technologiesTechnologyEmerging

Single-cell & spatial profiling

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

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.

Schematic · not to scale

Tumour niche · Immune cells, in place

How it works

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

Latest papers

Literature trend15,315 papers in the last 12 months+30% vs prior 12How this is computed

Latest papers · live from Europe PMC

Open in Europe PMC

Query for this technology: (TITLE:"single-cell RNA sequencing" OR ABSTRACT:"single-cell RNA sequencing" OR TITLE:"spatial transcriptomics" OR ABSTRACT:"spatial transcriptomics" OR TITLE:"single-cell" OR ABSTRACT:"single-cell") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about Single-cell & spatial profiling, not a curated reading list.

Connected

fronts

2

Diagnostics & Biomarkers Drug Discovery Platforms

technologies

8

Geneformer Nicheformer (spatial single-cell)scGPT Spatial biology instruments Spatial-omics-guided treatment selection State (Arc Institute perturbation model)Targeting the tumour's own microbes Targeting tumour mechanics and pressure

companies

3

10x Genomics Elucidate Bio Valius Sciences

institutions

10

BC Cancer Cancer Research UK Cambridge Centre / CRUK Cambridge Institute Chan Zuckerberg Biohub Garvan Institute of Medical Research / Kinghorn Cancer Centre Institut Pasteur Max Delbrück Center for Molecular Medicine University Hospital Zurich / Comprehensive Cancer Center Zurich Weizmann Institute of Science Wellcome Wellcome Sanger Institute

pathways

8

Chromosomal instability & aneuploidy Cold tumours: immune deserts and exclusion Epithelial–mesenchymal transition & drug efflux Fibroblast activation, desmoplasia & matrix stiffness Invasion: proteases, adhesion & the invasive front The metastatic cascade The pre-metastatic niche Tumour microenvironment (TME)

roadmaps

1

Virtual cell roadmap: from bulk omics to a predictive model of a cancer cell

ideas

27

A bone marrow niche on a chip to study human dormancy A global rapid tissue donation network for metastatic disease A national rapid research autopsy network for end-stage cancer A short pre-surgery drug window as the default early test of new agents An open foundation model of the cancer cell trained on perturbation data An open model of every cancer cell state, built from perturbation atlases Block the survival signals the tumour's neighbours provide Clear the suppressive neutrophils out of pancreatic tumours first Comparability by design: a digital twin and sentinel panel for cell process changes Find the parts of a tumour the drug never reaches Grow immune command posts inside tumours Implant a tiny device that tests twenty drugs inside the patient's own tumour Link single-cell and spatial tumour atlases to clinical outcomes Make every cold tumour hot: a coordinated programme to reprogramme immune-excluded tumours Map which tumour clones sit next to which immune cells before choosing therapy Match therapy to the type of scar-forming cell in the tumour Pool every immunotherapy trial's biomarker data into one commons Re-map the tumour's surface proteins before choosing the next antibody drug Reprogramme suppressive macrophages instead of trying to delete them Select patients for cell therapy by whether their tumour holds reactive T cells Standards for spatial and multiplex tissue biomarkers before they reach the clinic Test drugs on freshly cut slices of the patient's own tumour Turn the map of immune cells inside a tumour into a standardised test Two-week pre-operative windows to compare combination biology head to head Use pre-surgery immunotherapy windows as the field's biomarker engine What actually holds T cells at the tumour border?What decides which disseminated cells ever colonise?

collections

1

CZ CELLxGENE / Human Cell Atlas

people

4

Bradley E. Bernstein Miriam Merad Trevor J. Pugh Woong-Yang Park

bottlenecks

2

Cold tumours and the immunosuppressive microenvironment Tumour heterogeneity and clonal evolution

Evidence strength11/100 · Preliminary

How much and what kind of evidence, not how big the benefit. Click for the breakdown.

Status: emerging+11
No linked product0

Formula disclosed on the evidence page.

Not yet reviewedNeeds expert (scientific) review. Review this page or see the review queue and roster.

ProvenanceLast edited 2026-09-09 · Jude Gomila · Editing pass: every TL;DR and summary stands alone · diff · file · history

Wikipedia

Spatial transcriptomics

Data

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