biology,

Recognition

  • Dean's Award in International Exchange Section, Graduate School of Frontier Sciences, The University of Tokyo (awarded as the organizing committee of international conference) 2009
  • Scholarship at College of Bioresource Sciences, Nihon University 2001
  • Postdoctoral Travel Award, Annual Meeting of the Society for Molecular Biology and Evolution, Kyoto, Japan 2011
  • Research Fellowships of the Japan Society for the Promotion of Science for Young Scientists (PD) 2012
  • Research Fellowships of the Japan Society for the Promotion of Science for Young Scientists (DC2) 2009
  • Japan Society for the Promotion of Science Overseas Research Fellowships 2014
  • Dean's Prize, College of Bioresource Sciences, Nihon University 2005
  • European Society of Human Genetics Present
  • Society for Molecular Biology and Evolution Present
  • Irish Society of Human Genetics Present
  • The American Society of Human Genetics Present
  • Analysis Provider in GenomeAsia 100K 2018-Present
  • Review Editor for Frontier in Ecology and Evolution 2013-Present
  • Member of Asian DNA Repository Consortium 2013-Present
  • Member of Asian DNA Repository Consortium 2013-Present
  • Analysis Provider in GenomeAsia 100K 2018-Present
  • Review Editor for Frontier in Ecology and Evolution 2013-Present