Ronan Chaligné

This study shows that systemic iron sequestration via hepcidin reduces CD8+ T cells in pancreas cancer, linking iron dysregulation to tumoral immunity.

This study identifies an IL-1β/IL-6 signaling circuit in the tumor microenvironment that drives prostate cancer progression from pre-invasive to invasive stages.

The paper introduces Suco and Compocyte to classify immune cells from 3,965 patients, identifying new macrophage and monocyte states and T cell memory erosion in metastases.

This study uses spatial transcriptomics and single-cell analysis to reveal how MDS bone marrow microenvironments are altered, showing TGFβ dysregulation in malignant cells and immune escape mechanisms.

The paper integrates single-cell multiomics and CRISPR screening in prostate cancer organoids to reveal lineage-specific dependencies and heterogeneity effects on gene essentiality.

In mouse pancreatic cancer models, p53, CDKN2A and SMAD4 programs converge on a rare Kras-mutant progenitor-like state whose niche KRAS inhibition collapses and p53 loss expands.

The paper identifies MDF, a repair scar linked to POLQ-driven error-prone repair, as a marker of immune-responsive HRD pancreatic cancer with increased neoantigens and favorable clinical outcomes.

The paper analyzes transcriptomic changes in metastatic pancreatic cancer using a patient's autopsy data to identify site-specific gene programs and clonal phylogeny.

This study shows that metastatic site influences the function of driver genes like SMAD4 in pancreatic cancer, with organ-specific epigenetic states affecting tumor growth.

This study identifies MAPK activation and cellular plasticity as complementary resistance mechanisms to EGFR TKI in lung adenocarcinoma using single-nuclei RNA sequencing and clinical data.

This paper develops a method to engineer specific mtDNA deletions in human cells using end-joining machinery and targeted endonucleases, revealing a 75% heteroplasmy threshold for mitochondrial dysfunction.

This study shows aging reduces lung stem cell function and suppresses lung cancer by inducing iron deficiency through the NUPR1-lipocalin-2 pathway.

This study identifies ASCL1 as a critical driver of neuroendocrine lineage transition in prostate cancer using an in vivo model and spatial transcriptomics.

This paper introduces COVET and ENVI to model spatial niches and improve gene expression imputation and spatial context inference from single-cell data.

This paper introduces PERFF-seq, a method to profile rare cell states via scRNA-seq by enriching for specific RNA transcripts, demonstrating its application in immune and brain tissues.

SEACells identifies metacells from single-cell data, improving gene-peak associations and revealing chromatin dynamics in hematopoiesis and COVID-19.