Single-cell RNA sequencing reveals the tumor microenvironment and facilitates strategic choices to circumvent treatment failure in a chemorefractory bladder cancer patient

Personalised Medicine for Advanced Urothelial Cancer: What is the Right Way to Identify the Right Patient for the Right Treatment?

(2019) Simon J. Crabb   EUROPEAN UROLOGY

Targeting Tumor-Associated Macrophages in Cancer

(2019) Paulina Pathria et al.   TRENDS IN IMMUNOLOGY

Application of Cancer Organoid Model for Drug Screening and Personalized Therapy

(2019) Jumpei Kondo et al.   Cells

Cancer-Associated Fibroblasts Build and Secure the Tumor Microenvironment

(2019) Tianyi Liu et al.   Frontiers in Cell and Developmental Biology

Immune Responses in Bladder Cancer-Role of Immune Cell Populations, Prognostic Factors and Therapeutic Implications

(2019) Magdalene Joseph et al.   Frontiers in Oncology

Humanized Mice as Unique Tools for Human-Specific Studies

(2018) Kylie Su Mei Yong et al.   ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS

T Cell Dysfunction in Cancer

(2018) Daniela S. Thommen et al.   CANCER CELL

Immune checkpoint inhibitors for metastatic bladder cancer

(2018) Francesco Massari et al.   CANCER TREATMENT REVIEWS

European Association of Urology Guidelines on Upper Urinary Tract Urothelial Carcinoma: 2017 Update

(2018) Morgan Rouprêt et al.   EUROPEAN UROLOGY

Next generation of immune checkpoint therapy in cancer: new developments and challenges

(2018) Julian A. Marin-Acevedo et al.   Journal of Hematology & Oncology

Atezolizumab versus chemotherapy in patients with platinum-treated locally advanced or metastatic urothelial carcinoma (IMvigor211): a multicentre, open-label, phase 3 randomised controlled trial

(2018) Thomas Powles et al.   LANCET

Understanding the tumor immune microenvironment (TIME) for effective therapy

(2018) Mikhail Binnewies et al.   NATURE MEDICINE

Single-Cell Deconvolution of Fibroblast Heterogeneity in Mouse Pulmonary Fibrosis

(2018) Ting Xie et al.   Cell Reports

Bladder Cancer: New Insights into Its Molecular Pathology

(2018) Kentaro Inamura   Cancers

Precision medicine and bladder cancer heterogeneity

(2018) Guofeng Ma et al.   BULLETIN DU CANCER

Fundamental Mechanisms of Immune Checkpoint Blockade Therapy

(2018) Spencer C. Wei et al.   Cancer Discovery

Mutational analysis of 472 urothelial carcinoma across grades and anatomic sites

(2018) Amin H Nassar et al.   CLINICAL CANCER RESEARCH

Molecular tumor heterogeneity in muscle invasive bladder cancer: Biomarkers, subtypes, and implications for therapy

(2018) Jose Batista da Costa et al.   UROLOGIC ONCOLOGY-SEMINARS AND ORIGINAL INVESTIGATIONS

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

(2018) Manu P. Kumar et al.   Cell Reports

Updated 2016 EAU Guidelines on Muscle-invasive and Metastatic Bladder Cancer

(2017) J. Alfred Witjes et al.   EUROPEAN UROLOGY

Control of NK Cell Activation by Immune Checkpoint Molecules

(2017) Asma Beldi-Ferchiou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Spatiotemporal genomic architecture informs precision oncology in glioblastoma

(2017) Jin-Ku Lee et al.   NATURE GENETICS

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

Tumour-associated macrophages as treatment targets in oncology

(2017) Alberto Mantovani et al.   Nature Reviews Clinical Oncology

Single-cell analyses to tailor treatments

(2017) Alex K. Shalek et al.   Science Translational Medicine

Making Mouse Models That Reflect Human Immune Responses

(2017) Lili Tao et al.   TRENDS IN IMMUNOLOGY

Langerhans Cells – The Macrophage in Dendritic Cell Clothing

(2017) Thomas Doebel et al.   TRENDS IN IMMUNOLOGY

New tricks for human farnesyltransferase inhibitor: cancer and beyond

(2017) Jingyuan Wang et al.   MedChemComm

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

Reprogramming of Tumor-Associated Macrophages with Anticancer Therapies: Radiotherapy versus Chemo- and Immunotherapies

(2017) Géraldine Genard et al.   Frontiers in Immunology

Midkine derived from cancer-associated fibroblasts promotes cisplatin-resistance via up-regulation of the expression of lncRNA ANRIL in tumour cells

(2017) Dongya Zhang et al.   Scientific Reports

Turning tumour cells into antigen presenting cells: The next step to improve cancer immunotherapy?

(2016) Marie de Charette et al.   EUROPEAN JOURNAL OF CANCER

Intra-tumour heterogeneity - going beyond genetics

(2016) Francisco Caiado et al.   FEBS Journal

RAS isoforms and mutations in cancer at a glance

(2016) G. Aaron Hobbs et al.   JOURNAL OF CELL SCIENCE

Second Line Chemotherapy for Advanced and Metastatic Urothelial Carcinoma: Vinflunine and Beyond—A Comprehensive Review of the Current Literature

(2016) Christoph Oing et al.   JOURNAL OF UROLOGY

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial

(2016) Jonathan E Rosenberg et al.   LANCET

Clonal evolution of glioblastoma under therapy

(2016) Jiguang Wang et al.   NATURE GENETICS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Translating Mouse Models

(2016) Rani S. Sellers   TOXICOLOGIC PATHOLOGY

CXCL1-Mediated Interaction of Cancer Cells with Tumor-Associated Macrophages and Cancer-Associated Fibroblasts Promotes Tumor Progression in Human Bladder Cancer

(2016) Makito Miyake et al.   NEOPLASIA

JUN dependency in distinct early and late BRAF inhibition adaptation states of melanoma

(2016) Bjoern Titz et al.   Cell Discovery

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

Harnessing adaptive natural killer cells in cancer immunotherapy

(2015) Lisa L. Liu et al.   Molecular Oncology

Stromal contribution to the colorectal cancer transcriptome

(2015) Claudio Isella et al.   NATURE GENETICS

The prognostic effect of tumour-infiltrating lymphocytic subpopulations in bladder cancer

(2015) T. Horn et al.   WORLD JOURNAL OF UROLOGY

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

β2-Microglobulin-mediated Signaling as a Target for Cancer Therapy

(2014) Takeo Nomura et al.   Anti-Cancer Agents in Medicinal Chemistry

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Identification of Distinct Basal and Luminal Subtypes of Muscle-Invasive Bladder Cancer with Different Sensitivities to Frontline Chemotherapy

(2014) Woonyoung Choi et al.   CANCER CELL

Patient-Derived Xenografts from Non-Small Cell Lung Cancer Brain Metastases Are Valuable Translational Platforms for the Development of Personalized Targeted Therapy

(2014) H. W. Lee et al.   CLINICAL CANCER RESEARCH

The Erk2 MAPK Regulates CD8 T Cell Proliferation and Survival

(2014) W. N. D'Souza et al.   JOURNAL OF IMMUNOLOGY

Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma

(2014) Chong Sun et al.   NATURE

Drugging the undruggable RAS: Mission Possible?

(2014) Adrienne D. Cox et al.   NATURE REVIEWS DRUG DISCOVERY

IGFBP7, a novel tumor stroma marker, with growth-promoting effects in colon cancer through a paracrine tumor–stroma interaction

(2014) C Rupp et al.   ONCOGENE

Influence of tumour micro-environment heterogeneity on therapeutic response

(2013) Melissa R. Junttila et al.   NATURE

Cancer-associated fibroblasts and M2-polarized macrophages synergize during prostate carcinoma progression

(2013) G Comito et al.   ONCOGENE

Langerhans cell histiocytosis of the urinary bladder in a patient with bladder cancer previously treated with intravesical Bacillus Calmette–Guérin therapy

(2013) Satoe Numakura et al.   PATHOLOGY RESEARCH AND PRACTICE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Epithelial Plasticity, Cancer Stem Cells, and the Tumor-Supportive Stroma in Bladder Carcinoma

(2012) G. van der Horst et al.   MOLECULAR CANCER RESEARCH

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Tipifarnib-mediated suppression of T-bet-dependent signaling pathways

(2011) Fanqi Bai et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Notch Signaling Activated by Replication Stress-Induced Expression of Midkine Drives Epithelial-Mesenchymal Transition and Chemoresistance in Pancreatic Cancer

(2011) C. Gungor et al.   CANCER RESEARCH

Second-line systemic therapy and emerging drugs for metastatic transitional-cell carcinoma of the urothelium

(2010) Guru Sonpavde et al.   LANCET ONCOLOGY

FGFR3, HRAS, KRAS, NRAS and PIK3CA Mutations in Bladder Cancer and Their Potential as Biomarkers for Surveillance and Therapy

(2010) Lucie C. Kompier et al.   PLoS One

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS