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

Liver tumour immune microenvironment subtypes and neutrophil heterogeneity

(2022) Ruidong Xue et al.   NATURE

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

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

(2021) Hyuna Sung et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

(2021) Kevin Bi et al.   CANCER CELL

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

(2021) Sijin Cheng et al.   CELL

Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution

(2021) Yang Liu et al.   Nature Communications

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Neutrophil elastase selectively kills cancer cells and attenuates tumorigenesis

(2021) Chang Cui et al.   CELL

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

(2021) Ayse Bassez et al.   NATURE MEDICINE

Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers

(2021) Justina X. Caushi et al.   NATURE

Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

(2021) Giacomo Oliveira et al.   NATURE

Neoantigen-driven B cell and CD4 T follicular helper cell collaboration promotes anti-tumor CD8 T cell responses

(2021) Can Cui et al.   CELL

Randomized phase II trial evaluating treatment with EGFR-TKI associated with anti-estrogen in women with non-squamous advanced stage NSCLC: IFCT-1003 LADIE trial

(2020) Julien Mazieres et al.   CLINICAL CANCER RESEARCH

IASLC MULTIDISCIPLINARY RECOMMENDATIONS FOR PATHOLOGIC ASSESSMENT OF LUNG CANCER RESECTION SPECIMENS FOLLOWING NEOADJUVANT THERAPY

(2020) William D. Travis et al.   Journal of Thoracic Oncology

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

B cells and tertiary lymphoid structures promote immunotherapy response

(2020) Beth A. Helmink et al.   NATURE

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

(2020) Mirjana Efremova et al.   Nature Protocols

Complement Signals Determine Opposite Effects of B Cells in Chemotherapy-Induced Immunity

(2020) Yiwen Lu et al.   CELL

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

Elevated serum interleukin-8 is associated with enhanced intratumor neutrophils and reduced clinical benefit of immune-checkpoint inhibitors

(2020) Kurt A. Schalper et al.   NATURE MEDICINE

Cancer cell-intrinsic expression of MHC II in lung cancer cell lines is actively restricted by MEK/ERK signaling and epigenetic mechanisms

(2020) Alexander J Neuwelt et al.   Journal for ImmunoTherapy of Cancer

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Neoadjuvant chemotherapy and nivolumab in resectable non-small-cell lung cancer (NADIM): an open-label, multicentre, single-arm, phase 2 trial

(2020) Mariano Provencio et al.   LANCET ONCOLOGY

Efficacy and safety of neoadjuvant immunotherapy in resectable nonsmall cell lung cancer: A meta-analysis

(2020) Xiao-hui Jia et al.   LUNG CANCER

Reactivation of dormant tumor cells by modified lipids derived from stress-activated neutrophils

(2020) Michela Perego et al.   Science Translational Medicine

Tumor-Infiltrating Natural Killer Cells

(2020) Beatriz Cózar et al.   Cancer Discovery

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

CFP suppresses breast cancer cell growth by TES-mediated upregulation of the transcription factor DDIT3

(2019) Ines Block et al.   ONCOGENE

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

(2019) Xindong Liu et al.   NATURE

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

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Pembrolizumab versus chemotherapy for previously untreated, PD-L1-expressing, locally advanced or metastatic non-small-cell lung cancer (KEYNOTE-042): a randomised, open-label, controlled, phase 3 trial

(2019) Tony S K Mok et al.   LANCET

GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis

(2019) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

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

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

The estrogen pathway as a modulator of response to immunotherapy

(2019) Maria A Velez et al.   Immunotherapy

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

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

Metabolic adaptability in metastatic breast cancer by AKR1B10-dependent balancing of glycolysis and fatty acid oxidation

(2019) Antoinette van Weverwijk et al.   Nature Communications

MHC-II neoantigens shape tumour immunity and response to immunotherapy

(2019) Elise Alspach et al.   NATURE

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

(2019) David Liu et al.   NATURE MEDICINE

Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma

(2019) Sangeeta Goswami et al.   NATURE MEDICINE

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

IRAK1 Augments Cancer Stemness and Drug Resistance via the AP-1/AKR1B10 Signaling Cascade in Hepatocellular Carcinoma

(2018) Bowie Y. Cheng et al.   CANCER RESEARCH

Cancer immunotherapy efficacy and patients' sex: a systematic review and meta-analysis

(2018) Fabio Conforti et al.   LANCET ONCOLOGY

Randomized phase II study of fulvestrant and erlotinib compared with erlotinib alone in patients with advanced or metastatic non-small cell lung cancer

(2018) Edward B. Garon et al.   LUNG CANCER

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Understanding the tumor immune microenvironment (TIME) for effective therapy

(2018) Mikhail Binnewies et al.   NATURE MEDICINE

Neoadjuvant PD-1 Blockade in Resectable Lung Cancer

(2018) Patrick M. Forde et al.   NEW ENGLAND JOURNAL OF MEDICINE

S100A8/A9 in Inflammation

(2018) Siwen Wang et al.   Frontiers in Immunology

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Alveolar Macrophages in the Resolution of Inflammation, Tissue Repair, and Tolerance to Infection

(2018) Benoit Allard et al.   Frontiers in Immunology

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

Biological Consequences of Major Histocompatibility Class-II Expression by Tumor Cells in Cancer

(2018) Margaret L Axelrod et al.   CLINICAL CANCER RESEARCH

Upregulation of PD-L1 by SPP1 mediates macrophage polarization and facilitates immune escape in lung adenocarcinoma

(2017) Yan Zhang et al.   EXPERIMENTAL CELL RESEARCH

Intermediate Molecular Mass Hyaluronan and CD44 Receptor Interactions Enhance Neutrophil Phagocytosis and IL-8 Production via p38- and ERK1/2-MAPK Signalling Pathways

(2017) Cheng-Hsun Lu et al.   INFLAMMATION

AKR1B1 promotes basal-like breast cancer progression by a positive feedback loop that activates the EMT program

(2017) Xuebiao Wu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor–neutralizing therapy in patients with inflammatory bowel disease

(2017) Nathaniel R West et al.   NATURE MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Neutrophils dominate the immune cell composition in non-small cell lung cancer

(2017) Julia Kargl et al.   Nature Communications

FcRL4 Expression Identifies a Pro-inflammatory B Cell Subset in Viremic HIV-Infected Subjects

(2017) Basile Siewe et al.   Frontiers in 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

Tumor Cell–Independent Estrogen Signaling Drives Disease Progression through Mobilization of Myeloid-Derived Suppressor Cells

(2016) Nikolaos Svoronos et al.   Cancer Discovery

CCL2 and CCL5 Are Novel Therapeutic Targets for Estrogen-Dependent Breast Cancer

(2015) S. Svensson et al.   CLINICAL CANCER RESEARCH

Selenoprotein P influences colitis-induced tumorigenesis by mediating stemness and oxidative damage

(2015) Caitlyn W. Barrett et al.   JOURNAL OF CLINICAL INVESTIGATION

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Patrolling monocytes control tumor metastasis to the lung

(2015) R. N. Hanna et al.   SCIENCE

Expression of FcRL4 defines a pro-inflammatory, RANKL-producing B cell subset in rheumatoid arthritis

(2014) L Yeo et al.   ANNALS OF THE RHEUMATIC DISEASES

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Non-small-cell lung cancer

(2011) Peter Goldstraw et al.   LANCET

Synuclein γ Stimulates Membrane-Initiated Estrogen Signaling by Chaperoning Estrogen Receptor (ER)-α36, a Variant of ER-α

(2010) Yuenian Eric Shi et al.   AMERICAN JOURNAL OF PATHOLOGY

Human Cytosolic Hydroxysteroid Dehydrogenases of the Aldo-ketoreductase Superfamily Catalyze Reduction of Conjugated Steroids

(2009) Yi Jin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY