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Literature DB >> 31515541

Next-generation computational tools for interrogating cancer immunity.

Francesca Finotello¹, Dietmar Rieder¹, Hubert Hackl¹, Zlatko Trajanoski².

Abstract

The remarkable success of cancer therapies with immune checkpoint blockers is revolutionizing oncology and has sparked intensive basic and translational research into the mechanisms of cancer-immune cell interactions. In parallel, numerous novel cutting-edge technologies for comprehensive molecular and cellular characterization of cancer immunity have been developed, including single-cell sequencing, mass cytometry and multiplexed spatial cellular phenotyping. In order to process, analyse and visualize multidimensional data sets generated by these technologies, computational methods and software tools are required. Here, we review computational tools for interrogating cancer immunity, discuss advantages and limitations of the various methods and provide guidelines to assist in method selection.

Entities: Chemical

Mesh：

Year: 2019 PMID： 31515541 DOI： 10.1038/s41576-019-0166-7

Source DB: PubMed Journal: Nat Rev Genet ISSN： 1471-0056 Impact factor: 59.581

194 in total

1. Trial watch: The clinical trial landscape for PD1/PDL1 immune checkpoint inhibitors.

Authors: Jun Tang; Jia Xin Yu; Vanessa M Hubbard-Lucey; Svetoslav T Neftelinov; Jeffrey P Hodge; Yunqing Lin
Journal: Nat Rev Drug Discov Date: 2018-11-28 Impact factor: 84.694

Review 2. The hallmarks of successful anticancer immunotherapy.

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Journal: Sci Transl Med Date: 2018-09-19 Impact factor: 17.956

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Journal: Annu Rev Immunol Date: 2018-12-14 Impact factor: 28.527

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Authors: Wolf Herman Fridman; Franck Pagès; Catherine Sautès-Fridman; Jérôme Galon
Journal: Nat Rev Cancer Date: 2012-03-15 Impact factor: 60.716

5. Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade.

Authors: Pornpimol Charoentong; Francesca Finotello; Mihaela Angelova; Clemens Mayer; Mirjana Efremova; Dietmar Rieder; Hubert Hackl; Zlatko Trajanoski
Journal: Cell Rep Date: 2017-01-03 Impact factor: 9.423

Review 6. Update on Tumor Neoantigens and Their Utility: Why It Is Good to Be Different.

Authors: Chung-Han Lee; Roman Yelensky; Karin Jooss; Timothy A Chan
Journal: Trends Immunol Date: 2018-05-08 Impact factor: 16.687

Review 7. Oncology meets immunology: the cancer-immunity cycle.

Authors: Daniel S Chen; Ira Mellman
Journal: Immunity Date: 2013-07-25 Impact factor: 31.745

Review 8. Computational genomics tools for dissecting tumour-immune cell interactions.

Authors: Hubert Hackl; Pornpimol Charoentong; Francesca Finotello; Zlatko Trajanoski
Journal: Nat Rev Genet Date: 2016-07-04 Impact factor: 53.242

Review 9. Immunological Effects of Conventional Chemotherapy and Targeted Anticancer Agents.

Authors: Lorenzo Galluzzi; Aitziber Buqué; Oliver Kepp; Laurence Zitvogel; Guido Kroemer
Journal: Cancer Cell Date: 2015-12-14 Impact factor: 31.743

10. The Immune Landscape of Cancer.

Authors: Vésteinn Thorsson; David L Gibbs; Scott D Brown; Denise Wolf; Dante S Bortone; Tai-Hsien Ou Yang; Eduard Porta-Pardo; Galen F Gao; Christopher L Plaisier; James A Eddy; Elad Ziv; Aedin 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 Sy Vo; Jianfang Liu; Yuexin Liu; Janet Rader; Varsha Dhankani; Sheila M Reynolds; Reanne Bowlby; Andrea Califano; Andrew D Cherniack; Dimitris Anastassiou; Davide Bedognetti; Younes Mokrab; Aaron M Newman; Arvind Rao; Ken Chen; Alexander Krasnitz; Hai Hu; Tathiane M Malta; 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 Saltz; Robert A Holt; Charles S Rabkin; Alexander J Lazar; Jonathan S Serody; Elizabeth G Demicco; Mary L Disis; Benjamin G Vincent; Ilya Shmulevich
Journal: Immunity Date: 2018-04-05 Impact factor: 43.474

50 in total

Review 1. Online informatics resources to facilitate cancer target and chemical probe discovery.

Authors: Xuan Yang; Haian Fu; Andrey A Ivanov
Journal: RSC Med Chem Date: 2020-04-09

Review 2. Tackling TAMs for Cancer Immunotherapy: It's Nano Time.

Authors: Yishun Yang; Jianfeng Guo; Leaf Huang
Journal: Trends Pharmacol Sci Date: 2020-10 Impact factor: 14.819

3. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction.

Authors: Daniel K Wells; Marit M van Buuren; Kristen K Dang; Vanessa M Hubbard-Lucey; Kathleen C F Sheehan; Katie M Campbell; Andrew Lamb; Jeffrey P Ward; John Sidney; Ana B Blazquez; Andrew J Rech; Jesse M Zaretsky; Begonya Comin-Anduix; Alphonsus H C Ng; William Chour; Thomas V Yu; Hira Rizvi; Jia M Chen; Patrice Manning; Gabriela M Steiner; Xengie C Doan; Taha Merghoub; Justin Guinney; Adam Kolom; Cheryl Selinsky; Antoni Ribas; Matthew D Hellmann; Nir Hacohen; Alessandro Sette; James R Heath; Nina Bhardwaj; Fred Ramsdell; Robert D Schreiber; Ton N Schumacher; Pia Kvistborg; Nadine A Defranoux
Journal: Cell Date: 2020-10-09 Impact factor: 41.582

Review 4. Dissecting the Tumor-Immune Landscape in Chimeric Antigen Receptor T-cell Therapy: Key Challenges and Opportunities for a Systems Immunology Approach.

Authors: Gregory M Chen; Andrew Azzam; Yang-Yang Ding; David M Barrett; Stephan A Grupp; Kai Tan
Journal: Clin Cancer Res Date: 2020-03-03 Impact factor: 12.531

Review 5. Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group.

Authors: L De Mattos-Arruda; M Vazquez; F Finotello; R Lepore; E Porta; J Hundal; P Amengual-Rigo; C K Y Ng; A Valencia; J Carrillo; T A Chan; V Guallar; N McGranahan; J Blanco; M Griffith
Journal: Ann Oncol Date: 2020-06-28 Impact factor: 32.976

6. The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression.

Authors: Florent Petitprez; Sacha Levy; Cheng-Ming Sun; Maxime Meylan; Christophe Linhard; Etienne Becht; Nabila Elarouci; David Tavel; Lubka T Roumenina; Mira Ayadi; Catherine Sautès-Fridman; Wolf H Fridman; Aurélien de Reyniès
Journal: Genome Med Date: 2020-10-06 Impact factor: 11.117

Review 10. Immunoengineering has arrived.

Authors: Jordan J Green
Journal: J Biomed Mater Res A Date: 2020-08-04 Impact factor: 4.396