Pietro Andrei

Metabolic adaptations direct cell fate during tissue regeneration - Nature Metabolic enzymes of the tricarboxylic acid cycle, such as 2-oxoglutarate dehydrogenase, are differentially expressed in absorptive and secretory lineages, guiding cell fate establishment and offering insights for targeted regenerative therapies.

Nature research paper: Metabolic adaptations direct cell fate during tissue regeneration

https://go.nature.com/4l4GP5c

Segger logo

Message passing intuition behind the segger’s link-prediction model and the network architecture

1/ New preprint! 🍳

@elihei.bsky.social and our team at @embl.org , @dkfz.bsky.social, and @mskcancercenter.bsky.social built #segger - a fast, accurate cell segmentation tool for spatial transcriptomics that assigns transcripts to their cell origins!

doi.org/10.1101/2025...

I am excited to finally be able to share with you our work reporting the first Extracellular Vesicle with a personality! This video does not show a cell, it is a Blebbisome! #CellBiology
www.nature.com/articles/s41...

We have two open positions for #computationalbiologists to work on:
1. Early cancer initiation following our work in #NatureCancer (Ref 5028)
2. Response to cancer immunotherapy following our work in #CancerCell (Ref 5073)
To apply use the provided reference numbers: www.qmul.ac.uk/jobs/vacanci...

A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer Fewer than 50% of metastatic deficient mismatch repair (dMMR) colorectal cancer (CRC) patients respond to immune checkpoint inhibition (ICI). Identify…

New paper from our lab just out in @cp-cancercell.bsky.social! Integrating spatial omics, cell co-cultures and staining of clinical trial samples, we show that CD74 marks the right local microenvironment for #immunotherapy response. Excitingly, this may increase the number of treatable patients!

Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of esophageal cancer Nature Cancer - Ganguli et al. show that CDKN2A loss in Barrett’s esophagus prevents esophageal adenocarcinoma initiation by counterselecting subsequent TP53 loss and report context-dependent...

Best start of 2025: our study on the dual role of CDKN2A in cancer evolution (rdcu.be/d5pty) is out in @naturecancer.bsky.social! Big thanks to Piyali Ganguli who led it, all coauthors and @cancerresearchuk.org archuk.org @crick.ac.uk @qmbci.bsky.social bci.bsky.social for support! Summary below

#Immunology by First release now @science.org

Identification of APCs in the gut that promote Treg differentiation and how tolerance to food antigens is influenced by helminth infection

https://buff.ly/3DjNQ1e

By Maria Canesso, @danmucida.bsky.social , @victora.bsky.social and colleagues.

Sub-cellular Imaging of the Entire Protein-Coding Human Transcriptome (18933-plex) on FFPE Tissue Using Spatial Molecular Imaging
www.biorxiv.org/content/10.1...

With clear explanation of how this amazing technology achieves RNA (ISH) probe decoding at Hamming Distance of 4

NiCo is out! Our new algorithm for spatial transcriptomics data analysis predicts the crosstalk of cell types co-localized in tissue niches and sheds light on signalling mediators and downstream effects of cell-cell interactions by inferring covarying gene programs.

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

Excited to share a new algorithm that we have been working on over the last year.

💡 idea is to extend mutual nearest neighbors for
#spatial data. We call it spatial mutual nearest neighbors (spatialMNN) 😄

Thank you @haowen-zhou.bsky.social @pratibha-panwar.bsky.social who led this work! 👏 🧬🖥️🧪

Lgr5+ intestinal stem cells are required for organoid survival after genotoxic injury Summary: Primary intestinal organoids rely on Lgr5+ intestinal stem cells for survival following genotoxic injury induced by doxorubicin treatment, clarifying the cell types necessary for intestinal o...

Signal boosting our recent manuscript in @dev-journal.bsky.social since it’s now in “official” journal formatting (🥰)! 1/x

Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis - Nature Studies using mouse models of lung adenocarcinoma identify an association between age, iron homeostasis and tumour initiation potential that involves NUPR1 and lipocalin-2.

"Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis"

🧪
www.nature.com/articles/s41...

Phase I Results AMG 193, PRMT5 inhibitor targeting MTAP-deleted solid tumors: @AnnalsOncology

• 📊 ORR: 21.4% across 8 tumor types (incl. NSCLC, pancreatic & biliary)
• 🛡️ Safety: minimal myelosuppression; nausea & fatigue
• 🎯 MoA: Synthetic lethality in MTAP-deleted cells! @oncoalert.bsky.social

High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...

Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨
We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research!
Read more: bmcgenomics.biomedcentral.com/articles/10....
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Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues Patho-DBiT enables spatial profiling of a range of RNA species (i.e., mRNA, microRNA, tRNA, splicing isoform, etc.) all at once in clinical formalin-fixed paraffin-embedded tissue with high sensitivit...

This is why we are all in this field…to see, and one day to be able to produce work like this.

Patho-DBiT-seq

www.cell.com/cell/fulltex...

Interleukin-1α release during necrotic-like cell death generates myeloid-driven immunosuppression that restricts anti-tumor immunity Hänggi et al. investigate how tumor necroptosis regulates anti-tumor immunity and find an unexpected role for interleukin-1α (IL-1α) release by dying cells in promoting tumor growth by driving recruit...

IL-1 is SO RELEVANT in cancer 🔥 IL-1a released from dying tumor cells leads to myeloid cell recruitment and T cell suppression - targeting this pathway boosts efficacy of chemoTx and ICB

Beautiful study by @ruffell-lab.bsky.social lab n Cancer Cell

www.cell.com/cancer-cell/...

Graphical abstract of the paper.

How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...

Hi 👋🏻 can I join the group?