
Computational biologist at @IARCWHO. Views are my own. co-PI of the Computational Cancer Genomics team: https://xitter.cf/t.co/kbwe5cCyjX / @CancersRare
France
Joined May 2011
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Matthieu Foll retweeted
Could some lung neuroendocrine tumours be in the wrong box?
New research involving 319 lung NETs identified four distinct molecular groups, including a more aggressive supra-carcinoid group with biological links to small cell lung cancer.
The findings could help refine how these rare lung cancers are classified and studied.
link.springer.com/article/10…
#LCSM
New #IARCpaper establishes existence of4⃣molecular groups of lung neuroendocrine tumours with unique etiology, clinical & epidemiological features...
Potential implications for prevention, classification & clinical management.
Published in Molecular Cancer
iarc.who.int/news-events/dee…
Matthieu Foll retweeted
This is a fascinating but dense paper on molecular profiling of lung NENs.
A few take-home points:
-- There arefour strikingly different molecular groups that vary in patient characteristics, genomic and transcriptomic profiles, microenvironment, and morphology.
-- A new molecular group, enriched for highly aggressive supra‐carcinoids that displayed an immune‐rich microenvironment linked to tumour-macrophage crosstal
-- There appears to be an undifferentiated cell population within supra-carcinoids showing the transcriptomic similarities between supra-carcinoids and the recently identified atypical small cell lung cancer tumours, further demonstrating their molecular link to high-grade lung neuroendocrine carcinomas
-- There appear to be distinct evolutionary trajectories, suggesting that molecular groups are determined early in tumourigenesis by genomic events, and that transitions between groups, though infrequent, are possible for supra-carcinoids
link.springer.com/article/10…
New lungNENomics study: four molecular groups in lung neuroendocrine tumours, including supra-carcinoids.
Similar-looking tumours can follow different paths.
Congratulations @LexiLou_06 @EMathian @nl_alcala
@IARCWHO @CancersRare @CureNETs @ENETS_ORG
doi.org/10.1186/s12943-026-0…
Matthieu Foll retweeted
Are lung #Neuroendocrine #Tumor actually four different diseases with unique evolutionary trajectories? Checkout our latest article in #MolecularCancer link.springer.com/article/10… @EmilieMathian @digenoma @m_foll @CancersRare funded by @CureNETs
Matthieu Foll retweeted
ecDNA are rogue genetic material that amplify genes, contribute to treatment resistance and drive genomic heterogeneity. We report on the Origins and impact of extrachromosomal DNA today in @Nature nature.com/articles/s41586-0…
Matthieu Foll retweeted
'Emerging strategies to investigate the biology of early cancer'
nature.com/articles/s41568-0…
Matthieu Foll retweeted
Semi-supervised Omics Factor Analysis (SOFA) disentangles known sources of variation from latent factors in multi-omics data biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
Matthieu Foll retweeted
The Curated Cancer Cell Atlas: comprehensive characterisation of tumours at single-cell resolution biorxiv.org/cgi/content/shor… #biorxiv_cancer
Matthieu Foll retweeted
We are thrilled to welcome Yuliya Lim as a PhD student in the team, under the supervision of @nl_alcala, L. Fernandez-Cuesta, and @m_foll! Yuliya recieved a competitive PhD fellowship from @laliguecancer and will work on deciphering the mysteries of cancer ecosystem complexity.
Matthieu Foll retweeted
Very happy to share our latest work on pulmonary carcinoids published in @JCO_ASCO:
TERT Expression and Clinical Outcome in Pulmonary Carcinoids ascopubs.org/doi/10.1200/JCO…
Thanks to all involved!
@sfb1399 @DTG_Cologne @UKKoeln @charlesrudin @natasharekhtman @m_foll @digenoma
Matthieu Foll retweeted
Happy to share our first preprint using Chilean cancer data! 🎉 We developed a Nextflow pipeline for BRCA profiling, aiming to implement NGS testing in Chile's public health system. @uohiggins @uohiggins #brca #nextflow #ngs medrxiv.org/content/10.1101/…
Matthieu Foll retweeted
Very happy to share our opinion on the need for a naming convention for #peritumoral tissues (#PTT)!
Great work by Dzenis Koca with Dr Behnoush Abedi-Ardekani and Dr Joël Le Maoult!
nature.com/articles/s41416-0…
Matthieu Foll retweeted
Can tumours be described as complex ecological systems? What is the mathematical description of their dynamics and treatments? Check our @iScience_CP paper with @AguadeGuim and @ara_anderson in cell.com/iscience/fulltext/S…
Matthieu Foll retweeted
New research from @katherlab on #computational #pathology: We benchmark pathology foundation models 👇 Several of these are publicly available under permissive licenses.
arxiv.org/abs/2408.15823
Some takeaways:
1. The vision-language model CONCH (@AI4Pathology) outperforms vision-only models in many tasks.
2. Data diversity matters more than volume for improving pathology model performance.
3. Combining multiple models boosts accuracy, outperforming single models in most tasks.
Matthieu Foll retweeted
Assessment of methods to deconvolve cellular composition from bulk gene expression. #DREAM, #Immunotherapy, #deconvolution
nature.com/articles/s41467-0…
Matthieu Foll retweeted
Tumor heterogeneity is a major obstacle to effective cancer treatment. It is caused by multiple factors, including irreversible mutations and reversible phenotypic changes. But how can we model the interplay between both processes and what's their effect on cancer treatment? 1/
Matthieu Foll retweeted
Our opinion piece is out today, "The origin of novel traits in cancer"! Do the phenotypes come first and only later are they locked in by genetic or epigenetic changes? Insights from evolutionary biology are super useful for understanding cancer! cell.com/trends/cancer/abstr… #S_Frank
Matthieu Foll retweeted
Are computational biologists the drivers of research? 7 years ago I co-wrote an editorial about how computational biologists are no longer just supportive, but are now running the show. Today I would write how every biologist should also be computational.
genomebiology.biomedcentral.…
Matthieu Foll retweeted
💬 “Making #data publicly available should no longer be a by-product but a recognised part of the #research process”
💡Our Executive Director @cdessimoz was at the @scnatCH symposium “Open Research Data (ORD) – are we on track?” last 31 May.
more on👉 scnat.ch/en/uuid/i/6796a687-…




























