Lung tumor MHCII immunity depends on in situ antigen presentation by fibroblasts

Single-cell analysis defines a pancreatic fibroblast lineage that supports anti-tumor immunity

(2021) Colin Hutton et al.   CANCER CELL

Regulatory T Cells Restrain Interleukin-2- and Blimp-1-Dependent Acquisition of Cytotoxic Function by CD4+ T Cells

(2020) Anna Śledzińska et al.   IMMUNITY

B cells are associated with survival and immunotherapy response in sarcoma

(2020) Florent Petitprez et al.   NATURE

Tertiary lymphoid structures improve immunotherapy and survival in melanoma

(2020) Rita Cabrita et al.   NATURE

B cells and tertiary lymphoid structures promote immunotherapy response

(2020) Beth A. Helmink et al.   NATURE

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

DIVERSITY AND BIOLOGY OF CANCER-ASSOCIATED FIBROBLASTS

(2020) Giulia Biffi et al.   PHYSIOLOGICAL REVIEWS

Single-cell analysis reveals fibroblast clusters linked to immunotherapy resistance in cancer

(2020) Yann Kieffer et al.   Cancer Discovery

Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast Cancer

(2020) Aimy Sebastian et al.   Cancers

Integrative, normalization-insusceptible statistical analysis of RNA-Seq data, with improved differential expression and unbiased downstream functional analysis

(2020) Dionysios Fanidis et al.   BRIEFINGS IN BIOINFORMATICS

Visualizing Synaptic Transfer of Tumor Antigens among Dendritic Cells

(2020) Megan K. Ruhland et al.   CANCER CELL

Tissue-resident memory T cell reactivation by diverse antigen-presenting cells imparts distinct functional responses

(2020) Jun Siong Low et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Structural cells are key regulators of organ-specific immune responses

(2020) Thomas Krausgruber et al.   NATURE

cDC1 prime and are licensed by CD4+ T cells to induce anti-tumour immunity

(2020) Stephen T. Ferris et al.   NATURE

Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis

(2020) Maximilian Strunz et al.   Nature Communications

Conserved Interferon-γ Signaling Drives Clinical Response to Immune Checkpoint Blockade Therapy in Melanoma

(2020) Catherine S. Grasso et al.   CANCER CELL

The PD-1/PD-L1-Checkpoint Restrains T cell Immunity in Tumor-Draining Lymph Nodes

(2020) Floris Dammeijer et al.   CANCER CELL

TGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts

(2020) Angelo L. Grauel et al.   Nature Communications

T cells genetically engineered to overcome death signaling enhance adoptive cancer immunotherapy

(2019) Tori N. Yamamoto et al.   JOURNAL OF CLINICAL INVESTIGATION

Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity

(2019) Mikhail Binnewies et al.   CELL

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

(2019) Ela Elyada et al.   Cancer Discovery

MHC Class II Antigen Presentation by the Intestinal Epithelium Initiates Graft-versus-Host Disease and Is Influenced by the Microbiota

(2019) Motoko Koyama et al.   IMMUNITY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Autophagy inhibition-mediated epithelial–mesenchymal transition augments local myofibroblast differentiation in pulmonary fibrosis

(2019) Charlotte Hill et al.   Cell Death & Disease

MHC-II neoantigens shape tumour immunity and response to immunotherapy

(2019) Elise Alspach et al.   NATURE

Fibroblastic reticular cells enhance T cell metabolism and survival via epigenetic remodeling

(2019) Flavian D. Brown et al.   NATURE IMMUNOLOGY

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

(2019) Kroopa Joshi et al.   NATURE MEDICINE

Single-cell RNA sequencing reveals stromal evolution into LRRC15+ myofibroblasts as a determinant of patient response to cancer immunotherapy

(2019) Claudia X Dominguez et al.   Cancer Discovery

CD4+ T Cell Help Is Required for the Formation of a Cytolytic CD8+ T Cell Subset that Protects against Chronic Infection and Cancer

(2019) Ryan Zander et al.   IMMUNITY

An intra-tumoral niche maintains and differentiates stem-like CD8 T cells

(2019) Caroline S. Jansen et al.   NATURE

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

CD4+ T cell help creates memory CD8+ T cells with innate and help-independent recall capacities

(2019) Tomasz Ahrends et al.   Nature Communications

Complement and the Regulation of T Cell Responses

(2018) Erin E. West et al.   Annual Review of Immunology

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

C1q restrains autoimmunity and viral infection by regulating CD8+T cell metabolism

(2018) Guang Sheng Ling et al.   SCIENCE

MHC proteins confer differential sensitivity to CTLA-4 and PD-1 blockade in untreated metastatic melanoma

(2018) Scott J. Rodig et al.   Science Translational Medicine

Epithelial MHC Class II Expression and Its Role in Antigen Presentation in the Gastrointestinal and Respiratory Tracts

(2018) Jonathan E. Wosen et al.   Frontiers in Immunology

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Complement component 1, q subcomponent binding protein (C1QBP) in lipid rafts mediates hepatic metastasis of pancreatic cancer by regulating IGF-1/IGF-1R signaling

(2017) Haojun Shi et al.   INTERNATIONAL JOURNAL OF CANCER

Lung epithelial cells: therapeutically inducible effectors of antimicrobial defense

(2017) M M Leiva-Juárez et al.   Mucosal Immunology

Divergent roles for Clusterin in Lung Injury and Repair

(2017) David M. Habiel et al.   Scientific Reports

Tumor-induced stromal reprogramming drives lymph node transformation

(2016) Angela Riedel et al.   NATURE IMMUNOLOGY

Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy

(2016) Douglas B. Johnson et al.   Nature Communications

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Emerging and Novel Functions of Complement Protein C1q

(2015) Lubna Kouser et al.   Frontiers in Immunology

Depletion of Carcinoma-Associated Fibroblasts and Fibrosis Induces Immunosuppression and Accelerates Pancreas Cancer with Reduced Survival

(2014) Berna C. Özdemir et al.   CANCER CELL

Oncology Meets Immunology: The Cancer-Immunity Cycle

(2013) Daniel S. Chen et al.   IMMUNITY

Type 2 alveolar cells are stem cells in adult lung

(2013) Christina E. Barkauskas et al.   JOURNAL OF CLINICAL INVESTIGATION

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

DC-SIGN, C1q, and gC1qR form a trimolecular receptor complex on the surface of monocyte-derived immature dendritic cells

(2012) K. K. Hosszu et al.   BLOOD

Metabolic switching and fuel choice during T-cell differentiation and memory development

(2012) Gerritje J. W. Windt et al.   IMMUNOLOGICAL REVIEWS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Regulated release of nitric oxide by nonhematopoietic stroma controls expansion of the activated T cell pool in lymph nodes

(2011) Veronika Lukacs-Kornek et al.   NATURE IMMUNOLOGY

CD4+ T-Cell Help in the Tumor Milieu Is Required for Recruitment and Cytolytic Function of CD8+ T Lymphocytes

(2010) R. Bos et al.   CANCER RESEARCH

Accumulation and local proliferation of antigen-specific CD4+ T cells in antigen-bearing tissue

(2010) Cornelia Doebis et al.   IMMUNOLOGY AND CELL BIOLOGY

Bystander killing of cancer requires the cooperation of CD4+and CD8+T cells during the effector phase

(2010) Andrea Schietinger et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Mesenchymal cell targeting by TNF as a common pathogenic principle in chronic inflammatory joint and intestinal diseases

(2008) Maria Armaka et al.   JOURNAL OF EXPERIMENTAL MEDICINE