Marco Breinig

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

@science.org Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation | Science www.science.org/doi/10.1126/...

🚨 New paper from our lab just published in Nature🚨

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

Discover how 🌱 tumour formation is shaped by tissue context from the very beginning. Cancer is not driven by genetics alone

✨Fantastic team led by Greta Skrupskelyte, Eduardo Rojo, @hariajith.bsky.social

"Here, we present SPAtial Cell Exploration (SPACE), a spatial CRISPR screening platform that integrates whole-transcriptome profiling (~18,000 genes), multiplexed protein detection (~68 markers), and CRISPR perturbation mapping at subcellular resolution"

www.biorxiv.org/content/10.1...

Mohammad Vali Sanian, Arshia Hemmat, Amirhossein Vahidi, Jonas Maaskola, Jimmy Tsz Hang Lee, Stanislaw Makarchuk, Yeliz Demirci, ...
3D-Guided Scalable Flow Matching for Generating Volumetric Tissue Spatial Transcriptomics from Serial Histology
https://arxiv.org/abs/2511.14613

DeepSpaceDB
genomics.virus.kyoto-u.ac.jp/deepspacedb/

>2k #SpatialTranscriptomics Visium samples

👉Interactive, downloadable data analysis
👉Cross-sample/Cross-study comparison
👉Analyze your own data
👉Database-wide gene/pathway inquiry

#NucAcidRes 2026
academic.oup.com/nar/article/...

CytoTape in a neuron

Our CytoTape work is published today in Nature @nature.com! CytoTape is a genetically encoded, flexible, intracellular protein tape recorder for spatiotemporally scalable and multiplexed recording of cellular activities continuously across weeks in vitro and in vivo. www.nature.com/articles/s41...

Today I’m happy to release cyto, a tool I’ve developed at @arcinstitute.org to dramatically increase our computational throughput with 10x-flex single-cell processing by more than 16X!

Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus - Nature Methods DBiTplus represents an integrated experimental and computational workflow that unifies sequencing-based and imaging-based spatial omics, demonstrated by combining transcriptomic profiling and multiple...

DBiTplus: a workflow unifying sequencing-based and imaging-based spatial omics on the same tissue section.

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

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

A ‘time capsule for cells’ stores the secret experiences of their past Scientists have transformed enigmatic cell structures, called vaults, into storage units for messenger-RNA molecules made in the past.

The cellular storage units, called TimeVaults, could help unlock secrets to cancer-drug resistance and stem-cell biology

go.nature.com/49nE0ZY

SpatialZ generates virtual single-cell transcriptomics slices between experimentally measured sections, enabling accurate and efficient building of 3D cell atlases of different tissues.

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

Multiplexed Pan Soluble Ligandome Assaying via OASIS https://www.biorxiv.org/content/10.64898/2025.12.21.695830v1

Pan-cancer tumor classification by a holistic tumor microenvironment atlas #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2025.12.27.696641v1

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Towards Comprehensive Cellular Characterisation of H&E slides [new]
Enables detailed tumor microenvironment analysis via improved cell detection, segmentation, and classification across diverse cell types using a new pan-cancer dataset.

How do CRISPR edits actually change cells in real tissues?
Most single-cell CRISPR screens infer edits indirectly.
We present scPT-seq, a method that directly detects CRISPR mutations and transcriptomes in the same single cells in vivo, from John Hawkins and Siamak Redhai from Boutros Lab. 1/10

If you want to map the spatial composition of a tissue or organ, 3D mapping is not an option.

It is absolutely necessary.

Due to its inherent undersampling, 2D omic mapping is almost always misleading.

See details here: www.sciencedirect.com/science/arti...

Hepatic adaptation to chronic metabolic stress primes tumorigenesis Environmental stresses, such as a high-fat diet, disrupt liver cell balance by promoting pro-survival, developmental, and regenerative programs while impairing key tissue functions. These stress respo...

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

Transient hepatic reconstitution of trophic factors enhances aged immunity - Nature Using lipid nanoparticle delivery of mRNAs to the liver in aged mice, T cell function and declining immune cues can be restored.

Targeting T cells by delivering mRNAs encoding DLL1, FLT3L and IL-7 to liver improved peptide vaccine responses and restored anti-tumour immunity in aged mice. #NBThighlight
www.nature.com/articles/s41...

SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics Nature Methods - SpaceBar is a cellular barcoding strategy for simultaneous analysis of cell clonal and spatial identities.

Excited that SpaceBar is now out in Nature Methods!🥳

We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?

Most genes were driven by location, but some showed strong clonal patterns.

rdcu.be/eVhpc

Computational prediction of human genetic variants in the mouse genome - Nature Biotechnology A dictionary of human-to-mouse variants aids the design of mouse models of disease.

Computational prediction of human genetic variants in the mouse genome - @fsrmit.bsky.social @mitkochinstitute.bsky.social go.nature.com/4qbEfg1

Somatic evolution following cancer treatment in normal tissue - Nature High-depth sequencing of non-cancerous tissue from patients with metastatic cancer reveals single-base mutational signatures of alcohol, smoking and cancer treatments, and reveals how exogenous factors, including cancer therapies, affect somatic cell evolution.

Nature research paper: Somatic evolution following cancer treatment in normal tissue

go.nature.com/48MhLvf

NimbusImage: a cloud-computing platform for image analysis - Nature Methods Nature Methods - NimbusImage: a cloud-computing platform for image analysis

NimbusImage: a cloud computing platform for image analysis.

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

Multimodal AI generates virtual population for tumor microenvironment modeling GigaTIME leverages multimodal AI to generate virtual multiplex immunofluorescence (mIF) profiles from standard H&E slides, enabling comprehensive tumor immune microenvironment modeling across a large ...

A major advance in cancer using multimodal AI to do virtual proteomics of H&E slides, unraveling the tumor microenvironment, key proteins, biomarkers, and informing prognosis
@cellcellpress.bsky.social @hoifungpoon.bsky.social
@msftresearch.bsky.social

cell.com/cell/fulltex...

Cell-type deconvolution methods for spatial transcriptomics
rdcu.be/el1kC

High-fidelity human chromosome transfer and elimination The synthesis of human genomes and other gigabase-scale genomes will require new strategies. Here, we realized key steps in our pipeline for building synthetic human chromosomes. We established: (i) t...

@science.org🧬High-fidelity human chromosome transfer and elimination | Science www.science.org/doi/10.1126/... @wellcometrust.bsky.social @mrclmb.bsky.social

Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets - Nature Biotechnology A multi-institute, multi-platform initiative generates standard metrics and best practices for spatial transcriptomics analysis.

Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets - @jasmineplummer.bsky.social @lgmartelotto.bsky.social go.nature.com/4rBC1Z0

SpatialProp: tissue perturbation modeling with spatially resolved single-cell transcriptomics #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.64898/2025.11.30.691355v1

Decay of driver mutations shapes the landscape of intestinal transformation - Nature The order in which driver mutations of colorectal cancer occur in intestinal epithelium can determine whether clones are positively or negatively selected and can shape subsequent tumour development.

Nature research paper: Decay of driver mutations shapes the landscape of intestinal transformation

go.nature.com/49VIh7w

Inducible hepatic-associated lymphoid tissue (iHALT) unlocks liver functionality as a surrogate secondary lymphoid organ @nature.com @emoryuniversity.bsky.social @grakoui.bsky.social
www.nature.com/articles/s41...

Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks - Nature Methods This work introduces Deep-STARmap and Deep-RIBOmap, imaging-based sequencing platforms designed to profile transcriptional and translational activity in thick tissue blocks.

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