Literature DB >> 31430664

Multimodal single-cell approaches shed light on T cell heterogeneity.

Aparna Nathan1, Yuriy Baglaenko2, Chamith Y Fonseka1, Jessica I Beynor2, Soumya Raychaudhuri3.   

Abstract

Single-cell methods have revolutionized the study of T cell biology by enabling the identification and characterization of individual cells. This has led to a deeper understanding of T cell heterogeneity by generating functionally relevant measurements - like gene expression, surface markers, chromatin accessibility, T cell receptor sequences - in individual cells. While these methods are independently valuable, they can be augmented when applied jointly, either on separate cells from the same sample or on the same cells. Multimodal approaches are already being deployed to characterize T cells in diverse disease contexts and demonstrate the value of having multiple insights into a cell's function. But, these data sets pose new statistical challenges for integration and joint analysis.
Copyright © 2019 Elsevier Ltd. All rights reserved.

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Year:  2019        PMID: 31430664      PMCID: PMC6901721          DOI: 10.1016/j.coi.2019.07.002

Source DB:  PubMed          Journal:  Curr Opin Immunol        ISSN: 0952-7915            Impact factor:   7.486


  81 in total

1.  Two subsets of memory T lymphocytes with distinct homing potentials and effector functions.

Authors:  F Sallusto; D Lenig; R Förster; M Lipp; A Lanzavecchia
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2.  Cell sorting: automated separation of mammalian cells as a function of intracellular fluorescence.

Authors:  H R Hulett; W A Bonner; J Barrett; L A Herzenberg
Journal:  Science       Date:  1969-11-07       Impact factor: 47.728

3.  Whole-organism clone tracing using single-cell sequencing.

Authors:  Anna Alemany; Maria Florescu; Chloé S Baron; Josi Peterson-Maduro; Alexander van Oudenaarden
Journal:  Nature       Date:  2018-03-28       Impact factor: 49.962

4.  Multiplexed ion beam imaging of human breast tumors.

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Journal:  Nat Med       Date:  2014-03-02       Impact factor: 53.440

Review 5.  Integrative single-cell analysis.

Authors:  Tim Stuart; Rahul Satija
Journal:  Nat Rev Genet       Date:  2019-05       Impact factor: 53.242

6.  Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.

Authors:  Daniel Schulz; Vito Riccardo Tomaso Zanotelli; Jana Raja Fischer; Denis Schapiro; Stefanie Engler; Xiao-Kang Lun; Hartland Warren Jackson; Bernd Bodenmiller
Journal:  Cell Syst       Date:  2017-12-27       Impact factor: 10.304

7.  SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells.

Authors:  Kyung Yeon Han; Kyu-Tae Kim; Je-Gun Joung; Dae-Soon Son; Yeon Jeong Kim; Areum Jo; Hyo-Jeong Jeon; Hui-Sung Moon; Chang Eun Yoo; Woosung Chung; Hye Hyeon Eum; Sangmin Kim; Hong Kwan Kim; Jeong Eon Lee; Myung-Ju Ahn; Hae-Ock Lee; Donghyun Park; Woong-Yang Park
Journal:  Genome Res       Date:  2017-12-05       Impact factor: 9.043

8.  Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells.

Authors:  Zinaida Good; Luciene Borges; Nora Vivanco Gonzalez; Bita Sahaf; Nikolay Samusik; Robert Tibshirani; Garry P Nolan; Sean C Bendall
Journal:  Nat Biotechnol       Date:  2019-02-11       Impact factor: 54.908

9.  Highly multiplexed simultaneous detection of RNAs and proteins in single cells.

Authors:  Andreas P Frei; Felice-Alessio Bava; Eli R Zunder; Elena W Y Hsieh; Shih-Yu Chen; Garry P Nolan; Pier Federico Gherardini
Journal:  Nat Methods       Date:  2016-01-25       Impact factor: 28.547

10.  Induction and transcriptional regulation of the co-inhibitory gene module in T cells.

Authors:  Norio Chihara; Asaf Madi; Takaaki Kondo; Huiyuan Zhang; Nandini Acharya; Meromit Singer; Jackson Nyman; Nemanja D Marjanovic; Monika S Kowalczyk; Chao Wang; Sema Kurtulus; Travis Law; Yasaman Etminan; James Nevin; Christopher D Buckley; Patrick R Burkett; Jason D Buenrostro; Orit Rozenblatt-Rosen; Ana C Anderson; Aviv Regev; Vijay K Kuchroo
Journal:  Nature       Date:  2018-06-13       Impact factor: 49.962

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  6 in total

1.  Static array of droplets and on-demand recovery for biological assays.

Authors:  Syung Hun Han; Junhyong Kim; Daeyeon Lee
Journal:  Biomicrofluidics       Date:  2020-09-15       Impact factor: 2.800

2.  Multimodal detection of protein isoforms and nucleic acids from low starting cell numbers.

Authors:  Elisabet Rosàs-Canyelles; Andrew J Modzelewski; Ana E Gomez Martinez; Alisha Geldert; Anjali Gopal; Lin He; Amy E Herr
Journal:  Lab Chip       Date:  2021-06-15       Impact factor: 7.517

Review 3.  Computational methods for the integrative analysis of single-cell data.

Authors:  Mattia Forcato; Oriana Romano; Silvio Bicciato
Journal:  Brief Bioinform       Date:  2021-01-18       Impact factor: 11.622

Review 4.  Applications of Single-Cell Omics to Dissect Tumor Microenvironment.

Authors:  Tingting Guo; Weimin Li; Xuyu Cai
Journal:  Front Genet       Date:  2020-11-27       Impact factor: 4.599

5.  Distinguishing activated T regulatory cell and T conventional cells by single-cell technologies.

Authors:  Julia Reinhardt; Virag Sharma; Antigoni Stavridou; Annett Lindner; Susanne Reinhardt; Andreas Petzold; Mathias Lesche; Fabian Rost; Ezio Bonifacio; Anne Eugster
Journal:  Immunology       Date:  2022-03-02       Impact factor: 7.215

6.  Multimodally profiling memory T cells from a tuberculosis cohort identifies cell state associations with demographics, environment and disease.

Authors:  Aparna Nathan; Jessica I Beynor; Yuriy Baglaenko; Sara Suliman; Kazuyoshi Ishigaki; Samira Asgari; Chuan-Chin Huang; Yang Luo; Zibiao Zhang; Kattya Lopez; Cecilia S Lindestam Arlehamn; Joel D Ernst; Judith Jimenez; Roger I Calderón; Leonid Lecca; Ildiko Van Rhijn; D Branch Moody; Megan B Murray; Soumya Raychaudhuri
Journal:  Nat Immunol       Date:  2021-05-24       Impact factor: 25.606

  6 in total

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