# Single-cell & spatial profiling

Source: https://onco.cc/technologies/single-cell-spatial/  
OnCo record `single-cell-spatial` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

Reading the genes of each individual cell, and mapping where each cell sits in the tumour.

## Summary

scRNA-seq (10x Genomics) resolves tumour, immune, and stromal populations; spatial transcriptomics (Visium, Xenium, CosMx, MERFISH) and multiplex protein imaging (CODEX, IMC) keep tissue architecture. Revealing how ADC bystander killing, T-cell exclusion, and resistance niches work. Research-grade; entering trials as correlative science.

## Fields

- Kind: Technology
- Status: emerging
- Last checked: 2026-09-04
- Principle: RNA is captured with barcodes per cell or per spatial location, or read by imaging-based in situ hybridisation for hundreds to thousands of genes.
- Strengths: Resolves heterogeneity and microenvironment; Discovery engine for new targets
- Limitations: Cost, throughput, analysis burden; Not yet clinically actionable

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Spatial_transcriptomics
- Wikipedia: https://en.wikipedia.org/wiki/Spatial_transcriptomics

## Connected records

- ideas: [A bone marrow niche on a chip to study human dormancy](https://onco.cc/ideas/idea-bio2-marrow-niche-on-chip/), [A global rapid tissue donation network for metastatic disease](https://onco.cc/ideas/idea-bio2-rapid-autopsy-commons/), [A national rapid research autopsy network for end-stage cancer](https://onco.cc/ideas/idea-bio1-rapid-autopsy-network/), [A short pre-surgery drug window as the default early test of new agents](https://onco.cc/ideas/idea-tr1-window-of-opportunity-default/), [An open foundation model of the cancer cell trained on perturbation data](https://onco.cc/ideas/idea-data-open-cell-foundation-model/), [An open model of every cancer cell state, built from perturbation atlases](https://onco.cc/ideas/idea-moon-open-cancer-cell-state-model/), [Block the survival signals the tumour's neighbours provide](https://onco.cc/ideas/idea-bio1-stromal-resistance-blockade/), [Clear the suppressive neutrophils out of pancreatic tumours first](https://onco.cc/ideas/idea-bio2-cxcr2-neutrophil-blockade/), [Comparability by design: a digital twin and sentinel panel for cell process changes](https://onco.cc/ideas/idea-reg-comparability-by-design-digital-twin/), [Find the parts of a tumour the drug never reaches](https://onco.cc/ideas/idea-bio1-drug-exposure-sanctuary-mapping/), [Grow immune command posts inside tumours](https://onco.cc/ideas/idea-bio2-tertiary-lymphoid-induction/), [Implant a tiny device that tests twenty drugs inside the patient's own tumour](https://onco.cc/ideas/idea-bio2-implantable-microdevice-screen/), [Link single-cell and spatial tumour atlases to clinical outcomes](https://onco.cc/ideas/idea-data-atlas-to-outcome-linkage/), [Make every cold tumour hot: a coordinated programme to reprogramme immune-excluded tumours](https://onco.cc/ideas/idea-moon-cold-to-hot-programme/), [Map which tumour clones sit next to which immune cells before choosing therapy](https://onco.cc/ideas/idea-bio1-spatial-clone-immune-map/), [Match therapy to the type of scar-forming cell in the tumour](https://onco.cc/ideas/idea-bio2-caf-subtype-assignment/), [Pool every immunotherapy trial's biomarker data into one commons](https://onco.cc/ideas/idea-bio2-io-biomarker-data-commons/), [Re-map the tumour's surface proteins before choosing the next antibody drug](https://onco.cc/ideas/idea-bio1-antigen-mapping-at-progression/), [Reprogramme suppressive macrophages instead of trying to delete them](https://onco.cc/ideas/idea-bio2-trem2-myeloid-reprogramming/), [Select patients for cell therapy by whether their tumour holds reactive T cells](https://onco.cc/ideas/idea-bio2-til-reactivity-selection/), [Standards for spatial and multiplex tissue biomarkers before they reach the clinic](https://onco.cc/ideas/idea-tr2-spatial-biomarker-standards/), [Test drugs on freshly cut slices of the patient's own tumour](https://onco.cc/ideas/idea-bio1-tumour-slice-cultures/), [Turn the map of immune cells inside a tumour into a standardised test](https://onco.cc/ideas/idea-bio2-spatial-signature-cdx/), [Two-week pre-operative windows to compare combination biology head to head](https://onco.cc/ideas/idea-tr2-window-of-opportunity-triplets/), [Use pre-surgery immunotherapy windows as the field's biomarker engine](https://onco.cc/ideas/idea-bio2-neoadjuvant-biomarker-engine/), [What actually holds T cells at the tumour border?](https://onco.cc/ideas/idea-immune-exclusion-drivers/), [What decides which disseminated cells ever colonise?](https://onco.cc/ideas/idea-dtc-colonisation-determinants/)
- fronts: [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/), [Drug Discovery Platforms](https://onco.cc/fronts/drug-discovery/)
- companies: [10x Genomics](https://onco.cc/companies/10x-genomics/), [Elucidate Bio](https://onco.cc/companies/elucidate-bio/), [Immunai](https://onco.cc/companies/immunai/), [Menarini Silicon Biosystems](https://onco.cc/companies/menarini-silicon-biosystems/), [Mission Bio](https://onco.cc/companies/mission-bio/), [Noetik](https://onco.cc/companies/noetik/), [Nucleai](https://onco.cc/companies/nucleai/), [Origin Bio](https://onco.cc/companies/origin-bio/), [Valius Sciences](https://onco.cc/companies/valius/)
- technologies: [Flow cytometers](https://onco.cc/technologies/flow-cytometers/), [Geneformer](https://onco.cc/technologies/geneformer/), [Imaging mass cytometry](https://onco.cc/technologies/imaging-mass-cytometry/), [Nicheformer (spatial single-cell)](https://onco.cc/technologies/nicheformer/), [scGPT](https://onco.cc/technologies/scgpt/), [Spatial biology instruments](https://onco.cc/technologies/spatial-biology-instruments/), [Spatial transcriptomics](https://onco.cc/technologies/spatial-transcriptomics/), [Spatial-omics-guided treatment selection](https://onco.cc/technologies/spatial-omics-guided-therapy/), [State (Arc Institute perturbation model)](https://onco.cc/technologies/state-arc/), [Targeting the tumour's own microbes](https://onco.cc/technologies/tumour-microbiome-targeting/), [Targeting tumour mechanics and pressure](https://onco.cc/technologies/mechanobiology-therapy/)
- cancers: [Pancreatic ductal adenocarcinoma](https://onco.cc/cancers/pancreatic/)
- key papers: [Association of high tumor mutation burden in non-small cell lung cancers with increased immune infiltration and improved clinical outcomes of PD-L1 blockade across PD-L1 expression levels](https://onco.cc/key-papers/paper-ricciuti-tmb-pd-l1-levels-jama-oncol-2022/), [Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts](https://onco.cc/key-papers/paper-elyada-antigen-presenting-cafs-single-cell-cancer-discov-2019/), [Spatially confined sub-tumor microenvironments in pancreatic cancer](https://onco.cc/key-papers/paper-grunwald-subtme-pancreatic-cell-2021/), [The landscape of somatic mutation in normal colorectal epithelial cells](https://onco.cc/key-papers/paper-lee-six-somatic-mutation-normal-colorectal-crypts-nature-2019/), [Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution](https://onco.cc/key-papers/paper-chan-seng-yue-pancreatic-transcription-phenotypes-nat-genet-2020/)
- terms: [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [Fibroblast subtypes in the pancreatic cancer stroma (myCAF, iCAF and apCAF)](https://onco.cc/terms/caf-subtypes-pancreatic/), [Single-cell RNA sequencing (scRNA-seq, 10x Chromium)](https://onco.cc/terms/single-cell-rna-seq/), [Spatial transcriptomics platforms (Visium HD, Xenium, MERFISH, CosMx, CODEX)](https://onco.cc/terms/spatial-transcriptomics-platforms/)
- pathways: [Chromosomal instability & aneuploidy](https://onco.cc/pathways/chromosomal-instability/), [Cold tumours: immune deserts and exclusion](https://onco.cc/pathways/immune-desert-exclusion/), [Epithelial-mesenchymal transition & drug efflux](https://onco.cc/pathways/emt/), [Fibroblast activation, desmoplasia & matrix stiffness](https://onco.cc/pathways/caf-activation-desmoplasia/), [Invasion: proteases, adhesion & the invasive front](https://onco.cc/pathways/invasion-ecm-degradation/), [The metastatic cascade](https://onco.cc/pathways/metastatic-cascade/), [The pre-metastatic niche](https://onco.cc/pathways/pre-metastatic-niche/), [Tumour microenvironment (TME)](https://onco.cc/pathways/tumor-microenvironment/)
- collections: [CZ CELLxGENE / Human Cell Atlas](https://onco.cc/collections/cellxgene-hca/)
- people: [Bradley E. Bernstein](https://onco.cc/people/bradley-bernstein/), [Miriam Merad](https://onco.cc/people/miriam-merad/), [Trevor J. Pugh](https://onco.cc/people/trevor-pugh/), [Woong-Yang Park](https://onco.cc/people/park-woong-yang/)
- bottlenecks: [Cold tumours and the immunosuppressive microenvironment](https://onco.cc/bottlenecks/b-tme-immunosuppression/), [Tumour heterogeneity and clonal evolution](https://onco.cc/bottlenecks/b-tumor-heterogeneity/)
- institutions: [BC Cancer](https://onco.cc/institutions/bc-cancer/), [Cancer Research UK Cambridge Centre / CRUK Cambridge Institute](https://onco.cc/institutions/cruk-cambridge-centre/), [Chan Zuckerberg Biohub](https://onco.cc/institutions/cz-biohub/), [Garvan Institute of Medical Research / Kinghorn Cancer Centre](https://onco.cc/institutions/garvan-institute/), [Institut Pasteur](https://onco.cc/institutions/institut-pasteur/), [Max Delbrück Center for Molecular Medicine](https://onco.cc/institutions/mdc-berlin/), [University Hospital Zurich / Comprehensive Cancer Center Zurich](https://onco.cc/institutions/usz-zurich/), [Weizmann Institute of Science](https://onco.cc/institutions/weizmann/), [Wellcome](https://onco.cc/institutions/wellcome/), [Wellcome Sanger Institute](https://onco.cc/institutions/wellcome-sanger/)
- roadmaps: [Diagnostics roadmap: stains → gene panels → blood tests that decide treatment](https://onco.cc/roadmaps/diagnostics-roadmap/), [Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell](https://onco.cc/roadmaps/virtual-cell/)

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JSON: https://onco.cc/api/v1/entities/single-cell-spatial.json