Julien Vibert (李满山)

👉 Showcase your rare cancer research! #ESMORareCancers26 Chairs Prof. David Thomas, Prof. Eva Tiensuu Janson & Dr. Claudia Valverde highlight why abstracts matter: visibility, expert feedback & networking.
⏰ Submit by 9 Dec 2025.
🔗 buff.ly/0MGWMsn

Origin of Ewing sarcoma by embryonic reprogramming of neural crest to mesoderm Using a zebrafish genetic model of Ewing sarcoma, Vasileva et al. provide evidence for a neural crest origin of the disease. These findings offer new insight into how a single oncogenic fusion can hij...

1/9 Thrilled to share that our paper, “Origin of Ewing sarcoma by embryonic reprogramming of neural crest to mesoderm,” is now published in @cp-cellreports.bsky.social! @amatrudalab.bsky.social @crumplab.bsky.social www.cell.com/cell-reports...

📊 Oncologists don’t need to be #AI experts, but they should understand how AI makes predictions and its limits. ESMO President Fabrice André calls for education & interdisciplinary collaboration to improve patient care.

#ESMODailyReporter 👉 buff.ly/wei558Y

#HealthAI #ESMOAI25

Ultra-sensitive DNA sequencing maps mutations that precede cancer Scientists have used low-error genome-sequencing methods in normal tissues from large cohorts of individuals to scan for mutations that set the stage for cancer.

Scientists have used low-error genome-sequencing methods in normal tissues from large cohorts of individuals to scan for mutations that set the stage for cancer

go.nature.com/42vakWS

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.

🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China

A scientist’s guide to AI agents — how could they help your research? Researchers are increasingly turning to artificial-intelligence tools that can handle complex, multi-step processes.

Researchers are increasingly turning to artificial-intelligence tools that can handle complex, multi-step processes

go.nature.com/3IY9njc

The @ItalianSarcomaGroup consensus paper on extended molecular profiling in mesenchymal tumors is out!
Huge thanks to everyone who contributed to this collaborative effort!
@merlini-ale.bsky.social
doi.org/10.1016/j.cr...

Ancient viral DNA in the human genome shapes early development Stem-cell models provide evidence that viral DNA sequences that entered the human genome in the past were repurposed to aid early stages of embryonic development.

Stem-cell models provide evidence that viral DNA sequences that entered the human genome in the past were repurposed to aid early stages of embryonic development

go.nature.com/4nRJyA4

Distinct T cell functions enable efficient immunoediting and prevent tumor emergence of developing sarcomas Cheung et al. describe efficient T cell control of nascent neoantigen+ and nearby neoantigen-negative sarcoma cells, underlying a ∼50% reduction in tumor penetrance. This otherwise imperceptible immunoediting process is revealed by time-resolved profiling of autochthonously arising, muscle-derived sarcoma cells expressing fluorescent reporter-embedded model T cell antigens within the native tissue environment.

Online Now: Distinct T cell functions enable efficient immunoediting and prevent tumor emergence of developing sarcomas

Predicting drug responses of unseen cell types through transfer learning with foundation models - Nature Computational Science This work develops CRISP, a framework using foundation models to predict drug responses in previously unseen cell types at single-cell resolution, advancing drug repurposing and drug screening capabilities.

Out now! Yu Li and colleagues develop CRISP, a foundation-model-based framework for predicting drug responses at single-cell resolution. www.nature.com/articles/s43...

🔓 rdcu.be/eJlt9

Now online in Cancer Discovery @aacrjournals.bsky.social: Epigenetic and Transcriptional Programs Define #Osteosarcoma Subtypes and Establish Targetable Vulnerabilities - by Eunice López-Fuentes, Alejandro Sweet-Cordero, and colleagues doi.org/10.1158/2159... @ucsfchildrens.bsky.social

Online Now: Cell-free DNA fragmentomics in cancer

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...

InterPLM: discovering interpretable features in protein language models via sparse autoencoders - Nature Methods InterPLM is a computational framework to extract and analyze interpretable features from protein language models using sparse autoencoders. By training sparse autoencoders on ESM-2 embeddings, this study identifies thousands of interpretable biological features learned by the different layers of the ESM-2 model.

InterPLM: a computational framework for extracting and analyzing interpretable features from protein language models.

www.nature.com/articles/s41...

Spatial architecture of development and disease Nature Reviews Genetics, Published online: 30 September 2025; doi:10.1038/s41576-025-00892-5Spatial omics has empowered the discovery of developmental and disease-associated molecular signatures, cell states and multicellular niches, as well as the evaluation of disease heterogeneity within and across organs. The authors review spatially resolved molecular changes across diseases and discuss the potential of spatial multi-omics for clinical applications, including the recent impact of artificial intelligence.

New online! Spatial architecture of development and disease

New review in JCO Precision Oncology by the NEWTS group of the @euroewing.bsky.social consortium:

Recurrent and Refractory Ewing #Sarcoma Phase I/II Trials: Current Perspective From the Euro-Ewing Consortium

ascopubs.org/doi/10.1200/...

International collaboration is KEY for clinical trials!

Genomically matched therapy in advanced solid tumors: the randomized phase 2 ROME trial - Nature Medicine In the proof-of-concept phase 2 ROME trial, comprehensive genomic profiling followed by molecular tumor board evaluation and randomization of patients with metastatic solid cancer to receive personalized therapy or standard of care led to a significantly higher objective response rate and longer progression-free survival in patients who received personalized therapy.

A randomized trial of patients with advanced cancer who had genomically matched treatment vs standard of care showed substantial outcome improvement for the former
www.nature.com/articles/s41...

🚀 Excited to share scPortrait! Led by Sophia Mädler & Niklas Schmacke w/ the Mann lab — a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights.
🔗 www.biorxiv.org/content/10.1...

Taming cancer evolution surprises - Nature Methods With a focus on the evolutionary forces that shape cancer cell behavior, some researchers work out ways to outmaneuver cancer.

With a focus on the evolutionary forces that shape cancer cell behavior, some researchers work out ways to outmaneuver cancer, according to a feature in Nature Methods. #medsky 🧪

EpiAgent: foundation model for single-cell epigenomics - Nature Methods EpiAgent is a foundation model for analyzing scATAC-seq data that excels in standard downstream tasks such as feature extraction, cell type annotation and data imputation while also enabling simulation of cCRE knockouts and cell state changes.

EpiAgent: a foundation model for analyzing scATAC-seq data.

www.nature.com/articles/s41...

Single-cell multi-omic detection of DNA methylation and histone modifications reconstructs the dynamics of epigenomic maintenance - Nature Methods This work presents scEpi2-seq, a method for simultaneous single-cell profiling of DNA methylation and histone modifications, enabling direct investigation of the interplay between these two epigenomic marks.

scEpi2-seq: a method for simultaneous single-cell profiling of DNA methylation and histone modifications.
@jervdberg.bsky.social @hubrechtinstitute.bsky.social

www.nature.com/articles/s41...

New cell lines expanding the diversity of Ewing sarcoma models A chromosomal translocation between the EWSR1 and ETS genes is the key oncogenic driver in Ewing sarcoma. EWSR1::FLI1, the most frequent fusion, is subdivided into different fusion types with unclear...

New cell lines expanding the diversity of
#Ewing #sarcoma models

onlinelibrary.wiley.com/doi/10.1002/...

Single-cell nascent transcription reveals sparse genome usage and plasticity scFLUENT-seq is a single-cell method that sensitively captures nascent nuclear transcriptomes to reveal mRNA and ncRNA dynamics, heterogeneity across chromatin compartments, and transcriptional diversity linked to cellular plasticity.

Now online! Single-cell nascent transcription reveals sparse genome usage and plasticity

Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer - Nature Basal cells, rather than neuroendocrine cells, have been identified as the probable origin of small cell lung cancer and other neuroendocrine–tuft cancers, explaining neuroendocrine–tuft heterogeneity and offering new perspectives for targeting lineage plasticity.

Nature research paper: Basal cell of origin resolves neuroendocrine–tuft lineage plasticity in cancer

go.nature.com/3ViRTAP

The Biodiversity Cell Atlas white paper is out! A bold vision to map the diversity and evolution of cell types across the tree of life 🌍

EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors https://www.biorxiv.org/content/10.1101/2025.09.22.676906v1

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

@science.org🧬🔬Functional maps of a #genomic locus reveal confinement of an enhancer by its target #gene | Science www.science.org/doi/10.1126/...