Single‐cell dissection of cervical cancer reveals key subsets of the tumor immune microenvironment

Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer

(2022) Namrata S. Patil et al.   CANCER CELL

Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer

(2022) Maxime Meylan et al.   IMMUNITY

Pembrolizumab in soft-tissue sarcomas with tertiary lymphoid structures: a phase 2 PEMBROSARC trial cohort

(2022) A. Italiano et al.   NATURE MEDICINE

B cells and tertiary lymphoid structures as determinants of tumour immune contexture and clinical outcome

(2022) Wolf H. Fridman et al.   Nature Reviews Clinical Oncology

Tertiary lymphoid structures critical for prognosis in endometrial cancer patients

(2022) Nanda Horeweg et al.   Nature Communications

Interleukin-21, acting beyond the immunological synapse, independently controls T follicular helper and germinal center B cells

(2022) Isaak Quast et al.   IMMUNITY

Single cell sequencing reveals trajectory of tumor-infiltrating lymphocyte states in pancreatic cancer

(2022) Aislyn Schalck et al.   Cancer Discovery

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

(2021) Ruli Gao et al.   NATURE BIOTECHNOLOGY

Transcriptional and Metabolic Control of Memory B Cells and Plasma Cells

(2021) Tyler J. Ripperger et al.   Annual Review of Immunology

Insights Gained from Single-Cell Analysis of Immune Cells in the Tumor Microenvironment

(2021) Xianwen Ren et al.   Annual Review of Immunology

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

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

(2021) Sijin Cheng et al.   CELL

TCR-engineered T cells targeting E7 for patients with metastatic HPV-associated epithelial cancers

(2021) Nisha B. Nagarsheth et al.   NATURE MEDICINE

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Single-cell dissection of cellular components and interactions shaping the tumor immune phenotypes in ovarian cancer

(2021) Milena Hornburg et al.   CANCER CELL

TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data

(2021) Li Song et al.   NATURE METHODS

Tumor Immunity and Immunotherapy for HPV-Related Cancers

(2021) Achraf A. Shamseddine et al.   Cancer Discovery

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Cancer‐associated fibroblasts: Key players in shaping the tumor immune microenvironment

(2021) Mélanie Desbois et al.   IMMUNOLOGICAL REVIEWS

Functional HPV-specific PD-1+ stem-like CD8 T cells in head and neck cancer

(2021) Christiane S. Eberhardt et al.   NATURE

Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells

(2021) María Casanova-Acebes et al.   NATURE

Pembrolizumab for Persistent, Recurrent, or Metastatic Cervical Cancer

(2021) Nicoletta Colombo et al.   NEW ENGLAND JOURNAL OF MEDICINE

PD-1+CXCR5−CD4+ Th-CXCL13 cell subset drives B cells into tertiary lymphoid structures of nasopharyngeal carcinoma

(2021) Jiang-Ping Li et al.   Journal for ImmunoTherapy of Cancer

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

(2021) Can Cui et al.   CELL

Pan-cancer single-cell landscape of tumor-infiltrating T cells

(2021) Liangtao Zheng et al.   SCIENCE

scCODA is a Bayesian model for compositional single-cell data analysis

(2021) M. Büttner et al.   Nature Communications

An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates

(2020) Jermaine Goveia et al.   CANCER CELL

Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer

(2020) Anthony R. Cillo et al.   IMMUNITY

Tertiary lymphoid structures improve immunotherapy and survival in melanoma

(2020) Rita Cabrita et al.   NATURE

Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma

(2020) Benjamin P. Fairfax et al.   NATURE MEDICINE

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

B Cells Improve Overall Survival in HPV-Associated Squamous Cell Carcinomas and Are Activated by Radiation and PD-1 Blockade

(2020) Sangwoo S. Kim et al.   CLINICAL CANCER RESEARCH

The multifarious roles of the chemokine CXCL14 in cancer progression and immune responses

(2020) Joseph A. Westrich et al.   MOLECULAR CARCINOGENESIS

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

(2020) Andrew L. Ji et al.   CELL

Stromal cell diversity associated with immune evasion in human triple‐negative breast cancer

(2020) Sunny Z Wu et al.   EMBO JOURNAL

Omics-wide quantitative B-cell infiltration analyses identify GPR18 for human cancer prognosis with superiority over CD20

(2020) Yuchen Liu et al.   Communications Biology

Baseline immunity and impact of chemotherapy on immune microenvironment in cervical cancer

(2020) Yi Zhang et al.   BRITISH JOURNAL OF CANCER

Single-cell transcriptomic analysis defines the interplay between tumor cells, viral infection, and the microenvironment in nasopharyngeal carcinoma

(2020) Shanzhao Jin et al.   CELL RESEARCH

Camrelizumab Plus Apatinib in Patients With Advanced Cervical Cancer (CLAP): A Multicenter, Open-Label, Single-Arm, Phase II Trial

(2020) Chunyan Lan et al.   JOURNAL OF CLINICAL ONCOLOGY

Single-cell RNA sequencing highlights the role of inflammatory cancer-associated fibroblasts in bladder urothelial carcinoma

(2020) Zhaohui Chen et al.   Nature Communications

Infiltrating pattern and prognostic value of tertiary lymphoid structures in resected non-functional pancreatic neuroendocrine tumors

(2020) Wu-Hu Zhang et al.   Journal for ImmunoTherapy of Cancer

HPV post-infection microenvironment and cervical cancer

(2020) Yi Yuan et al.   CANCER LETTERS

Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma

(2020) Yunfan Sun et al.   CELL

Pembrolizumab plus GX-188E therapeutic DNA vaccine in patients with HPV-16-positive or HPV-18-positive advanced cervical cancer: interim results of a single-arm, phase 2 trial

(2020) Jin Won Youn et al.   LANCET ONCOLOGY

Defining HPV-specific B cell responses in patients with head and neck cancer

(2020) Andreas Wieland et al.   NATURE

3D models in the new era of immune oncology: focus on T cells, CAF and ECM

(2019) Francesca Di Modugno et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Cervical cancer-instructed stromal fibroblasts enhance IL-23 expression in dendritic cells to support expansion of Th17 cells

(2019) Barbara Walch-Rückheim et al.   CANCER RESEARCH

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

(2019) Rapolas Zilionis et al.   IMMUNITY

The hallmarks of CMV-specific CD8 T-cell differentiation

(2019) Sara P. H. van den Berg et al.   MEDICAL MICROBIOLOGY AND IMMUNOLOGY

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Key Molecular Events in Cervical Cancer Development

(2019) Shandra Devi Balasubramaniam et al.   Medicina-Lithuania

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

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

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

HPV16 drives cancer immune escape via NLRX1-mediated degradation of STING

(2019) Xiaobo Luo et al.   JOURNAL OF CLINICAL INVESTIGATION

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(2018) Stefano Serra et al.   JOURNAL OF CLINICAL PATHOLOGY

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates

(2018) Yannick Simoni et al.   NATURE

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

(2018) Hanjie Li et al.   CELL

Cancer immunoediting and resistance to T cell-based immunotherapy

(2018) Jake S. O’Donnell et al.   Nature Reviews Clinical Oncology

Local mutational diversity drives intratumoral immune heterogeneity in non-small cell lung cancer

(2018) Qingzhu Jia et al.   Nature Communications

Increased expression of PD-L1 by the human papillomavirus 16 E7 oncoprotein inhibits anticancer immunity

(2017) Chaoqi Liu et al.   Molecular Medicine Reports

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

(2017) Mikhail Shugay et al.   NUCLEIC ACIDS RESEARCH

Landscape of immunogenic tumor antigens in successful immunotherapy of virally induced epithelial cancer

(2017) Sanja Stevanović et al.   SCIENCE

Mast cells as therapeutic target in cancer

(2016) Domenico Ribatti   EUROPEAN JOURNAL OF PHARMACOLOGY

Tertiary lymphoid structures, drivers of the anti-tumor responses in human cancers

(2016) Marie-Caroline Dieu-Nosjean et al.   IMMUNOLOGICAL REVIEWS

The Papillomavirus Episteme: a major update to the papillomavirus sequence database

(2016) Koenraad Van Doorslaer et al.   NUCLEIC ACIDS RESEARCH

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

(2016) I. Tirosh et al.   SCIENCE

Tumor- and Neoantigen-Reactive T-cell Receptors Can Be Identified Based on Their Frequency in Fresh Tumor

(2016) A. Pasetto et al.   Cancer Immunology Research

Stromal Fibroblasts Induce CCL20 through IL6/C/EBP  to Support the Recruitment of Th17 Cells during Cervical Cancer Progression

(2015) B. Walch-Ruckheim et al.   CANCER RESEARCH

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Intramuscular Therapeutic Vaccination Targeting HPV16 Induces T Cell Responses That Localize in Mucosal Lesions

(2014) L. Maldonado et al.   Science Translational Medicine

High and Interrelated Rates of PD-L1+CD14+ Antigen-Presenting Cells and Regulatory T Cells Mark the Microenvironment of Metastatic Lymph Nodes from Patients with Cervical Cancer

(2014) A. M. Heeren et al.   Cancer Immunology Research

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Collective Invasion in Breast Cancer Requires a Conserved Basal Epithelial Program

(2013) Kevin J. Cheung et al.   CELL

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Therapeutic vaccination against human papilloma virus induced malignancies

(2011) Sjoerd H van der Burg et al.   CURRENT OPINION IN IMMUNOLOGY

A TNF-Regulated Recombinatorial Macrophage Immune Receptor Implicated in Granuloma Formation in Tuberculosis

(2011) Alexander W. Beham et al.   PLoS Pathogens

An Unexpectedly Large Polyclonal Repertoire of HPV-Specific T Cells Is Poised for Action in Patients with Cervical Cancer

(2010) Peggy J. de Vos van Steenwijk et al.   CANCER RESEARCH

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

(2009) David A. Barbie et al.   NATURE