Evidence map›Paper›PMID 42321208›Full record

ArticleNature communications2026

Single-cell RNA sequencing profiles drug activity within spatially engineered 3D cultures.

Jessica J King, Alireza Mowla, Jessica A Kretzmann, Nishka Bhalla, Giselle Sugianto, Marck Norret, Ulrich D Kadolsky, Munir Iqbal, Alka Saxena, Sebastian E Amos and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Jessica J KingSchool of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
Alireza MowlaBRITElab, Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, Australia.
Jessica A KretzmannSchool of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.ORCID http://orcid.org/0000-0002-8680-7766
Nishka BhallaSchool of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.ORCID http://orcid.org/0009-0004-9066-590X
Giselle SugiantoSchool of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
Marck NorretSchool of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
Ulrich D KadolskyGenomics WA, Harry Perkins Institute of Medical Research, The Kids Research Institute Australia, and The University of Western Australia, Nedlands, Perth, WA, Australia.ORCID http://orcid.org/0000-0002-7016-1956
Munir IqbalGenomics WA, Harry Perkins Institute of Medical Research, The Kids Research Institute Australia, and The University of Western Australia, Nedlands, Perth, WA, Australia.
Alka SaxenaGenomics WA, Harry Perkins Institute of Medical Research, The Kids Research Institute Australia, and The University of Western Australia, Nedlands, Perth, WA, Australia.
Sebastian E AmosSchool of Human Sciences, University of Western Australia, Perth, WA, Australia.
Yu Suk ChoiSchool of Human Sciences, University of Western Australia, Perth, WA, Australia.ORCID http://orcid.org/0000-0002-0241-0447
Brendan F KennedyBRITElab, Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, WA, Australia.
K Swaminathan IyerSchool of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.ORCID http://orcid.org/0000-0001-9329-4930
Nicole M SmithSchool of Molecular Sciences, The University of Western Australia, Perth, WA, Australia. nicole.smith@uwa.edu.au.
Cameron W EvansSchool of Molecular Sciences, The University of Western Australia, Perth, WA, Australia. cameron.evans@utas.edu.au.ORCID http://orcid.org/0000-0003-2312-9803

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Spatial transcriptomic techniques provide a wealth of information useful in guiding drug development, while three-dimensional (3D) cell cultures have demonstrated power in accelerating drug approvals. However, techniques for robust spatial analysis of 3D cultures are limited. Here, we present a transfection-based method for constructing cellular spheroids through a layer-by-layer approach, in which DNA barcodes encode the spatial positioning of cells. Our technique facilitates multiplex single-cell RNA sequencing, providing spatial maps of gene expression and drug response, while correlative imaging reveals the locations of barcoded cell populations and quantifies local tissue elasticity. We show that model HeLa 3D spheroids display heterogeneous responses to drugs, which may arise through diffusion gradients of the drug, or from differences in metabolism, nutrient supply, and cellular stressors. The ability to create spatially encoded cellular assemblies may help to reveal spatial variation in gene expression within 3D culture models.

Indexed as

Cell Culture Techniques, Three DimensionalSequence Analysis, RNASingle-Cell AnalysisHeLa CellsHumansSingle-Cell Gene Expression AnalysisSpatial TranscriptomicsSpheroids, CellularTransfection

Identifiers

PMID42321208
PMCPMC13434128

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.