Hiromi Sakamoto

Publications (69)428.61 Total impact

• Article: Regulatory Nexus of Synthesis and Degradation Deciphers Cellular Nrf2 Expression Levels.

  Takafumi Suzuki, Tatsuhiro Shibata, Kai Takaya, Kouya Shiraishi, Takashi Kohno, Hideo Kunitoh, Koji Tsuta, Koh Furuta, Koichi Goto, Fumie Hosoda, Hiromi Sakamoto, Hozumi Motohashi, Masayuki Yamamoto
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  ABSTRACT: Transcription factor Nrf2 (NF-E2-related factor-2) is essential for oxidative and electrophilic stress responses. While it has been well characterized that Nrf2 activity is tightly regulated at the protein level through proteasomal degradation via Keap1 (Kelch-like ECH-associated protein 1)-mediated ubiquitination, not much attention has been paid to the supply-side of Nrf2, especially regulation of Nrf2 gene transcription. Using genetically engineered mouse models, here we report that manipulation of Nrf2 transcription is effective in changing the final Nrf2 protein level and activity of cellular defense against oxidative stress even in the presence of Keap1 and under efficient Nrf2 degradation. In excellent agreement, we found that minor A/A homozygotes of a single nucleotide polymorphism (SNP) in human NRF2 upstream-promoter region (rs6721961) exhibited significantly diminished NRF2 gene expression and consequently an increased risk of lung cancer, especially in ever-smokers. Our results support the notion that in addition to control over proteasomal degradation and derepression from the degradation/repression, the transcriptional level of the Nrf2 gene acts as another important regulatory point to define cellular Nrf2 levels. These results thus verify the critical importance of human SNPs that influence transcription levels of the NRF2 gene for future personalized medicine.
  Molecular and cellular biology 04/2013; · 6.06 Impact Factor
• Article: Missense allele of a single nucleotide polymorphism rs2294008 attenuated antitumor effects of prostate stem cell antigen in gallbladder cancer cells.

  Hiroe Ono, Dai Chihara, Fumiko Chiwaki, Kazuyoshi Yanagihara, Hiroki Sasaki, Hiromi Sakamoto, Hideo Tanaka, Teruhiko Yoshida, Norihisa Saeki, Keitaro Matsuo
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  ABSTRACT: Prostate stem cell antigen (PSCA), an organ-dependent tumor suppressor, is down regulated in gallbladder cancer (GBC). It is anticipated that the missense allele C of the single nucleotide polymorphism (SNP) rs2294008 (T/C) in the translation initiation codon of the gene affects the gene's biological function and has some influence on GBC susceptibility. We examined the biological effect of the C allele on the function of the gene and the relation between the C allele and GBC susceptibility. Functional analysis of the SNP was conducted by introducing PSCA cDNA harboring the allele to a GBC cell line TGBC- 1TKB and performing colony formation assays in vitro and tumor formation assays in mice. The effect on transcriptional regulation was assessed by reporter assays. The association study was conducted on 44 Japanese GBC cases and 173 controls. The PSCA cDNA harboring the C allele showed lower cell growth inhibition activity (20% reduction) than that with the T allele. Concordantly, when injected into subcutaneous tissues of mice, the GBC cell line stably expressing the cDNA with the C allele formed tumors of almost the same size as that of the control cells, but the cell line expressing the cDNA with the T allele showed slower growth. The upstream DNA fragment harboring the C allele had more transcriptional activity than that with the T allele. The C allele showed positive correlation to GBC but no statistical significant odds ratio (OR = 1.77, 95% confidence interval 0.85-3.70, P value = 0.127 in dominant model). The missense allele was shown to have a biological effect, attenuating antitumor activities of PSCA, and consequently it may be a potential risk for GBC development. An association study in a larger sample size may reveal a significant association between the allele and GBC.
  Journal of Carcinogenesis 01/2013; 12:4.
• Article: Intraperitoneal delivery of a small interfering RNA targeting NEDD1 prolongs the survival of scirrhous gastric cancer model mice.

  Takeshi Fujita, Kazuyoshi Yanagihara, Fumitaka Takeshita, Kazuhiko Aoyagi, Takao Nishimura, Misato Takigahira, Fumiko Chiwaki, Takeo Fukagawa, Hitoshi Katai, Takahiro Ochiya, Hiromi Sakamoto, Hiroyuki Konno, Teruhiko Yoshida, Hiroki Sasaki
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  ABSTRACT: The prognosis of patients with advanced diffuse-type gastric cancer (GC, especially scirrhous gastric cancer (SGC) remains extremely poor. Peritoneal carcinomatosis is a frequent form of metastasis of SGC. With survival rates of patients with peritoneal metastasis at 3 and 5 years being only 9.8% and 0%, respectively, development of a new treatment is urgently crucial. For such development, the establishment of a therapeutic mouse model is required. Among the 11 GC cell lines we examined, HSC-60 showed the most well-preserved expression profiles of the Hedgehog and epithelial-mesenchymal transition pathways found in primary SGCs. After 6 cycles of harvest of ascitic tumor cells and their orthotopic inoculation in scid mice, a highly metastatic subclone of HSC-60, 60As6 was obtained, by means of which we successfully developed peritoneal metastasis model mice. The mice treated with small interfering (si) RNA targeting NEDD1, which encodes a gamma-tubulin ring complex-binding protein, by the atelocollagen-mediated delivery system showed a significantly prolonged survival. Our mouse model could thus be useful for the development of a new therapeutic modality. Intraperitoneal administration of siRNAs of targeted genes such as NEDD1 could provide a new opportunity in the treatment of the peritoneal metastasis of SGC.
  Cancer Science 10/2012; · 3.33 Impact Factor
• Article: Genetic factors related to gastric-cancer susceptibility identified by GWAS.

  Norihisa Saeki, Hiroe Ono, Hiromi Sakamoto, Teruhiko Yoshida
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  ABSTRACT: Gastric cancer (GC) is one of the major malignant diseases worldwide, especially in Asia, where Japan and Korea have the highest incidence in the world. GC is classified into intestinal and diffuse types. While the former is almost absolutely caused by Helicobacter pylori infection as initial insult, the latter seems to include the cases in which the role of the infection is limited, if any, and a contribution of genetic factors is anticipated. Previously, we performed a genome-wide association study (GWAS) on the diffuse-type GC by utilizing single nucleotide polymorphisms (SNPs) catalogued for Japanese (JSNP), and identified prostate stem cell antigen gene (PSCA) encoding a glycosylphosphatidylinositol-anchored cell surface antigen as a GC susceptibility gene. From the second candidate locus identified by the GWAS, 1q22, we found the Mucin 1 gene (MUC1) encoding a cell membrane-bound mucin protein as another gene related to diffuse-type GC. A two-allele analysis based on risk genotypes of the 2 genes revealed approximately 95 % of Japanese have at least one of the 2 risk genotypes, and about 56% of the population have both risk genotypes. The 2-SNP genotype may offer ample room to further stratify a high GC risk subpopulation in Japan and Asia by adding another genetic and/or non-genetic factor. Recently, a GWAS on the Chinese population disclosed additional 3 GC-susceptibility loci: 3q13.31, 5p13.1 and 10q23.
  Cancer Science 10/2012; · 3.33 Impact Factor
• Article: Association of dietary and genetic factors related to one-carbon metabolism with global methylation level of leukocyte DNA.

  Hiroe Ono, Motoki Iwasaki, Aya Kuchiba, Yoshio Kasuga, Shiro Yokoyama, Hiroshi Onuma, Hideki Nishimura, Ritsu Kusama, Sumiko Ohnami, Hiromi Sakamoto, Teruhiko Yoshida, Shoichiro Tsugane
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  ABSTRACT: Global hypomethylation of leukocyte DNA has been associated with an increased risk of cancer. As dietary and genetic factors related to one-carbon metabolism may influence both the methylation and synthesis of DNA, we investigated associations between these factors and the global methylation level of peripheral blood leukocyte DNA based on a cross-sectional study of 384 Japanese women. Dietary intake of folate and vitamins B2, B6, and B12 was assessed with a validated semiquantitative food frequency questionnaire. Five polymorphisms in methylenetetrahydrofolate reductase (MTHFR) (rs1801133 and rs1801131), methionine synthase (MTR) (rs1805087), and methionine synthase reductase (MTRR) (rs10380 and rs162049) were genotyped. Global DNA methylation of leukocyte DNA was quantified using Luminometric Methylation Assay. A linear trend of association between methylation and dietary and genetic factors was evaluated by regression coefficients in a multivariable linear regression model. Mean global methylation level (standard deviation) was 70.2% (3.4) and range was from 59.0% to 81.2%. Global methylation level significantly decreased by 0.36% (95% confidence interval, 0.03-0.69) per quartile category for folate level. Subgroup analysis suggested that alcohol drinking modified the association between folate intake and global methylation level (P(interaction) = 0.01). However, no statistically significant association was observed for intake of vitamins B2, B6, and B12, alcohol consumption, or five single nucleotide polymorphisms of MTHFR, MTR, and MTRR. We found that higher folate intake was significantly associated with a lower level of global methylation of leukocyte DNA in a group of healthy Japanese females.
  Cancer Science 09/2012; · 3.33 Impact Factor
• Article: Prostate stem cell antigen gene is expressed in islets of pancreas.

  Hiroe Ono, Kazuyoshi Yanagihara, Hiromi Sakamoto, Teruhiko Yoshida, Norihisa Saeki
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  ABSTRACT: Prostate stem cell antigen (PSCA) is a glycosylphosphatidylinositol-anchored cell surface antigen with an organ-dependent expression pattern in cancers; e.g., up-regulated in prostate cancer and down-regulated in gastric cancer. Previously it was reported that PSCA is not expressed in the normal pancreas but aberrantly expressed in pancreatic cancer. In this present study, we identified PSCA expression in islets of the pancreas by immunohistochemistry, which was co-localized with four islet-cell markers: insulin, glucagon, somatostatin and pancreatic polypeptide. In our investigation of the transcription start site of PSCA, we found a non-coding splicing variant of PSCA as well as authentic PSCA transcripts in mRNA samples from a normal pancreas. Both the transcripts were also identified in several pancreatic cancer cell lines. We previously reported that PSCA expression is correlated to the methylation status of the enhancer region in gastric and gallbladder cancer cell lines but not in pancreatic cancer cell lines, suggesting that PSCA expression is regulated in a diff erent mode in pancreatic cancer from that in gastric and gallbladder cancers.
  Anatomy & cell biology 09/2012; 45(3):149-54.
• Article: A genome-wide association study identifies two new susceptibility loci for lung adenocarcinoma in the Japanese population.

  Kouya Shiraishi, Hideo Kunitoh, Yataro Daigo, Atsushi Takahashi, Koichi Goto, Hiromi Sakamoto, Sumiko Ohnami, Yoko Shimada, Kyota Ashikawa, Akira Saito, Shun-ichi Watanabe, Koji Tsuta, Naoyuki Kamatani, Teruhiko Yoshida, Yusuke Nakamura, Jun Yokota, Michiaki Kubo, Takashi Kohno
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  ABSTRACT: Lung adenocarcinoma is the most common histological type of lung cancer, and its incidence is increasing worldwide. To identify genetic factors influencing risk of lung adenocarcinoma, we conducted a genome-wide association study and two validation studies in the Japanese population comprising a total of 6,029 individuals with lung adenocarcinoma (cases) and 13,535 controls. We confirmed two previously reported risk loci, 5p15.33 (rs2853677, P(combined) = 2.8 × 10(-40), odds ratio (OR) = 1.41) and 3q28 (rs10937405, P(combined) = 6.9 × 10(-17), OR = 1.25), and identified two new susceptibility loci, 17q24.3 (rs7216064, P(combined) = 7.4 × 10(-11), OR = 1.20) and 6p21.3 (rs3817963, P(combined) = 2.7 × 10(-10), OR = 1.18). These data provide further evidence supporting a role for genetic susceptibility in the development of lung adenocarcinoma.
  Nature Genetics 07/2012; 44(8):900-3. · 35.53 Impact Factor
• Article: KIF5B-RET fusions in lung adenocarcinoma.

  Takashi Kohno, Hitoshi Ichikawa, Yasushi Totoki, Kazuki Yasuda, Masaki Hiramoto, Takao Nammo, Hiromi Sakamoto, Koji Tsuta, Koh Furuta, Yoko Shimada, [......], Itaru Yamanaka, Yasuhito Arai, Shun-Ichi Watanabe, Ikuo Sekine, Seishi Ogawa, Curtis C Harris, Hitoshi Tsuda, Teruhiko Yoshida, Jun Yokota, Tatsuhiro Shibata
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  ABSTRACT: We identified in-frame fusion transcripts of KIF5B (the kinesin family 5B gene) and the RET oncogene, which are present in 1-2% of lung adenocarcinomas (LADCs) from people from Japan and the United States, using whole-transcriptome sequencing. The KIF5B-RET fusion leads to aberrant activation of RET kinase and is considered to be a new driver mutation of LADC because it segregates from mutations or fusions in EGFR, KRAS, HER2 and ALK, and a RET tyrosine kinase inhibitor, vandetanib, suppresses the fusion-induced anchorage-independent growth activity of NIH3T3 cells.
  Nature medicine 01/2012; 18(3):375-7. · 27.14 Impact Factor
• Article: Association between plasma 25-hydroxyvitamin D and colorectal adenoma according to dietary calcium intake and vitamin D receptor polymorphism.

  Taiki Yamaji, Motoki Iwasaki, Shizuka Sasazuki, Hiromi Sakamoto, Teruhiko Yoshida, Shoichiro Tsugane
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  ABSTRACT: The anticarcinogenic potential of vitamin D might be mediated by not only calcium metabolism but also other mechanisms initiated by vitamin D receptor (VDR). The authors measured plasma 25-hydroxyvitamin D in healthy volunteer examinees who underwent total colonoscopy in Tokyo, Japan, 2004-2005, and evaluated its influence on colorectal adenoma, both alone and in interaction with VDR polymorphisms, which correspond to the FokI and TaqI restriction sites. The main analysis of plasma 25-hydroxyvitamin D included 737 cases and 703 controls. Compared with the lowest quintile of plasma 25-hydroxyvitamin D, only the highest was related to a significantly decreased odds ratio of colorectal adenoma (odds ratio = 0.64, 95% confidence interval: 0.45, 0.92). In contrast, all but the lowest quintile of dietary calcium intake presented similarly reduced odds ratios (odds ratio for the highest = 0.67, 95% confidence interval: 0.47, 0.95). Of note, the association between plasma 25-hydroxyvitamin D levels and colorectal adenoma was modified by the TaqI polymorphism of the VDR gene (P(interaction) = 0.03) but not by dietary calcium intake (P(interaction) = 0.93). These observations highlight the importance of vitamin D in colorectal tumorigenesis. Vitamin D might protect against colorectal neoplasia, mainly through mechanisms other than the indirect mechanism via calcium metabolism.
  American journal of epidemiology 12/2011; 175(3):236-44. · 5.59 Impact Factor
• Article: Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency.

  Linghua Wang, Shuichi Tsutsumi, Tokuichi Kawaguchi, Koichi Nagasaki, Kenji Tatsuno, Shogo Yamamoto, Fei Sang, Kohtaro Sonoda, Minoru Sugawara, Akio Saiura, [......], Genta Nagae, Takayuki Isagawa, Hiroki Ueda, Satsuki Murayama-Hosokawa, Tatsuhiro Shibata, Hiromi Sakamoto, Yae Kanai, Atsushi Kaneda, Tetsuo Noda, Hiroyuki Aburatani
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  ABSTRACT: Whole-exome sequencing (Exome-seq) has been successfully applied in several recent studies. We here sequenced the exomes of 15 pancreatic tumor cell lines and their matched normal samples. We captured 162,073 exons of 16,954 genes and sequenced the targeted regions to a mean coverage of 56-fold. This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among cell lines. The diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-seq revealed intensive genomic instability in a cell line with MLH1 homozygous deletion, indicated by a dramatically elevated rate of somatic substitutions, small insertions/deletions (indels), as well as indels in microsatellites. Notably, we found that MLH1 expression was decreased by nearly half in cell lines with an allelic loss of MLH1. While these cell lines were negative in conventional microsatellite instability assay, they showed a 10.5-fold increase in the rate of somatic indels, e.g., truncating indels in TP53 and TGFBR2, indicating MLH1 haploinsufficiency in the correction of DNA indel errors. We further analyzed the exomes of 15 renal cell carcinomas and confirmed MLH1 haploinsufficiency. We observed a much higher rate of indel mutations in the affected cases and identified recurrent truncating indels in several cancer genes such as VHL, PBRM1, and JARID1C. Together, our data suggest that MLH1 hemizygous deletion, through increasing the rate of indel mutations, could drive the development and progression of sporadic cancers.
  Genome Research 12/2011; 22(2):208-19. · 13.61 Impact Factor
• Article: Identification of genes upregulated in ALK-positive and EGFR/KRAS/ALK-negative lung adenocarcinomas.

  Hirokazu Okayama, Takashi Kohno, Yuko Ishii, Yoko Shimada, Kouya Shiraishi, Reika Iwakawa, Koh Furuta, Koji Tsuta, Tatsuhiro Shibata, Seiichiro Yamamoto, [......], Hiromi Sakamoto, Kensuke Kumamoto, Seiichi Takenoshita, Noriko Gotoh, Hideaki Mizuno, Akinori Sarai, Shuichi Kawano, Rui Yamaguchi, Satoru Miyano, Jun Yokota
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  ABSTRACT: Activation of the EGFR, KRAS, and ALK oncogenes defines 3 different pathways of molecular pathogenesis in lung adenocarcinoma. However, many tumors lack activation of any pathway (triple-negative lung adenocarcinomas) posing a challenge for prognosis and treatment. Here, we report an extensive genome-wide expression profiling of 226 primary human stage I-II lung adenocarcinomas that elucidates molecular characteristics of tumors that harbor ALK mutations or that lack EGFR, KRAS, and ALK mutations, that is, triple-negative adenocarcinomas. One hundred and seventy-four genes were selected as being upregulated specifically in 79 lung adenocarcinomas without EGFR and KRAS mutations. Unsupervised clustering using a 174-gene signature, including ALK itself, classified these 2 groups of tumors into ALK-positive cases and 2 distinct groups of triple-negative cases (groups A and B). Notably, group A triple-negative cases had a worse prognosis for relapse and death, compared with cases with EGFR, KRAS, or ALK mutations or group B triple-negative cases. In ALK-positive tumors, 30 genes, including ALK and GRIN2A, were commonly overexpressed, whereas in group A triple-negative cases, 9 genes were commonly overexpressed, including a candidate diagnostic/therapeutic target DEPDC1, that were determined to be critical for predicting a worse prognosis. Our findings are important because they provide a molecular basis of ALK-positive lung adenocarcinomas and triple-negative lung adenocarcinomas and further stratify more or less aggressive subgroups of triple-negative lung ADC, possibly helping identify patients who may gain the most benefit from adjuvant chemotherapy after surgical resection.
  Cancer Research 11/2011; 72(1):100-11. · 7.86 Impact Factor
• Article: Prostate stem cell antigen, a presumable organ-dependent tumor suppressor gene, is down-regulated in gallbladder carcinogenesis.

  Hiroe Ono, Nobuyoshi Hiraoka, Yeon-Su Lee, Sang Myung Woo, Woo Jin Lee, Il Ju Choi, Akira Saito, Kazuyoshi Yanagihara, Yae Kanai, Sumiko Ohnami, Fumiko Chiwaki, Hiroki Sasaki, Hiromi Sakamoto, Teruhiko Yoshida, Norihisa Saeki
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  ABSTRACT: Gallbladder cancer (GBC) is relatively rare but has a high mortality rate. One candidate molecule which might be involved in GBC development is prostate stem cell antigen (PSCA), a glycosylphosphatidylinositol-anchored cell surface antigen with a tissue-specific pattern of expression in the epithelium of several organs, such as the prostate, stomach, bladder, and gallbladder. It is up-regulated in a number of cancers including prostate, urinary bladder, and pancreatic cancers, while it is down-regulated in esophageal and gastric cancers, suggesting that PSCA has an oncogenic activity in the former but a tumor suppressor activity in the latter. However, the precise function of PSCA and the regulatory mechanism for its expression in normal and cancer cells are yet to be determined. In this study, immunohistochemical analyses with a specific antibody revealed that PSCA is down-regulated in non-neoplastic gallbladder lesions such as cholesterolosis, cholecystolithiasis, and cholecystitis (9/17; 53%), and also in adenocarcinoma (40/44; 91%), a common neoplasm in gallbladder. Analyses of the DNA methylation status in the GBC cell lines by bisulfite-Pyrosequencing and a reporter assay for the PSCA promoter activity suggested that the down-regulation is explained, at least partly, by DNA methylation. Moreover, colony formation assay revealed that PSCA has cell-proliferation inhibition activity in the GBC cell lines, which was also observed in vivo. These lines of in vivo and in vitro evidence suggest that PSCA is acting as a tumor suppressor in GBC development.
  Genes Chromosomes and Cancer 09/2011; 51(1):30-41. · 3.31 Impact Factor
• Source

  Available from: Tomomitsu Hirota

  Article: Genome-wide association study identifies HLA-DP as a susceptibility gene for pediatric asthma in Asian populations.

  Emiko Noguchi, Hiromi Sakamoto, Tomomitsu Hirota, Kaori Ochiai, Yoshimasa Imoto, Masafumi Sakashita, Fumitake Kurosaka, Akira Akasawa, Shigemi Yoshihara, Noriko Kanno, [......], Nobuyuki Hizawa, Toru Sakamoto, Hironori Masuko, Yusuke Nakamura, Ichiro Nomura, Mayumi Tamari, Tadao Arinami, Teruhiko Yoshida, Hirohisa Saito, Kenji Matsumoto
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  ABSTRACT: Asthma is a complex phenotype influenced by genetic and environmental factors. We conducted a genome-wide association study (GWAS) with 938 Japanese pediatric asthma patients and 2,376 controls. Single-nucleotide polymorphisms (SNPs) showing strong associations (P<1×10(-8)) in GWAS were further genotyped in an independent Japanese samples (818 cases and 1,032 controls) and in Korean samples (835 cases and 421 controls). SNP rs987870, located between HLA-DPA1 and HLA-DPB1, was consistently associated with pediatric asthma in 3 independent populations (P(combined) = 2.3×10(-10), odds ratio [OR] = 1.40). HLA-DP allele analysis showed that DPA1*0201 and DPB1*0901, which were in strong linkage disequilibrium, were strongly associated with pediatric asthma (DPA1*0201: P = 5.5×10(-10), OR = 1.52, and DPB1*0901: P = 2.0×10(-7), OR = 1.49). Our findings show that genetic variants in the HLA-DP locus are associated with the risk of pediatric asthma in Asian populations.
  PLoS Genetics 07/2011; 7(7):e1002170. · 8.69 Impact Factor
• Article: High-resolution characterization of a hepatocellular carcinoma genome.

  Yasushi Totoki, Kenji Tatsuno, Shogo Yamamoto, Yasuhito Arai, Fumie Hosoda, Shumpei Ishikawa, Shuichi Tsutsumi, Kohtaro Sonoda, Hirohiko Totsuka, Takuya Shirakihara, [......], Linghua Wang, Hidenori Ojima, Kazuaki Shimada, Tomoo Kosuge, Takuji Okusaka, Kazuto Kato, Jun Kusuda, Teruhiko Yoshida, Hiroyuki Aburatani, Tatsuhiro Shibata
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  ABSTRACT: Hepatocellular carcinoma, one of the most common virus-associated cancers, is the third most frequent cause of cancer-related death worldwide. By massively parallel sequencing of a primary hepatitis C virus-positive hepatocellular carcinoma (36× coverage) and matched lymphocytes (>28× coverage) from the same individual, we identified more than 11,000 somatic substitutions of the tumor genome that showed predominance of T>C/A>G transition and a decrease of the T>C substitution on the transcribed strand, suggesting preferential DNA repair. Gene annotation enrichment analysis of 63 validated non-synonymous substitutions revealed enrichment of phosphoproteins. We further validated 22 chromosomal rearrangements, generating four fusion transcripts that had altered transcriptional regulation (BCORL1-ELF4) or promoter activity. Whole-exome sequencing at a higher sequence depth (>76× coverage) revealed a TSC1 nonsense substitution in a subpopulation of the tumor cells. This first high-resolution characterization of a virus-associated cancer genome identified previously uncharacterized mutation patterns, intra-chromosomal rearrangements and fusion genes, as well as genetic heterogeneity within the tumor.
  Nature Genetics 05/2011; 43(5):464-9. · 35.53 Impact Factor
• Article: Genome-wide association study on overall survival of advanced non-small cell lung cancer patients treated with carboplatin and paclitaxel.

  Yasunori Sato, Noboru Yamamoto, Hideo Kunitoh, Yuichiro Ohe, Hironobu Minami, Nan M Laird, Noriko Katori, Yoshiro Saito, Sumiko Ohnami, Hiromi Sakamoto, Jun-Ichi Sawada, Nagahiro Saijo, Teruhiko Yoshida, Tomohide Tamura
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  ABSTRACT: Our goal was to identify candidate polymorphisms that could influence overall survival (OS) in advanced non-small cell lung cancer (NSCLC) patients treated with carboplatin (CBDCA) and paclitaxel (PTX). Chemotherapy-naïve stage IIIB or IV NSCLC patients treated with CBDCA (area under the curve = 6 mg/mL/min) and PTX (200 mg/m, 3-hour period) were eligible for this study. The DNA samples were extracted from peripheral blood mononuclear cells before treatment, and genotypes at approximately 110,000 gene-centric single-nucleotide polymorphisms (SNPs) were obtained by Illumina's Sentrix Human-1 Genotyping BeadChip. Statistical analyses were performed by the log-rank test and Cox proportional hazards model. From July 2002 to May 2004, 105 patients received a total of 308 cycles of treatment. The median survival time (MST) of 105 patients was 17.1 months. In the genome-wide association study, three SNPs were associated significantly with shortened OS after multiple comparison adjustment: rs1656402 in the EIF4E2 gene (MST was 18.0 and 7.7 months for AG [n = 50] + AA [n = 40] and GG [n = 15], respectively; p = 8.4 × 10), rs1209950 in the ETS2 gene (MST = 17.7 and 7.4 months for CC [n = 94] and CT [n = 11] + TT [n = 0]; p = 2.8 × 10), and rs9981861 in the DSCAM gene (MST = 17.1 and 3.8 months for AA [n = 75] + AG [n = 26] and GG [n = 4]; p = 3.5 × 10). Three SNPs were identified as new prognostic biomarker candidates for advanced NSCLC treated with CBDCA and PTX. The agnostic genome-wide association study may unveil unexplored molecular pathways associated with the drug response, but our findings should be replicated by other investigators.
  Journal of thoracic oncology: official publication of the International Association for the Study of Lung Cancer 11/2010; 6(1):132-8. · 4.55 Impact Factor
• Article: A functional single nucleotide polymorphism in mucin 1, at chromosome 1q22, determines susceptibility to diffuse-type gastric cancer.

  Norihisa Saeki, Akira Saito, Il Ju Choi, Keitaro Matsuo, Sumiko Ohnami, Hirohiko Totsuka, Suenori Chiku, Aya Kuchiba, Yeon-Su Lee, Kyong-Ah Yoon, [......], Wataru Yasui, Kazuhiko Aoyagi, Hiroki Sasaki, Kazuyoshi Yanagihara, Hitoshi Katai, Tadakazu Shimoda, Teruhiko Yoshida, Yusuke Nakamura, Setsuo Hirohashi, Hiromi Sakamoto
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  ABSTRACT: Two major types of gastric cancer, intestinal and diffuse, develop through distinct mechanisms; the diffuse type is considered to be more influenced by genetic factors, although the mechanism is unknown. Our previous genome-wide association study associated 3 single nucleotide polymorphisms (SNPs) with diffuse-type gastric cancer (DGC); 1 was a functional SNP (rs2294008) in prostate stem cell antigen (PSCA), but the loci of the other 2 were not investigated. We performed high-density mapping to explore a linkage disequilibrium status of the 2 SNPs at chromosome 1q22. A DGC case-control study was conducted using DNA from 606 cases and 1264 controls (all Japanese individuals) and validated using DNA from Japanese (304 cases, 1465 controls) and Korean (452 cases, 372 controls) individuals. The effects of SNPs on function were analyzed by reporter assays and analyses of splice variants. A region of a strong linkage disequilibrium with the 2 SNPs contained mucin 1 (MUC1) and other 4 genes and SNPs significantly associated with DGC (rs2070803: P = 4.33 × 10(-13); odds ratio [OR], 1.71 by meta-analysis of the studies on the 3 panels) but not with intestinal-type gastric cancer. Functional studies demonstrated that rs4072037 (P = 1.43 × 10(-11); OR, 1.66 by meta-analysis) in MUC1 affects promoter activity and determines the major splicing variants of MUC1 in the gastric epithelium. Individuals that carry both SNPs rs2294008 in PSCA and rs4072037 in MUC1 have a high risk for developing DGC (OR, 8.38). MUC1 is the second major DGC susceptibility gene identified. The SNPs rs2070803 and rs4072037 in MUC1 might be used to identify individuals at risk for this type of gastric cancer.
  Gastroenterology 11/2010; 140(3):892-902. · 11.68 Impact Factor
• Article: Association of CYP19A1 polymorphisms with risks for atypical adenomatous hyperplasia and bronchioloalveolar carcinoma in the lungs.

  Takashi Kohno, Ryutaro Kakinuma, Motoki Iwasaki, Taiki Yamaji, Hideo Kunitoh, Kenji Suzuki, Yoko Shimada, Kouya Shiraishi, Yoshio Kasuga, Gerson Shigeaki Hamada, Koh Furuta, Koji Tsuta, Hiromi Sakamoto, Aya Kuchiba, Seiichiro Yamamoto, Yae Kanai, Shoichiro Tsugane, Jun Yokota
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  ABSTRACT: Estrogen has been indicated to play an etiological role in the development of lung adenocarcinoma (ADC), particularly bronchioloalveolar carcinoma (BAC), a type of ADC that develops from a benign adenomatous lesion, atypical adenomatous hyperplasia (AAH). Polymorphisms in the CYP19A1 gene cause interindividual differences in estrogen levels. Here, 13 CYP19A1 single-nucleotide polymorphisms (SNPs) were examined for associations with lung AAH risk. AAH is detected as ground-glass opacity (GGO) by computed tomography (CT) examination, and this study consisted of 100 individuals diagnosed with GGO in their lungs among 3088 CT-based cancer screening examinees and 424 without. Minor allele carriers for the rs3764221 SNP showed an elevated risk for GGO [odds ratio (OR) = 1.72, P = 0.017]. Associations of this SNP with risks for lung AAH and BAC in the lungs were next examined using 359 ADC cases whose resected lung lobes were subjected to a histological examination for AAH accompaniment and the presence of BAC components and 330 controls without cancer. The ORs were also increased for lung ADC accompanied by AAH (OR = 1.74, P = 0.029) as well as lung ADC with BAC components (OR = 1.41, P = 0.091). The minor allele was associated with an increased circulating estradiol level (P = 0.079) in a population of 363 postmenopausal women without cancer. These results indicate that CYP19A1 polymorphisms are involved in the risk for lung AAH and BAC in the lungs by causing differences in estrogen levels.
  Carcinogenesis 10/2010; 31(10):1794-9. · 5.70 Impact Factor
• Article: Genome-wide germline analyses on cancer susceptibility and GeMDBJ database: Gastric cancer as an example.

  Teruhiko Yoshida, Hiroe Ono, Aya Kuchiba, Norihisa Saeki, Hiromi Sakamoto
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  ABSTRACT: The power of an SNP-based genome-wide association study (GWAS) was first demonstrated in Japan using the JSNP database and is currently a major strategy adopted around the world for a number of common diseases including cancers. The hypothesis-free strategy can lead us to a novel hypothesis for carcinogenesis and may contribute to identifying a high risk group for research and, in the future, practice of personalized prevention. We performed a GWAS on diffuse-type gastric cancer and identified a significant association with SNPs in the PSCA (prostate stem cell antigen) gene. The association was validated by a Korean gastric case-control analysis. The PSCA protein is expressed predominantly in the stem cell/precursor-rich region of the gastric epithelium, which is considered as the origin of diffuse-type gastric cancer, and showed tumor suppressor-like characteristics. Individuals with a low PSCA promoter activity are susceptible to diffuse-type gastric cancer. By contrast, the polymorphism does not significantly predispose to intestinal-type gastric cancer, congruous to the hypothesis of the two distinct carcinogenesis pathways for the two major types of gastric cancer. In addition to publication on a specific gene, the sharing of GWAS data through a database on the web is expected to accelerate validation and discovery by other investigators. GeMDBJ (Genome Medicine Database of Japan), started in 2005 in Japan, is one of such attempts. Moreover, the advent of "next generation" sequencers may herald a new era in which the poorly explored domains of the genetic architecture of disease susceptibility may be unveiled.
  Cancer Science 07/2010; 101(7):1582-9. · 3.33 Impact Factor
• Article: Detection of inappropriate samples in association studies by an IBS-based method considering linkage disequilibrium between genetic markers.

  Masataka Andoh, Yasunori Sato, Hiromi Sakamoto, Teruhiko Yoshida, Megu Ohtaki
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  ABSTRACT: An association study is a popular study design to identify susceptibility genes for common complex diseases. In such a study, the presence of inappropriate samples, such as those derived from close relatives or showing DNA contamination, causes an inflation of type I error or a decrease of power. Here we propose an identity-by-state (IBS)-based detection method of inappropriate samples taking linkage disequilibrium (LD) into consideration. The test statistics is the mean of the proportion of alleles that are shared identical by state at each single nucleotide polymorphism (SNP) between each sample pair in an association study. A covariance of the number of shared alleles between two SNPs is introduced to consider LD. We show that type I error and power are estimated accurately in computer-simulated data, and that if the number of SNPs analyzed is small, the performance of detection of inappropriate samples is superior to the previous method in simulated LD. An application to real association study data showed that accuracy in estimating the distribution of test statistics improved if LD was considered. Sample pairs considered to be siblings were detected. These results suggested that an LD-considered IBS-based detection method is useful in identifying inappropriate samples in an association study.
  Journal of Human Genetics 05/2010; 55(7):436-40. · 2.57 Impact Factor
• Article: Analysis of poly(ADP-ribose) polymerase-1 (PARP1) gene alteration in human germ cell tumor cell lines.

  Hideki Ogino, Robert Nakayama, Hiromi Sakamoto, Teruhiko Yoshida, Takashi Sugimura, Mitsuko Masutani
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  ABSTRACT: The poly(ADP-ribose) polymerase-1 protein (PARP-1) functions in DNA repair, maintenance of genomic stability, induction of cell death, and transcriptional regulation. We previously analyzed alterations of the PARP1 gene in 16 specimens of human germ cell tumors, and found a heterozygous sequence alteration that causes the amino acid substitution Met129Thr (M129T) in both tumor and normal tissues in a single patient. In this study, aberration of the PARP1 gene and protein was further analyzed in human germ cell tumor cell lines. We found a nonheterozygous sequence alteration that causes the amino acid substitution Glu251Lys (E251K) located at a conserved peptide stretch of PARP-1 in cell line NEC8. Sequencing of 95 samples from Japanese healthy volunteers revealed that all the samples were homozygous for the wild-type alleles at M129T and E251K. The M129T allele is thus suggested to be a rare single-nucleotide polymorphism (SNP). We observed a decrease in auto-poly(ADP-ribosyl)ation activity of PARP-1 proteins harboring M129T or E251K amino acid substitution, but the difference was not statistically significant. The levels of PARP-1 and poly(ADP-ribosyl)ation were heterogeneous among germ cell tumor cell lines. The SNPs of the PARP1 gene, as well as differences in the levels of PARP-1 and poly(ADP-ribosyl)ation of proteins, may influence germ cell tumor development and responses to chemotherapy and radiotherapy.
  Cancer genetics and cytogenetics 02/2010; 197(1):8-15. · 1.54 Impact Factor