Development of mutation analysis system by multiplex PCR and suspension array for paraffin-embedded autopsy samples

2011 Fiscal Year Final Research Report

• Project/Area Number: 21590411
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Human pathology
• Research Institution: Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology
• Principal Investigator: HOSOYA Hiroko 地方独立行政法人東京都健康長寿医療センター(東京都健康長寿医療センター研究所), 東京都健康長寿医療センター研究所, 助手 (00158841)
• Co-Investigator(Kenkyū-buntansha): TANAKA Masashi 地方独立行政法人東京都健康長寿医療センター(東京都健康長寿医療センター研究所), 東京都健康長寿医療センター研究所, 研究部長 (60155166) ; NISHIGAKI Yutaka 地方独立行政法人東京都健康長寿医療センター(東京都健康長寿医療センター研究所), 東京都健康長寿医療センター研究所, 研究員 (80296988) ; FUKU Noriyuki 地方独立行政法人東京都健康長寿医療センター(東京都健康長寿医療センター研究所), 東京都健康長寿医療センター研究所, 研究員 (40392526)
• Project Period (FY): 2009 – 2011
• Keywords: 病理解剖 / パラフィン包埋切片 / 生活習慣病 / 脳梗塞 / 動脈硬化 / 健康長寿 / ミトコンドリアゲノム多型 / 遺伝子増幅

Research Abstract

Objective : To establish a suspension array-based analysis system for determining mitochondrial haplogroups, using DNA purified from formalin-fixed paraffin-embedded(FFPE) autopsy tissues. Background : Because the evolutionary rate of mitochondrial DNA(mtDNA) is much higher than that of nuclear DNA, and because mtDNA is highly polymorphic, mitochondrial single nucleotide polymorphisms(mtSNPs) are expected to contribute more extensively to the functional differences among individuals than those SNPs in the nuclear DNA. Design/Methods : We carefully purified total DNA from FFPE autopsy tissues by using ethanol precipitation. By using our system, we could estimate 7 major mitochondrial haplogroups for Japanese containing 17 subhaplogroups belonging to 2 super haplogroups(M and N), based on information obtained from the comprehensive analysis of mtSNPs in the coding region of mtDNA. We first tested approximately 100 DNA samples from blood and FFPE tissues of autopsy subjects whose haplogroups had been identified by DNA analysis of frozen-kidney tissues. To examine more fully the utility of the system, we analyzed 5, 161 DNA samples from FFPE tissues. Results : We could analyze 4, 485(87%) of them successfully. However, we could not analyze the remainder(13%) because of an insufficient PCR amplification due to severe DNA fragmentation. We had previously revealed the haplogroup frequencies of 1, 500 frozen-kidney DNA samples. In comparison, the haplogroup D4a was overestimated, but the haplogroups M7a, D4b1b and N9b were underestimated, by the present system we developed. Conclusions : We have established a method to purify DNA from FFPE tissues and developed a suspension array-based analytic system to estimate major haplogroups of Japanese individuals. We believe that our system for the classification of mitochondrial haplogroups will be very helpful not only for pathogenetical studies, but also for epidemiological cohort studies.

Research Products

• [Journal Article] Importance of mitochondrial haplotypes and maternal lineage in sprint performance among individuals of West African ancestry (2012)
  • Author(s): Deason M, Scott R, Irwin L, Macaulay V, Fuku N, Tanaka M, Irving R, Charlton V, Morrison E, Austin K, Pitsiladis YP
  • Journal Title: Scand J Med Sci Sports Volume: 22 Pages: 217-223
  • DOI: DOI:10.1111/j.1600-0838.2010.01289.x
  • Peer Reviewed
• [Journal Article] Association of 29C T Polymorphism in the Transforming Growth Factor-β1 Gene with Lean Body Mass in Community-Dwelling Japanese Population (2012)
  • Author(s): Fuku N, Mori S, Murakami H, Gando Y, Zhou H, Ito H, Tanaka M, Miyachi M
  • Journal Title: Geriatr Gerontol Int Volume: 12 Pages: 292-297
  • DOI: DOI:10.1111/j.1447-0594.2011.00768.x.
  • Peer Reviewed
• [Journal Article] Mitochondrial macrohaplogroup associated with muscle power in healthy adults (2012)
  • Author(s): Fuku N, Murakami H, Iemitsu M, Sanada K, Tanaka M, Miyachi M
  • Journal Title: Int J Sports Med Volume: 33 Pages: 410-414
  • DOI: DOI:10.1055/s-0031-1301317
  • Peer Reviewed
• [Journal Article] Beneficial effect of pyruvate therapy on Leigh syndrome due to a novel mutation in PDH E1a gene (2012)
  • Author(s): Koga Y, Povalko N, Katayama K, Kakimoto N, Matsuishi T, Naito E, Tanaka M
  • Journal Title: Brain Dev Volume: 34 Pages: 87-91
  • DOI: DOI:10.1016/j.braindev.2011.03.003
  • Peer Reviewed
• [Journal Article] Mitochondrial haplogroups A and M7a confer a genetic risk for coronary atherosclerosis in the Japanese elderly : An autopsy study of 1, 536 patients (2011)
  • Author(s): Sawabe M, Tanaka M, Chida K, Arai T, Nishigaki Y, Fuku N, Mieno MN, Kuchiba A, Tanaka N
  • Journal Title: J Atheroscler Thromb Volume: 18(2) Pages: 166-75
  • DOI: DOI:10.1002/ajpa.21561
  • Peer Reviewed
• [Journal Article] Mitochondrial DNA analysis of Hokkaido Jomon skeletons : Remnants of archaic maternal lineages at the southwestern edge of former Beringia (2011)
  • Author(s): Noboru Adachi, Ken-ichi Shinoda, Kazuo Umetsu, Takashi Kitano, Hirofumi, Matsumura, Ryuzo Fujiyama, Junmei Sawada, and Masashi Tanaka
  • Journal Title: Am J Phys Anthropol Volume: 146 Pages: 346-360
  • DOI: DOI:10.1002/ajpa.21561
  • Peer Reviewed
• [Journal Article] Association of a polymorphism of BTN2A1 with dyslipidemia in East Asian populations (2011)
  • Author(s): Tetsuo Fujimaki, Kimihiko Kato, Mitsutoshi Oguri, Tetsuro Yohida, Hideki Horibe, Kiyoshi Yokoi, Sachiro Watanabe, Kei Satoh, Yukitoshi Aoyagi, Masashi Tanaka, Hiroto Yoshida, Shoji Shinkai, Yoshinori Nozawa, Dong-Jik Shin, Jong-Ho Lee, Yangsoo Jang, Yoshiji Yamada
  • Journal Title: Exp Ther Med Volume: 2 Pages: 745-749
  • DOI: DOI:10.3892/etm.2011.266
  • Peer Reviewed
• [Journal Article] Association of a polymorphism of BTN2A1 with type 2 diabetes mellitus in Japanese individuals (2011)
  • Author(s): Mizuho Hiramatsu, Mitsutoshi Oguri, Kimihiko Kato, Tetsuro Yoshida, Tetsuo Fujimaki, Hideki Horibe, Kiyoshi Yokoi, Sachiro Watanabe, Kei Satoh, Yukitoshi Aoyagi, Masashi Tanaka, Hiroto Yoshida, Shoji Shinkai, Yoshinori Nozawa, Toyoaki Murohara, Yoshiji Yamada
  • Journal Title: Diabetic Med Volume: 28 Pages: 1381-1387
  • DOI: DOI:10.1111/j.1464-5491.2011.03358.x
  • Peer Reviewed
• [Journal Article] Association of a polymorphism of BTN2A1 with hypertension in Japanese individuals (2011)
  • Author(s): Hideki Horibe, Kimihiko Kato, Mitsutoshi Oguri, Tetsuro Yoshida, Tetsuo Fujimaki, Toshiki Kawamiya, Kiyoshi Yokoi, Sachiro Watanabe, Kei Satoh, Yukitoshi Aoyagi, Masashi Tanaka, Hiroto Yoshida, Shoji Shinkai, Yoshinori Nozawa, Toyoaki Murohara, Yoshiji Ya
  • Journal Title: Am J Hypertens Volume: 24 Pages: 924-929
  • DOI: DOI:10.1038/ajh.2011.74
  • Peer Reviewed
• [Journal Article] Association of polymorphisms of BTN2A1 and ILF3 with myocardial infarction in Japanese individuals with or without hypertension, diabetes mellitus, or chronic kidney disease (2011)
  • Author(s): Tetsuro Yoshida, Kimihiko Kato, Mitsutoshi Oguri, Hideki Horibe, Toshiki Kawamiya, Kiyoshi Yokoi, Tetsuo Fujimaki, Sachiro Watanabe, Kei Satoh, Yukitoshi Aoyagi, Masashi Tanaka, Hiroto Yoshida, Shoji Shinkai, Yoshinori Nozawa, Yoshiji Yamada
  • Journal Title: Int J Mol Med Volume: 27 Pages: 745-752
  • DOI: DOI:10.3892/ijmm.2011.623
  • Peer Reviewed
• [Journal Article] Association of polymorphisms of BTN2A1 and ILF3 with myocardial infarction in Japanese individuals with different lipid profiles (2011)
  • Author(s): Tetsuro Yoshida, Kimihiko Kato, Mitsutoshi Oguri, Hideki Horibe, Toshiki Kawamiya, Kiyoshi Yokoi, Tetsuo Fujimaki, Sachiro Watanabe, Kei Satoh, Yukitoshi Aoyagi, Masashi Tanaka, Hiroto Yoshida, Shoji Shinkai, Yoshinori Nozawa, Yoshiji Yamada
  • Journal Title: Mol Med Rep Volume: 4 Pages: 511-518
  • Peer Reviewed
• [Journal Article] Association of a polymorphism of BTN2A1 with chronic kidney disease in Japanese individuals with or without hypertension or diabetes mellitus (2011)
  • Author(s): Tetsuro Yoshida, Kimihiko Kato, Mitsutoshi Oguri, Hideki Horibe, Toshiki Kawamiya, Kiyoshi Yokoi, Tetsuo Fujimaki, Sachiro Watanabe, Kei Satoh, Yukitoshi Aoyagi, Masashi Tanaka, Hiroto Yoshida, Shoji Shinkai, Yoshinori Nozawa, Yoshiji Yamada
  • Journal Title: Exp Ther Med Volume: 2 Pages: 325-331
  • DOI: DOI:10.3892/etm.2011.191
  • Peer Reviewed
• [Journal Article] Association of a polymorphism of BTN2A1 with myocardial infarction in East Asian populations (2011)
  • Author(s): Yoshiji Yamada, Tamotsu Nishida, Sahoko Ichihara, Motoji Sawabe, Noriyuki Fuku, Yutaka Nishigaki, Yukitoshi Aoyagi, Masashi Tanaka, Yoshinori Fujiwara, Hiroto Yoshida, Shoji Shinkai, Kei Satoh, Kimihiko Kato, Tetsuo Fujimaki, Kiyoshi Yokoi, Mitsutoshi Oguri, Tetsuro Yoshida, Sachiro Watanabe, Yoshinori Nozawa, Aki Hasegawa, Toshio Kojima, Bok-Ghee Han, Younjin Ahn, Meehee Lee, Dong-Jik Shin, Jong Ho Lee, Yangsoo Jang
  • Journal Title: Atherosclerosis Volume: 215 Pages: 145-152
  • DOI: DOI:10.1016/j.atherosclerosis.2010.12.005
  • Peer Reviewed
• [Journal Article] Mitochondrial haplogroups associated with elite Japanese athlete status (2011)
  • Author(s): Mikami E, Fuku N, Takahashi H, Ohiwa N, Scott RA, Pitsiladis YP, Higuchi M, Kawahara T, Tanaka M
  • Journal Title: Br J Sports Med Volume: 45 Pages: 1179-83
  • DOI: DOI:10.1136/bjsm.2010.072371
  • Peer Reviewed
• [Journal Article] Trehalose extends longevity in the nematode Caenorhabditis elegans (2010)
  • Author(s): Honda Y, Tanaka M, Honda S
  • Journal Title: Aging Cell Volume: 9 Pages: 558-569
  • DOI: DOI:10.1111/j.1474-9726.2010.00582.x
  • Peer Reviewed
• [Journal Article] Mitochondrial haplogroups associated with lifestyle-related diseases and longevity in the Japanese population (2010)
  • Author(s): Yutaka Nishigaki, Noriyuki Fuku, Masashi Tanaka
  • Journal Title: Geriatr Gerontol Int Volume: 10 Pages: 221-235
  • DOI: DOI:10.1111/j.1447-0594.2010.00599.x
  • Peer Reviewed
• [Journal Article] Redox regulation, gene expression and longevity (2010)
  • Author(s): Honda Y, Tanaka M, Honda S
  • Journal Title: Geriatr Gerontol Int Volume: 10 Pages: 59-69
  • DOI: DOI:10.1111/j.1447-0594.2010.00591.x
  • Peer Reviewed
• [Journal Article] Pyruvate therapy for Leigh syndrome due to cytochrome c oxidase deficiency (2010)
  • Author(s): Komaki H, Nishigaki Y, Fuku N, Hosoya H, Murayama K, Ohtake A, Goto Y, Wakamoto H, Koga Y, Tanaka M
  • Journal Title: Biochim Biophys Acta Volume: 1800 Pages: 313-315
  • Peer Reviewed
• [Journal Article] Extensive screening system using suspension array technology to detect mitochondrial DNA point mutations (2010)
  • Author(s): Nishigaki Y, Ueno H, Coku J, Koga Y, Fujii T, Sahashi K, Nakano K, Yoneda M, Nonaka M, Tang L, Liou CW, Paquis-Flucklinger V, Harigaya Y, Ibi T, Goto Y, Hosoya H, DiMauro S, Hirano M, Tanaka M
  • Journal Title: Mitochondrion Volume: 10 Pages: 300-308
  • DOI: DOI:10.1016/j.mito.2010.01.003
  • Peer Reviewed
• [Journal Article] Extensive and rapid screening for major mitochondrial DNA point mutations in patients with hereditary hearing loss (2010)
  • Author(s): Kato T, Nishigaki Y, Noguchi Y, Ueno H, Hosoya H, Ito T, Kimura Y, Kitamura K, Tanaka M
  • Journal Title: J Hum Genet Volume: 55 Pages: 147-154
  • DOI: DOI:10.1038/jhg.2009.143
  • Peer Reviewed
• [Journal Article] Metabolic analysis of 13C-labeled pyruvate for noninvasive assessment of mitochondrial function (2010)
  • Author(s): Wu IC, Ohsawa I, Fuku N, Tanaka M
  • Journal Title: Ann N Y Acad Sci Volume: 1201 Pages: 111-120
  • DOI: DOI:10.1111/j.1749-6632.2010.05636.x
  • Peer Reviewed
• [Journal Article] Loss of mutant mitochondrial DNA harboring the MELAS A3243G mutation in human cybrid cells after cell-cell fusion with normal tissue-derived fibroblast cells (2010)
  • Author(s): Yano T, Tanaka M, Fukuda N, Ueda T, Nagase H
  • Journal Title: Int J Mol Med Volume: 25 Pages: 153-158
  • DOI: Doi:10.3892/ijmm_00000325
  • Peer Reviewed
• [Presentation] Comprehensive Mitochondrial Haplogroup Analysis System Based On Suspension-Array Technology Using DNA From Formalin-Fixed Paraffin-Embedded Autopsy TissuesComprehensive Mitochondrial Haplogroup Analysis System Based On Suspension-Array Technology Using DNA From Formalin-Fixed Paraffin-Embedded Autopsy Tissues (2012)
  • Author(s): Yutaka Nishigaki, Hiroko Hosoya, Makiko Naka-Mieno, Tomio Arai, Motoji Sawabe, Masashi Tanaka
  • Organizer: American Academy of Neurology 2012
  • Place of Presentation: アメリカ・ニューオリンズ
  • Year and Date: 2012-04-26
• [Presentation] Association of the transforming growth factor-β1 genetic polymorphism with lean body mass (2011)
  • Author(s): Noriyuki Fuku, Seijiro Mori, Haruka Murakami, Yuko Gando, Zhou Heying, Hideki Ito, Masashi Tanaka, Motohiko Miyachi
  • Organizer: Gerontological Society of America's 64th Annual Scientific Meeting
  • Place of Presentation: アメリカ・ボストン
  • Year and Date: 2011-11-20
• [Presentation] 日本人トップアスリートにおけるミトコンドリアDNA多型の網羅的解析 (2011)
  • Author(s): 三上恵里、福典之、川原貴、高橋英幸、大岩奈青、樋口満、田中雅嗣
  • Organizer: 第66回日本体力医学会大会
  • Place of Presentation: 山口市
  • Year and Date: 2011-09-17
• [Presentation] Polymorphisms in the Control Region of Mitochondrial DNA Associate with Elite Japanese Athlete Status (2011)
  • Author(s): Eri Mikami, Noriyuki Fuku, Hideyuki Takahashi, Nao Ohiwa, Yannis P Pitsiladis, Mitsuru Higuchi, Takashi Kawahara, Masashi Tanaka
  • Organizer: American College of Sports Medicine 58th Annual Meeting and 2nd World Congress on Exercise is Medicine
  • Place of Presentation: アメリカ・デンバー
  • Year and Date: 2011-06-02
• [Remarks]
  • URL: http://mtsnp.tmig.or.jp/mtsnp/index.shtml