J.-P. Mallm

Cell-state plasticity drives heterogeneity in Group 3/4 medulloblastoma

This study identifies cell-state plasticity as a driver of heterogeneity in Group 3/4 medulloblastomas, showing that transcription factor perturbation can redirect tumor cells along different differentiation trajectories.

Medulloblastoma oncogene aberrations are not involved in tumor initiation, but essential for disease progression and therapy resistance

The paper uses single-cell technologies to show that large-scale chromosomal aberrations drive medulloblastoma initiation, while single-gene oncogenic events like MYC contribute to progression and therapy resistance.

Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage

The paper uses single-cell transcriptomics to show how two compartments in medulloblastoma are connected through a migrating precursor stage, revealing spatial and developmental links between proliferating and differentiated tumor cells.

Oncogenic RAS-Pathway Activation Drives Oncofetal Reprogramming and Creates Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia

This study identifies oncofetal reprogramming in juvenile myelomonocytic leukemia, linking RAS-pathway activation to fetal gene expression and revealing CD52 as a therapeutic target.

Spatial and temporal transcriptomics of SHH-medulloblastoma with chromothripsis identifies multiple genetic clones that resist to treatment and lead to relapse

This study uses spatial transcriptomics to analyze chromothriptic medulloblastomas, revealing higher intra-tumour heterogeneity, treatment resistance, and relapse mechanisms through clone-specific features.

A multidimensional atlas of human glioblastoma organoids reveals highly coordinated molecular networks and effective drugs

This study characterizes human glioblastoma organoids using multi-omics analysis and identifies drug targets linked to glycerol lipid reprogramming.

High-dimensional single-cell definition of CLL T cells identifies Galectin-9 as novel immunotherapy target

The paper defines CLL T cell subtypes and identifies Galectin-9 as a novel immunotherapy target through single-cell and multi-omics analyses.

Establishment of a simplified preparation method for single-nucleus RNA-sequencing and its application to long-term frozen tumor tissues

The paper develops a simplified method for isolating nuclei from frozen tumor tissues and applies it to analyze pediatric central nervous system tumors using snRNA-seq.

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability

This study examines DNA methylation heterogeneity in multiple myeloma, linking it to transcriptomic variability and poor patient outcomes through epigenetic and structural changes.

Hematopoietic stem cells fail to regenerate following inflammatory challenge.

This study shows that repeated inflammatory challenges lead to progressive depletion of functional HSCs with no recovery, contributing to age-related hematopoietic decline.

Methylome-based cell-of-origin modeling (Methyl-COOM) identifies aberrant expression of immune regulatory molecules in CLL

This study introduces Methyl-COOM, a method to identify cell-of-origin and CLL-specific epigenetic aberrations by analyzing DNA methylation patterns.

Dissecting intratumor heterogeneity of nodal B cell lymphomas on the transcriptional, genetic, and drug response level

This study examines intratumor heterogeneity in B cell lymphomas by analyzing transcriptional, genetic, and drug response profiles across malignant subclones and immune cells.

Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming

The paper uses single-cell RNA sequencing to analyze fibroblast subpopulations in young and old human skin, finding that aging reduces fibroblast priming and alters their interactions with other skin cells.

Retrieving chromatin patterns from deep sequencing data using correlation functions

The paper introduces MCORE, a method to quantify and compare chromatin patterns across length scales using correlation functions, applied to mouse chromatin data.