Pan-cancer spatially resolved single-cell analysis reveals the crosstalk between cancer-associated fibroblasts and tumor microenvironment

Single-cell analysis reveals prognostic fibroblast subpopulations linked to molecular and immunological subtypes of lung cancer

(2023) Christopher J. Hanley et al.   Nature Communications

Single-cell dissection of cellular and molecular features underlying human cervical squamous cell carcinoma initiation and progression

(2023) Chao Liu et al.   Science Advances

TGF-β Regulation of T Cells

(2023) WanJun Chen   Annual Review of Immunology

Fibroblasts in cancer: Unity in heterogeneity

(2023) Yash Chhabra et al.   CELL

Galectin-1: A Traditionally Immunosuppressive Protein Displays Context-Dependent Capacities

(2023) Xizhi Yu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

MIF inhibition alleviates vitiligo progression by suppressing CD8+ T cell activation and proliferation

(2023) Jianru Chen et al.   JOURNAL OF PATHOLOGY

Extracellular matrix remodeling in tumor progression and immune escape: from mechanisms to treatments

(2023) Zhennan Yuan et al.   Molecular Cancer

Roles of cancer-associated fibroblasts (CAFs) in anti- PD-1/PD-L1 immunotherapy for solid cancers

(2023) Liping Pei et al.   Molecular Cancer

Targeting angiogenesis in oncology, ophthalmology and beyond

(2023) Yihai Cao et al.   NATURE REVIEWS DRUG DISCOVERY

Single-cell transcriptome profiling of the stepwise progression of head and neck cancer

(2023) Ji-Hye Choi et al.   Nature Communications

Tumor microenvironment remodeling after neoadjuvant immunotherapy in non-small cell lung cancer revealed by single-cell RNA sequencing

(2023) Junjie Hu et al.   Genome Medicine

Harnessing type I interferon-mediated immunity to target malignant brain tumors

(2023) Juhee Lim et al.   Frontiers in Immunology

Basement membrane promotes tumor development by attenuating T cell activation

(2022) Xiangming Liu et al.   Journal of Molecular Cell Biology

‘Reverse Warburg effect’ of cancer‑associated fibroblasts (Review)

(2022) Lin Liang et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

Spatial charting of single-cell transcriptomes in tissues

(2022) Runmin Wei et al.   NATURE BIOTECHNOLOGY

Single-Cell RNA Sequencing Reveals the Tissue Architecture in Human High-Grade Serous Ovarian Cancer

(2022) Junfen Xu et al.   CLINICAL CANCER RESEARCH

Cancer-associated fibroblasts: Vital suppressors of the immune response in the tumor microenvironment

(2022) Xuan Xiang et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Recent progress on vascular endothelial growth factor receptor inhibitors with dual targeting capabilities for tumor therapy

(2022) Yun Liu et al.   Journal of Hematology & Oncology

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

(2022) Dalia Barkley et al.   NATURE GENETICS

A single-cell atlas of the multicellular ecosystem of primary and metastatic hepatocellular carcinoma

(2022) Yiming Lu et al.   Nature Communications

Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk

(2022) Xin Shao et al.   Nature Communications

Targeting the tumor stroma for cancer therapy

(2022) Maosen Xu et al.   Molecular Cancer

The expanding vistas of spatial transcriptomics

(2022) Luyi Tian et al.   NATURE BIOTECHNOLOGY

Major pathways involved in macrophage polarization in cancer

(2022) Clément Kerneur et al.   Frontiers in Immunology

Decoding Strategies to Evade Immunoregulators Galectin-1, -3, and -9 and Their Ligands as Novel Therapeutics in Cancer Immunotherapy

(2022) Lee Seng Lau et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Liver tumour immune microenvironment subtypes and neutrophil heterogeneity

(2022) Ruidong Xue et al.   NATURE

Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment

(2022) Han Luo et al.   Nature Communications

A single-cell analysis reveals tumor heterogeneity and immune environment of acral melanoma

(2022) Chao Zhang et al.   Nature Communications

Systematic single-cell pathway analysis to characterize early T cell activation

(2022) Jack A. Bibby et al.   Cell Reports

Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Implication of cancer associated fibroblast subtypes on cancer pathogenesis, prognosis, and immunotherapy resistance

(2021) Phillip M Galbo et al.   CLINICAL CANCER RESEARCH

Type I interferon activating type I dendritic cells for anti-tumor immunity

(2021) Yong Liang et al.   CLINICAL CANCER RESEARCH

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

ShinyCell: simple and sharable visualization of single-cell gene expression data

(2021) John F Ouyang et al.   BIOINFORMATICS

Fibroblast-macrophage reciprocal interactions in health, fibrosis, and cancer

(2021) Matthew B. Buechler et al.   IMMUNITY

A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

(2021) Ayse Bassez et al.   NATURE MEDICINE

Anti-angiogenic agents — overcoming tumour endothelial cell anergy and improving immunotherapy outcomes

(2021) Zowi R. Huinen et al.   Nature Reviews Clinical Oncology

Conserved pan-cancer microenvironment subtypes predict response to immunotherapy

(2021) Alexander Bagaev et al.   CANCER CELL

Mitogen‐activated protein kinase activity drives cell trajectories in colorectal cancer

(2021) Florian Uhlitz et al.   EMBO Molecular Medicine

A single-cell and spatially resolved atlas of human breast cancers

(2021) Sunny Z. Wu et al.   NATURE GENETICS

Spatiotemporal Immune Landscape of Colorectal Cancer Liver Metastasis at Single-Cell Level

(2021) Yingcheng Wu et al.   Cancer Discovery

Cancer biology deciphered by single-cell transcriptomic sequencing

(2021) Yanmeng Li et al.   Protein & Cell

Matrix Stiffness Induces Pericyte-Fibroblast Transition Through YAP Activation

(2021) Feng Feng et al.   Frontiers in Pharmacology

Recombinant Mycobacterium smegmatis delivering a fusion protein of human macrophage migration inhibitory factor (MIF) and IL-7 exerts an anticancer effect by inducing an immune response against MIF in a tumor-bearing mouse model

(2021) Hyein Jeong et al.   Journal for ImmunoTherapy of Cancer

Single-cell analysis of pancreatic ductal adenocarcinoma identifies a novel fibroblast subtype associated with poor prognosis but better immunotherapy response

(2021) Yu Wang et al.   Cell Discovery

Galectins as Emerging Glyco-Checkpoints and Therapeutic Targets in Glioblastoma

(2021) Guillermo A. Videla-Richardson et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Pan-cancer single-cell landscape of tumor-infiltrating T cells

(2021) Liangtao Zheng et al.   SCIENCE

Single-cell transcriptomic analysis of the tumor ecosystems underlying initiation and progression of papillary thyroid carcinoma

(2021) Weilin Pu et al.   Nature Communications

Comprehensive analysis of spatial architecture in primary liver cancer

(2021) Rui Wu et al.   Science Advances

GeneSwitches: Ordering gene-expression and functional events in single-cell experiments

(2020) Elaine Y Cao et al.   BIOINFORMATICS

Tertiary lymphoid structures improve immunotherapy and survival in melanoma

(2020) Rita Cabrita et al.   NATURE

KLF16 Affects the MYC Signature and Tumor Growth in Prostate Cancer

(2020) Jun Zhang et al.   OncoTargets and Therapy

Identification of Distinct Immune Subtypes in Colorectal Cancer Based on the Stromal Compartment

(2020) Rongfang Shen et al.   Frontiers in Oncology

Emergence of a High-Plasticity Cell State during Lung Cancer Evolution

(2020) Nemanja Despot Marjanovic et al.   CANCER CELL

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

Single-cell RNA sequencing highlights the role of inflammatory cancer-associated fibroblasts in bladder urothelial carcinoma

(2020) Zhaohui Chen et al.   Nature Communications

Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy

(2019) Tuba N. Gide et al.   CANCER CELL

Tumor Mutational Burden and Efficacy of Nivolumab Monotherapy and in Combination with Ipilimumab in Small-Cell Lung Cancer

(2019) Matthew D. Hellmann et al.   CANCER CELL

TISIDB: an integrated repository portal for tumor-immune system interactions

(2019) Beibei Ru et al.   BIOINFORMATICS

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Type I Interferons and Cancer: An Evolving Story Demanding Novel Clinical Applications

(2019) Eleonora Aricò et al.   Cancers

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas

(2018) Shengbao Suo et al.   Cell Reports

Identification of an Immune-specific Class of Hepatocellular Carcinoma, Based on Molecular Features

(2017) Daniela Sia et al.   GASTROENTEROLOGY

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

(2017) Mark Ayers et al.   JOURNAL OF CLINICAL INVESTIGATION

KLF4-dependent perivascular cell plasticity mediates pre-metastatic niche formation and metastasis

(2017) Meera Murgai et al.   NATURE MEDICINE

Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

(2017) Whijae Roh et al.   Science Translational Medicine

Type I Interferon in Chronic Virus Infection and Cancer

(2017) Laura M. Snell et al.   TRENDS IN IMMUNOLOGY

CDX2 is involved in microRNA‑associated inflammatory carcinogenesis in gastric cancer

(2017) Motonobu Saito et al.   Oncology Letters

Pericyte–fibroblast transition promotes tumor growth and metastasis

(2016) Kayoko Hosaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic Mutations and Neoepitope Homology in Melanomas Treated with CTLA-4 Blockade

(2016) Tavi Nathanson et al.   Cancer Immunology Research

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Stromal miR-200s contribute to breast cancer cell invasion through CAF activation and ECM remodeling

(2015) X Tang et al.   CELL DEATH AND DIFFERENTIATION

The Transcription Factor NFAT Promotes Exhaustion of Activated CD8 + T Cells

(2015) Gustavo J. Martinez et al.   IMMUNITY

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

(2015) Antonio Colaprico et al.   NUCLEIC ACIDS RESEARCH

NFATc1 Regulates PD-1 Expression upon T Cell Activation

(2014) K. J. Oestreich et al.   JOURNAL OF IMMUNOLOGY

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

‘Cancer associated fibroblasts’ – more than meets the eye

(2013) Shalom Madar et al.   TRENDS IN MOLECULAR MEDICINE

Inferring tumour purity and stromal and immune cell admixture from expression data

(2013) Kosuke Yoshihara et al.   Nature Communications

Robust rank aggregation for gene list integration and meta-analysis

(2012) Raivo Kolde et al.   BIOINFORMATICS

Therapeutic applications of macrophage colony-stimulating factor-1 (CSF-1) and antagonists of CSF-1 receptor (CSF-1R) signaling

(2011) D. A. Hume et al.   BLOOD

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY