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Radiation-related genomic profile of papillary thyroid carcinoma after the Chernobyl accident 期刊论文
Science, 2021
作者:  Lindsay M. Morton;  Danielle M. Karyadi;  Chip Stewart;  Tetiana I. Bogdanova;  Eric T. Dawson;  Mia K. Steinberg;  Jieqiong Dai;  Stephen W. Hartley;  Sara J. Schonfeld;  Joshua N. Sampson;  Yosef E. Maruvka;  Vidushi Kapoor;  Dale A. Ramsden;  Juan Carvajal-Garcia;  Charles M. Perou;  Joel S. Parker;  Marko Krznaric;  Meredith Yeager;  Joseph F. Boland;  Amy Hutchinson;  Belynda D. Hicks;  Casey L. Dagnall;  Julie M. Gastier-Foster;  Jay Bowen;  Olivia Lee;  Mitchell J. Machiela;  Elizabeth K. Cahoon;  Alina V. Brenner;  Kiyohiko Mabuchi;  Vladimir Drozdovitch;  Sergii Masiuk;  Mykola Chepurny;  Liudmyla Yu. Zurnadzhy;  Maureen Hatch;  Amy Berrington de Gonzalez;  Gerry A. Thomas;  Mykola D. Tronko;  Gad Getz;  Stephen J. Chanock
收藏  |  浏览/下载:15/0  |  提交时间:2021/05/21
Lack of transgenerational effects of ionizing radiation exposure from the Chernobyl accident 期刊论文
Science, 2021
作者:  Meredith Yeager;  Mitchell J. Machiela;  Prachi Kothiyal;  Michael Dean;  Clara Bodelon;  Shalabh Suman;  Mingyi Wang;  Lisa Mirabello;  Chase W. Nelson;  Weiyin Zhou;  Cameron Palmer;  Bari Ballew;  Leandro M. Colli;  Neal D. Freedman;  Casey Dagnall;  Amy Hutchinson;  Vibha Vij;  Yosi Maruvka;  Maureen Hatch;  Iryna Illienko;  Yuri Belayev;  Nori Nakamura;  Vadim Chumak;  Elena Bakhanova;  David Belyi;  Victor Kryuchkov;  Ivan Golovanov;  Natalia Gudzenko;  Elizabeth K. Cahoon;  Paul Albert;  Vladimir Drozdovitch;  Mark P. Little;  Kiyohiko Mabuchi;  Chip Stewart;  Gad Getz;  Dimitry Bazyka;  Amy Berrington de Gonzalez;  Stephen J. Chanock
收藏  |  浏览/下载:9/0  |  提交时间:2021/05/21
Cell type–specific genetic regulation of gene expression across human tissues 期刊论文
Science, 2020
作者:  Sarah Kim-Hellmuth;  François Aguet;  Meritxell Oliva;  Manuel Muñoz-Aguirre;  Silva Kasela;  Valentin Wucher;  Stephane E. Castel;  Andrew R. Hamel;  Ana Viñuela;  Amy L. Roberts;  Serghei Mangul;  Xiaoquan Wen;  Gao Wang;  Alvaro N. Barbeira;  Diego Garrido-Martín;  Brian B. Nadel;  Yuxin Zou;  Rodrigo Bonazzola;  Jie Quan;  Andrew Brown;  Angel Martinez-Perez;  José Manuel Soria;  GTEx Consortium§;  Gad Getz;  Emmanouil T. Dermitzakis;  Kerrin S. Small;  Matthew Stephens;  Hualin S. Xi;  Hae Kyung Im;  Roderic Guigó;  Ayellet V. Segrè;  Barbara E. Stranger;  Kristin G. Ardlie;  Tuuli Lappalainen
收藏  |  浏览/下载:12/0  |  提交时间:2020/09/14
Ice front blocking of ocean heat transport to an Antarctic ice shelf 期刊论文
NATURE, 2020, 578 (7796) : 568-+
作者:  Alexandrov, Ludmil B.;  Kim, Jaegil;  Haradhvala, Nicholas J.;  Huang, Mi Ni;  Ng, Alvin Wei Tian;  Wu, Yang;  Boot, Arnoud;  Covington, Kyle R.;  Gordenin, Dmitry A.;  Bergstrom, Erik N.;  Islam, S. M. Ashiqul;  Lopez-Bigas, Nuria;  Klimczak, Leszek J.;  McPherson, John R.;  Morganella, Sandro;  Sabarinathan, Radhakrishnan;  Wheeler, David A.;  Mustonen, Ville;  Getz, Gad;  Rozen, Steven G.;  Stratton, Michael R.
收藏  |  浏览/下载:11/0  |  提交时间:2020/05/13

The front of the Getz Ice Shelf in West Antarctica creates an abrupt topographic step that deflects ocean currents, suppressing 70% of the heat delivery to the ice sheet.


Mass loss from the Antarctic Ice Sheet to the ocean has increased in recent decades, largely because the thinning of its floating ice shelves has allowed the outflow of grounded ice to accelerate(1,2). Enhanced basal melting of the ice shelves is thought to be the ultimate driver of change(2,3), motivating a recent focus on the processes that control ocean heat transport onto and across the seabed of the Antarctic continental shelf towards the ice(4-6). However, the shoreward heat flux typically far exceeds that required to match observed melt rates(2,7,8), suggesting that other critical controls exist. Here we show that the depth-independent (barotropic) component of the heat flow towards an ice shelf is blocked by the marked step shape of the ice front, and that only the depth-varying (baroclinic) component, which is typically much smaller, can enter the sub-ice cavity. Our results arise from direct observations of the Getz Ice Shelf system and laboratory experiments on a rotating platform. A similar blocking of the barotropic component may occur in other areas with comparable ice-bathymetry configurations, which may explain why changes in the density structure of the water column have been found to be a better indicator of basal melt rate variability than the heat transported onto the continental shelf(9). Representing the step topography of the ice front accurately in models is thus important for simulating ocean heat fluxes and induced melt rates.


  
Live-animal imaging of native haematopoietic stem and progenitor cells 期刊论文
NATURE, 2020, 578 (7794) : 278-+
作者:  Gerstung, Moritz;  Jolly, Clemency;  Leshchiner, Ignaty;  Dentro, Stefan C.;  Gonzalez, Santiago;  Rosebrock, Daniel;  Mitchell, Thomas J.;  Rubanova, Yulia;  Anur, Pavana;  Yu, Kaixian;  Tarabichi, Maxime;  Deshwar, Amit;  Wintersinger, Jeff;  Kleinheinz, Kortine;  Vazquez-Garcia, Ignacio;  Haase, Kerstin;  Jerman, Lara;  Sengupta, Subhajit;  Macintyre, Geoff;  Malikic, Salem;  Donmez, Nilgun;  Livitz, Dimitri G.;  Cmero, Marek;  Demeulemeester, Jonas;  Schumacher, Steven;  Fan, Yu;  Yao, Xiaotong;  Lee, Juhee;  Schlesner, Matthias;  Boutros, Paul C.;  Bowtell, David D.;  Zhu, Hongtu;  Getz, Gad;  Imielinski, Marcin;  Beroukhim, Rameen;  Sahinalp, S. Cenk;  Ji, Yuan;  Peifer, Martin;  Markowetz, Florian;  Mustonen, Ville;  Yuan, Ke;  Wang, Wenyi;  Morris, Quaid D.;  Spellman, Paul T.;  Wedge, David C.;  Van Loo, Peter;  Deshwar, Amit G.;  Adams, David J.;  Campbell, Peter J.;  Cao, Shaolong;  Christie, Elizabeth L.;  Cun, Yupeng;  Dawson, Kevin J.;  Drews, Ruben M.;  Eils, Roland;  Fittall, Matthew;  Garsed, Dale W.;  Ha, Gavin;  Lee-Six, Henry;  Martincorena, Inigo;  Oesper, Layla;  Peto, Myron;  Raphael, Benjamin J.;  Salcedo, Adriana;  Shi, Ruian;  Shin, Seung Jun;  Spiro, Oliver;  Stein, Lincoln D.;  Vembu, Shankar;  Wheeler, David A.;  Yang, Tsun-Po
收藏  |  浏览/下载:15/0  |  提交时间:2020/07/03

The biology of haematopoietic stem cells (HSCs) has predominantly been studied under transplantation conditions(1,2). It has been particularly challenging to study dynamic HSC behaviour, given that the visualization of HSCs in the native niche in live animals has not, to our knowledge, been achieved. Here we describe a dual genetic strategy in mice that restricts reporter labelling to a subset of the most quiescent long-term HSCs (LT-HSCs) and that is compatible with current intravital imaging approaches in the calvarial bone marrow(3-5). We show that this subset of LT-HSCs resides close to both sinusoidal blood vessels and the endosteal surface. By contrast, multipotent progenitor cells (MPPs) show greater variation in distance from the endosteum and are more likely to be associated with transition zone vessels. LT-HSCs are not found in bone marrow niches with the deepest hypoxia and instead are found in hypoxic environments similar to those of MPPs. In vivo time-lapse imaging revealed that LT-HSCs at steady-state show limited motility. Activated LT-HSCs show heterogeneous responses, with some cells becoming highly motile and a fraction of HSCs expanding clonally within spatially restricted domains. These domains have defined characteristics, as HSC expansion is found almost exclusively in a subset of bone marrow cavities with bone-remodelling activity. By contrast, cavities with low bone-resorbing activity do not harbour expanding HSCs. These findings point to previously unknown heterogeneity within the bone marrow microenvironment, imposed by the stages of bone turnover. Our approach enables the direct visualization of HSC behaviours and dissection of heterogeneity in HSC niches.


A dual genetic strategy enables the labelling and in vivo imaging of native long-term haematopoietic stem cells in the mouse calvarial bone marrow.


  
RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues 期刊论文
SCIENCE, 2019, 364 (6444) : 970-+
作者:  Yizhak, Keren;  Aguet, Francois;  Kim, Jaegil;  Hess, JulianM.;  Kubler, Kirsten;  Grimsby, Jonna;  Frazer, Ruslana;  Zhang, Hailei;  Haradhvala, Nicholas J.;  Rosebrock, Daniel;  Livitz, Dimitri;  Li, Xiao;  Arich-Landkof, Eila;  Shoresh, Noam;  Stewart, Chip;  Segre, Ayellet V.;  Branton, Philip A.;  Polak, Paz;  Ardlie, Kristin G.;  Getz, Gad
收藏  |  浏览/下载:23/0  |  提交时间:2019/11/27
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (vol 483, pg 603, 2012) 期刊论文
NATURE, 2019, 565 (7738) : E5-E6
作者:  Barretina, Jordi;  Caponigro, Giordano;  Stransky, Nicolas;  Venkatesan, Kavitha;  Margolin, Adam A.;  Kim, Sungjoon;  Wilson, Christopher J.;  Lehar, Joseph;  Kryukov, Gregory V.;  Sonkin, Dmitriy;  Reddy, Anupama;  Liu, Manway;  Murray, Lauren;  Berger, Michael F.;  Monahan, John E.;  Morais, Paula;  Meltzer, Jodi;  Korejwa, Adam;  Jane-Valbuena, Judit;  Mapa, Felipa A.;  Thibault, Joseph;  Bric-Furlong, Eva;  Raman, Pichai;  Shipway, Aaron;  Engels, Ingo H.;  Cheng, Jill;  Yu, Guoying K.;  Yu, Jianjun;  Aspesi, Peter, Jr.;  de Silva, Melanie;  Jagtap, Kalpana;  Jones, Michael D.;  Wang, Li;  Hatton, Charles;  Palescandolo, Emanuele;  Gupta, Supriya;  Mahan, Scott;  Sougnez, Carrie;  Onofrio, Robert C.;  Liefeld, Ted;  MacConaill, Laura;  Winckler, Wendy;  Reich, Michael;  Li, Nanxin;  Mesirov, Jill P.;  Gabriel, Stacey B.;  Getz, Gad;  Ardlie, Kristin;  Chan, Vivien;  Myer, Vic E.;  Weber, Barbara L.;  Porter, Jeff;  Warmuth, Markus;  Finan, Peter;  Harris, Jennifer L.;  Meyerson, Matthew;  Golub, Todd R.;  Morrissey, Michael P.;  Sellers, William R.;  Schlegel, Robert;  Garraway, Levi A.
收藏  |  浏览/下载:22/0  |  提交时间:2019/11/27
Comment on "DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification" 期刊论文
SCIENCE, 2018, 361 (6409)
作者:  Stewart, Chip;  Leshchiner, Ignaty;  Hess, Julian;  Getz, Gad
收藏  |  浏览/下载:10/0  |  提交时间:2019/11/27
Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq 期刊论文
SCIENCE, 2018, 360 (6386) : 331-335
作者:  Filbin, Mariella G.;  Tirosh, Itay;  Hovestadt, Volker;  Shaw, McKenzie L.;  Escalante, Leah E.;  Mathewson, Nathan D.;  Neftel, Cyril;  Frank, Nelli;  Pelton, Kristine;  Hebert, ChristineM.;  Haberler, Christine;  Yizhak, Keren;  Gojo, Johannes;  Egervari, Kristof;  Mount, Christopher;  van Galen, Peter;  Bonal, Dennis M.;  Quang-De Nguyen;  Beck, Alexander;  Sinai, Claire;  Czech, Thomas;  Dorfer, Christian;  Goumnerova, Liliana;  Lavarino, Cinzia;  Carcaboso, Angel M.;  Mora, Jaume;  Mylvaganam, Ravindra;  Luo, Christina C.;  Peyrl, Andreas;  Popovic, Mara;  Azizi, Amedeo;  Batchelor, Tracy T.;  Frosch, Matthew P.;  Martinez-Lage, Maria;  Kieran, Mark W.;  Bandopadhayay, Pratiti;  Beroukhim, Rameen;  Fritsch, Gerhard;  Getz, Gad;  Rozenblatt-Rosen, Orit;  Wucherpfennig, Kai W.;  Louis, David N.;  Monje, Michelle;  Slavc, Irene;  Ligon, Keith L.;  Golub, Todd R.;  Regev, Aviv;  Bernstein, Bradley E.;  Suva, Mario L.
收藏  |  浏览/下载:17/0  |  提交时间:2019/11/27
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq 期刊论文
SCIENCE, 2017, 355 (6332)
作者:  Venteicher, Andrew S.;  Tirosh, Itay;  Hebert, Christine;  Yizhak, Keren;  Neftel, Cyril;  Filbin, Mariella G.;  Hovestadt, Volker;  Escalante, Leah E.;  Shaw, McKenzie L.;  Rodman, Christopher;  Gillespie, Shawn M.;  Dionne, Danielle;  Luo, Christina C.;  Ravichandran, Hiranmayi;  Mylvaganam, Ravindra;  Mount, Christopher;  Onozato, Maristela L.;  Nahed, Brian V.;  Wakimoto, Hiroaki;  Curry, William T.;  Iafrate, A. John;  Rivera, Miguel N.;  Frosch, Matthew P.;  Golub, Todd R.;  Brastianos, Priscilla K.;  Getz, Gad;  Patel, Anoop P.;  Monje, Michelle;  Cahill, Daniel P.;  Rozenblatt-Rosen, Orit;  Louis, David N.;  Bernstein, Bradley E.;  Regev, Aviv;  Suva, Mario L.
收藏  |  浏览/下载:12/0  |  提交时间:2019/11/27