Literature DB >> 34329587

From bench to bedside: Single-cell analysis for cancer immunotherapy.

Emily F Davis-Marcisak1, Atul Deshpande2, Genevieve L Stein-O'Brien1, Won J Ho2, Daniel Laheru2, Elizabeth M Jaffee2, Elana J Fertig3, Luciane T Kagohara4.   

Abstract

Single-cell technologies are emerging as powerful tools for cancer research. These technologies characterize the molecular state of each cell within a tumor, enabling new exploration of tumor heterogeneity, microenvironment cell-type composition, and cell state transitions that affect therapeutic response, particularly in the context of immunotherapy. Analyzing clinical samples has great promise for precision medicine but is technically challenging. Successfully identifying predictors of response requires well-coordinated, multi-disciplinary teams to ensure adequate sample processing for high-quality data generation and computational analysis for data interpretation. Here, we review current approaches to sample processing and computational analysis regarding their application to translational cancer immunotherapy research.
Copyright © 2021 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  computational biology; single-cell proteomics; single-cell transcriptomics; spatial proteomics; spatial transcriptomics; translational medicine; tumor immunology

Mesh:

Year:  2021        PMID: 34329587      PMCID: PMC8406623          DOI: 10.1016/j.ccell.2021.07.004

Source DB:  PubMed          Journal:  Cancer Cell        ISSN: 1535-6108            Impact factor:   38.585


  156 in total

Review 1.  When tissue antigens and antibodies get along: revisiting the technical aspects of immunohistochemistry--the red, brown, and blue technique.

Authors:  J A Ramos-Vara; M A Miller
Journal:  Vet Pathol       Date:  2013-10-15       Impact factor: 2.221

Review 2.  Dendritic cells in cancer immunology and immunotherapy.

Authors:  Stefanie K Wculek; Francisco J Cueto; Adriana M Mujal; Ignacio Melero; Matthew F Krummel; David Sancho
Journal:  Nat Rev Immunol       Date:  2019-08-29       Impact factor: 53.106

3.  High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

Authors:  Yang Liu; Mingyu Yang; Yanxiang Deng; Graham Su; Archibald Enninful; Cindy C Guo; Toma Tebaldi; Di Zhang; Dongjoo Kim; Zhiliang Bai; Eileen Norris; Alisia Pan; Jiatong Li; Yang Xiao; Stephanie Halene; Rong Fan
Journal:  Cell       Date:  2020-11-13       Impact factor: 41.582

4.  SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes.

Authors:  Marc Elosua-Bayes; Paula Nieto; Elisabetta Mereu; Ivo Gut; Holger Heyn
Journal:  Nucleic Acids Res       Date:  2021-05-21       Impact factor: 16.971

5.  The single-cell pathology landscape of breast cancer.

Authors:  Hartland W Jackson; Jana R Fischer; Vito R T Zanotelli; H Raza Ali; Robert Mechera; Savas D Soysal; Holger Moch; Simone Muenst; Zsuzsanna Varga; Walter P Weber; Bernd Bodenmiller
Journal:  Nature       Date:  2020-01-20       Impact factor: 49.962

6.  Quantifying the effect of experimental perturbations at single-cell resolution.

Authors:  Daniel B Burkhardt; Jay S Stanley; Alexander Tong; Ana Luisa Perdigoto; Scott A Gigante; Kevan C Herold; Guy Wolf; Antonio J Giraldez; David van Dijk; Smita Krishnaswamy
Journal:  Nat Biotechnol       Date:  2021-02-08       Impact factor: 54.908

7.  Distinct predictive biomarker candidates for response to anti-CTLA-4 and anti-PD-1 immunotherapy in melanoma patients.

Authors:  Priyanka B Subrahmanyam; Zhiwan Dong; Daniel Gusenleitner; Anita Giobbie-Hurder; Mariano Severgnini; Jun Zhou; Michael Manos; Lauren M Eastman; Holden T Maecker; F Stephen Hodi
Journal:  J Immunother Cancer       Date:  2018-03-06       Impact factor: 13.751

8.  GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data.

Authors:  Ye Yuan; Ziv Bar-Joseph
Journal:  Genome Biol       Date:  2020-12-10       Impact factor: 13.583

9.  Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data.

Authors:  Jean Fan; Hae-Ock Lee; Soohyun Lee; Da-Eun Ryu; Semin Lee; Catherine Xue; Seok Jin Kim; Kihyun Kim; Nikolaos Barkas; Peter J Park; Woong-Yang Park; Peter V Kharchenko
Journal:  Genome Res       Date:  2018-06-13       Impact factor: 9.043

Review 10.  Single-cell multiomics: technologies and data analysis methods.

Authors:  Jeongwoo Lee; Do Young Hyeon; Daehee Hwang
Journal:  Exp Mol Med       Date:  2020-09-15       Impact factor: 8.718

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  12 in total

Review 1.  The use of machine learning to discover regulatory networks controlling biological systems.

Authors:  Rossin Erbe; Jessica Gore; Kelly Gemmill; Daria A Gaykalova; Elana J Fertig
Journal:  Mol Cell       Date:  2022-01-10       Impact factor: 17.970

Review 2.  Next-generation sequencing: unraveling genetic mechanisms that shape cancer immunotherapy efficacy.

Authors:  Ahmed Halima; Winston Vuong; Timothy A Chan
Journal:  J Clin Invest       Date:  2022-06-15       Impact factor: 19.456

3.  Integrative immune transcriptomic classification improves patient selection for precision immunotherapy in advanced gastro-oesophageal adenocarcinoma.

Authors:  Manuel Cabeza-Segura; Valentina Gambardella; Francisco Gimeno-Valiente; Juan Antonio Carbonell-Asins; Lorena Alarcón-Molero; Arturo González-Vilanova; Sheila Zuñiga-Trejos; Pilar Rentero-Garrido; Rosana Villagrasa; Mireia Gil; Ana Durá; Paula Richart; Noelia Alonso; Marisol Huerta; Susana Roselló; Desamparados Roda; Noelia Tarazona; Carolina Martínez-Ciarpaglini; Josefa Castillo; Andrés Cervantes; Tania Fleitas
Journal:  Br J Cancer       Date:  2022-10-17       Impact factor: 9.075

Review 4.  Challenges and the Evolving Landscape of Assessing Blood-Based PD-L1 Expression as a Biomarker for Anti-PD-(L)1 Immunotherapy.

Authors:  Tao Wang; Desirée Denman; Silvia M Bacot; Gerald M Feldman
Journal:  Biomedicines       Date:  2022-05-20

Review 5.  The Molecular Biology of Soft Tissue Sarcomas: Current Knowledge and Future Perspectives.

Authors:  Julien Vibert; Sarah Watson
Journal:  Cancers (Basel)       Date:  2022-05-22       Impact factor: 6.575

6.  Single Cell Technologies to Dissect Heterogenous Immune Cell Therapy Products.

Authors:  Katherine Mueller; Krishanu Saha
Journal:  Curr Opin Biomed Eng       Date:  2021-09-15

Review 7.  The changing role of natural killer cells in cancer metastasis.

Authors:  Isaac S Chan; Andrew J Ewald
Journal:  J Clin Invest       Date:  2022-03-15       Impact factor: 14.808

Review 8.  Tumor heterogeneity reshapes the tumor microenvironment to influence drug resistance.

Authors:  Aiping Zhang; Kai Miao; Heng Sun; Chu-Xia Deng
Journal:  Int J Biol Sci       Date:  2022-04-24       Impact factor: 10.750

9.  Metastasis Related Epithelial-Mesenchymal Transition Signature Predicts Prognosis and Response to Immunotherapy in Gastric Cancer.

Authors:  Junquan Song; Rongyuan Wei; Shiying Huo; Jianpeng Gao; Xiaowen Liu
Journal:  Front Immunol       Date:  2022-06-13       Impact factor: 8.786

10.  Identification of the immune subtype of ovarian cancer patients by integrated analyses of transcriptome and single-cell sequencing data.

Authors:  Sixue Wang; Xi Wang; Xiaomeng Xia; Tingting Zhang; Mingyu Yi; Zeying Li; Li Jiang; Yalan Yang; Jie Fu; Xiaoling Fang
Journal:  Sci Rep       Date:  2022-08-02       Impact factor: 4.996

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