Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis

High-fat diet activates a PPAR-δ program to enhance intestinal stem cell function

(2021) Semir Beyaz et al.   Cell Stem Cell

DolphinNext: a distributed data processing platform for high throughput genomics

(2020) Onur Yukselen et al.   BMC GENOMICS

Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis

(2020) Timur Tuganbaev et al.   CELL

DEBrowser: interactive differential expression analysis and visualization tool for count data

(2019) Alper Kucukural et al.   BMC GENOMICS

WNT/β-catenin pathway activation correlates with immune exclusion across human cancers

(2019) Jason J. Luke et al.   CLINICAL CANCER RESEARCH

FXR Regulates Intestinal Cancer Stem Cell Proliferation

(2019) Ting Fu et al.   CELL

The nutritional environment determines which and how intestinal stem cells contribute to homeostasis and tumorigenesis

(2019) Wenge Li et al.   CARCINOGENESIS

T Cell Recruitment to the Intestinal Stem Cell Compartment Drives Immune-Mediated Intestinal Damage after Allogeneic Transplantation

(2019) Ya-Yuan Fu et al.   IMMUNITY

MHC Class II Antigen Presentation by the Intestinal Epithelium Initiates Graft-versus-Host Disease and Is Influenced by the Microbiota

(2019) Motoko Koyama et al.   IMMUNITY

Phospholipid Remodeling and Cholesterol Availability Regulate Intestinal Stemness and Tumorigenesis

(2018) Bo Wang et al.   Cell Stem Cell

Quiescent Tissue Stem Cells Evade Immune Surveillance

(2018) Judith Agudo et al.   IMMUNITY

An aberrant SREBP-dependent lipogenic program promotes metastatic prostate cancer

(2018) Ming Chen et al.   NATURE GENETICS

Colonoscopy-based colorectal cancer modeling in mice with CRISPR–Cas9 genome editing and organoid transplantation

(2018) Jatin Roper et al.   Nature Protocols

Genetic Mechanisms of Immune Evasion in Colorectal Cancer

(2018) Catherine S. Grasso et al.   Cancer Discovery

A Map of Toll-like Receptor Expression in the Intestinal Epithelium Reveals Distinct Spatial, Cell Type-Specific, and Temporal Patterns

(2018) April E. Price et al.   IMMUNITY

Two to Tango: Dialog between Immunity and Stem Cells in Health and Disease

(2018) Shruti Naik et al.   CELL

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation

(2018) Moshe Biton et al.   CELL

Discovery of common and rare genetic risk variants for colorectal cancer

(2018) Jeroen R. Huyghe et al.   NATURE GENETICS

Association Between Inflammatory Diet Pattern and Risk of Colorectal Carcinoma Subtypes Classified by Immune Responses to Tumor

(2017) Li Liu et al.   GASTROENTEROLOGY

Dietary Fat Intake and Lung Cancer Risk: A Pooled Analysis

(2017) Jae Jeong Yang et al.   JOURNAL OF CLINICAL ONCOLOGY

Treatment of Patients With Metastatic Cancer Using a Major Histocompatibility Complex Class II–Restricted T-Cell Receptor Targeting the Cancer Germline Antigen MAGE-A3

(2017) Yong-Chen Lu et al.   JOURNAL OF CLINICAL ONCOLOGY

Inflammatory memory sensitizes skin epithelial stem cells to tissue damage

(2017) Shruti Naik et al.   NATURE

In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis

(2017) Jatin Roper et al.   NATURE BIOTECHNOLOGY

Expression of the MHC class II in triple-negative breast cancer is associated with tumor-infiltrating lymphocytes and interferon signaling

(2017) In Ah Park et al.   PLoS One

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

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

CD4 CTL, a Cytotoxic Subset of CD4+ T Cells, Their Differentiation and Function

(2017) Arata Takeuchi et al.   Frontiers in Immunology

CML cells actively evade host immune surveillance through cytokine-mediated downregulation of MHC-II expression

(2016) Anuradha Tarafdar et al.   BLOOD

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Obesity and Cancer: The Oil that Feeds the Flame

(2016) Joan Font-Burgada et al.   Cell Metabolism

Molecular Pathways: Dietary Regulation of Stemness and Tumor Initiation by the PPAR-  Pathway

(2016) S. Beyaz et al.   CLINICAL CANCER RESEARCH

High-fat diet enhances stemness and tumorigenicity of intestinal progenitors

(2016) Semir Beyaz et al.   NATURE

Persistent microbiome alterations modulate the rate of post-dieting weight regain

(2016) Christoph A. Thaiss et al.   NATURE

Targeting metastasis-initiating cells through the fatty acid receptor CD36

(2016) Gloria Pascual et al.   NATURE

The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells

(2016) Semir Beyaz et al.   NATURE IMMUNOLOGY

High-fat diet modifies the PPAR-γ pathway leading to disruption of microbial and physiological ecosystem in murine small intestine

(2016) Julie Tomas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antimicrobial Defense of the Intestine

(2015) Sohini Mukherjee et al.   IMMUNITY

Idiotype-specific CD4+ T cells eradicate disseminated myeloma

(2015) O A Haabeth et al.   LEUKEMIA

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

Interleukin-22 promotes intestinal-stem-cell-mediated epithelial regeneration

(2015) Caroline A. Lindemans et al.   NATURE

Obesity and Diabetes: The Increased Risk of Cancer and Cancer-Related Mortality

(2015) Emily Jane Gallagher et al.   PHYSIOLOGICAL REVIEWS

High Fat Diet Causes Depletion of Intestinal Eosinophils Associated with Intestinal Permeability

(2015) Andrew M. F. Johnson et al.   PLoS One

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

Toll-like receptor expression in crypt epithelial cells, putative stem cells and intestinal myofibroblasts isolated from controls and patients with inflammatory bowel disease

(2014) M. Brown et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

NOD1 and NOD2: Signaling, Host Defense, and Inflammatory Disease

(2014) Roberta Caruso et al.   IMMUNITY

Cutting Edge: New Chimeric NOD2/TLR2 Adjuvant Drastically Increases Vaccine Immunogenicity

(2014) Vincent Pavot et al.   JOURNAL OF IMMUNOLOGY

High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity

(2014) Manon D. Schulz et al.   NATURE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Interferon-γ Induces Expression of MHC Class II on Intestinal Epithelial Cells and Protects Mice from Colitis

(2014) Christoph Thelemann et al.   PLoS One

Cancer Immunotherapy Based on Mutation-Specific CD4+ T Cells in a Patient with Epithelial Cancer

(2014) E. Tran et al.   SCIENCE

Allospecific Rejection of MHC Class I-Deficient Bone Marrow by CD8 T Cells

(2013) F. Haspot et al.   AMERICAN JOURNAL OF TRANSPLANTATION

The Intestinal Crypt, A Prototype Stem Cell Compartment

(2013) Hans Clevers   CELL

High- and Low-Fat Dairy Intake, Recurrence, and Mortality After Breast Cancer Diagnosis

(2013) C. H. Kroenke et al.   JNCI-Journal of the National Cancer Institute

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Secreted and Transmembrane 1A Is a Novel Co-Stimulatory Ligand

(2013) Duncan Howie et al.   PLoS One

Toll-like Receptor 4 Is Expressed on Intestinal Stem Cells and Regulates Their Proliferation and Apoptosis via the p53 Up-regulated Modulator of Apoptosis

(2012) Matthew D. Neal et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Induction of tumoricidal function in CD4+T cells is associated with concomitant memory and terminally differentiated phenotype

(2012) Daniel Hirschhorn-Cymerman et al.   JOURNAL OF EXPERIMENTAL MEDICINE

mTORC1 in the Paneth cell niche couples intestinal stem-cell function to calorie intake

(2012) Ömer H. Yilmaz et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Lineage Tracing Reveals Lgr5+ Stem Cell Activity in Mouse Intestinal Adenomas

(2012) A. G. Schepers et al.   SCIENCE

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

The Dual PI3K/mTOR Inhibitor NVP-BEZ235 Induces Tumor Regression in a Genetically Engineered Mouse Model of PIK3CA Wild-Type Colorectal Cancer

(2011) Jatin Roper et al.   PLoS One

Expression Regulation of Major Histocompatibility Complex Class I and Class II Encoding Genes

(2011) Peter J. van den Elsen   Frontiers in Immunology

CYT387, a novel JAK2 inhibitor, induces hematologic responses and normalizes inflammatory cytokines in murine myeloproliferative neoplasms

(2010) J. W. Tyner et al.   BLOOD

Regulation of major histocompatibility complex class II genes

(2010) Nancy M Choi et al.   CURRENT OPINION IN IMMUNOLOGY

Naive tumor-specific CD4+T cells differentiated in vivo eradicate established melanoma

(2010) Ying Xie et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Obesity and Cancer Risk: Recent Review and Evidence

(2010) Karen Basen-Engquist et al.   Current Oncology Reports

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The role of CD4 T cell help for CD8 CTL activation

(2009) Sheng Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Dietary Induction of Colonic Tumors in a Mouse Model of Sporadic Colon Cancer

(2008) K. Yang et al.   CANCER RESEARCH

CD4+Foxp3+ regulatory T cell expansion induced by antigen-driven interaction with intestinal epithelial cells independent of local dendritic cells

(2008) A M Westendorf et al.   GUT

Crypt stem cells as the cells-of-origin of intestinal cancer

(2008) Nick Barker et al.   NATURE