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

Mesothelial cell-derived antigen-presenting cancer-associated fibroblasts induce expansion of regulatory T cells in pancreatic cancer

(2022) Huocong Huang et al.   CANCER CELL

Identification of Functional Heterogeneity of Carcinoma-Associated Fibroblasts with Distinct IL6-Mediated Therapy Resistance in Pancreatic Cancer

(2022) Kathleen M. McAndrews et al.   Cancer Discovery

Single-cell analysis reveals transcriptomic remodellings in distinct cell types that contribute to human prostate cancer progression

(2021) Sujun Chen et al.   NATURE CELL BIOLOGY

Method of the Year: spatially resolved transcriptomics

(2021) Vivien Marx   NATURE METHODS

A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

(2021) Sijin Cheng et al.   CELL

Galectin-9 interacts with PD-1 and TIM-3 to regulate T cell death and is a target for cancer immunotherapy

(2021) Riyao Yang et al.   Nature Communications

The IKZF1–IRF4/IRF5 Axis Controls Polarization of Myeloma-Associated Macrophages

(2021) Dimitrios Mougiakakos et al.   Cancer Immunology Research

Transcriptional networks controlling stromal cell differentiation

(2021) Alexander Rauch et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Clinical and therapeutic relevance of cancer-associated fibroblasts

(2021) Yang Chen et al.   Nature Reviews Clinical Oncology

Single-cell analysis of the pan-cancer immune microenvironment and scTIME portal

(2021) Fang Hong et al.   Cancer Immunology Research

Characterizing dedifferentiation of thyroid cancer by integrated analysis

(2021) Han Luo et al.   Science Advances

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

(2021) Liangtao Zheng et al.   SCIENCE

Single-Cell Atlas of Lineage States, Tumor Microenvironment, and Subtype-Specific Expression Programs in Gastric Cancer

(2021) Vikrant Kumar et al.   Cancer Discovery

FOXP3+ T cells in uterine sarcomas are associated with favorable prognosis, low extracellular matrix expression and reduced YAP activation

(2021) Okan Gultekin et al.   npj Precision Oncology

Oncogenic ERG represses PI3K signaling through down-regulation of IRS2

(2020) Ninghui Mao et al.   CANCER RESEARCH

Single cell genomic characterization reveals the cellular reprogramming of the gastric tumor microenvironment

(2020) Anuja Sathe et al.   CLINICAL CANCER RESEARCH

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

Sufficiency of CD40 activation and immune checkpoint blockade for T cell priming and tumor immunity

(2020) Alexander H. Morrison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Loss of Spry1 reduces growth of BRAFV600-mutant cutaneous melanoma and improves response to targeted therapy

(2020) Barbara Montico et al.   Cell Death & Disease

Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

(2020) Nayoung Kim et al.   Nature Communications

A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

(2020) Junbin Qian et al.   CELL RESEARCH

Neural transcription factor Pou4f1 promotes renal fibrosis via macrophage–myofibroblast transition

(2020) Patrick Ming-Kuen Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a distinct luminal subgroup diagnosing and stratifying early stage prostate cancer by tissue-based single-cell RNA sequencing

(2020) Xiaoshi Ma et al.   Molecular Cancer

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

(2020) Zhaohui Chen et al.   Nature Communications

Single-cell transcriptome analysis of tumor and stromal compartments of pancreatic ductal adenocarcinoma primary tumors and metastatic lesions

(2020) Wei Lin et al.   Genome Medicine

Immunometabolic Interplay in the Tumor Microenvironment

(2020) Irem Kaymak et al.   CANCER CELL

CCL22 controls immunity by promoting regulatory T cell communication with dendritic cells in lymph nodes

(2019) Moritz Rapp et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma

(2019) Junya Peng et al.   CELL RESEARCH

CD24 signalling through macrophage Siglec-10 is a target for cancer immunotherapy

(2019) Amira A. Barkal et al.   NATURE

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

(2019) Ela Elyada et al.   Cancer Discovery

Transition of Macrophages to Fibroblast-Like Cells in Healing Myocardial Infarction

(2019) Nezam Haider et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

Notch Signaling in the Tumor Microenvironment

(2018) Olivier Meurette et al.   CANCER CELL

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

(2018) Sanjeev Mariathasan et al.   NATURE

FAP delineates heterogeneous and functionally divergent stromal cells in immune-excluded breast tumors

(2018) Viviana Cremasco et al.   Cancer Immunology Research

Oncofoetal insulin receptor isoform A marks the tumour endothelium; an underestimated pathway during tumour angiogenesis and angiostatic treatment

(2018) Patrycja Nowak-Sliwinska et al.   BRITISH JOURNAL OF CANCER

Tumour-vasculature development via endothelial-to-mesenchymal transition after radiotherapy controls CD44v6+ cancer cell and macrophage polarization

(2018) Seo-Hyun Choi et al.   Nature Communications

MAFB Determines Human Macrophage Anti-Inflammatory Polarization: Relevance for the Pathogenic Mechanisms Operating in Multicentric Carpotarsal Osteolysis

(2017) Víctor D. Cuevas et al.   JOURNAL OF IMMUNOLOGY

Macrophage-to-Myofibroblast Transition Contributes to Interstitial Fibrosis in Chronic Renal Allograft Injury

(2017) Ying-Ying Wang et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Dectin 1 activation on macrophages by galectin 9 promotes pancreatic carcinoma and peritumoral immune tolerance

(2017) Donnele Daley et al.   NATURE MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

SOXF transcription factors in cardiovascular development

(2017) Andrew J. Lilly et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

Targeting the tumor microenvironment: removing obstruction to anticancer immune responses and immunotherapy

(2016) J. M. Pitt et al.   ANNALS OF ONCOLOGY

Galectin-9: From cell biology to complex disease dynamics

(2016) Sebastian John et al.   JOURNAL OF BIOSCIENCES

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

Anti–PD-1/PD-L1 therapy of human cancer: past, present, and future

(2015) Lieping Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Esm1 Modulates Endothelial Tip Cell Behavior and Vascular Permeability by Enhancing VEGF Bioavailability

(2014) Susana F. Rocha et al.   CIRCULATION RESEARCH

PGC-1α Induces SPP1 to Activate Macrophages and Orchestrate Functional Angiogenesis in Skeletal Muscle

(2014) Glenn C. Rowe et al.   CIRCULATION RESEARCH

T Cells Are Smad’ly in Love with Galectin-9

(2014) Richard D. Cummings   IMMUNITY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Carcinoma-Associated Fibroblast Expressing Fibroblast Activation Protein and Escape from Immune Surveillance

(2014) D. T. Fearon   Cancer Immunology Research

Microenvironmental regulation of tumor progression and metastasis

(2013) Daniela F Quail et al.   NATURE MEDICINE

Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer

(2013) C. Feig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accessories to the Crime: Functions of Cells Recruited to the Tumor Microenvironment

(2012) Douglas Hanahan et al.   CANCER CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Sox10 is required for Schwann-cell homeostasis and myelin maintenance in the adult peripheral nerve

(2011) Magdalena Bremer et al.   GLIA

The role of pericytes in angiogenesis

(2011) Domenico Ribatti et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Macrophage-specific gene functions in Spi1-directed innate immunity

(2010) A. Zakrzewska et al.   BLOOD

Suppression of Antitumor Immunity by Stromal Cells Expressing Fibroblast Activation Protein- 

(2010) M. Kraman et al.   SCIENCE

Granzyme B produced by human plasmacytoid dendritic cells suppresses T-cell expansion

(2009) B. Jahrsdorfer et al.   BLOOD

Ets1 and Ets2 are required for endothelial cell survival during embryonic angiogenesis

(2009) G. Wei et al.   BLOOD

PDGF-C Mediates the Angiogenic and Tumorigenic Properties of Fibroblasts Associated with Tumors Refractory to Anti-VEGF Treatment

(2009) Yongping Crawford et al.   CANCER CELL

TGF-β: A Master of All T Cell Trades

(2008) Ming O. Li et al.   CELL

Systemic Endocrine Instigation of Indolent Tumor Growth Requires Osteopontin

(2008) Sandra S. McAllister et al.   CELL

CD44 Mediates Successful Interstitial Navigation by Killer T Cells and Enables Efficient Antitumor Immunity

(2008) Paulus Mrass et al.   IMMUNITY