Matouš Elphick

Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...

u-Segment3D: a universal framework for 2D to 3D cell segmentation that generalizes across cell types and imaging modalities.

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

TGF-β builds a dual immune barrier in colorectal cancer by impairing T cell recruitment and instructing immunosuppressive SPP1+ macrophages - Nature Genetics Targeting TGFBR1 in transplantable mouse colorectal tumor organoids improves response to anti-PD-L1 therapy. Mechanistically, TGF-β abrogates clonal expansion of T effector and memory phenotypes and i...

1/17 🧵
🙌Thrilled to share our first hard-core immunology paper out today in Nature Genetics! 👇

➡️We unravel how TGFβ suppresses the innate and adaptive immune system in microsatellite stable colorectal cancer (MSS CRC).

Very proud of the team and efforts behind it.

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

Crick Crash Course: Immunotherapy Our series of morning lectures sharing science from across the Crick in a simple and accessible way continues.

How does immunotherapy work, and why do some patients respond while others don’t?

Book our free talk by Samra Turajlic, head of the Cancer Dynamics Lab here at the Crick, Director of @cruk-mi.bsky.social and head of the UK-wide MANIFEST programme.

www.eventbrite.co.uk/e/crick-cras...

Lipid droplet growth is orchestrated by the seipin complex, which provides a structural platform for droplet nucleation and expansion. The microprotein adipogenin fine-tunes seipin’s conformation, remodeling its architecture to regulate lipid storage capacity. This modulation results in the formation of fewer but larger lipid droplets, revealing a key mechanism in lipid homeostasis.

Fat storage in the body relies on specialized structures called lipid droplets. In a new Science study, researchers identified the microprotein adipogenin as a regulator of adipocyte lipid droplet size, revealing a key mechanism in lipid homeostasis.

Learn more this week: https://scim.ag/4nFEGO7

7 basic science discoveries that changed the world Ozempic, MRI machines and flat screen televisions all emerged out of fundamental research decades earlier — the very types of study being slashed by the US government.

Scientists point to a long list of findings that emerged out of fundamental research, the type of studies the US government is cutting, and went on to change the world. Nature lists a few of their examples. 🧪

STORIES: learning cell fate landscapes from spatial transcriptomics using optimal transport - Nature Methods By learning a differentiation potential using an optimal transport-based approach, STORIES models and infers cell fate trajectories using spatiotemporal omics data.

Happy to share STORIES out now on Nature Methods

STORIES learns cell fate landscapes from spatial tramscripromics data profiled at several time points, thus allowing prediction of future cell states.

Led by Geert-Jan Huizing and Jules Samaran

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

@pasteur.fr

An Introduction to OME-Zarr for Big Bioimaging Data

Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data".

ome-zarr-book.readthedocs.io

High-resolution imaging mass cytometry enables highly multiplexed imaging of nuclear foci and mitochondrial networks.

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

Cancer cells tighten the belt around their neighbours forcing them to die - Research Cancerous cells can expand in our tissues by killing neighbouring healthy cells. Researchers in Institut Pasteur, CNRS and the Université Paris Cité found a new mechanism used by cancerous cells to ki...

🧬🩸 Cancer cells “tighten the belt” on their neighbors — Institut Pasteur, CNRS & Université Paris Cité uncover a mechanical killing strategy: tumor cells surround healthy ones and squeeze them to death via a contractile belt.

Read more 👉 research.pasteur.fr/en/news/canc...

Hunger influences the behaviour of female mice towards pups Researchers find that virgin female mice can become aggressive towards pups when hungry, but only in certain hormonal states.

Researchers at the Crick found that virgin female mice can become aggressive towards pups when hungry, but only in certain hormonal states.

It highlights the importance of understanding hormones when observing how different physical states interact in the brain.

www.crick.ac.uk/news/2025-10...

👏We are pleased to announce Laura Marandino as the 2025 recipient of the ESMO José Baselga Fellowship for Clinician Scientists. This fellowship, supported by AZ, provides the resources & #mentorship for #ClinicianScientists. #ESMO25

@science.org High-resolution spatial mapping of cell state and lineage dynamics in vivo with PEtracer | Science www.science.org/doi/10.1126/... @lukekoblan.bsky.social @weissmanlab.bsky.social @zhuanglab.bsky.social @whiteheadinstitute.bsky.social et al.

Sex and smoking bias in the selection of somatic mutations in human bladder - Nature Sex bias and association with smoking history identified in the landscape of driver mutations and clonal expansions in normal human bladder tissue may explain the higher bladder cancer risk in men and smokers.

Ultra-sensitive DNA sequencing maps mutations that precede cancer @nature.com @imartincorena.bsky.social
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/s41... @bbglab.bsky.social @irbbarcelona.org @nlbigas.bsky.social

Automated classification of cellular expression in multiplexed imaging data with Nimbus - Nature Methods Nimbus, a deep learning model, uses a large multiplexed imaging dataset to predict the likelihood of marker positivity in single cells.

Nimbus predicts the likelihood of marker positivity from multiplexed image data in single cells.

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...

SPP1 is required for maintaining mesenchymal cell fate in pancreatic cancer - Nature Mutual paracrine regulation of the cytokines GREM1 and SPP1 mediate mesenchymal and epithelial cell fate in pancreatic cancer.

new out in Nature www.nature.com/articles/s41...

Global matrisome changes in obese lung are linked to fibroblastic stroma and premature aging Rottmann et al. use multi-omics and functional assays to show that obesity remodels the lung matrisome and enhances fibroblast contractility, exhibiting hallmarks of aging. These changes mirror premature aging signatures in the lung, linking overnutrition to impaired pulmonary function.

Global matrisome changes in obese lung are linked to fibroblastic stroma and premature aging

Come join us next year at the @embo.org meeting "The Many Faces of #Cancer evolution"! Organised by @ciriellolab.bsky.social @magnanilab.bsky.social @turajliclab.bsky.social & Céline Vaillot! In beautiful Rimini 🇮🇹

More information in the poster below ⬇️ and at

meetings.embo.org/event/26-cancer-evo

CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.

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

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)

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

Systematic Growth Factor Profiling Platform for 3D Tumor Models Reveals Estradiol-Responsive Cellular Mechanisms of Immunotherapy Resistance https://www.biorxiv.org/content/10.1101/2025.09.04.674374v1

Unravelling the genetics and epigenetics of the ageing tumour microenvironment in cancer Nature Reviews Cancer, Published online: 08 September 2025; doi:10.1038/s41568-025-00868-xIn this Review, Easwaran and Weeraratna outline how ageing leads to epigenetic alterations in the tissue microenvironment, enhancing clonal expansion of mutations and ultimately increasing cancer risk.

NEW content online!

Evidence that mitochondria in macrophages are destroyed by microautophagy - Nature Communications Mitophagy, the selective degradation of mitochondria, has been thought to occur via macroautophagy. Here, the authors present data indicating that microautophagy also mediates mitophagy in macrophages...

Evidence that mitochondria in macrophages are destroyed by microautophagy
www.nature.com/articles/s41...

Mechanical confinement governs phenotypic plasticity in melanoma - Nature Mechanical confinement of cancer cells at the tumour–microenvironment interface induces phenotype switching through chromatin remodelling by HMGB2, leading to a more invasive and drug-resistant state ...

new out in Nature this week www.nature.com/articles/s41...

In-depth proteomic profiling of the extracellular matrix of pancreatic ductal adenocarcinomas identifies signatures correlating with lymphocyte infiltration The extracellular matrix (ECM) is a complex assembly of proteins surrounding cells. It is a critical component of the tumor microenvironment that plays an active role in tumor progression and modulati...

🤔 Wondering to what extent the #ECM influences immune cell infiltration in tumors? In collaboration with @boehringerglobal.bsky.social, we applied #matrisomics to identify signatures distinguishing hot and cold #PDACs. Check out our preprint to learn what we found! www.biorxiv.org/content/10.1...

Your DNA sequence reveals a rare mutation. Will you get the disease, i.e. penetrance? A new study using machine learning predicts this across 10 common diseases, 1,600 genomic variants
New @science.org
science.org/doi/10.1126/...

Next up at #CBIAS2025 is @helenajambor.bsky.social‬ from the University of Applied Sciences of the Grisons. Helena researches data visualisation in the life sciences, combining their expertise with large datasets and their interest in data communication

🔗👇
helenajamborwrites.netlify.app/about

A 3D genome compendium of breast cancer progression Genomics; Chromosome organization; Molecular Genetics; Cancer

We all know that cancers -even from the same subtype- are highly heterogeneous right? In a new study we asked whether this was also the case for the three-dimensional organization of the genome in breast cancer. The answer: it’s complicated. www.cell.com/iscience/ful...

Large-scale CRISPR screening in stomach organoids reveals gene-drug interactions Large-scale CRISPR screening in stomach organoids reveals gene-drug interactions

Researchers used large-scale CRISPR screening in stomach organoids to uncover how tumors respond to cancer drugs. These findings could inform more personalized treatment strategies.

Learn more: spr.ly/63329fsVJF #EndCancer #OncSky