H. Clevers

Divergent lineage trajectories and genetic landscapes in human gastric intestinal metaplasia organoids associated with early neoplastic progression

Tuft cells act as regenerative stem cells in the human intestine

The paper identifies four human tuft cell states, showing they function as radiation-resistant stem cells capable of regenerating the intestinal epithelium.

Multi-omic dataset of patient-derived tumor organoids of neuroendocrine neoplasms

The paper presents a multi-omic dataset of patient-derived tumor organoids for neuroendocrine neoplasms, including whole-genome and RNA-seq data, and provides analysis tools for re-use.

Multi-dimensional profiling of hepatoblastomas and patient-derived tumor organoids uncovers tumor subpopulations with divergent WNT activation profiles and identifies pan-hepatoblastoma drug sensitivities

This study identifies two hepatoblastoma subtypes with distinct WNT activation profiles and discovers drug sensitivities in patient-derived tumor organoids.

Establishment and characterization of a new Pseudomonas aeruginosa infection model using 2D airway organoids and dual RNA sequencing

This study establishes a Pseudomonas aeruginosa infection model using 2D airway organoids and dual RNA sequencing to investigate host-bacterial interactions and quorum sensing effects.

Druggable Growth Dependencies and Tumor Evolution Analysis in Patient-Derived Organoids of Neuroendocrine Cancer

This study establishes patient-derived tumor organoids (PDTOs) for neuroendocrine cancers, identifies therapeutic vulnerabilities, and highlights EGF dependency in pulmonary neuroendocrine tumors.

Functional and spatial proteomics profiling reveals intra- and intercellular signaling crosstalk in colorectal cancer

The paper uses patient-derived organoids and phosphoproteomics to study signaling crosstalk in colorectal cancer and identify off-target effects of kinase inhibitors.

Paecilomycone inhibits quorum sensing in Gram-negative bacteria

This paper identifies paecilomycone as a quorum sensing inhibitor in Pseudomonas aeruginosa, reducing virulence factors and biofilm formation with low eukaryotic toxicity.

Nanoblades allow high-level genome editing in organoids

This paper introduces nanoblade technology for efficient, low-toxicity genome editing in organoids, achieving up to 80% gene knockout in murine and human organoids.

Chromatin Remodeling in Patient-Derived Colorectal Cancer Models

This study compares chromatin remodeling in colorectal cancer patient-derived models and identifies transcription factors driving differences in growth and drug response.

Following cell type transitions in space and time by combining live-cell tracking and endpoint cell identity in intestinal organoids

The paper introduces TypeTracker, a method combining live-cell tracking and endpoint cell identity to study differentiation trajectories in intestinal organoids, revealing new insights into cell type transitions and spatial organization.

Oncogenic signalling is coupled to colorectal cancer cell differentiation state

This study shows oncogenic signalling in colorectal cancer is linked to cell differentiation states through a defined axis, with mutations affecting stemness and differentiation.

Druggable redox pathways against M. abscessus in cystic fibrosis patient-derived airway organoids

This study uses airway organoids to investigate M. abscessus infection in CF patients, showing antioxidant pathways can inhibit bacterial growth and enhance antibiotic efficacy.

A turquoise fluorescence lifetime-based biosensor for quantitative imaging of intracellular calcium

This paper introduces a new calcium biosensor based on fluorescence lifetime imaging, which provides accurate and pH-insensitive quantification of intracellular calcium concentrations.

Loss of Rnf43 accelerates Kras-mediated neoplasia and remodels the tumor immune microenvironment in pancreatic adenocarcinoma

This study shows that loss of Rnf43 accelerates Kras-driven pancreatic cancer and alters the tumor immune microenvironment by increasing lymphocytes and immune checkpoint expression.

Behavioral-transcriptomic landscape of engineered T cells targeting human cancer organoids

The paper develops BEHAV3D, a 3D imaging-transcriptomics platform to study T cell behavior and molecular mechanisms in cancer organoids, identifying a super engager cluster with unique gene signatures and IFN-I priming capabilities.

Human organoid systems reveal in vitro correlates of fitness for SARS-CoV-2 B.1.1.7

The paper assesses the replicative fitness of SARS-CoV-2 B.1.1.7 variant in human organoid models and finds higher infectious virus production and fitness compared to an ancestral strain.

Phospholipid peroxidation fuels ExoU phospholipase-dependent cell necrosis and supports Pseudomonas aeruginosa-driven pathology

This study identifies phospholipid peroxidation as a mechanism enhancing ExoU phospholipase activity, leading to cell necrosis and supporting Pseudomonas aeruginosa pathogenesis.

Serine Palmitoyltransferase Controls Stemness of Intestinal Progenitors

The paper shows that serine palmitoyltransferase (SPT) modulates intestinal stem cell homeostasis by promoting stemness through sphingolipid production and PPAR-alpha activation, linking diet to cancer risk.

Human liver organoids; a patient-derived primary model for HBV Infection and Related Hepatocellular Carcinoma

This paper establishes human liver organoids as a model for HBV infection and HCC, showing they support viral replication, produce infectious HBV, and exhibit cancer-related gene signatures.

Early invasion of uropathogenic Escherichia coli into the bladder wall by solitary bacteria that are protected from antibiotics and neutrophil swarms in an organoid model

This study uses a bladder organoid model to show that UPEC can invade deeper bladder layers as solitary bacteria, evading antibiotics and neutrophils, forming reservoirs that contribute to recurrent infections.

SARS-CoV-2 Productively Infects Human Gut Enterocytes

The paper shows SARS-CoV-2 infects human gut enterocytes in small intestinal organoids, leading to viral replication and a strong immune response.

Cysteamine-bicalutamide combination treatment restores alpha-ketoglutarate and corrects proximal tubule phenotype in cystinosis

This study identifies alpha-ketoglutarate as a key metabolite in cystinosis and shows that combining cysteamine with bicalutamide corrects proximal tubule defects in cell models and zebrafish.

Mathematical Model of Colorectal Cancer Initiation

The paper develops a mathematical model of colorectal cancer initiation, showing that mutation rates and fitness effects determine the order of driver events and that immune suppression may not significantly affect colorectal lesions.

Fast and efficient generation of knock-in human organoids using homology-independent CRISPR/Cas9 precision genome editing

This paper introduces CRISPR-HOT, a method for efficient knock-in of exogenous DNA in human organoids without requiring homology templates or TP53 inactivation, and demonstrates its application in studying hepatocyte division and ploidy.

Novel Conformation Specific Inhibitors of Activated GTPases reveal Ras-dependency of Patient-Derived Cancer Organoids

The paper develops RBD variants that inhibit Ras effector binding, inducing senescence in non-tumorigenic cells and revealing Ras dependency in cancer organoids.

A rectal cancer model establishes a platform to study individual responses to chemoradiation

This study develops a rectal cancer organoid model that mimics patient tumor responses to chemoradiation and metastasis in mice.

Modelling cancer immunomodulation using epithelial organoid cultures

This study uses CRC organoids to model immune-cancer interactions and assess immunomodulation by co-culturing with cytotoxic T cells.

Long-term expanding human airway organoids for disease modelling.

This study establishes long-term-expanding human airway organoids from broncho-alveolar biopsies or lavage material, enabling disease modeling of cystic fibrosis, lung cancer, and RSV infection.

Hematopoietic stem cells differentiate into restricted myeloid progenitors before cell division

This study shows hematopoietic stem cells can differentiate into restricted progenitors without dividing or entering the S phase, indicating fate decisions are uncoupled from cell division.