Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy

Top 10 Challenges in Cancer Immunotherapy

(2020) Priti S. Hegde et al.   IMMUNITY

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

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

(2020) Mirjana Efremova et al.   Nature Protocols

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

(2020) Orit Rozenblatt-Rosen et al.   CELL

Analyzing the Mycobacterium tuberculosis immune response by T-cell receptor clustering with GLIPH2 and genome-wide antigen screening

(2020) Huang Huang et al.   NATURE BIOTECHNOLOGY

The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes

(2020) Peter C de Greef et al.   eLife

A committed tissue-resident memory T cell precursor within the circulating CD8+ effector T cell pool

(2020) Lianne Kok et al.   JOURNAL OF EXPERIMENTAL MEDICINE

TGF-β suppresses type 2 immunity to cancer

(2020) Ming Liu et al.   NATURE

Transcriptomic Profiling of the Tumor Microenvironment Reveals Distinct Subgroups of Clear cell Renal Cell Cancer - Data from a Randomized Phase III Trial

(2019) A. Ari Hakimi et al.   Cancer Discovery

Avelumab plus Axitinib versus Sunitinib for Advanced Renal-Cell Carcinoma

(2019) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Pembrolizumab plus Axitinib versus Sunitinib for Advanced Renal-Cell Carcinoma

(2019) Brian I. Rini et al.   NEW ENGLAND JOURNAL OF MEDICINE

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis identifies NR4A1 as a key mediator of T cell dysfunction

(2019) Xindong Liu et al.   NATURE

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets

(2019) Luca Cassetta et al.   CANCER CELL

Biomarker analyses from JAVELIN Renal 101: Avelumab + axitinib (A+Ax) versus sunitinib (S) in advanced renal cell carcinoma (aRCC).

(2019) Toni K. Choueiri et al.   JOURNAL OF CLINICAL ONCOLOGY

Atezolizumab plus bevacizumab versus sunitinib in patients with previously untreated metastatic renal cell carcinoma (IMmotion151): a multicentre, open-label, phase 3, randomised controlled trial

(2019) Brian I Rini et al.   LANCET

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

Single T Cell Sequencing Demonstrates the Functional Role of αβ TCR Pairing in Cell Lineage and Antigen Specificity

(2019) Jason A. Carter et al.   Frontiers in Immunology

Tissue-Resident Memory T Cells in Cancer Immunosurveillance

(2019) Simone L. Park et al.   TRENDS IN IMMUNOLOGY

NCCN Guidelines Insights: Kidney Cancer, Version 2.2020

(2019) Robert J. Motzer et al.   Journal of the National Comprehensive Cancer Network

A clonal expression biomarker associates with lung cancer mortality

(2019) Dhruva Biswas et al.   NATURE MEDICINE

Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy

(2019) Diego Chowell et al.   NATURE MEDICINE

Tissue-resident memory CD8+ T cells amplify anti-tumor immunity by triggering antigen spreading through dendritic cells

(2019) Evelyn Menares et al.   Nature Communications

Adenosine 2A Receptor Blockade as an Immunotherapy for Treatment-Refractory Renal Cell Cancer

(2019) Lawrence Fong et al.   Cancer Discovery

Macrophage-derived granulin drives resistance to immune checkpoint inhibition in metastatic pancreatic cancer

(2018) Valeria Quaranta et al.   CANCER RESEARCH

Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer

(2018) Allen W. Zhang et al.   CELL

Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal

(2018) Samra Turajlic et al.   CELL

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

(2018) Samra Turajlic et al.   CELL

Tissue-resident memory T cells are epigenetically cytotoxic with signs of exhaustion in human urinary bladder cancer

(2018) Ciputra Adijaya Hartana et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection

(2018) Federica Pierini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma

(2018) David F. McDermott et al.   NATURE MEDICINE

Nivolumab plus Ipilimumab versus Sunitinib in Advanced Renal-Cell Carcinoma

(2018) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

(2018) Diana Miao et al.   SCIENCE

Tissue-Resident Memory CD8+ T Cells: From Phenotype to Function

(2018) David J. Topham et al.   Frontiers in Immunology

Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity

(2018) William S DeWitt et al.   eLife

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

CD169+ Macrophages Capture and Dendritic Cells Instruct: The Interplay of the Gatekeeper and the General of the Immune System

(2018) Joanna Grabowska et al.   Frontiers in Immunology

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA–seq data

(2017) Bo Li et al.   NATURE GENETICS

Induction of resident memory T cells enhances the efficacy of cancer vaccine

(2017) Mevyn Nizard et al.   Nature Communications

Role of the CXCL8-CXCR1/2 Axis in Cancer and Inflammatory Diseases

(2017) Helen Ha et al.   Theranostics

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Cancer Immunosurveillance by Tissue-Resident Innate Lymphoid Cells and Innate-like T Cells

(2016) Saïda Dadi et al.   CELL

CD103 defines intraepithelial CD8+ PD1+ tumour-infiltrating lymphocytes of prognostic significance in endometrial adenocarcinoma

(2016) Hagma H. Workel et al.   EUROPEAN JOURNAL OF CANCER

Atezolizumab versus docetaxel for patients with previously treated non-small-cell lung cancer (POPLAR): a multicentre, open-label, phase 2 randomised controlled trial

(2016) Louis Fehrenbacher et al.   LANCET

Macrophage-secreted granulin supports pancreatic cancer metastasis by inducing liver fibrosis

(2016) Sebastian R. Nielsen et al.   NATURE CELL BIOLOGY

Landscape of tumor-infiltrating T cell repertoire of human cancers

(2016) Bo Li et al.   NATURE GENETICS

Granulocyte macrophage colony-stimulating factor predicts postoperative recurrence of clear-cell renal cell carcinoma

(2016) Yuan Chang et al.   Oncotarget

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

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

(2015) Michael S. Rooney et al.   CELL

Cyclooxygenase-Dependent Tumor Growth through Evasion of Immunity

(2015) Santiago Zelenay et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

FLT1 signaling in metastasis-associated macrophages activates an inflammatory signature that promotes breast cancer metastasis

(2015) Bin-Zhi Qian et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CD8+CD103+Tumor–Infiltrating Lymphocytes Are Tumor-Specific Tissue-Resident Memory T Cells and a Prognostic Factor for Survival in Lung Cancer Patients

(2015) Fayçal Djenidi et al.   JOURNAL OF IMMUNOLOGY

Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma

(2015) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Immune biomarkers associated with clinical benefit from atezolizumab (MPDL3280a; anti-PD-L1) in advanced urothelial bladder cancer (UBC)

(2015) Thomas Powles et al.   Journal for ImmunoTherapy of Cancer

RGS5 promotes arterial growth during arteriogenesis

(2014) C. Arnold et al.   EMBO Molecular Medicine

The CXCL8/IL-8 chemokine family and its receptors in inflammatory diseases

(2014) Remo C Russo et al.   Expert Review of Clinical Immunology

Tissue-Resident Exhausted Effector Memory CD8+ T Cells Accumulate in the Retina during Chronic Experimental Autoimmune Uveoretinitis

(2014) J. Boldison et al.   JOURNAL OF IMMUNOLOGY

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

The cellular and molecular origin of tumor-associated macrophages

(2014) R. A. Franklin et al.   SCIENCE

The Dendritic Cell Lineage: Ontogeny and Function of Dendritic Cells and Their Subsets in the Steady State and the Inflamed Setting

(2013) Miriam Merad et al.   Annual Review of Immunology

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Identification and Analysis of In Vivo VEGF Downstream Markers Link VEGF Pathway Activity with Efficacy of Anti-VEGF Therapies

(2013) M. J. Brauer et al.   CLINICAL CANCER RESEARCH

Spatiotemporal Dynamics of Intratumoral Immune Cells Reveal the Immune Landscape in Human Cancer

(2013) Gabriela Bindea et al.   IMMUNITY

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Macrophage biology in development, homeostasis and disease

(2013) Thomas A. Wynn et al.   NATURE

Pazopanib versus Sunitinib in Metastatic Renal-Cell Carcinoma

(2013) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2013) Kosuke Yoshihara et al.   Nature Communications

Sequence analysis of T-cell repertoires in health and disease

(2013) Daniel J Woodsworth et al.   Genome Medicine

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

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

(2012) Douglas Hanahan et al.   CANCER CELL

The structural basis of αβ T-lineage immune recognition: TCR docking topologies, mechanotransduction, and co-receptor function

(2012) Jia-huai Wang et al.   IMMUNOLOGICAL REVIEWS

The pro- and anti-inflammatory properties of the cytokine interleukin-6

(2011) Jürgen Scheller et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

A Mechanism for TCR Sharing between T Cell Subsets and Individuals Revealed by Pyrosequencing

(2011) Vanessa Venturi et al.   JOURNAL OF IMMUNOLOGY

Interactions between lymphocytes and myeloid cells regulate pro- versus anti-tumor immunity

(2010) David G. DeNardo et al.   CANCER AND METASTASIS REVIEWS

Macrophage Diversity Enhances Tumor Progression and Metastasis

(2010) Bin-Zhi Qian et al.   CELL

The Mysterious Ways of the Chemokine CXCL5

(2010) Ekaterina K. Koltsova et al.   IMMUNITY

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE