RIKEN IMS AnnualReport 2021
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91 184 Ota M, Nagafuchi Y, Hatano H, Ishigaki K, Terao C, Takeshima Y, Yanaoka H, Kobayashi S, Okubo M, Shirai H, Sugimori Y, Maeda J, Nakano M, Yamada S, Yoshida R, Tsuchiya H, Tsuchida Y, Akizuki S, Yoshifuji H, Ohmura K, Mimori T, Yoshida K, Kurosaka D, Okada M, Setoguchi K, Kaneko H, Ban N, Yabuki N, Matsuki K, Mutoh H, Oyama S, Okazaki M, Tsunoda H, Iwasaki Y, Sumitomo S, Shoda H, Kochi Y, Okada Y, Yamamoto K, Okamura T, Fujio K. Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases. Cell 184, 3006-3021.e17 (2021) 185 Otani S, Date Y, Ueno T, Ito T, Kajikawa S, Omori K, Taniuchi I, Umeda M, Komori T, Toguchida J, Ito K. Runx3 is required for oncogenic Myc upregulation in p53-deficient osteosarcoma. Oncogene, doi: 10.1038/s41388-021-02120-w (Epub 2021) 186 Otomo N, Lu HF, Koido M, Kou I, Takeda K, Momozawa Y, Kubo M, Kamatani Y, Ogura Y, Takahashi Y, Nakajima M, Minami S, Uno K, Kawakami N, Ito M, Sato T, Watanabe K, Kaito T, Yanagida H, Taneichi H, Harimaya K, Taniguchi Y, Shigematsu H, Iida T, Demura S, Sugawara R, Fujita N, Yagi M, Okada E, Hosogane N, Kono K, Nakamura M, Chiba K, Kotani T, Sakuma T, Akazawa T, Suzuki T, Nishida K, Kakutani K, Tsuji T, Sudo H, Iwata A, Kaneko K, Inami S, Kochi Y, Chang WC, Matsumoto M, Watanabe K, Ikegawa S, Terao C. Polygenic Risk Score of Adolescent Idiopathic Scoliosis for Potential Clinical Use. J Bone Miner Res 36, 1481-1491 (2021) 187 Ozaki K, Irioka T, Uchihara T, Yamada A, Nakamura A, Majima T, Igarashi S, Shintaku H, Yakeishi M, Tsuura Y, Okazaki Y, Ishikawa K, Yokota T. Neuropathology of SCA34 show-ing widespread oligodendroglial pathology with vacuolar white matter degeneration: a case study. Acta Neuropathol Commun 9, 172 (2021) 188 Ozturk M, Chia JE, Hazra R, Saqib M, Maine RA, Guler R, Suzuki H, Mishra BB, Brom-bacher F, Parihar SP. Evaluation of Berberine as an Adjunct to TB Treatment. Front Immunol 12, 656419 (2021) 189 Palihati M, Tsubouchi H, Argunhan B, Kajitani R, Bakenova O, Han YW, Murayama Y, Itoh T, Iwasaki H. Homology length dictates the requirement for Rad51 and Rad52 in gene targeting in the Basidiomycota yeast Naganishia liquefaciens. Curr Genet 67, 919-936 (2021) 190 Patel PN, Ito K, Willcox JAL, Haghighi A, Jang MY, Gorham JM, DePalma SR, Lam L, McDonough B, Johnson R, Lakdawala NK, Roberts A, Barton PJR, Cook SA, Fatkin D, Seidman CE, Seidman JG. Contribution of Noncanonical Splice Variants to TTN Truncat-ing Variant Cardiomyopathy. Circ Genom Precis Med 14, e003389 (2021) 191 Pillay S, Takahashi H, Carninci P, Kanhere A. Antisense RNAs during early vertebrate development are divided in groups with distinct features. Genome Res 31, 995-1010 (2021) 192 Pretemer Y, Kawai S, Nagata S, Nishio M, Watanabe M, Tamaki S, Alev C, Yamanaka Y, Jing-yi X, Wang Z, Fukiage K, Tsukanaka M, Futami T, Ikegawa S, Toguchida J. Differen-tiation of Hypertrophic Chondrocytes from Human iPSCs for the In Vitro Modeling of Chondrodysplasias. Stem Cell Reports 16, 610-625 (2021) 193 Raju S, Xia Y, Daniel B, Yost KE, Bradshaw E, Tonc E, Verbaro DJ, Kometani K, Yokoyama WM, Kurosaki T, Satpathy AT, Egawa T. Identification of a T-bethi Quiescent Exhausted CD8 T Cell Subpopulation That Can Differentiate into TIM3+ CX3CR1+ Effectors and Memory-like Cells. J Immunol 206, 2924-2936 (2021) 194 Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoff-man MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Udara Liyanage I, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nak-agawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O'Connor BD, Oesterle S, Ogishima S, Wang VO, Paglione LAD, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: Building standards for data sharing across genomic research and healthcare. Cell Genom 1, 100029 (2021) 195 Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD; Immunological Genome Consortium. A microRNA expression and regulatory element activity atlas of the mouse immune system. Nat Immunol 22, 914-927 (2021) 196 Rozenblatt-Rosen O, Shin JW, Rood J, Hupalowska A, ** H, Regev A, Heyn H. Building a high-quality Human Cell Atlas. Nat Biotechnol 39, 149-153 (2021) 197 Runcharoen C, Fukunaga K, Sensorn I, Iemwimangsa N, Klumsathian S, Tong H, Vo NS, Le L, Hlaing TM, Thant M, Zain SM, Mohamed Z, Pung Y, Capule F, Nevado J, Silao CL, Al-Mahayri ZN, Ali BR, Yuliwulandari R, Prayuni K, Zahroh H, Noor DA, Xangsayarath P, Xayavong D, Kounnavong S, Sayasone S, Kordou Z, Liopetas I, Tsikrika A, Tsermpini E, Koromina M, Mitropoulou C, Patrinos GP, Kesornsit A, Charoenyingwattana A, Wat-tanapokayakit S, Mahasirimongkol S, Mushiroda T, Chantratita W. Prevalence of phar-macogenomic variants in 100 pharmacogenes among Southeast Asian populations under the collaboration of the Southeast Asian Pharmacogenomics Research Network (SEAPharm). Hum Genome Var 8, 7 (2021) 198 Saika A, Nagatake T, Hirata SI, Sawane K, Adachi J, Abe Y, Isoyama J, Morimoto S, Node E, Tiwari P, Hosomi K, Matsunaga A, Honda T, Tomonaga T, Arita M, Kabashima K, Kunisawa J. ω3 fatty acid metabolite, 12‐hydroxyeicosapentaenoic acid, alleviates contact hypersensitivity by downregulation of CXCL1 and CXCL2 gene expression in keratinocytes via retinoid X receptor α. FASEB J 35, e21354 (2021) 199 Saiki R, Momozawa Y, Nannya Y, Nakagawa MM, Ochi Y, Yoshizato T, Terao C, Kuroda Y, Shiraishi Y, Chiba K, Tanaka H, Niida A, Imoto S, Matsuda K, Morisaki T, Murakami Y, Kamatani Y, Matsuda S, Kubo M, Miyano S, Makishima H, Ogawa S. Combined landscape of single-nucleotide variants and copy number alterations in clonal hema-topoiesis. Nat Med 27, 1239-1249 (2021) 200 Saito K, Inoue T, Ariyasu H, Shimada T, Itoh H, Tanaka I, Terao C. Usefulness of subclas-sification of adult diabetes mellitus among inpatients in Japan. J Diabetes Investig, doi: 10.1111/jdi.13707 (Epub 2021) 201 Sakai M, Takahashi N, Ikeda H, Furutani Y, Higuchi S, Suzuki T, Dohmae N, Kobayashi S, Harada H, Kojima S, Matsuura T, Hattori A, Kakeya H. Design, synthesis, and tar-get identification of new hypoxia-inducible factor 1 (HIF-1) inhibitors containing 1-alkyl-1H-pyrazole-3-carboxamide moiety. Bioorg Med Chem 46, 116375 (2021) 202 Sakaue S, Akiyama M, Hirata M, Matsuda K, Murakami Y, Kubo, Kamatani Y, Okada Y. Functional variants in ADH1B and ALDH2 are non-additively associated with all-cause mortality in Japanese population. Eur J Hum Genet 28, 378-382 (2021) 203 Sakaue S, Hirata J, Kanai M, Suzuki K, Akiyama M, Too CL, Arayssi T, Hammoudeh M, Emadi SA, Masri BK, Halabi H, Badsha H, Uthman Iw, Sexena R, Padyukov L, Hirata M, Matsuda K, Murakami Y, Kamatani Y, Okada Y. Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction. Nat Commun 11, 1569 (2021) 204 Sakaue S, Kanai M, Karjalainen J, Akiyama M, Kurki M, Matoba N, Takahashi A, Hirata M, Kubo, Matsuda K, Murakami Y, Gen F, Daly MJ, Kamatani Y, Okada Y. Trans-biobank analysis with 676,000 individuals elucidates the association of polygenic risk scores of complex traits with human lifespan. Nat Med 26, 542-548 (2021) 205 Sakaue S, Kanai M, Tanigawa Y, Karjalainen J, Kurki M, Koshiba S, Narita A, Konuma T, Yamamoto K, Akiyama M, Ishigaki K, Suzuki A, Suzuki K, Obara W, Yamaji K, Takahashi K, Asai S, Takahashi Y, Suzuki T, Shinozaki N, Yamaguchi H, Minami S, Murayama S, Yo-shimori K, Nagayama S, Obata D, Higashiyama M, Masumoto A, Koretsune Y; FinnGen, Ito K, Terao C, Yamauchi T, Komuro I, Kadowaki T, Tamiya G, Yamamoto M, Nakamura Y, Kubo M, Murakami Y, Yamamoto K, Kamatani Y, Palotie A, Rivas MA, Daly MJ, Matsuda K, Okada Y. A cross-population atlas of genetic associations for 220 human pheno-types. Nat Genet 53, 1415-1424 (2021) 206 Sasaki K, Oguchi A, Cheng K, Murakawa Y, Okamoto I, Ohta H, Yabuta Y, Iwatani C, Tsuchiya H, Yamamoto T, Seita Y, Saitou M. The embryonic ontogeny of the gonadal somatic cells in mice and monkeys. Cell Rep 35, 109075 (2021) 207 Sato T, Kojima T, Samura O, Kawaguchi S, Nakamura A, Nakajima M, Tanuma-Takahashi A, Nakabayashi K, Hata K, Ikegawa S, Nishimura G, Okamoto A, Yamada T. Two unrelated pedigrees with achondrogenesis type 1b carrying a Japan-specific pathogenic variant in SLC26A2. Am J Med Genet A 182, 735-739 (2021) 208 Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S, Kearney SM, Suda W, Takeshita K, Sasaki T, Okamoto S, Skelly AN, Okamura Y, Vlamakis H, Li Y, Tanoue T, Takei H, Nittono H, Narushima S, Irie J, Itoh H, Moriya K, Sugiura Y, Suematsu M, Moritoki N, Shibata S, Littman DR, Fischbach MA, Uwamino Y, Inoue T, Honda A, Hattori M, Murai T, Xavier

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