Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response DOI Creative Commons
Alexander Coulton, Jun Murai, Danwen Qian

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: July 6, 2024

Abstract The paradigm for macrophage characterization has evolved from the simple M1/M2 dichotomy to a more complex model that encompasses broad spectrum of phenotypic diversity, due differences in ontogeny and/or local stimuli. We currently lack an in-depth pan-cancer single cell RNA-seq (scRNAseq) atlas tumour-associated macrophages (TAMs) fully captures this complexity. In addition, increased understanding diversity could help explain variable responses cancer patients immunotherapy. Our includes well established subsets as number additional ones. associate composition with tumour phenotype and show can vary between primary metastatic tumours growing sites like liver. also examine macrophage-T functional cross talk identify two TAMs associated T activation. Analysis TAM signatures large cohort immune checkpoint inhibitor-treated (CPI1000 + ) multiple response, including presence subset upregulate collagen-related genes. Finally, we demonstrate utility our data resource reference mapping novel datasets using projection. Overall, these advances represent important step both classification overcoming resistance immunotherapies cancer.

Language: Английский

Uveal melanoma DOI
Martine J. Jager, Carol L. Shields, Colleen M. Cebulla

et al.

Nature Reviews Disease Primers, Journal Year: 2020, Volume and Issue: 6(1)

Published: April 9, 2020

Language: Английский

Citations

603
Single-cell RNA landscape of intratumoral heterogeneity and immunosuppressive microenvironment in advanced osteosarcoma DOI Creative Commons
Yan Zhou, Yang Dong,

Qingcheng Yang

et al.

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

Published: Dec. 10, 2020

Osteosarcoma is the most frequent primary bone tumor with poor prognosis. Through RNA-sequencing of 100,987 individual cells from 7 primary, 2 recurrent, and lung metastatic osteosarcoma lesions, 11 major cell clusters are identified based on unbiased clustering gene expression profiles canonical markers. The transcriptomic properties, regulators dynamics malignant together their microenvironment particularly stromal immune characterized. transdifferentiation osteoblastic chondroblastic revealed by analyses inferred copy-number variation trajectory. A proinflammatory FABP4

Language: Английский

Citations

424
Transfer learning enables predictions in network biology DOI
Christina V. Theodoris, Ling Xiao,

Anant Chopra

et al.

Nature, Journal Year: 2023, Volume and Issue: 618(7965), P. 616 - 624

Published: May 31, 2023

Language: Английский

Citations

408
Endoplasmic reticulum stress: molecular mechanism and therapeutic targets DOI Creative Commons
Xingyi Chen, Chaoran Shi,

Meihui He

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: Sept. 15, 2023

Abstract The endoplasmic reticulum (ER) functions as a quality-control organelle for protein homeostasis, or “proteostasis”. quality control systems involve ER-associated degradation, chaperons, and autophagy. ER stress is activated when proteostasis broken with an accumulation of misfolded unfolded proteins in the ER. activates adaptive response to restore by initiating kinase R-like kinase, activating transcription factor 6, inositol requiring enzyme 1. multifaceted, acts on aspects at epigenetic level, including processing. Accumulated data indicates its key role homeostasis other diverse involved various ocular diseases, such glaucoma, diabetic retinopathy, age-related macular degeneration, retinitis pigmentosa, achromatopsia, cataracts, tumors, surface myopia. This review summarizes molecular mechanisms underlying aforementioned diseases from perspective. Drugs (chemicals, neurotrophic factors, nanoparticles), gene therapy, stem cell therapy are used treat alleviating stress. We delineate advancement targeting provide new treatment strategies diseases.

Language: Английский

Citations

368
Insights Gained from Single-Cell Analysis of Immune Cells in the Tumor Microenvironment DOI
Xianwen Ren, Lei Zhang, Yuanyuan Zhang

et al.

Annual Review of Immunology, Journal Year: 2021, Volume and Issue: 39(1), P. 583 - 609

Published: Feb. 27, 2021

Understanding tumor immune microenvironments is critical for identifying modifiers of cancer progression and developing immunotherapies. Recent applications single-cell RNA sequencing (scRNA-seq) in dissecting have brought important insights into the biology tumor-infiltrating cells, including their heterogeneity, dynamics, potential roles both disease response to checkpoint inhibitors other This review focuses on advances knowledge acquired from scRNA-seq studies across multiple types human tumors, with a particular emphasis study phenotypic plasticity lineage dynamics cells environment. We also discuss several imminent questions emerging observations solutions horizon.

Language: Английский

Citations

260
Advancing Cancer Research and Medicine with Single-Cell Genomics DOI Creative Commons
Bora Lim, Yiyun Lin, Nicholas E. Navin

et al.

Cancer Cell, Journal Year: 2020, Volume and Issue: 37(4), P. 456 - 470

Published: April 1, 2020

Language: Английский

Citations

249
Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy DOI
Satyen H. Gohil, J. Bryan Iorgulescu, David A. Braun

et al.

Nature Reviews Clinical Oncology, Journal Year: 2020, Volume and Issue: 18(4), P. 244 - 256

Published: Dec. 4, 2020

Language: Английский

Citations

216
Integrated analysis of single-cell and bulk RNA sequencing data reveals a pan-cancer stemness signature predicting immunotherapy response DOI Creative Commons
Zhen Zhang, Zixian Wang,

Yan‐Xing Chen

et al.

Genome Medicine, Journal Year: 2022, Volume and Issue: 14(1)

Published: April 29, 2022

Although immune checkpoint inhibitor (ICI) is regarded as a breakthrough in cancer therapy, only limited fraction of patients benefit from it. Cancer stemness can be the potential culprit ICI resistance, but direct clinical evidence lacking.

Language: Английский

Citations

175
Tumor immune microenvironment lncRNAs DOI Creative Commons

Eun-Gyeong Park,

Sung-Jin Pyo,

Youxi Cui

et al.

Briefings in Bioinformatics, Journal Year: 2021, Volume and Issue: 23(1)

Published: Nov. 5, 2021

Abstract Long non-coding ribonucleic acids (RNAs) (lncRNAs) are key players in tumorigenesis and immune responses. The nature of their cell type-specific gene expression other functional evidence support the idea that lncRNAs have distinct cellular functions tumor microenvironment (TIME). To date, majority lncRNA studies heavily relied on bulk RNA-sequencing data which various types contribute to an averaged signal, limiting discovery functions. Single-cell (scRNA-seq) is a potential solution for tackling this limitation despite lack annotations low abundance yet lncRNAs. Hence, updated further understanding will be necessary characterizing genes TIME. In review, we discuss specifically expressed cells, summarize regulatory at type level highlight how scRNA-seq approach can help study TIME

Language: Английский

Citations

162
Unraveling B cell trajectories at single cell resolution DOI Creative Commons

Dhakshayini Morgan,

Vinay Tergaonkar

Trends in Immunology, Journal Year: 2022, Volume and Issue: 43(3), P. 210 - 229

Published: Jan. 25, 2022

During adaptive immunity, B cells differentiate either into memory or plasma and produce antibodies against foreign antigens to fight infection. Additionally, they behave as antigen-presenting participate in T cell activation during cellular immune responses. However, their functional dysregulation can result various autoimmune diseases cancers. With significant breakthroughs single technologies, assessing individual genomics, transcriptomics, proteomics give deeper insights mammalian development, differentiation, antibody repertoire, responses under conditions of homeostasis, infection, aberrations disease. In this review, we discuss the adoption approaches identify different gene signatures biomarkers normal diseased tissues, subsequent benefits for future therapeutic discoveries.

Language: Английский

Citations

150