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Kageyama S, Sakata S, Ma J, Asakawa M, Takeshita T, Furuta M, Ninomiya T, Yamashita Y. High-Resolution Detection of Translocation of Oral Bacteria to the Gut. J Dent Res 2023:220345231160747. [PMID: 37204134 DOI: 10.1177/00220345231160747] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
Ectopic enrichment of oral microbes in the gut is a notable alteration in gut microbial balance. These microbes are likely delivered from the oral cavity with saliva and food; however, evidence of oral-gut microbial transmission is insufficient and needs further investigation. In this observational study, we examined 144 pairs of saliva and stool samples collected from community-dwelling adults to verify the oral-gut microbial link and identify the relevant influencing factors on the increased abundance of oral microbes within the gut. The bacterial composition of each sample was determined using PacBio single-molecule long-read sequencing of the full-length 16S ribosomal RNA gene and amplicon sequence variant (ASV) analysis. Although the bacterial compositions of salivary and gut microbiota were distinctly different, at least 1 ASV was shared between salivary and gut microbiota in 72.9% of subjects. Shared ASVs accounted for 0.0% to 63.1% (median 0.14%) of the gut microbiota in each subject and frequently included abundant Streptococcus salivarius and Streptococcus parasanguinis. Their total relative abundance in the gut was significantly higher in older subjects or those with dental plaque accumulation. The gut microbiota with ≥5% of shared ASVs displayed a higher abundance of Streptococcus, Lactobacillus, and Klebsiella and a lower abundance of Faecalibacterium, Blautia, Megamonas, and Parabacteroides. Our study presents evidence for the translocation of oral bacteria to the gut in community-dwelling adults and suggests that aging and dental plaque accumulation contribute to an increased abundance of oral microbes in the gut, which might be relevant to the compositional shift in the gut commensals.
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Affiliation(s)
- S Kageyama
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - S Sakata
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - J Ma
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - M Asakawa
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - T Takeshita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
- OBT Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - M Furuta
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - T Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Y Yamashita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
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Author Correction: The evolutionary history of 2,658 cancers. Nature 2023; 614:E42. [PMID: 36697833 PMCID: PMC9931577 DOI: 10.1038/s41586-022-05601-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK. .,European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. .,Wellcome Sanger Institute, Cambridge, UK.
| | - Clemency Jolly
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Ignaty Leshchiner
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Stefan C. Dentro
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK
| | - Santiago Gonzalez
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Daniel Rosebrock
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Thomas J. Mitchell
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Yulia Rubanova
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Pavana Anur
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - Kaixian Yu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Maxime Tarabichi
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Amit Deshwar
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Jeff Wintersinger
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | - Kortine Kleinheinz
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Heidelberg University, Heidelberg, Germany
| | - Ignacio Vázquez-García
- grid.10306.340000 0004 0606 5382Wellcome Sanger Institute, Cambridge, UK ,grid.5335.00000000121885934University of Cambridge, Cambridge, UK
| | - Kerstin Haase
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK
| | - Lara Jerman
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK ,grid.8954.00000 0001 0721 6013University of Ljubljana, Ljubljana, Slovenia
| | - Subhajit Sengupta
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA
| | - Geoff Macintyre
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Salem Malikic
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Nilgun Donmez
- grid.61971.380000 0004 1936 7494Simon Fraser University, Burnaby, British Columbia Canada ,grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada
| | - Dimitri G. Livitz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Marek Cmero
- grid.1008.90000 0001 2179 088XUniversity of Melbourne, Melbourne, Victoria Australia ,grid.1042.70000 0004 0432 4889Walter and Eliza Hall Institute, Melbourne, Victoria Australia
| | - Jonas Demeulemeester
- grid.451388.30000 0004 1795 1830The Francis Crick Institute, London, UK ,grid.5596.f0000 0001 0668 7884University of Leuven, Leuven, Belgium
| | - Steven Schumacher
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Yu Fan
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Xiaotong Yao
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Juhee Lee
- grid.205975.c0000 0001 0740 6917University of California Santa Cruz, Santa Cruz, CA USA
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul C. Boutros
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.419890.d0000 0004 0626 690XOntario Institute for Cancer Research, Toronto, Ontario Canada ,grid.19006.3e0000 0000 9632 6718University of California, Los Angeles, CA USA
| | - David D. Bowtell
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, Victoria Australia
| | - Hongtu Zhu
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Gad Getz
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA USA ,grid.32224.350000 0004 0386 9924Department of Pathology, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Marcin Imielinski
- grid.5386.8000000041936877XWeill Cornell Medicine, New York, NY USA ,grid.429884.b0000 0004 1791 0895New York Genome Center, New York, NY USA
| | - Rameen Beroukhim
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - S. Cenk Sahinalp
- grid.412541.70000 0001 0684 7796Vancouver Prostate Centre, Vancouver, British Columbia Canada ,grid.411377.70000 0001 0790 959XIndiana University, Bloomington, IN USA
| | - Yuan Ji
- grid.240372.00000 0004 0400 4439NorthShore University HealthSystem, Evanston, IL USA ,grid.170205.10000 0004 1936 7822The University of Chicago, Chicago, IL USA
| | - Martin Peifer
- grid.6190.e0000 0000 8580 3777University of Cologne, Cologne, Germany
| | - Florian Markowetz
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Ville Mustonen
- grid.7737.40000 0004 0410 2071University of Helsinki, Helsinki, Finland
| | - Ke Yuan
- grid.5335.00000000121885934Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK ,grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Wenyi Wang
- grid.240145.60000 0001 2291 4776The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Quaid D. Morris
- grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada ,grid.494618.6Vector Institute, Toronto, Ontario Canada
| | | | - Paul T. Spellman
- grid.5288.70000 0000 9758 5690Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR USA
| | - David C. Wedge
- grid.4991.50000 0004 1936 8948Big Data Institute, University of Oxford, Oxford, UK ,grid.454382.c0000 0004 7871 7212Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, UK. .,University of Leuven, Leuven, Belgium.
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Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Wu K, Yang H, Fonseca NA, Kahles A, Lehmann KV, Urban L, Soulette CM, Shiraishi Y, Liu F, He Y, Demircioğlu D, Davidson NR, Calabrese C, Zhang J, Perry MD, Xiang Q, Greger L, Li S, Liu D, Stark SG, Zhang F, Amin SB, Bailey P, Chateigner A, Cortés-Ciriano I, Craft B, Erkek S, Frenkel-Morgenstern M, Goldman M, Hoadley KA, Hou Y, Huska MR, Khurana E, Kilpinen H, Korbel JO, Lamaze FC, Li C, Li X, Li X, Liu X, Marin MG, Markowski J, Nandi T, Nielsen MM, Ojesina AI, Pan-Hammarström Q, Park PJ, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Pedamallu CS, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pedersen JS, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Siebert R, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Su H, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Tan P, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Teh BT, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Wang J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Waszak SM, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Xiong H, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Yakneen S, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Ye C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Yung C, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Zhang X, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Zheng L, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Zhu J, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Zhu S, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Awadalla P, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Creighton CJ, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Meyerson M, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Ouellette BFF, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Wu K, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Yang H, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Göke J, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Schwarz RF, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Stegle O, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Zhang Z, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Brazma A, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Rätsch G, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Brooks AN, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Brazma A, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Brooks AN, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Göke J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Rätsch G, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Schwarz RF, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Stegle O, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Zhang Z, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Aaltonen LA, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Abascal F, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Abeshouse A, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Aburatani H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Adams DJ, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Agrawal N, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Ahn KS, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Ahn SM, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Aikata H, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, Akbani R, von Mering C, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, 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Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, 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Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV. Author Correction: Genomic basis for RNA alterations in cancer. Nature 2023; 614:E37. [PMID: 36697831 PMCID: PMC9931574 DOI: 10.1038/s41586-022-05596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | - Claudia Calabrese
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Natalie R. Davidson
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.5386.8000000041936877XWeill Cornell Medical College, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Deniz Demircioğlu
- grid.4280.e0000 0001 2180 6431National University of Singapore, Singapore, Singapore ,grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Nuno A. Fonseca
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Yao He
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - André Kahles
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Kjong-Van Lehmann
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Fenglin Liu
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Yuichi Shiraishi
- grid.26999.3d0000 0001 2151 536XThe University of Tokyo, Minato-ku, Japan
| | - Cameron M. Soulette
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Lara Urban
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Liliana Greger
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Siliang Li
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Dongbing Liu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Marc D. Perry
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.266102.10000 0001 2297 6811University of California, San Francisco, San Francisco, CA USA
| | - Qian Xiang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fan Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
| | - Junjun Zhang
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Peter Bailey
- grid.8756.c0000 0001 2193 314XUniversity of Glasgow, Glasgow, UK
| | - Serap Erkek
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Katherine A. Hoadley
- grid.10698.360000000122483208The University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - Yong Hou
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Matthew R. Huska
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Helena Kilpinen
- grid.83440.3b0000000121901201University College London, London, UK
| | - Jan O. Korbel
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Maximillian G. Marin
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA
| | - Julia Markowski
- grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Tannistha Nandi
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore
| | - Qiang Pan-Hammarström
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.4714.60000 0004 1937 0626Karolinska Institutet, Stockholm, Sweden
| | - Chandra Sekhar Pedamallu
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | - Reiner Siebert
- grid.410712.10000 0004 0473 882XUlm University and Ulm University Medical Center, Ulm, Germany
| | - Stefan G. Stark
- grid.5801.c0000 0001 2156 2780ETH Zurich, Zurich, Switzerland ,grid.51462.340000 0001 2171 9952Memorial Sloan Kettering Cancer Center, New York, NY USA ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.412004.30000 0004 0478 9977University Hospital Zurich, Zurich, Switzerland
| | - Hong Su
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Patrick Tan
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Sebastian M. Waszak
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Christina Yung
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shida Zhu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Philip Awadalla
- grid.17063.330000 0001 2157 2938Ontario Institute for Cancer Research, Toronto, Ontario, Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, Ontario Canada
| | - Chad J. Creighton
- grid.39382.330000 0001 2160 926XBaylor College of Medicine, Houston, TX USA
| | - Matthew Meyerson
- grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XHarvard Medical School, Boston, MA USA
| | | | - Kui Wu
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China ,grid.507779.b0000 0004 4910 5858China National GeneBank-Shenzhen, Shenzhen, China
| | - Huanming Yang
- grid.21155.320000 0001 2034 1839BGI-Shenzhen, Shenzhen, China
| | | | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
| | - Angela N. Brooks
- grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Santa Cruz, CA USA ,grid.66859.340000 0004 0546 1623Broad Institute, Cambridge, MA USA ,grid.65499.370000 0001 2106 9910Dana-Farber Cancer Institute, Boston, MA USA
| | - Jonathan Göke
- grid.418377.e0000 0004 0620 715XGenome Institute of Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745National Cancer Centre Singapore, Singapore, Singapore
| | - Gunnar Rätsch
- ETH Zurich, Zurich, Switzerland. .,Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA. .,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland. .,University Hospital Zurich, Zurich, Switzerland.
| | - Roland F. Schwarz
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.419491.00000 0001 1014 0849Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), partner site Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oliver Stegle
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK ,grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zemin Zhang
- grid.11135.370000 0001 2256 9319Peking University, Beijing, China
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Yokouchi H, Mizugaki H, Ikezawa Y, Morita R, Tateishi K, Yokoo K, Sumi T, Kikuchi H, Nakamura A, M. kobayashi, Aso M, Tsukita Y, Yoshiike F, Furuta M, Tanaka H, Sekikawa M, Hachiya T, Nakamura K, Kitamura Y. 335P Real-world data of first-line treatment with pembrolizumab for non-small cell lung cancer with high PD-L1 expression (HOT/NJLCG2001). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.10.373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
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5
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Vo KC, Wada A, Iwata R, Asada R, Sakamoto JJ, Furuta M, Tsuchido T. Evaluation of distinct modes of oxidative secondary injury generated in heat-treated cells of Escherichia coli with solid/liquid and complex/semi-synthetic media sets. J Appl Microbiol 2022; 133:2361-2374. [PMID: 35771133 DOI: 10.1111/jam.15697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022]
Abstract
AIMS To characterize and evaluate oxidative secondary injury generated in heat-treated Escherichia coli cells during recovery cultivation either on agar or in a broth of a semi-synthetic enriched M9 (EM9) medium and a complex Luria broth (LB) medium with different types of antioxidants. METHODS AND RESULTS E. coli cells grown in the EM9 and LB broth were heated at 50o C in a buffer (pH7.0). Heated cells were recovered on the same kind of agar medium as that used for growth, with or without different antioxidants. Although these antioxidants mostly protected the cells from oxidative secondary injury on the recovery media, sodium thiosulfate and sodium pyruvate were most protective on EM9 and LB agars, respectively. Determination of viability using the most probable number and growth delay analysis methods showed significant reductions in the protective effects of antioxidants in the EM9 and LB media. CONCLUSION Oxidative secondary injury generated in heated E. coli cells was found to be qualitatively and quantitatively diverse under cellular and environmental conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Our results suggest that different modes of oxidation should be considered in viability determination and injured cell enumeration of heat-treated cells.
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Affiliation(s)
- K C Vo
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan
| | - A Wada
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan
| | - R Iwata
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan
| | - R Asada
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan.,Radiation Research Center, Organization for Research Promotion, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan.,Research Center of Microorganism Control, Organization for Research Promotion, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan
| | - J J Sakamoto
- Research Center of Microorganism Control, Organization for Research Promotion, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan.,Faculty of Materials, Chemistry, Engineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka, Japan
| | - M Furuta
- Department of Quantum and Radiation Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan.,Radiation Research Center, Organization for Research Promotion, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan.,Research Center of Microorganism Control, Organization for Research Promotion, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan
| | - T Tsuchido
- Research Center of Microorganism Control, Organization for Research Promotion, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Japan
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Kobayashi M, Mizugaki H, Ikezawa Y, Morita R, Tateishi K, Yokoo K, Sumi T, Kikuchi H, Nagano Y, Nakamura A, Aso M, Kimura N, Yoshiike F, Furuta M, Tanaka H, Sekikawa M, Hachiya T, Fujita Y, Oizumi S. P16.05 Real World Data of First-Line Treatment With Pembrolizumab for Highly PD-L1-Expressing NSCLC. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Nakamura A, Mizugaki H, Ikezawa Y, Morita R, Tateishi K, Yokoo K, Sumi T, Kikuchi H, Kitamura Y, Morita M, Aso M, Tsukita Y, Yoshiike F, Furuta M, Tanaka H, Sekikawa M, Hachiya T, Nakamura K, Yokouchi H. 1306P Real-world data of first-line treatment with pembrolizumab for highly PD-L1 expressing NSCLC (HOT/NJLCG2001). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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8
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Kondo Y, Sakakibara T, Furuta M, Kato J, Kato A, Mase S, Sasaki H, Miyake Y. 333MO Cost-utility analysis of olanzapine in Japanese patients treated with cisplatin-containing highly emetogenic chemotherapy. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Aaltonen LA, Abascal F, Abeshouse A, Aburatani H, Adams DJ, Agrawal N, Ahn KS, Ahn SM, Aikata H, Akbani R, Akdemir KC, Al-Ahmadie H, Al-Sedairy ST, Al-Shahrour F, Alawi M, Albert M, Aldape K, Alexandrov LB, Ally A, Alsop K, Alvarez EG, Amary F, Amin SB, Aminou B, Ammerpohl O, Anderson MJ, Ang Y, Antonello D, Anur P, Aparicio S, Appelbaum EL, Arai Y, Aretz A, Arihiro K, Ariizumi SI, Armenia J, Arnould L, Asa S, Assenov Y, Atwal G, Aukema S, Auman JT, Aure MRR, Awadalla P, Aymerich M, Bader GD, Baez-Ortega A, Bailey MH, Bailey PJ, Balasundaram M, Balu S, Bandopadhayay P, Banks RE, Barbi S, Barbour AP, Barenboim J, Barnholtz-Sloan J, Barr H, Barrera E, Bartlett J, Bartolome J, Bassi C, Bathe OF, Baumhoer D, Bavi P, Baylin SB, Bazant W, Beardsmore D, Beck TA, Behjati S, Behren A, Niu B, Bell C, Beltran S, Benz C, Berchuck A, Bergmann AK, Bergstrom EN, Berman BP, Berney DM, Bernhart SH, Beroukhim R, Berrios M, Bersani S, Bertl J, Betancourt M, Bhandari V, Bhosle SG, Biankin AV, Bieg M, Bigner D, Binder H, Birney E, Birrer M, Biswas NK, Bjerkehagen B, Bodenheimer T, Boice L, Bonizzato G, De Bono JS, Boot A, Bootwalla MS, Borg A, Borkhardt A, Boroevich KA, Borozan I, Borst C, Bosenberg M, Bosio M, Boultwood J, Bourque G, Boutros PC, Bova GS, Bowen DT, Bowlby R, Bowtell DDL, Boyault S, Boyce R, Boyd J, Brazma A, Brennan P, Brewer DS, Brinkman AB, Bristow RG, Broaddus RR, Brock JE, Brock M, Broeks A, Brooks AN, Brooks D, Brors B, Brunak S, Bruxner TJC, Bruzos AL, Buchanan A, Buchhalter I, Buchholz C, Bullman S, Burke H, Burkhardt B, Burns KH, Busanovich J, Bustamante CD, Butler AP, Butte AJ, Byrne NJ, Børresen-Dale AL, Caesar-Johnson SJ, Cafferkey A, Cahill D, Calabrese C, Caldas C, Calvo F, Camacho N, Campbell PJ, Campo E, Cantù C, Cao S, Carey TE, Carlevaro-Fita J, Carlsen R, Cataldo I, Cazzola M, Cebon J, Cerfolio R, Chadwick DE, Chakravarty D, Chalmers D, Chan CWY, Chan K, Chan-Seng-Yue M, Chandan VS, Chang DK, Chanock SJ, Chantrill LA, Chateigner A, Chatterjee N, Chayama K, Chen HW, Chen J, Chen K, Chen Y, Chen Z, Cherniack AD, Chien J, Chiew YE, Chin SF, Cho J, Cho S, Choi JK, Choi W, Chomienne C, Chong Z, Choo SP, Chou A, Christ AN, Christie EL, Chuah E, Cibulskis C, Cibulskis K, Cingarlini S, Clapham P, Claviez A, Cleary S, Cloonan N, Cmero M, Collins CC, Connor AA, Cooke SL, Cooper CS, Cope L, Corbo V, Cordes MG, Cordner SM, Cortés-Ciriano I, Covington K, Cowin PA, Craft B, Craft D, Creighton CJ, Cun Y, Curley E, Cutcutache I, Czajka K, Czerniak B, Dagg RA, Danilova L, Davi MV, Davidson NR, Davies H, Davis IJ, Davis-Dusenbery BN, Dawson KJ, De La Vega FM, De Paoli-Iseppi R, Defreitas T, Tos APD, Delaneau O, Demchok JA, Demeulemeester J, Demidov GM, Demircioğlu D, Dennis NM, Denroche RE, Dentro SC, Desai N, Deshpande V, Deshwar AG, Desmedt C, Deu-Pons J, Dhalla N, Dhani NC, Dhingra P, Dhir R, DiBiase A, Diamanti K, Ding L, Ding S, Dinh HQ, Dirix L, Doddapaneni H, Donmez N, Dow MT, Drapkin R, Drechsel O, Drews RM, Serge S, Dudderidge T, Dueso-Barroso A, Dunford AJ, Dunn M, Dursi LJ, Duthie FR, Dutton-Regester K, Eagles J, Easton DF, Edmonds S, Edwards PA, Edwards SE, Eeles RA, Ehinger A, Eils J, Eils R, El-Naggar A, Eldridge M, Ellrott K, Erkek S, Escaramis G, Espiritu SMG, Estivill X, Etemadmoghadam D, Eyfjord JE, Faltas BM, Fan D, Fan Y, Faquin WC, Farcas C, Fassan M, Fatima A, Favero F, Fayzullaev N, Felau I, Fereday S, Ferguson ML, Ferretti V, Feuerbach L, Field MA, Fink JL, Finocchiaro G, Fisher C, Fittall MW, Fitzgerald A, Fitzgerald RC, Flanagan AM, Fleshner NE, Flicek P, Foekens JA, Fong KM, Fonseca NA, Foster CS, Fox NS, Fraser M, Frazer S, Frenkel-Morgenstern M, Friedman W, Frigola J, Fronick CC, Fujimoto A, Fujita M, Fukayama M, Fulton LA, Fulton RS, Furuta M, Futreal PA, Füllgrabe A, Gabriel SB, Gallinger S, Gambacorti-Passerini C, Gao J, Gao S, Garraway L, Garred Ø, Garrison E, Garsed DW, Gehlenborg N, Gelpi JLL, George J, Gerhard DS, Gerhauser C, Gershenwald JE, Gerstein M, Gerstung M, Getz G, Ghori M, Ghossein R, Giama NH, Gibbs RA, Gibson B, Gill AJ, Gill P, Giri DD, Glodzik D, Gnanapragasam VJ, Goebler ME, Goldman MJ, Gomez C, Gonzalez S, Gonzalez-Perez A, Gordenin DA, Gossage J, Gotoh K, Govindan R, Grabau D, Graham JS, Grant RC, Green AR, Green E, Greger L, Grehan N, Grimaldi S, Grimmond SM, Grossman RL, Grundhoff A, Gundem G, Guo Q, Gupta M, Gupta S, Gut IG, Gut M, Göke J, Ha G, Haake A, Haan D, Haas S, Haase K, Haber JE, Habermann N, Hach F, Haider S, Hama N, Hamdy FC, Hamilton A, Hamilton MP, Han L, Hanna GB, Hansmann M, Haradhvala NJ, Harismendy O, Harliwong I, Harmanci AO, Harrington E, Hasegawa T, Haussler D, Hawkins S, Hayami S, Hayashi S, Hayes DN, Hayes SJ, Hayward NK, Hazell S, He Y, Heath AP, Heath SC, Hedley D, Hegde AM, Heiman DI, Heinold MC, Heins Z, Heisler LE, Hellstrom-Lindberg E, Helmy M, Heo SG, Hepperla AJ, Heredia-Genestar JM, Herrmann C, Hersey P, Hess JM, Hilmarsdottir H, Hinton J, Hirano S, Hiraoka N, Hoadley KA, Hobolth A, Hodzic E, Hoell JI, Hoffmann S, Hofmann O, Holbrook A, Holik AZ, Hollingsworth MA, Holmes O, Holt RA, Hong C, Hong EP, Hong JH, Hooijer GK, Hornshøj H, Hosoda F, Hou Y, Hovestadt V, Howat W, Hoyle AP, Hruban RH, Hu J, Hu T, Hua X, Huang KL, Huang M, Huang MN, Huang V, Huang Y, Huber W, Hudson TJ, Hummel M, Hung JA, Huntsman D, Hupp TR, Huse J, Huska MR, Hutter B, Hutter CM, Hübschmann D, Iacobuzio-Donahue CA, Imbusch CD, Imielinski M, Imoto S, Isaacs WB, Isaev K, Ishikawa S, Iskar M, Islam SMA, Ittmann M, Ivkovic S, Izarzugaza JMG, Jacquemier J, Jakrot V, Jamieson NB, Jang GH, Jang SJ, Jayaseelan JC, Jayasinghe R, Jefferys SR, Jegalian K, Jennings JL, Jeon SH, Jerman L, Ji Y, Jiao W, Johansson PA, Johns AL, Johns J, Johnson R, Johnson TA, Jolly C, Joly Y, Jonasson JG, Jones CD, Jones DR, Jones DTW, Jones N, Jones SJM, Jonkers J, Ju YS, Juhl H, Jung J, Juul M, Juul RI, Juul S, Jäger N, Kabbe R, Kahles A, Kahraman A, Kaiser VB, Kakavand H, Kalimuthu S, von Kalle C, Kang KJ, Karaszi K, Karlan B, Karlić R, Karsch D, Kasaian K, Kassahn KS, Katai H, Kato M, Katoh H, Kawakami Y, Kay JD, Kazakoff SH, Kazanov MD, Keays M, Kebebew E, Kefford RF, Kellis M, Kench JG, Kennedy CJ, Kerssemakers JNA, Khoo D, Khoo V, Khuntikeo N, Khurana E, Kilpinen H, Kim HK, Kim HL, Kim HY, Kim H, Kim J, Kim J, Kim JK, Kim Y, King TA, Klapper W, Kleinheinz K, Klimczak LJ, Knappskog S, Kneba M, Knoppers BM, Koh Y, Komorowski J, Komura D, Komura M, Kong G, Kool M, Korbel JO, Korchina V, Korshunov A, Koscher M, Koster R, Kote-Jarai Z, Koures A, Kovacevic M, Kremeyer B, Kretzmer H, Kreuz M, Krishnamurthy S, Kube D, Kumar K, Kumar P, Kumar S, Kumar Y, Kundra R, Kübler K, Küppers R, Lagergren J, Lai PH, Laird PW, Lakhani SR, Lalansingh CM, Lalonde E, Lamaze FC, Lambert A, Lander E, Landgraf P, Landoni L, Langerød A, Lanzós A, Larsimont D, Larsson E, Lathrop M, Lau LMS, Lawerenz C, Lawlor RT, Lawrence MS, Lazar AJ, Lazic AM, Le X, Lee D, Lee D, Lee EA, Lee HJ, Lee JJK, Lee JY, Lee J, Lee MTM, Lee-Six H, Lehmann KV, Lehrach H, Lenze D, Leonard CR, Leongamornlert DA, Leshchiner I, Letourneau L, Letunic I, Levine DA, Lewis L, Ley T, Li C, Li CH, Li HI, Li J, Li L, Li S, Li S, Li X, Li X, Li X, Li Y, Liang H, Liang SB, Lichter P, Lin P, Lin Z, Linehan WM, Lingjærde OC, Liu D, Liu EM, Liu FFF, Liu F, Liu J, Liu X, Livingstone J, Livitz D, Livni N, Lochovsky L, Loeffler M, Long GV, Lopez-Guillermo A, Lou S, Louis DN, Lovat LB, Lu Y, Lu YJ, Lu Y, Luchini C, Lungu I, Luo X, Luxton HJ, Lynch AG, Lype L, López C, López-Otín C, Ma EZ, Ma Y, MacGrogan G, MacRae S, Macintyre G, Madsen T, Maejima K, Mafficini A, Maglinte DT, Maitra A, Majumder PP, Malcovati L, Malikic S, Malleo G, Mann GJ, Mantovani-Löffler L, Marchal K, Marchegiani G, Mardis ER, Margolin AA, Marin MG, Markowetz F, Markowski J, Marks J, Marques-Bonet T, Marra MA, Marsden L, Martens JWM, Martin S, Martin-Subero JI, Martincorena I, Martinez-Fundichely A, Maruvka YE, Mashl RJ, Massie CE, Matthew TJ, Matthews L, Mayer E, Mayes S, Mayo M, Mbabaali F, McCune K, McDermott U, McGillivray PD, McLellan MD, McPherson JD, McPherson JR, McPherson TA, Meier SR, Meng A, Meng S, Menzies A, Merrett ND, Merson S, Meyerson M, Meyerson W, Mieczkowski PA, Mihaiescu GL, Mijalkovic S, Mikkelsen T, Milella M, Mileshkin L, Miller CA, Miller DK, Miller JK, Mills GB, Milovanovic A, Minner S, Miotto M, Arnau GM, Mirabello L, Mitchell C, Mitchell TJ, Miyano S, Miyoshi N, Mizuno S, Molnár-Gábor F, Moore MJ, Moore RA, Morganella S, Morris QD, Morrison C, Mose LE, Moser CD, Muiños F, Mularoni L, Mungall AJ, Mungall K, Musgrove EA, Mustonen V, Mutch D, Muyas F, Muzny DM, Muñoz A, Myers J, Myklebost O, Möller P, Nagae G, Nagrial AM, Nahal-Bose HK, Nakagama H, Nakagawa H, Nakamura H, Nakamura T, Nakano K, Nandi T, Nangalia J, Nastic M, Navarro A, Navarro FCP, Neal DE, Nettekoven G, Newell F, Newhouse SJ, Newton Y, Ng AWT, Ng A, Nicholson J, Nicol D, Nie Y, Nielsen GP, Nielsen MM, Nik-Zainal S, Noble MS, Nones K, Northcott PA, Notta F, O’Connor BD, O’Donnell P, O’Donovan M, O’Meara S, O’Neill BP, O’Neill JR, Ocana D, Ochoa A, Oesper L, Ogden C, Ohdan H, Ohi K, Ohno-Machado L, Oien KA, Ojesina AI, Ojima H, Okusaka T, Omberg L, Ong CK, Ossowski S, Ott G, Ouellette BFF, P’ng C, Paczkowska M, Paiella S, Pairojkul C, Pajic M, Pan-Hammarström Q, Papaemmanuil E, Papatheodorou I, Paramasivam N, Park JW, Park JW, Park K, Park K, Park PJ, Parker JS, Parsons SL, Pass H, Pasternack D, Pastore A, Patch AM, Pauporté I, Pea A, Pearson JV, Pedamallu CS, Pedersen JS, Pederzoli P, Peifer M, Pennell NA, Perou CM, Perry MD, Petersen GM, Peto M, Petrelli N, Petryszak R, Pfister SM, Phillips M, Pich O, Pickett HA, Pihl TD, Pillay N, Pinder S, Pinese M, Pinho AV, Pitkänen E, Pivot X, Piñeiro-Yáñez E, Planko L, Plass C, Polak P, Pons T, Popescu I, Potapova O, Prasad A, Preston SR, Prinz M, Pritchard AL, Prokopec SD, Provenzano E, Puente XS, Puig S, Puiggròs M, Pulido-Tamayo S, Pupo GM, Purdie CA, Quinn MC, Rabionet R, Rader JS, Radlwimmer B, Radovic P, Raeder B, Raine KM, Ramakrishna M, Ramakrishnan K, Ramalingam S, Raphael BJ, Rathmell WK, Rausch T, Reifenberger G, Reimand J, Reis-Filho J, Reuter V, Reyes-Salazar I, Reyna MA, Reynolds SM, Rheinbay E, Riazalhosseini Y, Richardson AL, Richter J, Ringel M, Ringnér M, Rino Y, Rippe K, Roach J, Roberts LR, Roberts ND, Roberts SA, Robertson AG, Robertson AJ, Rodriguez JB, Rodriguez-Martin B, Rodríguez-González FG, Roehrl MHA, Rohde M, Rokutan H, Romieu G, Rooman I, Roques T, Rosebrock D, Rosenberg M, Rosenstiel PC, Rosenwald A, Rowe EW, Royo R, Rozen SG, Rubanova Y, Rubin MA, Rubio-Perez C, Rudneva VA, Rusev BC, Ruzzenente A, Rätsch G, Sabarinathan R, Sabelnykova VY, Sadeghi S, Sahinalp SC, Saini N, Saito-Adachi M, Saksena G, Salcedo A, Salgado R, Salichos L, Sallari R, Saller C, Salvia R, Sam M, Samra JS, Sanchez-Vega F, Sander C, Sanders G, Sarin R, Sarrafi I, Sasaki-Oku A, Sauer T, Sauter G, Saw RPM, Scardoni M, Scarlett CJ, Scarpa A, Scelo G, Schadendorf D, Schein JE, Schilhabel MB, Schlesner M, Schlomm T, Schmidt HK, Schramm SJ, Schreiber S, Schultz N, Schumacher SE, Schwarz RF, Scolyer RA, Scott D, Scully R, Seethala R, Segre AV, Selander I, Semple CA, Senbabaoglu Y, Sengupta S, Sereni E, Serra S, Sgroi DC, Shackleton M, Shah NC, Shahabi S, Shang CA, Shang P, Shapira O, Shelton T, Shen C, Shen H, Shepherd R, Shi R, Shi Y, Shiah YJ, Shibata T, Shih J, Shimizu E, Shimizu K, Shin SJ, Shiraishi Y, Shmaya T, Shmulevich I, Shorser SI, Short C, Shrestha R, Shringarpure SS, Shriver C, Shuai S, Sidiropoulos N, Siebert R, Sieuwerts AM, Sieverling L, Signoretti S, Sikora KO, Simbolo M, Simon R, Simons JV, Simpson JT, Simpson PT, Singer S, Sinnott-Armstrong N, Sipahimalani P, Skelly TJ, Smid M, Smith J, Smith-McCune K, Socci ND, Sofia HJ, Soloway MG, Song L, Sood AK, Sothi S, Sotiriou C, Soulette CM, Span PN, Spellman PT, Sperandio N, Spillane AJ, Spiro O, Spring J, Staaf J, Stadler PF, Staib P, Stark SG, Stebbings L, Stefánsson ÓA, Stegle O, Stein LD, Stenhouse A, Stewart C, Stilgenbauer S, Stobbe MD, Stratton MR, Stretch JR, Struck AJ, Stuart JM, Stunnenberg HG, Su H, Su X, Sun RX, Sungalee S, Susak H, Suzuki A, Sweep F, Szczepanowski M, Sültmann H, Yugawa T, Tam A, Tamborero D, Tan BKT, Tan D, Tan P, Tanaka H, Taniguchi H, Tanskanen TJ, Tarabichi M, Tarnuzzer R, Tarpey P, Taschuk ML, Tatsuno K, Tavaré S, Taylor DF, Taylor-Weiner A, Teague JW, Teh BT, Tembe V, Temes J, Thai K, Thayer SP, Thiessen N, Thomas G, Thomas S, Thompson A, Thompson AM, Thompson JFF, Thompson RH, Thorne H, Thorne LB, Thorogood A, Tiao G, Tijanic N, Timms LE, Tirabosco R, Tojo M, Tommasi S, Toon CW, Toprak UH, Torrents D, Tortora G, Tost J, Totoki Y, Townend D, Traficante N, Treilleux I, Trotta JR, Trümper LHP, Tsao M, Tsunoda T, Tubio JMC, Tucker O, Turkington R, Turner DJ, Tutt A, Ueno M, Ueno NT, Umbricht C, Umer HM, Underwood TJ, Urban L, Urushidate T, Ushiku T, Uusküla-Reimand L, Valencia A, Van Den Berg DJ, Van Laere S, Van Loo P, Van Meir EG, Van den Eynden GG, Van der Kwast T, Vasudev N, Vazquez M, Vedururu R, Veluvolu U, Vembu S, Verbeke LPC, Vermeulen P, Verrill C, Viari A, Vicente D, Vicentini C, VijayRaghavan K, Viksna J, Vilain RE, Villasante I, Vincent-Salomon A, Visakorpi T, Voet D, Vyas P, Vázquez-García I, Waddell NM, Waddell N, Wadelius C, Wadi L, Wagener R, Wala JA, Wang J, Wang J, Wang L, Wang Q, Wang W, Wang Y, Wang Z, Waring PM, Warnatz HJ, Warrell J, Warren AY, Waszak SM, Wedge DC, Weichenhan D, Weinberger P, Weinstein JN, Weischenfeldt J, Weisenberger DJ, Welch I, Wendl MC, Werner J, Whalley JP, Wheeler DA, Whitaker HC, Wigle D, Wilkerson MD, Williams A, Wilmott JS, Wilson GW, Wilson JM, Wilson RK, Winterhoff B, Wintersinger JA, Wiznerowicz M, Wolf S, Wong BH, Wong T, Wong W, Woo Y, Wood S, Wouters BG, Wright AJ, Wright DW, Wright MH, Wu CL, Wu DY, Wu G, Wu J, Wu K, Wu Y, Wu Z, Xi L, Xia T, Xiang Q, Xiao X, Xing R, Xiong H, Xu Q, Xu Y, Xue H, Yachida S, Yakneen S, Yamaguchi R, Yamaguchi TN, Yamamoto M, Yamamoto S, Yamaue H, Yang F, Yang H, Yang JY, Yang L, Yang L, Yang S, Yang TP, Yang Y, Yao X, Yaspo ML, Yates L, Yau C, Ye C, Ye K, Yellapantula VD, Yoon CJ, Yoon SS, Yousif F, Yu J, Yu K, Yu W, Yu Y, Yuan K, Yuan Y, Yuen D, Yung CK, Zaikova O, Zamora J, Zapatka M, Zenklusen JC, Zenz T, Zeps N, Zhang CZ, Zhang F, Zhang H, Zhang H, Zhang H, Zhang J, Zhang J, Zhang J, Zhang X, Zhang X, Zhang Y, Zhang Z, Zhao Z, Zheng L, Zheng X, Zhou W, Zhou Y, Zhu B, Zhu H, Zhu J, Zhu S, Zou L, Zou X, deFazio A, van As N, van Deurzen CHM, van de Vijver MJ, van’t Veer L, von Mering C. Pan-cancer analysis of whole genomes. Nature 2020; 578:82-93. [PMID: 32025007 PMCID: PMC7025898 DOI: 10.1038/s41586-020-1969-6] [Citation(s) in RCA: 1435] [Impact Index Per Article: 358.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.
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Shoji T, Kikuchi E, Kikuchi J, Maeda M, Takashima Y, Furuta M, Takahashi H, Kinoshita I, Dosaka-Akita H, Sakakibara-Konishi J, Konno S. P2.03-53 Immunoproteasome as a Potential Therapeutic Target in Cisplatin-Resistant Small and Non-Small Cell Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Takeuchi K, Matsumoto K, Furuta M, Fukuyama S, Takeshita T, Ogata H, Suma S, Shibata Y, Shimazaki Y, Hata J, Ninomiya T, Nakanishi Y, Inoue H, Yamashita Y. Periodontitis Is Associated with Chronic Obstructive Pulmonary Disease. J Dent Res 2019; 98:534-540. [DOI: 10.1177/0022034519833630] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Although they are known to share pathophysiological processes, the relationship between periodontitis and chronic obstructive pulmonary disease (COPD) is not fully understood. The aim of the present study was to test the hypothesis that periodontitis is associated with a greater risk of development of COPD, when smoking is taken into account. The analysis in a 5-y follow-up population-based cohort study was based on 900 community-dwelling Japanese adults (age: 68.8 ± 6.3 [mean ± SD], 46.0% male) without COPD aged 60 or older with at least 1 tooth. Participants were classified into 3 categories according to baseline periodontitis severity (no/mild, moderate, and severe). COPD was spirometrically determined by a fixed ratio of <0.7 for forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) and by FEV1/FVC below the lower limit of normal. Poisson regression was used to calculate the relative risk (RR) of developing COPD according to the severity of periodontitis. The population attributable fraction (PAF) was also calculated. During follow-up, 22 (2.4%) subjects developed COPD. Compared with no/mild periodontitis subjects, a significantly increased risk of COPD occurred among severe periodontitis subjects (RR = 3.55; 95% confidence interval [CI], 1.18 to 10.67), but no significant differences were observed between the no/mild and moderate categories (RR = 1.48; 95% CI, 0.56 to 3.90). After adjustment for potential confounders, including smoking intensity, the relationship between severe periodontitis and risk of COPD remained significant (RR = 3.51; 95% CI, 1.15 to 10.74). Likewise, there was a positive association of periodontitis severity with risk of COPD ( P for trend = 0.043). The PAF for COPD due to periodontitis was 22.6%. These data highlight the potential importance of periodontitis as a risk factor for COPD.
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Affiliation(s)
- K. Takeuchi
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
- OBT Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - K. Matsumoto
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - M. Furuta
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - S. Fukuyama
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - T. Takeshita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
- OBT Research Center, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - H. Ogata
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - S. Suma
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Y. Shibata
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Y. Shimazaki
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
- Department of Preventive Dentistry and Dental Public Health, School of Dentistry, Aichi Gakuin University, Aichi, Japan
| | - J. Hata
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - T. Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Y. Nakanishi
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - H. Inoue
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Y. Yamashita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
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Shirasu H, Yokota T, Fushiki K, Inoue H, Shibata M, Furuta M, Kawakami T, Kawai S, Hamauchi S, Todaka A, Tsushima T, Machida N, Yamazaki K, Fukutomi A, Onozawa Y, Yasui H. Risk factors for aspiration pneumonia during concurrent chemoradiotherapy or bio-radiotherapy for head and neck cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy287.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Furuta M, Watanabe J, Aramaki T. Clinical utility of hepatic arterial infusion chemotherapy for heavily pretreated metastatic breast cancer patients: A review of a single institution. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy272.308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Taniguchi H, Fujimoto A, Kono H, Furuta M, Fujita M, Nakagawa H. Loss-of-function mutations in Zn-finger DNA-binding domain of HNF4A cause aberrant transcriptional regulation in liver cancer. Oncotarget 2018; 9:26144-26156. [PMID: 29899848 PMCID: PMC5995239 DOI: 10.18632/oncotarget.25456] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 05/02/2018] [Indexed: 11/25/2022] Open
Abstract
Hepatocyte nuclear factors (HNF) are transcription factors that crucially regulate cell-specific gene expression in many tissues, including the liver. Of these factors, HNF4A acts both as a master regulator of liver organogenesis and a tumor suppressor in the liver. In our whole genome sequencing analysis, we found seven somatic mutations (three Zn-finger mutations, three deletion mutants, and one intron mutation) of HNF4A in liver cancers. Interestingly, three out of seven mutations were clustered in its Zn-finger DNA-binding domain; G79 and F83 are positioned in the DNA recognition helix and the sidechain of M125 is sticking into the core of domain. These mutations are likely to affect DNA interaction from a structural point of view. We then generated these mutants and performed in-vitro promoter assays as well as DNA binding assays. These three mutations reduced HNF4 transcriptional activity at promoter sites of HNF4A-target genes. Expectedly, this decrease in transcriptional activity was associated with a change in DNA binding. RNA-Seq analysis observed a strong correlation between HNF4A expression and expression of its target genes, ApoB and HNF1A, in liver cancers. Since knockdown of HNF4A caused a reduction in ApoB and HNF1A expression, possibly loss of HNF4 reduces the expression of these genes and subsequently tumor growth is triggered. Therefore, we propose that HNF4A mutations G79C, F83C, and M125I are functional mutations found in liver cancers and that loss of HNF4A function, through its mutation, leads to a reduction in HNF1A and ApoB gene expression with a concomitant increased risk of liver tumorigenesis.
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Affiliation(s)
- Hiroaki Taniguchi
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.,Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec 05-552, Poland
| | - Akihiro Fujimoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| | - Mayuko Furuta
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Masashi Fujita
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
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15
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Furuta M, Tanaka H, Shiraishi Y, Unida T, Imamura M, Fujimoto A, Fujita M, Sasaki-Oku A, Maejima K, Nakano K, Kawakami Y, Arihiro K, Aikata H, Ueno M, Hayami S, Ariizumi SI, Yamamoto M, Gotoh K, Ohdan H, Yamaue H, Miyano S, Chayama K, Nakagawa H. Characterization of HBV integration patterns and timing in liver cancer and HBV-infected livers. Oncotarget 2018; 9:25075-25088. [PMID: 29861854 PMCID: PMC5982772 DOI: 10.18632/oncotarget.25308] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/06/2018] [Indexed: 12/17/2022] Open
Abstract
Integration of Hepatitis B virus (HBV) into the human genome can cause genetic instability, leading to selective advantages for HBV-induced liver cancer. Despite the large number of studies for HBV integration into liver cancer, little is known about the mechanism of initial HBV integration events owing to the limitations of materials and detection methods. We conducted an HBV sequence capture, followed by ultra-deep sequencing, to screen for HBV integrations in 111 liver samples from human-hepatocyte chimeric mice with HBV infection and human clinical samples containing 42 paired samples from non-tumorous and tumorous liver tissues. The HBV infection model using chimeric mice verified the efficiency of our HBV-capture analysis and demonstrated that HBV integration could occur 23 to 49 days after HBV infection via microhomology-mediated end joining and predominantly in mitochondrial DNA. Overall HBV integration sites in clinical samples were significantly enriched in regions annotated as exhibiting open chromatin, a high level of gene expression, and early replication timing in liver cells. These data indicate that HBV integration in liver tissue was biased according to chromatin accessibility, with additional selection pressures in the gene promoters of tumor samples. Moreover, an integrative analysis using paired non-tumorous and tumorous samples and HBV-related transcriptional change revealed the involvement of TERT and MLL4 in clonal selection. We also found frequent and non-tumorous liver-specific HBV integrations in FN1 and HBV-FN1 fusion transcript. Extensive survey of HBV integrations facilitates and improves the understanding of the timing and biology of HBV integration during infection and HBV-related hepatocarcinogenesis.
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Affiliation(s)
- Mayuko Furuta
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takuro Unida
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Michio Imamura
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Akihiro Fujimoto
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Masahi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Aya Sasaki-Oku
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Kaoru Nakano
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Yoshiiku Kawakami
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Koji Arihiro
- Department of Anatomical Pathology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Masaki Ueno
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Shinya Hayami
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Shun-Ichi Ariizumi
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Masakazu Yamamoto
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Kunihito Gotoh
- Department of Surgery, Osaka International Cancer Institute, Osaka 537-8511, Japan
| | - Hideki Ohdan
- Department of Gastroenterological Surgery, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
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Wardell CP, Fujita M, Yamada T, Simbolo M, Fassan M, Karlic R, Polak P, Kim J, Hatanaka Y, Maejima K, Lawlor RT, Nakanishi Y, Mitsuhashi T, Fujimoto A, Furuta M, Ruzzenente A, Conci S, Oosawa A, Sasaki-Oku A, Nakano K, Tanaka H, Yamamoto Y, Michiaki K, Kawakami Y, Aikata H, Ueno M, Hayami S, Gotoh K, Ariizumi SI, Yamamoto M, Yamaue H, Chayama K, Miyano S, Getz G, Scarpa A, Hirano S, Nakamura T, Nakagawa H. Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations. J Hepatol 2018; 68:959-969. [PMID: 29360550 DOI: 10.1016/j.jhep.2018.01.009] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous and respond poorly to treatment. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed large-scale genome sequencing analyses on BTCs to investigate their somatic and germline driver events and characterize their genomic landscape. METHODS We analyzed 412 BTC samples from Japanese and Italian populations, 107 by whole-exome sequencing (WES), 39 by whole-genome sequencing (WGS), and a further 266 samples by targeted sequencing. The subtypes were 136 intrahepatic cholangiocarcinomas (ICCs), 101 distal cholangiocarcinomas (DCCs), 109 peri-hilar type cholangiocarcinomas (PHCs), and 66 gallbladder or cystic duct cancers (GBCs/CDCs). We identified somatic alterations and searched for driver genes in BTCs, finding pathogenic germline variants of cancer-predisposing genes. We predicted cell-of-origin for BTCs by combining somatic mutation patterns and epigenetic features. RESULTS We identified 32 significantly and commonly mutated genes including TP53, KRAS, SMAD4, NF1, ARID1A, PBRM1, and ATR, some of which negatively affected patient prognosis. A novel deletion of MUC17 at 7q22.1 affected patient prognosis. Cell-of-origin predictions using WGS and epigenetic features suggest hepatocyte-origin of hepatitis-related ICCs. Deleterious germline mutations of cancer-predisposing genes such as BRCA1, BRCA2, RAD51D, MLH1, or MSH2 were detected in 11% (16/146) of BTC patients. CONCLUSIONS BTCs have distinct genetic features including somatic events and germline predisposition. These findings could be useful to establish treatment and diagnostic strategies for BTCs based on genetic information. LAY SUMMARY We here analyzed genomic features of 412 BTC samples from Japanese and Italian populations. A total of 32 significantly and commonly mutated genes were identified, some of which negatively affected patient prognosis, including a novel deletion of MUC17 at 7q22.1. Cell-of-origin predictions using WGS and epigenetic features suggest hepatocyte-origin of hepatitis-related ICCs. Deleterious germline mutations of cancer-predisposing genes were detected in 11% of patients with BTC. BTCs have distinct genetic features including somatic events and germline predisposition.
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Affiliation(s)
- Christopher P Wardell
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Masashi Fujita
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Toru Yamada
- Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Michele Simbolo
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Matteo Fassan
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Rosa Karlic
- Bioinformatics Group, Department of Molecular Biology, Division of Biology, Faculty of Science, University of Zagreb, Croatia
| | - Paz Polak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jaegil Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yutaka Hatanaka
- Research Division of Companion Diagnostics, Hokkaido University Hospital, Sapporo 060-8648, Japan
| | - Kazuhiro Maejima
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Rita T Lawlor
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Yoshitsugu Nakanishi
- Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Tomoko Mitsuhashi
- Department of Surgical Pathology, Hokkaido University Hospital, Sapporo 060-8648, Japan
| | - Akihiro Fujimoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Mayuko Furuta
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Andrea Ruzzenente
- Department of Surgery, General and Hepatobiliary Surgery, University Hospital G.B. Rossi, University and Hospital Trust of Verona, Verona, Italy
| | - Simone Conci
- Department of Surgery, General and Hepatobiliary Surgery, University Hospital G.B. Rossi, University and Hospital Trust of Verona, Verona, Italy
| | - Ayako Oosawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Aya Sasaki-Oku
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Kaoru Nakano
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yujiro Yamamoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan; Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kubo Michiaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yoshiiku Kawakami
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University School of Medicine, Hiroshima 734-8551, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University School of Medicine, Hiroshima 734-8551, Japan
| | - Masaki Ueno
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Shinya Hayami
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Kunihito Gotoh
- Department of Surgery, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka 537-8511, Japan
| | - Shun-Ichi Ariizumi
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Masakazu Yamamoto
- Department of Gastroenterological Surgery, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Hiroki Yamaue
- Second Department of Surgery, Wakayama Medical University, Wakayama 641-8510, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Institute of Biomedical and Health Sciences, Hiroshima University School of Medicine, Hiroshima 734-8551, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aldo Scarpa
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Satoshi Hirano
- Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Toru Nakamura
- Department of Gastroenterological Surgery II, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo 108-8639, Japan.
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Fujita M, Matsubara N, Matsuda I, Maejima K, Oosawa A, Yamano T, Fujimoto A, Furuta M, Nakano K, Oku-Sasaki A, Tanaka H, Shiraishi Y, Mateos RN, Nakai K, Miyano S, Tomita N, Hirota S, Ikeuchi H, Nakagawa H. Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in the Wnt signaling. Oncotarget 2018; 9:969-981. [PMID: 29416670 PMCID: PMC5787528 DOI: 10.18632/oncotarget.22867] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/16/2017] [Indexed: 01/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) increases the risk of colorectal cancer, known as colitis-associated cancer (CAC). It is still unclear what driver mutations are caused by chronic inflammation and lead to CAC development. To get insight into this issue, we investigated somatic alterations in CAC. We performed exome sequencing of 22 fresh CACs and targeted sequencing of 43 genes on 90 archive specimens from Japanese CAC patients, of which 58 were ulcerative colitis (UC) and 32 were Crohn's disease (CD). Consistently with the previous reports, TP53 was commonly mutated (66%) whereas APC, KRAS and SMAD4 were mutated less frequently (16%, 11% and 11%, respectively). Mucinous CD-CACs in the anus, an Asian-specific subtype of CD-CAC, had less somatic mutations in our target genes. We also found that RNF43, a negative regulator of the Wnt signaling, was somatically mutated in a significant fraction of CACs (10 of 90; 11%). Two lines of evidence indicated that somatic mutations of RNF43 were related to chronic inflammation. First, somatic mutations of RNF43 were significantly associated with longer duration of IBD. Second, clinico-pathological features suggested many of the APC-mutated CACs were actually sporadic colorectal cancer whereas RNF43-mutated CACs did not have this tendency. RNA-Seq analysis showed that RNF43-mutated CACs had elevated expression of c-Myc and its target genes, suggesting that RNF43 is a bona fide driver of CAC development. This study provides evidence that somatic mutation of RNF43 is the driver genetic alteration that links chronic inflammation and cancer development in about 10% of CACs.
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Affiliation(s)
- Masashi Fujita
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Nagahide Matsubara
- Division of Lower Gastrointestinal Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Ikuo Matsuda
- Department of Surgical Pathology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Kazuhiro Maejima
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Ayako Oosawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Tomoki Yamano
- Division of Lower Gastrointestinal Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mayuko Furuta
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kaoru Nakano
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Aya Oku-Sasaki
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Raúl Nicolás Mateos
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
- Laboratory of Functional Analysis in silico, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Kenta Nakai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa-shi, Chiba, Japan
- Laboratory of Functional Analysis in silico, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naohiro Tomita
- Division of Lower Gastrointestinal Surgery, Department of Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Seiichi Hirota
- Department of Surgical Pathology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Hiroki Ikeuchi
- Department of Inflammatory Bowel Disease Surgery, Hyogo College of Medicine, Nishinomiya, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
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18
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Takeuchi K, Furuta M, Okabe Y, Suma S, Takeshita T, Akifusa S, Adachi M, Kinoshita T, Kikutani T, Yamashita Y. Swallowing disorders and 1-year functional decline in community-dwelling older adults receiving home care. J Oral Rehabil 2017; 44:982-987. [DOI: 10.1111/joor.12577] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 11/30/2022]
Affiliation(s)
- K. Takeuchi
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - M. Furuta
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - Y. Okabe
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - S. Suma
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - T. Takeshita
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
- OBT Research Center; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - S. Akifusa
- Department of Health Management; School of Oral Health Science; Kyushu Dental College; Kitakyushu Japan
| | - M. Adachi
- Itoshima Dental Association; Itoshima Japan
| | | | - T. Kikutani
- Rehabilitation Clinic for Speech and Swallowing Disorders; The Nippon Dental University Hospital; Tokyo Japan
| | - Y. Yamashita
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
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Kimura T, Furuta M, Masayuki N, Tsuyoshi M, Harutoshi F, Jinnai K, Takahashi M, Mochizuki H, Yoshikawa H. Macroscopic and microscopic diversity of mis-splicing in the central nervous system of myotonic dystrophy type 1. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.3544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Furuta M, Natsumi F, Kouki M, Kazuaki N, Fujita Y, Ikeda Y. Clinical and epidemiological analysis of sporadic inclusion body myositis. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Nozaki S, Furuta M, Yorifuji S, Yoshikawa H. Rhythm treatment for dysphagia with metronome modified respiratory-swallowing coordination. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Kubota T, Watanabe D, Kokubun N, Furuta M, Kokunai Y, Abe T, Takahashi M. Arginine-to-lysine mutations in the voltage sensor are associated with hypokalemic periodic paralysis. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.1857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Zakaria MN, Furuta M, Takeshita T, Shibata Y, Sundari R, Eshima N, Ninomiya T, Yamashita Y. Oral mycobiome in community-dwelling elderly and its relation to oral and general health conditions. Oral Dis 2017; 23:973-982. [PMID: 28419681 DOI: 10.1111/odi.12682] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/31/2017] [Accepted: 04/11/2017] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Oral fungal infection is generally associated with dysbiosis related to antibiotic use, immunodeficiency, or frailty. However, fungal colonization in a typical population without apparent symptoms and its associated conditions are poorly understood. In this study, oral fungal colonization in community-dwelling and independently living elderly populations was evaluated and factors affecting fungal colonization were analyzed. SUBJECTS AND METHODS The subjects (410; 181 males and 229 females) were 75-99 years of age; those under prior antibiotic use were excluded. Fungal populations in the saliva were evaluated by PCR-based molecular techniques. Body mass index (BMI), smoking habits, and oral health conditions were examined. RESULTS Salivary fungal amounts exceeded 104 CFU/ml in 63 (15.4%) of 410 subjects. Candida albicans was most frequently detected (98.4%), followed by Candida glabrata (54.0%), and Candida dubliniensis (38.1%) in those subjects with fungi at 104 CFU/ml or over. Fungi at 104 CFU/ml or over in the presence of C. glabrata or C. dubliniensis was significantly associated with low BMI. CONCLUSIONS Candida albicans, C. glabrata, and C. dubliniensis dominated the oral mycobiome in Japanese community-dwelling elderly. Lower BMI might signify compromised health status and thus could result in susceptibility to specific candidiasis by C. glabrata and C. dubliniensis.
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Affiliation(s)
- M N Zakaria
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan.,Department of Operative Dentistry and Endodontology, Study Program of Dentistry, Faculty of Medicine, Jenderal Achmad Yani University, Jawa Barat, Indonesia
| | - M Furuta
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - T Takeshita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan.,OBT Research Center, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - Y Shibata
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
| | - R Sundari
- Department of Operative Dentistry and Endodontology, Study Program of Dentistry, Faculty of Medicine, Jenderal Achmad Yani University, Jawa Barat, Indonesia
| | - N Eshima
- Center for Educational Outreach and Admissions, Kyoto University, Kyoto, Japan
| | - T Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Y Yamashita
- Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka, Japan
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Okabe Y, Takeuchi K, Izumi M, Furuta M, Takeshita T, Shibata Y, Kageyama S, Ganaha S, Yamashita Y. Posterior teeth occlusion and dysphagia risk in older nursing home residents: a cross-sectional observational study. J Oral Rehabil 2017; 44:89-95. [DOI: 10.1111/joor.12472] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Y. Okabe
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - K. Takeuchi
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - M. Izumi
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - M. Furuta
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - T. Takeshita
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - Y. Shibata
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - S. Kageyama
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
| | - S. Ganaha
- Kizuna-kai; Aso-kizuna Dental Clinic; Aso Japan
| | - Y. Yamashita
- Section of Preventive and Public Health Dentistry; Division of Oral Health, Growth and Development; Faculty of Dental Science; Kyushu University; Fukuoka Japan
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25
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Naganuma A, Ogawa Y, Hoshino T, Hatanaka T, Tanaka H, Inagawa M, Tanaka T, Ogawa T, Sato K, Kakizaki S, Furuta M, Akiyama K. SUN-P050: Effect of the Medical Walking and Leucine Enriched Amino Acid Containing Food for Female Non-Alcoholic Fatty Liver Disease : Randomized Controlled Trial. Clin Nutr 2016. [DOI: 10.1016/s0261-5614(16)30393-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Fujimoto A, Furuta M, Totoki Y, Tsunoda T, Kato M, Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, Gotoh K, Ariizumi SI, Wardell CP, Hayami S, Nakamura T, Aikata H, Arihiro K, Boroevich KA, Abe T, Nakano K, Maejima K, Sasaki-Oku A, Ohsawa A, Shibuya T, Nakamura H, Hama N, Hosoda F, Arai Y, Ohashi S, Urushidate T, Nagae G, Yamamoto S, Ueda H, Tatsuno K, Ojima H, Hiraoka N, Okusaka T, Kubo M, Marubashi S, Yamada T, Hirano S, Yamamoto M, Ohdan H, Shimada K, Ishikawa O, Yamaue H, Chayama K, Miyano S, Aburatani H, Shibata T, Nakagawa H. Erratum: Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet 2016; 48:700. [PMID: 27230686 DOI: 10.1038/ng0616-700a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Okabe Y, Furuta M, Akifusa S, Takeuchi K, Adachi M, Kinoshita T, Kikutani T, Nakamura S, Yamashita Y. Swallowing Function and Nutritional Status in Japanese Elderly People Receiving Home-care Services: A 1-year Longitudinal Study. J Nutr Health Aging 2016; 20:697-704. [PMID: 27499302 DOI: 10.1007/s12603-015-0645-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Malnutrition is a serious health concern for frail elderly people. Poor oral function leading to insufficient food intake can contribute to the development of malnutrition. In the present study, we explored the longitudinal association of malnutrition with oral function, including oral health status and swallowing function, in elderly people receiving home nursing care. DESIGN Prospective observational cohort study with 1-year follow-up. SETTING Two mid-sized cities in Fukuoka, Japan from November 2010 to March 2012. PARTICIPANTS One hundred and ninety-seven individuals, aged ≥ 60 years, living at home and receiving home-care services because of physical disabilities, without malnutrition. MEASUREMENTS Oral health status, swallowing function, taking modified-texture diets such as minced or pureed foods, nutritional status, cognitive function, and activities of daily living were assessed at baseline. The associations between malnutrition at 1-year follow-up and these related factors were analyzed using a logistic regression model. RESULTS Swallowing disorders [risk ratio (RR): 5.21, 95% confidence interval (95% CI): 1.65-16.43] were associated with malnutrition. On the other hand, oral health status did not have a direct association with malnutrition. CONCLUSION Swallowing disorders may be associated with the incidence of malnutrition in elderly people receiving home-care. The findings indicate that maintaining swallowing function may contribute to the prevention of malnutrition in frail elderly people.
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Affiliation(s)
- Y Okabe
- Yoshihisa Yamashita, Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan. E-mail:
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Nakagawa H, Fujimoto A, Furuta M, Gotoh K, Nakamura T, Yamamoto M, Yamaue H, Chayama K, Miyano S, Tsunoda T. Abstract 3890: Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Primary liver cancer is the third leading cause of cancer death worldwide. Virus infection is the most common and strongest etiological factor for liver cancer development. Pathologically, primary liver cancer can be classified into ∼90% hepatocellular carcinoma (HCC), and 5∼10% intrahepatic cholangiocarcinoma (ICC), and the combined hepatocellular-cholangiocarcinoma (cHCC/CC) representing only a small portion. Clinically, ICC and cHCC/CC show much more aggressive behavior with poorer prognosis than HCC, and no standard treatment currently exists, other than surgical resection. ICC and cHCC/CC show varying degrees of biliary epithelial differentiation, which can be defined as liver cancer displaying a biliary phenotype (LCB). To gain insight into molecular alterations of LCBs, we performed whole genome sequencing analysis on 30 LCBs. Here we show the genome-wide substitution patterns of LCBs developed in chronic hepatitis livers overlapped with those of 60 HCCs, while those of hepatitis-negative LCBs diverged. The subsequent validation study on 68 LCBs identified recurrent mutations in TERT promoter, chromatin regulators (BAP1, PBRM1 and ARID2), a synapse organization gene (PCLO), IDH genes and KRAS. The frequencies of KRAS and IDHs mutations, which are associated with poor disease-free survival, were significantly higher in hepatitis-negative LCBs. This study reveals the strong impact of chronic hepatitis on the mutational landscape in liver cancer and the genetic diversity among LCBs.
Citation Format: Hidewaki Nakagawa, Akihiro Fujimoto, Mayuko Furuta, Kunihito Gotoh, Toru Nakamura, Masakazu Yamamoto, Hiroki Yamaue, Kazuaki Chayama, Satoru Miyano, Tatsuhiko Tsunoda. Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3890. doi:10.1158/1538-7445.AM2015-3890
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Affiliation(s)
| | | | | | - Kunihito Gotoh
- 2Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Toru Nakamura
- 3Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | | | | | | | - Satoru Miyano
- 7The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Furuta M, Fujimoto A, Ueno M, Hayami S, Kawakami YI, Gotoh K, Tsunoda T, Miyano S, Ohdan H, Chayama K, Yamaue H, Nakagawa H. Abstract 2970: Whole genome sequencing analysis of multiple liver cancer nodules for determination of causal events for multi-occurrence. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Despite the recent progress in diagnostic accuracy and therapeutic efficacy, its five-year survival rate is still low. Characteristically, HCC shows a high rate of intrahepatic metastasis (IM) or multi-centric (MC) occurrence within the liver, and discrimination of IM/MC is difficult and important for therapeutic decision. Previously we reported that there were no common somatic mutations between whole genomes of MC tumors, indicating that MC tumors independently developed in their genetic aspect (Nat Genet, 44: 760-764, 2012). Here we performed whole genome sequencing (WGS) analysis on 43 multiple liver cancer nodules derived from 20 patients, which were clinically defined as IM or MC occurrence. We first analyzed common and unique somatic mutations in each individual and divided the cases into IM or MC by using the information of common somatic mutations between the multiple nodules. Interestingly, the clinical and pathological diagnoses of MC/IM in five of 20 cases were not concordant with the judgments from WGS, indicating the usefulness of WGS for a precise IM/MC judgment. Analysis of common somatic alterations in IM tumors enabled to extract early and late event in hepatocarcinogenesis among a large number of somatic events in each cases, while MC pairs shared only a few numbers of common alterations, including false positives. Importantly, one somatic mutation in non-coding region was exceptionally detected commonly among MC tumor pairs from three cases. Sanger sequencing confirmed that this mutation was also commonly detected in 10.9% (35/321) of liver cancer samples somatically. These results indicate the significance of this function-unknown and recurrent mutation in liver cancer development. To illuminate common driver events in MC tumors, we analyzed all detectable genetic alterations, including copy number alterations and rearrangements, on multi-time point or MC tumors derived from same individuals and extracted significant genetic alterations from them, which can help the understanding of driver genetic alterations in liver cancers.
Citation Format: Mayuko Furuta, Akihiro Fujimoto, Masaki Ueno, Shinya Hayami, Yoshi-iku Kawakami, Kunihito Gotoh, Tatsuhiko Tsunoda, Satoru Miyano, Hideki Ohdan, Kazuaki Chayama, Hiroki Yamaue, Hidewaki Nakagawa. Whole genome sequencing analysis of multiple liver cancer nodules for determination of causal events for multi-occurrence. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2970. doi:10.1158/1538-7445.AM2015-2970
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Affiliation(s)
| | | | - Masaki Ueno
- 2Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Shinya Hayami
- 2Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
| | - Yoshi-iku Kawakami
- 3Department of Medicine & Molecular Science, Hiroshima University School of Medicine, Hiroshima, Japan
| | - Kunihito Gotoh
- 4Department of Surgery, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | | | - Satoru Miyano
- 5Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hideki Ohdan
- 6Department of Gastroenterological Surgery, Hiroshima University School of Medicine, Hiroshima, Japan
| | - Kazuaki Chayama
- 3Department of Medicine & Molecular Science, Hiroshima University School of Medicine, Hiroshima, Japan
| | - Hiroki Yamaue
- 2Second Department of Surgery, Wakayama Medical University, Wakayama, Japan
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Ono A, Fujimoto A, Yamamoto Y, Akamatsu S, Hiraga N, Imamura M, Kawaoka T, Tsuge M, Abe H, Hayes CN, Miki D, Furuta M, Tsunoda T, Miyano S, Kubo M, Aikata H, Ochi H, Kawakami YI, Arihiro K, Ohdan H, Nakagawa H, Chayama K. Circulating Tumor DNA Analysis for Liver Cancers and Its Usefulness as a Liquid Biopsy. Cell Mol Gastroenterol Hepatol 2015; 1:516-534. [PMID: 28210698 PMCID: PMC5301414 DOI: 10.1016/j.jcmgh.2015.06.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/03/2015] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Circulating tumor DNA (ctDNA) carrying tumor-specific sequence alterations has been found in the cell-free fraction of blood. Liver cancer tumor specimens are difficult to obtain, and noninvasive methods are required to assess cancer progression and characterize underlying genomic features. METHODS We analyzed 46 patients with hepatocellular carcinoma who underwent hepatectomy or liver transplantation and for whom whole-genome sequencing data was available. We designed personalized assays targeting somatic rearrangements of each tumor to quantify serum ctDNA. Exome sequencing was performed using cell-free DNA paired primary tumor tissue DNA from a patient with recurrent liver cancer after transcatheter arterial chemoembolization (TACE). RESULTS We successfully detected ctDNA from 100 μL of serum samples in 7 of the 46 patients before surgery, increasing with disease progression. The cumulative incidence of recurrence and extrahepatic metastasis in the ctDNA-positive group were statistically significantly worse than in the ctDNA-negative group (P = .0102 and .0386, respectively). Multivariate analysis identified ctDNA (OR 6.10; 95% CI, 1.11-33.33, P = .038) as an independent predictor of microscopic vascular invasion of the portal vein (VP). We identified 45 nonsynonymous somatic mutations in cell-free DNA after TACE and 71 nonsynonymous somatic mutations in primary tumor tissue by exome sequencing. We identified 25 common mutations in both samples, and 83% of mutations identified in the primary tumor could be detected in the cell-free DNA. CONCLUSIONS The presence of ctDNA reflects tumor progression, and detection of ctDNA can predict VP and recurrence, especially extrahepatic metastasis within 2 years. Our study demonstrated the usefulness of ctDNA detection and sequencing analysis of cell-free DNA for personalized treatment of liver cancer.
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Key Words
- AFP, α-fetoprotein
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- Circulating Tumor DNA
- DCP, des-γ-carboxy prothrombin
- Exome Sequencing
- HAIC, hepatic arterial infusion chemotherapy
- HBV, hepatitis B virus
- HCC, hepatocellular carcinoma
- HCV, hepatitis C virus
- Hepatocellular Carcinoma
- PCR, polymerase-chain-reaction
- TACE, transcatheter arterial chemoembolization
- VP, microscopic vascular invasion to portal vein
- Whole-Genome Sequencing
- cHCC/CC, combined hepatocellular and cholangiocarcinoma
- ctDNA, circulating tumor DNA
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Affiliation(s)
- Atsushi Ono
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan,Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences, Hiroshima, Japan
| | - Akihiro Fujimoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yujiro Yamamoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Sakura Akamatsu
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan,Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences, Hiroshima, Japan
| | - Nobuhiko Hiraga
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Michio Imamura
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Tomokazu Kawaoka
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Masataka Tsuge
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Hiromi Abe
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan,Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences, Hiroshima, Japan
| | - C. Nelson Hayes
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan,Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences, Hiroshima, Japan
| | - Daiki Miki
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan,Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences, Hiroshima, Japan
| | - Mayuko Furuta
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroshi Aikata
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Hidenori Ochi
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan,Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences, Hiroshima, Japan
| | - Yoshi-iku Kawakami
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Koji Arihiro
- Department of Anatomical Pathology, Hiroshima University School of Medicine, Hiroshima, Japan
| | - Hideki Ohdan
- Department of Gastroenterological Surgery, Hiroshima University School of Medicine, Hiroshima, Japan
| | - Hidewaki Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan,Hidewaki Nakagawa, MD, PhD, Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan. fax: +81-3-5449-5785.
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Applied Life Science, Institute of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan,Liver Research Project Center, Hiroshima University, Hiroshima, Japan,Laboratory for Digestive Diseases, RIKEN Center for Integrative Medical Sciences, Hiroshima, Japan,Correspondence Address correspondence to: Kazuaki Chayama, MD, PhD, Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734–8551, Japan. fax: +81-82-255-6220.
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Nakagawa H, Wardell CP, Furuta M, Taniguchi H, Fujimoto A. Cancer whole-genome sequencing: present and future. Oncogene 2015; 34:5943-50. [PMID: 25823020 DOI: 10.1038/onc.2015.90] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/27/2015] [Accepted: 02/27/2015] [Indexed: 12/26/2022]
Abstract
Recent explosive advances in next-generation sequencing technology and computational approaches to massive data enable us to analyze a number of cancer genome profiles by whole-genome sequencing (WGS). To explore cancer genomic alterations and their diversity comprehensively, global and local cancer genome-sequencing projects, including ICGC and TCGA, have been analyzing many types of cancer genomes mainly by exome sequencing. However, there is limited information on somatic mutations in non-coding regions including untranslated regions, introns, regulatory elements and non-coding RNAs, and rearrangements, sometimes producing fusion genes, and pathogen detection in cancer genomes remain widely unexplored. WGS approaches can detect these unexplored mutations, as well as coding mutations and somatic copy number alterations, and help us to better understand the whole landscape of cancer genomes and elucidate functions of these unexplored genomic regions. Analysis of cancer genomes using the present WGS platforms is still primitive and there are substantial improvements to be made in sequencing technologies, informatics and computer resources. Taking account of the extreme diversity of cancer genomes and phenotype, it is also required to analyze much more WGS data and integrate these with multi-omics data, functional data and clinical-pathological data in a large number of sample sets to interpret them more fully and efficiently.
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Affiliation(s)
- H Nakagawa
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - C P Wardell
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - M Furuta
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - H Taniguchi
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - A Fujimoto
- Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
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Furuta M, Fuimoto A, Shiraishi Y, Miyano S, Tsunoda T, Nakagawa H. Abstract 5177: Genome-wide profiling of somatic mutations in liver cancers revealed significantly mutated genes and non-coding regions in liver cancers. Mol Cell Biol 2014. [DOI: 10.1158/1538-7445.am2014-5177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Abstract
OBJECTIVES Although the presence of dysphagia is a key determinant of nutritional status among older adults, few studies have focused on the association between malnutrition and dysphagia risk in community-dwelling frail older adults. This study estimated the prevalence of malnutrition and quantified the association between malnutrition and dysphagia risk among community-dwelling older Japanese adults requiring long-term care. DESIGN Cross-sectional study. SETTING This study was conducted with the cooperation of the Japan Dental Association and local dental associations in all 47 prefectures from January to February 2012. PARTICIPANTS Individuals aged ≥65 years capable of oral nutrient intake who were living at home and receiving home dental care and treatment. MEASUREMENTS Individual demographic characteristics and factors associated with health loss-related functional decline were obtained through interviews by home-visit dentists and self-administered questionnaires. Nutritional status and dysphagia risk were evaluated using the Mini Nutritional Assessment Short Form and the Dysphagia Risk Assessment for the Community-dwelling Elderly. RESULTS Among 874 respondents (345 men and 529 women), 24.6% were malnourished, 67.4% were at risk of malnutrition, and 8.0% were well nourished. Dysphagia risk was related to an increased likelihood of malnutrition at an old age, even after adjusting for covariates (PR = 1.30, 95% CI = 1.01-1.67). CONCLUSION Malnutrition is highly prevalent among community-dwelling frail older adults, and dysphagia risk is independently associated with malnutrition. Dysphagia may be an important predictor of malnutrition progression in aged populations.
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Affiliation(s)
- K Takeuchi
- K. Takeuchi, Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka-ken 812-8582, Japan, +81-92-642-6353, FAX: +81-92-642-6354,
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Kokunai Y, Nakata T, Furuta M, Sakata S, Kimura H, Aiba T, Yoshinaga M, Osaki Y, Nakamori M, Itoh H, Sato T, Kubota T, Kadota K, Shindo K, Mochizuki H, Shimizu W, Horie M, Okamura Y, Ohno K, Takahashi MP. A Kir3.4 mutation causes Andersen-Tawil syndrome by an inhibitory effect on Kir2.1. Neurology 2014; 82:1058-64. [DOI: 10.1212/wnl.0000000000000239] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Takemura Y, Umeji S, Ito K, Furuya S, Furuta M. Inactivation Treatment of Bacterial Spores Contaminated Spices by Atmospheric Plasma Jet. Plasma Med 2014. [DOI: 10.1615/plasmamed.2014011969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Matsuura H, Onishi Y, Maeda Y, Kongmany S, Furuta M, Imamura K, Okuda S. Effect of Active Radical Production on Plasma Degradation of Phorbol 12-Myristate 13-Acetate in Methanolic and Aqueous Solution. Plasma Med 2014. [DOI: 10.1615/plasmamed.2014011904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Kimura A, Ishida Y, Furuta M, Nosaka M, Kuninaka Y, Kawaguchi M, Mukaida N, Kondo T. Pivotal involvement of IFN-gamma/Stat5 axis in compensatory cardiac hypertrophy induced by pressure overload. Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht310.p5013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Furuta M, Nguyen HH, Fujimoto A, Shiraishi Y, Miyano S, Tsunoda T, Nakagawa H. Abstract 5200: Genome-wide integrative analysis for the determination of the consequence of AT-rich interacting domain 2 (ARID2) depletion in hepatocellular carcinoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-5200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We previously reported the genomic aberrations obtained by the whole genome sequencing of 27 HCCs derived from Japanese patients (Nature Genetics 44, 760, 2012). The statistical and functional analyses yielded frequently and recurrently mutated genes involved in chromatin regulation, including ARID1A, ARID1B, ARID2, MLL and MLL3. Among the chromatin regulators mutated in HCCs, we here focused on ARID2, a component of Polybromo-associated BRG1-associated factor (PBAF) complex, which is one of the SNI/SNF chromatin remodeling complex involved in ligand-dependent transcriptional activation by nuclear receptors. Most of the somatic mutations in ARID2 detected in HCCs by our sequencing studies indicated its loss-of-function, suggesting their role as a tumor-suppressor. Although its somatic mutation in HCC and other types of cancer have been recently reported, its detailed function and role in tumorigenesis is poorly understood. To determine its role in hepatocarcionogenesis, we first analyzed their activity on cell growth using HCC cell lines. Knockdown (KD) of ARID2 in ARID2-intact HCC cell lines, JHH4 and JHH5, promoted cell growth, while overexpression of ARID2 in ARID2-null HuH28 suppressed cell growth compared with controls. These findings are consistent with its role as a tumor-suppressor in HCC. We also performed RNA-Seq using the ARID2-KD RNA samples from ARID2-intact cell lines to predict its down-stream target genes, which might be affected by ARID2 depletion in HCCs. Pathway analysis of genes up- or down-regulated by ARID2-KD revealed that a large number of cancer-related genes showed their expression changes. In addition, some cytokines and kinases involved in carcinogenesis significantly appeared to be activated on the basis of down-stream target gene expression profile. These results indicate that somatic loss-of-function mutations in a component of chromatin regulator such as ARID2 could lead the genome-wide gene expression change appeared in HCCs.
Citation Format: Mayuko Furuta, Ha H. Nguyen, Akihiro Fujimoto, Yuichi Shiraishi, Satoru Miyano, Tatsuhiko Tsunoda, Hidewaki Nakagawa. Genome-wide integrative analysis for the determination of the consequence of AT-rich interacting domain 2 (ARID2) depletion in hepatocellular carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5200. doi:10.1158/1538-7445.AM2013-5200
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Affiliation(s)
| | | | | | - Yuichi Shiraishi
- 2Laboratory of DNA Informatics Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- 2Laboratory of DNA Informatics Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Furuta M, Kozaki KI, Tanimoto K, Tanaka S, Arii S, Shimamura T, Niida A, Miyano S, Inazawa J. The tumor-suppressive miR-497-195 cluster targets multiple cell-cycle regulators in hepatocellular carcinoma. PLoS One 2013; 8:e60155. [PMID: 23544130 PMCID: PMC3609788 DOI: 10.1371/journal.pone.0060155] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/21/2013] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression and commonly deregulated in carcinogenesis. To explore functionally crucial tumor-suppressive (TS)-miRNAs in hepatocellular carcinoma (HCC), we performed integrative function- and expression-based screenings of TS-miRNAs in six HCC cell lines. The screenings identified seven miRNAs, which showed growth-suppressive activities through the overexpression of each miRNA and were endogenously downregulated in HCC cell lines. Further expression analyses using a large panel of HCC cell lines and primary tumors demonstrated four miRNAs, miR-101, -195, -378 and -497, as candidate TS-miRNAs frequently silenced in HCCs. Among them, two clustered miRNAs miR-195 and miR-497 showed significant growth-suppressive activity with induction of G1 arrest. Comprehensive exploration of their targets using Argonute2-immunoprecipitation-deep-sequencing (Ago2-IP-seq) and genome-wide expression profiling after their overexpression followed by pathway analysis, revealed a significant enrichment of cell cycle regulators. Among the candidates, we successfully identified CCNE1, CDC25A, CCND3, CDK4, and BTRC as direct targets for miR-497 and miR-195. Moreover, target genes frequently upregulated in HCC in a tumor-specific manner, such as CDK6, CCNE1, CDC25A and CDK4, showed an inverse correlation in the expression of miR-195 and miR-497, and their targets. These results suggest the molecular pathway regulating cell cycle progression to be integrally altered by downregulation of miR-195 and miR-497 expression, leading to the aberrant cell proliferation in hepatocarcinogenesis.
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Affiliation(s)
- Mayuko Furuta
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Global Center of Excellence (GCOE) Program for International Research Center for Molecular Science in Tooth and Bone Diseases, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Ken-ichi Kozaki
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Therapeutic Genomics, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Hard Tissue Genome Research Center, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kousuke Tanimoto
- Genome Laboratory, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shinji Tanaka
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shigeki Arii
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Teppei Shimamura
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Atsushi Niida
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Global Center of Excellence (GCOE) Program for International Research Center for Molecular Science in Tooth and Bone Diseases, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- Hard Tissue Genome Research Center, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
- * E-mail:
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Endo H, Muramatsu T, Furuta M, Uzawa N, Pimkhaokham A, Amagasa T, Inazawa J, Kozaki KI. Potential of tumor-suppressive miR-596 targeting LGALS3BP as a therapeutic agent in oral cancer. Carcinogenesis 2012; 34:560-9. [PMID: 23233740 DOI: 10.1093/carcin/bgs376] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The incidence and mortality statistics for oral squamous cell carcinoma (OSCC) were 10th and 12th, respectively, in human cancers diagnosed worldwide in 2008. In this study, to identify novel tumor-suppressive microRNAs (TS-miRNAs) and their direct targets in OSCC, we performed methylation-based screening for 43 miRNAs encoded by 46 miRNA genes located within 500 bp downstream of 40 CpG islands and genome-wide gene expression profiling in combination with a prediction database analysis, respectively, in 18 cell lines, resulting in the identification of a novel TS-miRNA miR-596 directly targeting LGALS3BP/Mac-2 BP/90K. DNA hypermethylation of CpG island located 5'-upstream of miR-596 gene was frequently observed in OSCC cell lines (100% of 18 cell lines) and primary OSCC cases (46.2 and 76.3% of 26 Japanese and 38 Thais primary cases, respectively) in a tumor-specific manner. The ectopic transfection of double-stranded RNA (dsRNA) mimicking miR-596 or specific small interfering RNA for LGALS3BP significantly induced growth inhibition and apoptosis in cell lines lacking miR-596 expression or overexpressing LGALS3BP, respectively, in a manner associated with a suppression of ERK1/2 phosphorylation. Moreover, we also mention the effect of dsRNA mimicking miR-596 on the growth of an OSCC cell line in vivo. Our findings define a central role for miR-596 in OSCC and suggest the potential of miR-596 as an anticancer agent for miRNA replacement therapy in OSCC.
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Affiliation(s)
- Hironori Endo
- Department of Molecular Cytogenetics, Tokyo Medical and Dental University, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan
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Morita S, Shimajiri Y, Sakagashira S, Furuta M, Sanke T. Effect of exposure to non-esterified fatty acid on progressive deterioration of insulin secretion in patients with Type 2 diabetes: a long-term follow-up study. Diabet Med 2012; 29:980-5. [PMID: 22221293 DOI: 10.1111/j.1464-5491.2011.03566.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM The aim of the study was to determine whether fasting serum non-esterified fatty acid (NEFA) could be associated with long-term progressive deterioration of insulin secretion in patients with Type 2 diabetes. METHODS Seventy-seven Japanese patients with Type 2 diabetes (mean BMI 23.3 kg/m(2) ) were followed for 10 years. We measured fasting C-peptide level every 1-2 years. By using the slope of regression line between fasting C-peptide level and duration, we calculated its individual annual decline as an index of insulin secretion. During the follow-up periods of C-peptide, the patients were evaluated for fasting serum non-esterified fatty acid, LDL cholesterol, HDL cholesterol and HbA(1c) levels for the last 8 years. We excluded patients who had renal dysfunction or anti-insulin antibodies from among the insulin-treated patients. Association between the individual annual decline of fasting C-peptide level and related factors were evaluated. RESULTS The mean individual annual decline of fasting serum C-peptide level was -0.013 ± 0.027 nmol/l/year. Fasting serum non-esterified fatty acid level had no significant difference between the first and the last 2 years of the 8-year observation period of non-esterified fatty acid. Using multiple regression analysis, mean fasting serum non-esterified fatty acid level was associated with the individual annual decline of fasting serum C-peptide level (standardized regression coefficient -0.358, P=0.0056), although other related factors, including HbA(1c) level, were not associated. CONCLUSIONS Mean fasting serum non-esterified fatty acid level during an 8-year observation was independently associated with long-term progressive deterioration of insulin secretion in Japanese patients with Type 2 diabetes.
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Affiliation(s)
- S Morita
- Department of Clinical Laboratory Medicine, Wakayama Medical University, Wakayama, Japan.
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Li H, Takeshita T, Furuta M, Tomioka M, Shibata Y, Shimazaki Y, Makimura K, Yamashita Y. Molecular characterization of fungal populations on the tongue dorsum of institutionalized elderly adults. Oral Dis 2012; 18:771-7. [DOI: 10.1111/j.1601-0825.2012.01944.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Matsumura S, Imoto I, Kozaki KI, Matsui T, Muramatsu T, Furuta M, Tanaka S, Sakamoto M, Arii S, Inazawa J. Integrative array-based approach identifies MZB1 as a frequently methylated putative tumor suppressor in hepatocellular carcinoma. Clin Cancer Res 2012; 18:3541-51. [PMID: 22573353 DOI: 10.1158/1078-0432.ccr-11-1007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The aim of this study was the identification of novel tumor suppressor genes (TSG) silenced by DNA hypermethylation in hepatocellular carcinoma (HCC). EXPERIMENTAL DESIGN We conducted integrative array-based approach for genome-wide screening of methylation targets using a methylated DNA immunoprecipitation-CpG island microarray and expression array in three universal hepatoma cell lines and normal liver tissue. Through detailed expression and functional analyses using hepatoma cell lines and primary HCC samples, we isolated novel TSGs for HCC. RESULTS A total of 642 genes were identified as methylated in three hepatoma cell lines but unmethylated in normal liver tissue, whereas 204 genes on autosomes were identified as genes unexpressed but restored after treatment with 5-aza-2'-deoxycytidine in these cell lines and expressed in normal tissue. Through the integration of results of the two-array analyses and further validation analyses of expression and methylation status in 17 cell lines and 30 primary tumors of hepatoma, we identified MZB1, marginal zone B and B1 cell-specific protein, encoding an endoplasmic reticulum protein, as a putative TSG frequently methylated within its CpG island in hepatoma. Among 162 patients with primary HCC, silencing of MZB1 protein was significantly and independently associated with a worse outcome. Restoration of MZB1 expression in hepatoma cells reduced cell proliferation in vitro and in vivo through G(1)-arrest. CONCLUSIONS These results suggest that methylation-mediated silencing of MZB1 expression leads to loss of its tumor-suppressive activity, which may be a factor in the hepatocarcinogenesis, and is a useful prognosticator in HCC.
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Affiliation(s)
- Satoshi Matsumura
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
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Takasawa K, Takaeda C, Higuchi M, Maeda T, Tomosugi N, Ueda N, Sasaki Y, Ikezoe M, Hagiwara M, Furuhata S, Murakami M, Shimonaka Y, Yamazaki S, Hamahata S, Hamahata S, Oue M, Kuragano T, Furuta M, Yahiro M, Kida A, Otaki Y, Hasuike Y, Nonoguchi H, Nakanishi T, Sarafidis P, Rumjon A, Ackland D, Maclaughlin H, Bansal SS, Macdougall IC, Panichi V, Rosati A, Malagnino E, Giusti R, Casani A, Betti G, Conti P, Bernabini G, Bernabini G, Gabrielli C, Caiani D, Scatena A, Migliori M, Pizzarelli F, Mitsopoulos E, Tsiatsiou M, Minasidis I, Kousoula V, Intzevidou E, Passadakis P, Vargemezis V, Tsakiris D, Yahiro M, Kida A, Otaki Y, Hasuike Y, Nonoguchi H, Nakanishi T, Kuragano T, Lines SW, Carter AM, Dunn EJ, Wright MJ, Aoyagi R, Miura T, De Paola L, Lombardi G, Coppolino G, Lombardi L, Hasuike Y, Fukumoto H, Kaibe S, Tokuyama M, Kida A, Otaki Y, Kuragano T, Nonoguchi H, Hiwasa M, Miyamoto T, Ohue H, Matsumoto A, Toyoda K, Nakanishi T, Rottembourg J, Emery C, Lafuma A, Wernli J, Zakin L, Mahi L, Borzych-Duzalka D, Bilginer Y, Pape L, Ha IS, Bak M, Chua A, Rees L, Pesle S, Cano F, Urzykowska A, Emre S, Russcasso J, Ramela V, Printza N, White C, Kuzmanovska D, Andrea V, Muller-Wiefel D, Warady B, Schaefer F, Chung JH, Park MK, Kim HL, Shin BC, Fujikawa T, Kuji T, Kakimoto M, Shibata K, Satta H, Nishihara M, Kawata S, Koguchi N, Toya Y, Umemura S, David V, Michel G, Maxime H, Paul L, Sebastien K, Francois V, Kuntsevich V, Dou Y, Thijssen S, Levin NW, Kotanko P, Kim BS, Kim BS, Park WD, Song HC, Kim HG, Kim YO, Woodburn K, Fong KL, Moriya Y, Tagawa Y, Maeda T, Kanda F, Morita N, Tomosugi N, London G, London G, Zaoui P, Covic A, Dellanna F, Goldsmith D, Gesualdo L, Mann J, Combe C, Turner M, Meunzberg M, Macdonald K, Abraham I, Gesualdo L, Combe C, Covic A, Dellanna F, Goldsmith D, London G, Mann J, Zaoui P, Turner M, Meunzberg M, Macdonald K, Abraham I, Rottembourg J, Guerin A, Diaconita M, Apruzzese R, Dou Y, Thijssen S, Kruse A, Ouellet G, Levin NW, Kotanko P, Bond C, Jensen D, Wang S, Pham E, Rubin J, Sika M, Niecestro R, Woodburn K, Fong KL, Sloneker S, Strzemienski P, Solon E, Moriya Y, Tagawa Y, Stamopoulos D, Mpakirtzi N, Grapsa E, Gogola B, Manios E, Afentakis N, Ewer J, Macdougall IC. Renal anaemia - CKD 5D. Nephrol Dial Transplant 2012. [DOI: 10.1093/ndt/gfs244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Donadio C, Kanaki A, Martin-Gomez A, Garcia S, Palacios-Gomez M, Donadio C, Calia D, Colombini E, DI Francesco F, Ghimenti S, Kanaki A, Onor M, Tognotti D, Fuoco R, Marka-Castro E, Torres Zamora MI, Giron-Mino J, Jaime-Solis MA, Arteaga LM, Romero H, Marka-Castro E, Akonur A, Leypoldt K, Asola M, Culleton B, Eloot S, Glorieux G, Nathalie N, Vanholder R, Perez de Jose A, Verdalles Guzman U, Abad Esttebanez S, Vega Martinez A, Barraca D, Yuste C, Bucalo L, Rincon A, Lopez-Gomez JM, Bataille P, Celine P, Raymond A, Francois G, Herve L, Michel D, Jean Louis R, Zhu F, Kotanko P, Thijssen S, Levin NW, Papamichail N, Bougiakli M, Gouva C, Antoniou S, Gianitsi S, Vlachopanou A, Chachalos S, Naka K, Kaarsavvidou D, Katopodis K, Michalis L, Sasaki K, Yasuda K, Yamato M, Surace A, Rovatti P, Steckiph D, Bandini R, Severi S, Dellacasa Bellingegni A, Santoro A, Arias M, Arias M, Sentis A, Perez N, Fontsere N, Vera M, Rodriguez N, Arcal C, Ortega N, Uriza F, Cases A, Maduell F, Abbas SR, Abbas SR, Zhu F, Kotanko P, Levin NW, Georgianos P, Sarafidis P, Nikolaidis P, Lasaridis A, Ahmed A, Ahmed A, Kaoutar H, Mohammed B, Zouhir O, Balter P, Ginsberg N, Taylor P, Sullivan T, Usvyat LA, Levin NW, Kotanko P, Zabetakis P, Moissl U, Ferrario M, Garzotto F, Wabel P, Cruz D, Tetta C, Signorini MG, Cerutti S, Brendolan A, Ronco C, Heaf J, Axelsen M, Pedersen RS, Ahmed A, Ahmed A, Amine H, Oualim Z, Ammirati AL, Guimaraes de Souza NK, Nemoto Matsui T, Luiz Vieira M, Alves de Oliveira WA, Fischer CH, Dias Carneiro F, Iizuka IJ, Aparecida de Souza M, Mallet AC, Cruz Andreoli MC, Cardoso Dos Santos BF, Rosales L, Dou Y, Carter M, Thijssen S, Kotanko P, Testa A, Sottini L, Giacon B, Prati E, Loschiavo C, Brognoli M, Marseglia C, Tommasi A, Sereni L, Palladino G, Bove S, Bosticardo G, Schillaci E, Detoma P, Bergia R, Park JW, Moon SJ, Choi HY, Ha SK, Park HC, Liao Y, Zhang L, Fu P, Igarashi H, Suzuki N, Esashi S, Masakane I, Panichi V, De Ferrari G, Saffiotti S, Sidoti A, Biagioli M, Bianchi S, Imperiali P, Gabrielli C, Conti P, Patrone P, Rombola G, Falqui V, Mura C, Icardi A, Rosati A, Santori F, Mannarino A, Bertucci A, Steckiph D, Jeong J, Jeong J, Kim OK, Kim NH, Bots M, Den Hoedt C, Grooteman MP, Van der Weerd NC, Mazairac AHA, Levesque R, Ter Wee PM, Nube MJ, Blankestijn P, Van den Dorpel MA, Park Y, Jeon J, Tessitore N, Tessitore N, Bedogna V, Girelli D, Corazza L, Jacky P, Guillaume Q, Julien B, Marcinkowski W, Drozdz M, Milkowski A, Rydzynska T, Prystacki T, August R, Benedyk-Lorens E, Bladek K, Cina J, Janiszewska G, Kaczmarek A, Lewinska T, Mendel M, Paszkot M, Trafidlo E, Trzciniecka-Kloczkowska M, Vasilevsky A, Konoplev G, Lopatenko O, Komashnya A, Visnevsky K, Gerasimchuk R, Neivelt I, Frorip A, Vostry M, Racek J, Rajdl D, Eiselt J, Malanova L, Pechter U, Selart A, Ots-Rosenberg M, Krieter DH, Seidel S, Merget K, Lemke HD, Wanner C, Krieter DH, Canaud B, Lemke HD, Rodriguez A, Morgenroth A, Von Appen K, Dragoun GP, Wanner C, Fluck R, Fouque D, Lockridge R, Motomiya Y, Uji Y, Hiramatsu T, Ando Y, Furuta M, Furuta M, Kuragano T, Kida A, Yahiro M, Otaki Y, Hasuike Y, Nonoguchi H, Nakanishi T, Sain M, Sain M, Kovacic V, Ljutic D, Radic J, Jelicic I, Yalin SF, Yalin SF, Trabulus S, Yalin AS, Altiparmak MR, Serdengecti K, Ohtsuka A, Fukami K, Ishikawa K, Ando R, Kaida Y, Adachi T, Sugi K, Okuda S, Nesterova OB, Nesterova OB, Suglobova ED, Golubev RV, Vasiliev AN, Lazeba VA, Smirnov AV, Arita K, Kihara E, Maeda K, Oda H, Doi S, Masaki T, Hidaka S, Ishioka K, Oka M, Moriya H, Ohtake T, Nomura S, Kobayashi S, Wagner S, Gmerek A, Wagner J, Wizemann V, Eftimovska - Otovic N, Spaseska-Gjurovska K, Bogdanovska S, Babalj - Banskolieva E, Milovanceva M, Grozdanovski R, Pisani A, Riccio E, Mancini A, Ambuhl P, Astrid S, Ivana P, Martin H, Thomas K, Hans-Rudolf R, Daniel A, Denes K, Marco M, Wuthrich RP, Andreas S, Andrulli S, Altieri P, Sau G, Bolasco P, Pedrini LA, Basile C, David S, Feriani M, Nebiolo PE, Ferrara R, Casu D, Logias F, Tarchini R, Cadinu F, Passaghe M, Fundoni G, Villa G, DI Iorio BR, Zoccali C, Locatelli F, Kihara E, Arita K, Hamamoto M, Maeda K, Oda H, Doi S, Masaki T, Lee DY, Kim B, Moon KH, LI Z, Fu P, Ahrenholz P, Ahrenholz P, Winkler RE, Waitz G, Wolf H, Grundstrom G, Alquist M, Holmquist M, Christensson A, Bjork P, Abdgawad M, Ekholm L, Segelmark M, Corsi C, Santoro A, De Bie J, Mambelli E, Mortara D, Santoro A, Severi S, Arroyo D, Arroyo D, Panizo N, Quiroga B, Reque J, Melero R, Rodriguez-Ferrero M, Rodriguez-Benitez P, Anaya F, Luno J, Ragon A, James A, Brunet P, Ribeiro S, Faria MS, Rocha S, Rodrigues S, Catarino C, Reis F, Nascimento H, Fernandes J, Miranda V, Quintanilha A, Belo L, Costa E, Santos-Silva A, Arund J, Tanner R, Fridolin I, Luman M, Clajus C, Clajus C, Kielstein JT, Haller H, David S, Basile C, Basile C, Libutti P, Lisi P, Vernaglione L, Casucci F, Losurdo N, Teutonico A, Lomonte C, Krisp C, Gmerek A, Wagner J, Wolters DA, Pedrini LA, Matsuyama M, Tomo T, Ishida K, Matsuyama K, Nakata T, Kadota J, Caiazzo M, Monari E, Cuoghi A, Bellei E, Bergamini S, Palladino G, Tomasi A, Baranger T, Seniuta P, Berge F, Drouillat V, Frangie C, Rosier E, Labonia W, Lescano A, Rubio D, Von der Lippe N, Jorgensen JA, Osthus TB, Waldum B, Os I, Bossola M, DI Stasio E, Antocicco M, Tazza L, Griveas I, Karameris A, Pasadakis P, Savica V, Santoro D, Saitta S, Tigano V, Bellinghieri G, Gangemi S, Daniela R, Checherita IA, Ciocalteu A, Vacaroiu IA, Niculae A, Bladek K, Stefaniak E, Pietrzak I, Krupa D, Garred L, Santoro A, Mancini E, Corrazza L, Atti M, Afsar B, Stamopoulos D, Mpakirtzi N, Gogola B, Zeibekis M, Stivarou D, Panagiotou M, Grapsa E, Vega Vega O, Barraca Nunez D, Abad Esttebanez S, Bucalo L, Yuste C, Lopez-Gomez JM, Fernandez-Lucas M, Gomis A, Teruel JL, Elias S, Quereda C, Hignell L, Humphrey S, Pacy N, Stamopoulos D, Mpakirtzi N, Afentakis N, Grapsa E. Extracorporeal dialysis: techniques and adequacy. Nephrol Dial Transplant 2012. [DOI: 10.1093/ndt/gfs224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Tsuruta T, Kozaki KI, Uesugi A, Furuta M, Hirasawa A, Imoto I, Susumu N, Aoki D, Inazawa J. miR-152 is a tumor suppressor microRNA that is silenced by DNA hypermethylation in endometrial cancer. Cancer Res 2011; 71:6450-62. [PMID: 21868754 DOI: 10.1158/0008-5472.can-11-0364] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The etiology and development of human cancers that remain little understood might be enlightened by defining tumor suppressor microRNAs (TS-miRNA). In this study, we identified TS-miRNAs silenced by aberrant DNA hypermethylation in endometrial cancer. Functional screening of 327 synthetic miRNAs in an endometrial cancer cell proliferation assay identified 103 miRNAs that inhibited cell growth. We then determined the sequence, DNA methylation status, and expression levels of these miRNAs in endometrial cancer cell lines and primary tumors. These determinations led to the identification of miR-152 as a candidate TS-miRNA gene in endometrial cancer. Epigenetic silencing documented in miR-152 was consistent with its location at 17q21.32 in intron 1 of the COPZ2 gene, which is also silenced often in endometrial cancer by DNA hypermethylation, and also with evidence that miR-152 targets the DNA methyltransferase DNMT1. Notably, restoration of miR-152 expression in endometrial cancer cell lines was sufficient to inhibit tumor cell growth in vitro and in vivo. We identified E2F3, MET, and Rictor as novel candidate targets of miR-152, suggesting how its epigenetic silencing can drive endometrial carcinogenesis. Our findings define a central role for miR-152 in endometrial cancer, and they also suggest its use in new therapeutic strategies to treat this cancer.
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Affiliation(s)
- Tomohiko Tsuruta
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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Uesugi A, Kozaki KI, Tsuruta T, Furuta M, Morita KI, Imoto I, Omura K, Inazawa J. The tumor suppressive microRNA miR-218 targets the mTOR component Rictor and inhibits AKT phosphorylation in oral cancer. Cancer Res 2011; 71:5765-78. [PMID: 21795477 DOI: 10.1158/0008-5472.can-11-0368] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The incidence of oral squamous cell carcinoma (OSCC) is rising rapidly in developed countries, posing a growing challenge due to the poor management of this type of malignancy at present. In this study, we profiled tumor suppressive microRNAs (miRNAs) that are silenced by DNA hypermethylation in OSCC using a function-based screening approach. This approach employed a cell proliferation assay for 327 synthetic miRNAs in two OSCC cell lines. Among the 110 miRNAs identified in this set that exhibited inhibitory properties, we compared DNA methylation and expression status in a wider panel of OSCC cell lines and primary tumor tissues, resulting in the identification of miR-218 and miR-585 as functionally significant miRNA genes that are frequently silenced in OSCC by DNA hypermethylation. Ectopic expression of miR-218 and miR-585 in OSCC cells lacking endogenous expression reduced cell growth in part through caspase-mediated apoptosis. Notably, miR-218 reduced levels of the rapamycin-insensitive component of mTOR, Rictor, in a manner associated with a suppression of Akt S473 phosphorylation. Together our findings define miR-585 as a tumor suppressive function that is often epigenetically silenced in OSCC, and they identify Rictor as a novel target of miR-218, suggesting that activation of the mTOR-Akt signaling pathway induced by Rictor contributes centrally to oral carcinogenesis.
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Affiliation(s)
- Atsushi Uesugi
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo, Japan
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Takahashi K, Shibasaki A, Hirose T, Kaneko K, Nakamura M, Ohba K, Kato I, Totsune K, Zumrutdal A, Calayoglu R, Mescigil P, Kutlay S, Sengul S, Erturk S, Ibrahim M, Ahmed T, Awadalla A, El Naggar A, Yokoyama T, Onodera Y, Shimonaka Y, Sasaki Y, Kuragano T, Furuta M, Kida A, Kitamura R, Yahiro M, Otaki T, Hasuike Y, Nonoguchi H, Nishihara F, Nakanishi T, Sedlackova T, Racek J, Trefil L, Eiselt J, Kielberger L, Malanova L, Youssef D, Tawfeek D, Desoki T, Khalifa N, Takasawa K, Takaeda C, Higuchi M, Maeda T, Tomosugi N, Bratescu LO, Barsan L, Garneata L, Stanciu A, Lipan M, Stancu SH, Mircescu G, Zager P, Paine S, Myers O, Chang JH, Jung JY, Lee HH, Chung W, Kim S, Tutal E, Erkmen Uyar M, Sezer S, Bal Z, Wabel P, Machek P, Moissl U, Chamney P, Jirka T, Moissl U, Wabel P, Chamney P, Wieskotten S, Amato C, Mari F, Korol L, Dudar I, Van Wyck D, Goykhman I, Weldon J, Krishnan M, Nissenson A, Kinugasa E, Sanaka T, Mochizuki T, Kuno T, Kojima K, Kobayashi S, Satoh M, Noiri E, Kusano E, Owada S, Shimada N, Nakao K, Nakazawa R, Nishimura H, Tomo T, Shigematsu T, Maeda T, Rottembourg J, Guerin A, Diaconita M, Dumont JC, Dansaert A, Chailimpamontree W, Gojaseni P, Pajareya T, Chittinandana A, Bachmakov I, Meissner R, Benkenstein C, Migliori M, Bernabini G, Beati S, Paoletti S, De Pietro S, Ferrandello FP, Panichi V, Senol E, Ersoy A, Erdinc S, Sarandol E, Mikami S, Hamano T, Iba O, Inoue T, Toki M, Takamitsu Y, Mikami H, Fujii M. Anaemia in CKD 5D. Clin Kidney J 2011. [DOI: 10.1093/ndtplus/4.s2.56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Woodburn K, Holmes C, Fong KL, Sloneker S, Strzemienski P, Solon E, Ryckelynck JP, Lang P, Bataille P, Choukroun G, Esnault V, Knebelman B, Laville M, Fellous M, Legrand E, Portoles J, Vega NJ, Fernandez-Fresnedo G, Perez A, Bea S, Camba MJ, Leistikow F, Heidenreich S, Cases A, Portoles J, Calls J, Martinez Castelao A, Sanchez-Guisande D, Espinel E, Carreno A, Campistol JM, Arias M, Morales JM, Pallardo L, Franco A, Shestakova M, Heidenreich S, Tsubakihara Y, Bessho M, Suzuki M, Correa-Rotter R, Niihata K, Tomosugi N, Uehata T, Shoji T, Sonoda M, Kawabata H, Sakaguchi Y, Suzuki A, Okada N, Tsubakihara Y, Kuragano T, Shimonaka Y, Kida A, Kitamura R, Furuta M, Yahiro M, Otaki Y, Nisihara F, Nonoguchi H, Nakanishi T, Mircescu G, Stancu S, Stanciu A, Viasu L, Capusa C, Petrescu L, Zugravu A, Aydin Z, Gursu M, Uzun S, Karadag S, Tatli E, Sumnu A, Doventas Y, Koldas M, Ozturk S, Kazancioglu R, Malyszko Y, Levin-Iaina N, Malyszko J, Kozminski P, Koc-Zorawska E, Mysliwiec M, Hara M, Ando M, Tsuchiya K, Nitta K, Mirescu G, Deray G, Garneata L, Goldsmith D, Gorriz Teruel JL, Martin PY, Mitchell D, Mori C, Schafer R, Guerin A, Addison J, Bridges I, Di Giulio S, Farouk M, Winearls C, Kiss I, Claes K, Galle J, Costa E, Rocha-Pereira P, Sameiro-Faria M, Miranda V, Afonso C, Belo L, Marinho C, Bicho M, Santos-Silva A, Kim HW, Jang EH, Mercadal L, Metzger M, Casadevall N, Haymann JP, Boffa JJ, Flamant M, Vrtovsnik F, Stengel B, Froissart M, Ode M, Roth K, Locatelli F, Horl WH. Anaemia in CKD 1-5. Clin Kidney J 2011. [DOI: 10.1093/ndtplus/4.s2.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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