Lymph node colonization induces tumor-immune tolerance to promote distant metastasis

Interferon Receptor Trafficking and Signaling: Journey to the Cross Roads

(2021) Natacha Zanin et al.   Frontiers in Immunology

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

Attenuation of TCR-induced transcription by Bach2 controls regulatory T cell differentiation and homeostasis

(2020) Tom Sidwell et al.   Nature Communications

Tumor invasion in draining lymph nodes is associated with Treg accumulation in breast cancer patients

(2020) Nicolas Gonzalo Núñez et al.   Nature Communications

Tumor-educated B cells selectively promote breast cancer lymph node metastasis by HSPA4-targeting IgG

(2019) Yan Gu et al.   NATURE MEDICINE

The role of SOX family members in solid tumours and metastasis

(2019) Daniela Grimm et al.   SEMINARS IN CANCER BIOLOGY

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

(2019) Mikhail Binnewies et al.   CELL

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

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

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

Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade

(2019) Joseph L. Benci et al.   CELL

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

TGFβ drives immune evasion in genetically reconstituted colon cancer metastasis

(2018) Daniele V. F. Tauriello et al.   NATURE

Chromosomal instability drives metastasis through a cytosolic DNA response

(2018) Samuel F. Bakhoum et al.   NATURE

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Lymph node metastases can invade local blood vessels, exit the node, and colonize distant organs in mice

(2018) Ethel R. Pereira et al.   SCIENCE

Lymph node blood vessels provide exit routes for metastatic tumor cell dissemination in mice

(2018) M. Brown et al.   SCIENCE

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

(2018) Sanjeev Mariathasan et al.   NATURE

Minimal functional driver gene heterogeneity among untreated metastases

(2018) Johannes G. Reiter et al.   SCIENCE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Interleukin 2 modulates thymic-derived regulatory T cell epigenetic landscape

(2018) Laurent Chorro et al.   Nature Communications

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

The regulatory network behind MHC class I expression

(2017) Marlieke L.M. Jongsma et al.   MOLECULAR IMMUNOLOGY

Limited heterogeneity of known driver gene mutations among the metastases of individual patients with pancreatic cancer

(2017) Alvin P Makohon-Moore et al.   NATURE GENETICS

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Completion Dissection or Observation for Sentinel-Node Metastasis in Melanoma

(2017) Mark B. Faries et al.   NEW ENGLAND JOURNAL OF MEDICINE

Origins of lymphatic and distant metastases in human colorectal cancer

(2017) Kamila Naxerova et al.   SCIENCE

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

(2017) Moshe Sade-Feldman et al.   Nature Communications

Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses

(2017) Andrew E. Shaw et al.   PLOS BIOLOGY

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

Critical Role for CD103 + /CD141 + Dendritic Cells Bearing CCR7 for Tumor Antigen Trafficking and Priming of T Cell Immunity in Melanoma

(2016) Edward W. Roberts et al.   CANCER CELL

Tumor Interferon Signaling Regulates a Multigenic Resistance Program to Immune Checkpoint Blockade

(2016) Joseph L. Benci et al.   CELL

Metastatic Latency and Immune Evasion through Autocrine Inhibition of WNT

(2016) Srinivas Malladi et al.   CELL

Combination Cancer Therapies with Immune Checkpoint Blockade: Convergence on Interferon Signaling

(2016) Andy J. Minn et al.   CELL

Genomic Profiling of Patient-Derived Xenografts for Lung Cancer Identifies B2M Inactivation Impairing Immunorecognition

(2016) Carolina Pereira et al.   CLINICAL CANCER RESEARCH

Expansion and Activation of CD103 + Dendritic Cell Progenitors at the Tumor Site Enhances Tumor Responses to Therapeutic PD-L1 and BRAF Inhibition

(2016) Hélène Salmon et al.   IMMUNITY

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

SCS macrophages suppress melanoma by restricting tumor-derived vesicle-B cell interactions

(2016) F. Pucci et al.   SCIENCE

Comparing nodal versus bony metastatic spread using tumour phylogenies

(2016) Stefano Mangiola et al.   Scientific Reports

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

A shed NKG2D ligand that promotes natural killer cell activation and tumor rejection

(2015) W. Deng et al.   SCIENCE

The lymph node microenvironment and its role in the progression of metastatic cancer

(2015) Ethel R. Pereira et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

SOX2 boosts major tumor progression genes in prostate cancer and is a functional biomarker of lymph node metastasis

(2015) Marco Vincenzo Russo et al.   Oncotarget

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Continuous requirement for the TCR in regulatory T cell function

(2014) Andrew G Levine et al.   NATURE IMMUNOLOGY

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Genenames.org: the HGNC resources in 2015

(2014) Kristian A. Gray et al.   NUCLEIC ACIDS RESEARCH

Lymph node-independent liver metastasis in a model of metastatic colorectal cancer

(2014) Ida B. Enquist et al.   Nature Communications

Advanced Heat Map and Clustering Analysis Using Heatmap3

(2014) Shilin Zhao et al.   Biomed Research International

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

Tracking the clonal origin of lethal prostate cancer

(2013) Michael C. Haffner et al.   JOURNAL OF CLINICAL INVESTIGATION

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Up-Regulation of PD-L1, IDO, and Tregs in the Melanoma Tumor Microenvironment Is Driven by CD8+ T Cells

(2013) S. Spranger et al.   Science Translational Medicine

Genetic Ablation of SOX18 Function Suppresses Tumor Lymphangiogenesis and Metastasis of Melanoma in Mice

(2012) T. Duong et al.   CANCER RESEARCH

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Safety and Activity of Anti–PD-L1 Antibody in Patients with Advanced Cancer

(2012) Julie R. Brahmer et al.   NEW ENGLAND JOURNAL OF MEDICINE

INTERFEROME v2.0: an updated database of annotated interferon-regulated genes

(2012) Irina Rusinova et al.   NUCLEIC ACIDS RESEARCH

Colocalization of Inflammatory Response with B7-H1 Expression in Human Melanocytic Lesions Supports an Adaptive Resistance Mechanism of Immune Escape

(2012) J. M. Taube et al.   Science Translational Medicine

VEGF-C Promotes Immune Tolerance in B16 Melanomas and Cross-Presentation of Tumor Antigen by Lymph Node Lymphatics

(2012) Amanda W. Lund et al.   Cell Reports

SOX2 expression correlates with lymph-node metastases and distant spread in right-sided colon cancer

(2011) Jens Neumann et al.   BMC CANCER

ERK1/2 Regulation of CD44 Modulates Oral Cancer Aggressiveness

(2011) N. P. Judd et al.   CANCER RESEARCH

Impact of nodal status and tumor burden in sentinel lymph nodes on the clinical outcomes of cancer patients

(2011) Stanley P.L. Leong et al.   JOURNAL OF SURGICAL ONCOLOGY

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Cancer Immunoediting: Integrating Immunity's Roles in Cancer Suppression and Promotion

(2011) R. D. Schreiber et al.   SCIENCE

A Perspective on Cancer Cell Metastasis

(2011) C. L. Chaffer et al.   SCIENCE

Development of an Orthotopic Model of Invasive Pancreatic Cancer in an Immunocompetent Murine Host

(2010) W. W. Tseng et al.   CLINICAL CANCER RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Kupfer-type immunological synapse characteristics do not predict anti-brain tumor cytolytic T-cell function in vivo

(2010) J. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

WNT/TCF Signaling through LEF1 and HOXB9 Mediates Lung Adenocarcinoma Metastasis

(2009) Don X. Nguyen et al.   CELL

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Genes that mediate breast cancer metastasis to the brain

(2009) Paula D. Bos et al.   NATURE

BrafV600E cooperates with Pten loss to induce metastatic melanoma

(2009) David Dankort et al.   NATURE GENETICS

Hue-shifted monomeric variants of Clavularia cyan fluorescent protein: identification of the molecular determinants of color and applications in fluorescence imaging

(2008) Hui-wang Ai et al.   BMC BIOLOGY

TGFβ in Cancer

(2008) Joan Massagué   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY