Hans C. Clevers

Highly plastic macrophage niches orchestrate acquired quiescence and reactivation in breast-cancer bone metastasis

The paper identifies CXCL16 macrophages in bone metastases that transiently restrain cancer growth and G-CSF niches that promote reactivation, revealing CAF-bone-marrow interactions as a therapeutic target.

Single-Cell Inference of Structural States Of Ribosomes

SCISSOR infers global translation activity in single cells using ribosomal RNA protection signatures, revealing cell cycle and differentiation-related translation variations in human and murine cells.

The immediate cellular response to whole-genome doubling is conserved across polyploid contexts

The paper compares the immediate cellular response to polyploidization across different contexts and finds conserved scaling of cell size and protein translation, with cell-cycle adaptations influencing outcomes.

A Dual-Pathway Wnt-IL-13 Fusion Protein Enhances Human Intestinal Regeneration Through Tuft Cell Activation

This paper develops a Wnt-IL-13 fusion protein that activates tuft cells to enhance intestinal regeneration in human organoids.

A human organoid model of alveolar regeneration reveals distinct epithelial responses to interferon-gamma

This study develops a human organoid model to investigate interferon-gamma's effects on alveolar epithelial cell regeneration, showing divergent impacts on AT1 and AT2 cells.

WNT7B drives a program for pancreatic cancer subtype switching and progression

This study shows WNT7B drives pancreatic cancer subtype switching and progression by promoting a basal-like state and influencing cell communication within tumors.

A robust human airway organoid platform enables scalable expansion and trajectory mapping of pulmonary neuroendocrine cells

This paper develops a human airway organoid platform to expand and map the differentiation trajectories of pulmonary neuroendocrine cells.

The mood stabilizer lithium alters behaviour and physiology via the gut brain axis.

This study shows lithium affects behavior and physiology through the gut-brain axis by activating gut enterochromaffin cells, challenging the belief that lithium acts directly on the brain.

Fetal reversion from diverse lineages sustains the intestinal stem cell pool and confers stress resilience

This study shows that fetal reversion from diverse lineages sustains the intestinal stem cell pool and enhances stress resilience through bidirectional interconversion between CBCs and revSCs.

Human embryo implantation involves Syncytin-2/MFSD2A-mediated heterokaryon formation with maternal endometrium

The paper shows that human embryo implantation involves Syncytin-2/MFSD2A-mediated cell fusion between blastoids and endometrial epithelial cells, preventing implantation when MFSD2A is knocked out.

A collection of patient-derived intestinal organoid lines reveals epithelial phenotypes associated with genetic drivers of pediatric inflammatory bowel disease

The paper generates intestinal organoids from pediatric IBD patients and controls to study epithelial phenotypes linked to genetic drivers of the disease, identifying gene expression patterns and pathways associated with inflammation.

BEST4/CA7+ and goblet cells are interdependent regulators of intestinal mucus homeostasis

The paper shows that BEST4/CA7+ cells and goblet cells depend on each other for survival and differentiation in the intestinal mucus layer.

Mature tuft cell phenotypes are sequentially expressed along the intestinal crypt-villus axis following cytokine-induced tuft cell hyperplasia

The paper identifies sequential transcriptomic states of tuft cells along the intestinal crypt-villus axis and shows cytokine-specific differentiation into distinct tuft cell phenotypes.

Human colon stem cells are the principal epithelial responders to bacterial antigens

The paper investigates how human intestinal epithelial cells respond to bacterial antigens, finding that stem cells are the primary responders and that WNT signaling plays a key role in regulating microbial responses.

Mapping the complete influenza A virus infection cycle through single vRNP imaging

This study maps the complete influenza A virus infection cycle in individual cells, identifying key factors driving infection heterogeneity.

Integrin-activating Yersinia protein Invasin sustains long-term expansion of primary epithelial cells as 2D organoid sheets

The paper shows that Invasin-coated plates enable long-term 2D expansion of epithelial organoids from multiple species, offering an alternative to Matrigel/BME.

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

Sensitivity to Vγ9Vδ2TCR T cells is imprinted after single mutations during early oncogenesis

This study shows that single mutations during early oncogenesis can upregulate BTN2A1, enabling Vγ9Vδ2 TCR binding, but full activation requires subsequent phosphorylation of BTN3A1.

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.

Lgr5+ ductal cells of von Ebner's glands are stem cells for turnover of posterior tongue taste buds

Stimulation-responsive enhancers regulate inflammatory gene activation through retention and modification of H2A.Z-variant accessible nucleosomes

The paper identifies how dmPGE2 regulates inflammatory gene activation in HSPCs by modulating enhancer chromatin structure through H2A.Z-variant nucleosome retention and acetylation.

Mycobacteria-host interactions in human bronchiolar airway organoids

This study uses human airway organoids to model tuberculosis infection, showing mycobacteria infect epithelial cells with low efficiency and the organoid microenvironment controls but does not eliminate the pathogen.

A CRISPR/Cas9 genetically engineered organoid biobank reveals essential host factors for coronaviruses

The paper uses CRISPR/Cas9 to generate mutant intestinal organoids and identifies TMPRSS2 as a critical host factor for multiple coronaviruses.

Evaluating CRISPR-based Prime Editing for cancer modeling and CFTR repair in intestinal organoids

This study evaluates prime editing for modeling cancer mutations and repairing CFTR in intestinal organoids, showing its potential but also highlighting challenges in efficiency and off-target effects.

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.