Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization DOI
Jianfeng Li, Ben‐Ben Miao, Shixiang Wang

et al.

Briefings in Bioinformatics, Journal Year: 2022, Volume and Issue: 23(4)

Published: July 5, 2022

Abstract Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud- visualization-based mining techniques. However, the scientific community still lacks an easy-to-use web service for comprehensive visualization of data, particularly high-quality publication-ready graphics that allow easy scaling updatability according to user demands. Therefore, we propose a community-driven modern service, Hiplot (https://hiplot.org), with concise top-quality applications life sciences fields. This permits users conveniently interactively complete few specialized tasks previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most daily demands researchers its equipped 240+ functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Moreover, improve efficiency in use development plugins, introduced some core advantages on client-/server-side website, such as spreadsheet-based importing, cross-platform command-line controller (Hctl), multi-user plumber workers, JavaScript Object Notation-based plugin system, data/parameters, results errors reproduction real-time updates mode. Meanwhile, using demo/real sets benchmark tests, explored statistical parameters, cancer genomic landscapes, disease factors performance website based selected native plugins. The statistics visits numbers further reflect potential impact this relevant Thus, devoted would benefit from emerging free service.

Language: Английский

TIMER2.0 for analysis of tumor-infiltrating immune cells DOI Creative Commons
Taiwen Li, Jingxin Fu, Zexian Zeng

et al.

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 48(W1), P. W509 - W514

Published: May 17, 2020

Abstract Tumor progression and the efficacy of immunotherapy are strongly influenced by composition abundance immune cells in tumor microenvironment. Due to limitations direct measurement methods, computational algorithms often used infer cell from bulk transcriptome profiles. These estimated infiltrate populations have been associated with genomic transcriptomic changes tumors, providing insight into tumor–immune interactions. However, such investigations on large-scale public data remain challenging. To lower barriers for analysis complex interactions, we significantly improved our previous web platform TIMER. Instead just using one algorithm, TIMER2.0 (http://timer.cistrome.org/) provides more robust estimation infiltration levels The Cancer Genome Atlas (TCGA) or user-provided profiles six state-of-the-art algorithms. four modules investigating associations between infiltrates genetic clinical features, exploring cancer-related TCGA cohorts. Each module can generate a functional heatmap table, enabling user easily identify significant multiple cancer types simultaneously. Overall, server comprehensive visualization functions infiltrating cells.

Language: Английский

Citations

3724
Approaches to treat immune hot, altered and cold tumours with combination immunotherapies DOI
Jérôme Galon, Daniela Bruni

Nature Reviews Drug Discovery, Journal Year: 2019, Volume and Issue: 18(3), P. 197 - 218

Published: Jan. 4, 2019

Language: Английский

Citations

2622
Ferroptosis, necroptosis, and pyroptosis in anticancer immunity DOI Creative Commons
Rong Tang, Jin Xu, Bo Zhang

et al.

Journal of Hematology & Oncology, Journal Year: 2020, Volume and Issue: 13(1)

Published: Aug. 10, 2020

Abstract In recent years, cancer immunotherapy based on immune checkpoint inhibitors (ICIs) has achieved considerable success in the clinic. However, ICIs are significantly limited by fact that only one third of patients with most types respond to these agents. The induction cell death mechanisms other than apoptosis gradually emerged as a new treatment strategy because tumors harbor innate resistance apoptosis. date, possibility combining two modalities not been discussed systematically. Recently, few studies revealed crosstalk between distinct and antitumor immunity. pyroptosis, ferroptosis, necroptosis combined showed synergistically enhanced activity, even ICI-resistant tumors. Immunotherapy-activated CD8+ T cells traditionally believed induce tumor via following main pathways: (i) perforin-granzyme (ii) Fas-FasL. identified mechanism which suppress growth inducing ferroptosis provoked review relationship system activation. Hence, this review, we summarize knowledge reciprocal interaction immunity mechanisms, particularly necroptosis, three potentially novel immunogenic death. Because evidence is derived from using animal models, also reviewed related bioinformatics data available for human tissues public databases, partially confirmed presence interactions activation

Language: Английский

Citations

968
ImmuCellAI: A Unique Method for Comprehensive T‐Cell Subsets Abundance Prediction and its Application in Cancer Immunotherapy DOI Creative Commons
Ya‐Ru Miao, Qiong Zhang, Qian Lei

et al.

Advanced Science, Journal Year: 2020, Volume and Issue: 7(7)

Published: Feb. 11, 2020

The distribution and abundance of immune cells, particularly T-cell subsets, play pivotal roles in cancer immunology therapy. T cells have many subsets with specific function current methods are limited estimating them, thus, a method for predicting comprehensive is urgently needed research. Here, Immune Cell Abundance Identifier (ImmuCellAI), gene set signature-based method, introduced precisely the 24 cell types including 18 from expression data. Performance evaluation on both sequencing data flow cytometry results public indicate that ImmuCellAI can estimate superior accuracy to other especially subsets. Application immunotherapy datasets reveals dendritic cytotoxic T, gamma delta significantly higher comparisons on-treatment versus pre-treatment responders non-responders. Meanwhile, an result-based model built response high (area under curve 0.80-0.91). These demonstrate powerful unique tumor infiltration estimation prediction.

Language: Английский

Citations

766
Tissue-resident FOLR2+ macrophages associate with CD8+ T cell infiltration in human breast cancer DOI Creative Commons
Rodrigo Nalio Ramos, Yoann Missolo-Koussou, Yohan Gerber-Ferder

et al.

Cell, Journal Year: 2022, Volume and Issue: 185(7), P. 1189 - 1207.e25

Published: March 1, 2022

Language: Английский

Citations

351
Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers DOI Creative Commons
Yongsheng Li,

Tiantongfei Jiang,

Weiwei Zhou

et al.

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Feb. 21, 2020

Abstract Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and they play fundamental roles in immune regulation. Here we introduce an integrated algorithm, ImmLnc, for identifying lncRNA immune-related pathways. We comprehensively chart the landscape regulation immunome across 33 cancer types show that cancers with similar tissue origin likely to share regulators. Moreover, lncRNAs perturbation significantly correlated cell infiltration. ImmLnc can help prioritize cancer-related further identify three molecular subtypes (proliferative, intermediate, immunological) non-small lung cancer. These characterized by differences mutation burden, infiltration, immunomodulatory genes, response chemotherapy, prognosis. In summary, pipeline resulting data serve a valuable resource understanding function advance identification immunotherapy targets.

Language: Английский

Citations

346
Quantifying tumor-infiltrating immune cells from transcriptomics data DOI
Francesca Finotello, Zlatko Trajanoski

Cancer Immunology Immunotherapy, Journal Year: 2018, Volume and Issue: 67(7), P. 1031 - 1040

Published: March 14, 2018

Language: Английский

Citations

339
Blockade of the Phagocytic Receptor MerTK on Tumor-Associated Macrophages Enhances P2X7R-Dependent STING Activation by Tumor-Derived cGAMP DOI Creative Commons
Yi Zhou,

Mingjian Fei,

Gu Zhang

et al.

Immunity, Journal Year: 2020, Volume and Issue: 52(2), P. 357 - 373.e9

Published: Feb. 1, 2020

Language: Английский

Citations

316
Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment DOI Creative Commons
Han Luo, Xuyang Xia, Li‐Bin Huang

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Nov. 4, 2022

Abstract Cancer-associated fibroblasts (CAFs) are the predominant components of tumor microenvironment (TME) and influence cancer hallmarks, but without systematic investigation on their ubiquitous characteristics across different types. Here, we perform pan-cancer analysis 226 samples 10 solid types to profile TME at single-cell resolution, illustrating commonalities/plasticity heterogenous CAFs. Activation trajectory major CAF is divided into three states, exhibiting distinct interactions with other cell components, relating prognosis immunotherapy. Moreover, minor represent alternative origin from (e.g., endothelia macrophages). Particularly, presentation endothelial-to-mesenchymal transition CAF, which may interact proximal SPP 1 + tumor-associated macrophages, implicated in survival stratifications. Our study comprehensively profiles shared dynamics CAFs, highlight heterogeneity plasticity Browser integrated information available https://gist-fgl.github.io/sc-caf-atlas/ .

Language: Английский

Citations

292
LAYN Is a Prognostic Biomarker and Correlated With Immune Infiltrates in Gastric and Colon Cancers DOI Creative Commons
Jinghua Pan, Hong Zhou, Laura Cooper

et al.

Frontiers in Immunology, Journal Year: 2019, Volume and Issue: 10

Published: Jan. 28, 2019

Background: Layilin (LAYN) is a critical gene that regulates T cell function. However, the correlations of LAYN to prognosis and tumor-infiltrating lymphocytes in different cancers remain unclear. Methods: expression was analyzed via Oncomine database Tumor Immune Estimation Resource (TIMER) site. We evaluated influence on clinical using Kaplan-Meier plotter, PrognoScan Gene Expression Profiling Interactive Analysis (GEPIA). The between cancer immune infiltrates investigated TIMER. In addition, marker sets were by TIMER GEPIA. Results: A cohort (GSE17536) colorectal patients showed high associated with poorer overall survival (OS), disease-specific (DSS) disease-free (DFS). significantly correlated poor OS progression-free (PFS) gastric (OS HR = 1.97, P 3.6e-10; PFS 2.12, 2.3e-10). Moreover, LYAN impacts diverse Cancer Genome Atlas (TCGA). Specifically, worse stage 2 4 but not 1 N0 (P 0.28, 0.34; 0.073, 0.092). positively infiltrating levels CD4+ CD8+ cells, macrophages, neutrophils dendritic cells (DCs) colon adenocarcinoma (COAD) stomach (STAD). strong COAD STAD. Conclusions: These findings suggest of, including those DCs multiple cancers, especially patients. potentially contributes regulation tumor-associated macrophages (TAMs), DCs, exhaustion Tregs cancer. can be used as prognostic biomarker for determining infiltration cancers.

Language: Английский

Citations

285