Robust enumeration of cell subsets from tissue expression profiles
Aaron M. Newman,Chih Long Liu,Michael R. Green,Andrew J. Gentles,Weiguo Feng,Yue Xu,Chuong D. Hoang,Maximilian Diehn,Arash Ash Alizadeh +8 more
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TLDR
CIBERSORT outperformed other methods with respect to noise, unknown mixture content and closely related cell types when applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors.Abstract:
We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content and closely related cell types CIBERSORT should enable large-scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets (http://cibersortstanfordedu/)read more
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The Immune Landscape of Cancer
Vesteinn Thorsson,David L Gibbs,Scott D. Brown,Denise M. Wolf,Dante S. Bortone,Tai-Hsien Ou Yang,Eduard Porta-Pardo,Galen F. Gao,Christopher L. Plaisier,James A. Eddy,Elad Ziv,Aedín C. Culhane,Evan O. Paull,I K Ashok Sivakumar,Andrew J. Gentles,Raunaq Malhotra,Farshad Farshidfar,Antonio Colaprico,Joel S. Parker,Lisle E. Mose,Nam S Vo,Jianfang Liu,Yuexin Liu,Janet S. Rader,Varsha Dhankani,Sheila Reynolds,Reanne Bowlby,Andrea Califano,Andrew D. Cherniack,Dimitris Anastassiou,Davide Bedognetti,Arvind Rao,Ken Chen,Alexander Krasnitz,Hai Hu,Tathiane M. Malta,Houtan Noushmehr,Houtan Noushmehr,Chandra Sekhar Pedamallu,Susan Bullman,Akinyemi I. Ojesina,Andrew Lamb,Wanding Zhou,Hui Shen,Toni K. Choueiri,John N. Weinstein,Justin Guinney,Joel H. Saltz,Robert A. Holt,Charles E Rabkin,Alexander J. Lazar +50 more
TL;DR: An extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA identifies six immune subtypes that encompass multiple cancer types and are hypothesized to define immune response patterns impacting prognosis.
Journal ArticleDOI
TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells
Taiwen Li,Taiwen Li,Jingyu Fan,Binbin Wang,Nicole Traugh,Qianming Chen,Jun Liu,Bo Li,X. Shirley Liu,X. Shirley Liu +9 more
TL;DR: Tumor Immune Estimation Resource (TIMER) is presented to comprehensively investigate molecular characterization of tumor-immune interactions and provides a user-friendly web interface for dynamic analysis and visualization of these associations, which will be of broad utilities to cancer researchers.
Journal ArticleDOI
Understanding the tumor immune microenvironment (TIME) for effective therapy.
Mikhail Binnewies,Edward W. Roberts,Kelly Kersten,Vincent Chan,Douglas F. Fearon,Miriam Merad,Lisa M. Coussens,Dmitry I. Gabrilovich,Suzanne Ostrand-Rosenberg,Suzanne Ostrand-Rosenberg,Catherine C. Hedrick,Robert H. Vonderheide,Mikael J. Pittet,Rakesh K. Jain,Weiping Zou,T. Kevin Howcroft,Elisa C. Woodhouse,Robert A. Weinberg,Matthew F. Krummel +18 more
TL;DR: By parsing the unique classes and subclasses of tumor immune microenvironment (TIME) that exist within a patient’s tumor, the ability to predict and guide immunotherapeutic responsiveness will improve, and new therapeutic targets will be revealed.
Journal ArticleDOI
Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade
Pornpimol Charoentong,Francesca Finotello,Mihaela Angelova,Clemens Mayer,Mirjana Efremova,Dietmar Rieder,Hubert Hackl,Zlatko Trajanoski +7 more
TL;DR: The immunophenoscore was a superior predictor of response to anti-cytotoxic T lymphocyte antigen-4 (CTLA-4) and anti-programmed cell death protein 1 (anti-PD-1) antibodies in two independent validation cohorts and may help inform cancer immunotherapy and facilitate the development of precision immuno-oncology.
Journal ArticleDOI
The prognostic landscape of genes and infiltrating immune cells across human cancers
Andrew J. Gentles,Aaron M. Newman,Chih Long Liu,Scott V. Bratman,Scott V. Bratman,Weiguo Feng,Dongkyoon Kim,Viswam S. Nair,Yue Xu,Amanda Khuong,Chuong D. Hoang,Maximilian Diehn,Robert B. West,Sylvia K. Plevritis,Ash A. Alizadeh +14 more
TL;DR: A pan-cancer resource and meta-analysis of expression signatures from ∼18,000 human tumors with overall survival outcomes across 39 malignancies is presented and it is found that expression of favorably prognostic genes, including KLRB1 (encoding CD161), largely reflect tumor-associated leukocytes.
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