The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice
Elizabeth C. Townsend,Mark A. Murakami,Alexandra N. Christodoulou,Amanda L. Christie,Johannes Köster,Tiffany DeSouza,Elizabeth A. Morgan,Scott P. Kallgren,Huiyun Liu,Shuo-Chieh Wu,Olivia Plana,Joan Montero,Kristen E. Stevenson,Prakash Rao,Raga Vadhi,Michael Andreeff,Philippe Armand,Karen K. Ballen,Patrizia Barzaghi-Rinaudo,Sarah Cahill,Rachael A. Clark,Vesselina G. Cooke,Matthew S. Davids,Daniel J. DeAngelo,David M. Dorfman,Hilary Eaton,Benjamin L. Ebert,Julia Etchin,Brant Firestone,David C. Fisher,Arnold S. Freedman,Ilene Galinsky,Hui Gao,Jacqueline S. Garcia,Francine Garnache-Ottou,Timothy A. Graubert,Alejandro Gutierrez,Alejandro Gutierrez,Ensar Halilovic,Marian H. Harris,Zachary T. Herbert,Steven M. Horwitz,Giorgio Inghirami,Andrew M. Intlekofer,Moriko Ito,Shai Izraeli,Eric D. Jacobsen,Caron A. Jacobson,Sébastien Jeay,Irmela Jeremias,Michelle A. Kelliher,Raphael Koch,Marina Konopleva,Nadja Kopp,Steven M. Kornblau,Andrew L. Kung,Thomas S. Kupper,Nicole R. LeBoeuf,Ann S. LaCasce,Emma Lees,Loretta S. Li,A. Thomas Look,Masato Murakami,Markus Müschen,Donna Neuberg,Samuel Y. Ng,Oreofe O. Odejide,Stuart H. Orkin,Rachel R. Paquette,Andrew E. Place,Justine E. Roderick,Jeremy Ryan,Stephen E. Sallan,Brent Shoji,Lewis B. Silverman,Robert J. Soiffer,David P. Steensma,Kimberly Stegmaier,Richard Stone,Jerome Tamburini,Aaron R. Thorner,Paul Van Hummelen,Martha Wadleigh,Marion Wiesmann,Andrew P. Weng,Jens Wuerthner,David A. Williams,Bruce M. Wollison,Andrew A. Lane,Anthony Letai,Monica M. Bertagnolli,Jerome Ritz,Myles Brown,Henry W. Long,Jon C. Aster,Margaret A. Shipp,James D. Griffin,David M. Weinstock,David M. Weinstock +98 more
TLDR
It is demonstrated that large studies of acute leukemia PDXs that mimic human randomized clinical trials can characterize drug efficacy and generate transcriptional, functional, and proteomic biomarkers in both treatment-naive and relapsed/refractory disease.About:
This article is published in Cancer Cell.The article was published on 2016-04-11 and is currently open access. It has received 261 citations till now.read more
Citations
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Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
Alexandra-Chloé Villani,Alexandra-Chloé Villani,Rahul Satija,Rahul Satija,Gary Reynolds,Siranush Sarkizova,Karthik Shekhar,James Fletcher,Morgane Griesbeck,Andrew Butler,Shiwei Zheng,Suzan Lazo,Laura Jardine,David Dixon,Emily Stephenson,Emil Nilsson,Ida Grundberg,David McDonald,Andrew Filby,Weibo Li,Weibo Li,Philip L. De Jager,Philip L. De Jager,Orit Rozenblatt-Rosen,Andrew A. Lane,Andrew A. Lane,Muzlifah Haniffa,Muzlifah Haniffa,Aviv Regev,Aviv Regev,Aviv Regev,Nir Hacohen,Nir Hacohen +32 more
TL;DR: This refined analysis has identified, among others, a previously unknown dendritic cell population that potently activates T cells and reclassify pDCs as the originally described “natural interferon-producing cells (IPCs)” with weaker T cell proliferation induction ability.
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
Alexandra-Chloé Villani,Alexandra-Chloé Villani,Rahul Satija,Rahul Satija,Gary Reynolds,Siranush Sarkizova,Karthik Shekhar,James Fletcher,Morgane Griesbeck,Andrew Butler,Shiwei Zheng,Suzan Lazo,Laura Jardine,David Dixon,Emily Stephenson,Emil Nilsson,Ida Grundberg,David McDonald,Andrew Filby,Weibo Li,Weibo Li,Philip L. De Jager,Philip L. De Jager,Orit Rozenblatt-Rosen,Andrew A. Lane,Andrew A. Lane,Muzlifah Haniffa,Muzlifah Haniffa,Aviv Regev,Aviv Regev,Aviv Regev,Nir Hacohen,Nir Hacohen +32 more
TL;DR: In this paper, the authors performed single-cell RNA sequencing of ~2400 cells isolated from healthy blood donors and enriched for HLA-DR + lineage − cells, which led them to identify and validate six Dendritic cells (DCs) and four monocyte subtypes.
Journal ArticleDOI
Interrogating open issues in cancer precision medicine with patient-derived xenografts
Annette T. Byrne,D Alferez,Frédéric Amant,Daniela Annibali,Joaquín Arribas,Andrew V. Biankin,Andrew V. Biankin,Alejandra Bruna,Eva Budinská,Carlos Caldas,David K. Chang,Robert Clarke,Hans Clevers,George Coukos,Virginie Dangles-Marie,S. Gail Eckhardt,Eva González-Suárez,Els Hermans,Manuel Hidalgo,Monika A. Jarzabek,Steven de Jong,Jos Jonkers,Kristel Kemper,Luisa Lanfrancone,Gunhild Mari Mælandsmo,Elisabetta Marangoni,Jean-Christophe Marine,Enzo Medico,Jens Henrik Norum,Héctor G. Palmer,Daniel S. Peeper,Pier Giuseppe Pelicci,Alejandro Piris-Giménez,Sergio Roman-Roman,Oscar M. Rueda,Joan Seoane,Violeta Serra,Laura Soucek,Dominique Vanhecke,Alberto Villanueva,Emilie Vinolo,Andrea Bertotti,Livio Trusolino +42 more
TL;DR: Patient derived xenografts (PDXs) have emerged as an important platform to elucidate new treatments and biomarkers in oncology as mentioned in this paper, and the ability of PDX models to predict clinical outcomes is being improved through mouse humanization strategies and the implementation of co-clinical trials, within which patients and PDXs reciprocally inform therapeutic decisions.
Journal ArticleDOI
Functional precision cancer medicine—moving beyond pure genomics
TL;DR: The entire project of precision cancer medicine is called into question and the tools employed must be broadened, with a focus on acquiring highly actionable functional information by perturbing—for example, with cancer therapies—viable primary tumor cells from patients with cancer.
Journal ArticleDOI
Why do BCL-2 inhibitors work and where should we use them in the clinic?
Joan Montero,Antony Letai +1 more
TL;DR: By determining cells’ readiness for apoptosis and anti-apoptotic dependence, this work can use novel BH3 mimetics to overwhelm this apoptotic blockade and possibly combine them with other anti-cancer agents using dynamic BH 3 profiling (DBP) to improve personalized cancer treatment.
References
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limma powers differential expression analyses for RNA-sequencing and microarray studies
Matthew E. Ritchie,Belinda Phipson,Di Wu,Yifang Hu,Charity W. Law,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Jordi Barretina,Giordano Caponigro,Nicolas Stransky,Kavitha Venkatesan,Adam A. Margolin,Adam A. Margolin,Sungjoon Kim,Christine D. Wilson,Joseph Lehar,Gregory V. Kryukov,Dmitriy Sonkin,Anupama Reddy,Manway Liu,Lauren Murray,Michael F. Berger,Michael F. Berger,John Monahan,Paula Morais,Jodi Meltzer,Adam Korejwa,Judit Jané-Valbuena,Judit Jané-Valbuena,Felipa A. Mapa,Joseph Thibault,Eva Bric-Furlong,Pichai Raman,Aaron Shipway,Ingo H. Engels,Jill Cheng,Guoying K. Yu,Jianjun Yu,Peter Aspesi,Melanie de Silva,Kalpana Jagtap,Michael D. Jones,Li Wang,Charlie Hatton,Emanuele Palescandolo,Supriya Gupta,Scott Mahan,Carrie Sougnez,Robert C. Onofrio,Ted Liefeld,Laura E. MacConaill,Wendy Winckler,Michael R. Reich,Nanxin Li,Jill P. Mesirov,Stacey Gabriel,Gad Getz,Kristin G. Ardlie,Vivien W. Chan,Vic E. Myer,Barbara L. Weber,Jeffrey A. Porter,Markus Warmuth,Peter Finan,Jennifer L. Harris,Matthew Meyerson,Matthew Meyerson,Todd R. Golub,Michael Morrissey,William R. Sellers,Robert Schlegel,Levi A. Garraway,Levi A. Garraway +65 more
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Can the pharmaceutical industry reduce attrition rates
Ismail Kola,John Landis +1 more
TL;DR: The pharmaceutical industry faces considerable challenges, both politically and fiscally, and the fiscal pressures that face the industry from the perspective of R&D are dealt with.
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Snakemake--a scalable bioinformatics workflow engine.
Johannes Köster,Sven Rahmann +1 more
TL;DR: Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.
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Transcriptional control of human p53-regulated genes
TL;DR: The most comprehensive list so far of human p53-regulated genes and their experimentally validated, functional binding sites that confer p53 regulation is presented.
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