Evidence map›Paper›PMID 37348462›Full record

ArticleCell systems2023

Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics.

David B Morse, Aleksandra M Michalowski, Michele Ceribelli, Joachim De Jonghe, Maria Vias, Deanna Riley, Theresa Davies-Hill, Ty Voss, Stefania Pittaluga, Christoph Muus and 7 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed, 1 pooled it
2.2field-weighted citation impact, top 13% of its field
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

11 citing papers in PubMed, 1 synthesis or guideline pooled it, 14 citations in OpenAlex.

  1. Pooled it
  2. Article
  3. Article
  4. Metabolic starvation-induced cell swelling drives solid stress in tumors.bioRxiv : the preprint server for biology · 2026
    Article
  5. Article
  6. Review
  7. Article
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  10. Review
  11. Lamination-based organoid spatially resolved transcriptomics technique for primary lung and liver organoid characterization.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
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

17 authors at 6 institutions in 3 countries.

David B MorseCavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, UK; Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Aleksandra M MichalowskiLaboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Michele CeribelliDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
Joachim De JongheDepartment of Biochemistry, University of Cambridge, Cambridge, UK.
Maria ViasCancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK.
Deanna RileyLaboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Theresa Davies-HillLaboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Ty VossDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
Stefania PittalugaLaboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Christoph MuusJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Jiamin LiuAdvanced Imaging and Microscopy Resource, National Institutes of Health Clinical Center, Bethesda, MD, USA.
Samantha BoyleCancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK.
David A WeitzJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Department of Physics, Harvard University, Cambridge, MA, USA.
James D BrentonCancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK.
Jason D BuenrostroBroad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Tuomas P J KnowlesCavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK. Electronic address: tpjk2@cam.ac.uk.
Craig J ThomasDivision of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA; Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. Electronic address: craigt@mail.nih.gov.
National Institutes of Health · USBroad Institute · USCancer Research UK · GBUniversity of Cambridge · GBHarvard University · USNational Institutes of Health Clinical Center · US

Funding

Research Services Section (RSS)ZICTR000242 · NCATS · NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES · PI WILSON, KELLI · 2015 to 2025
$64.9M
Medical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0M
Disease model design and evaluationZIATR000473 · NCATS · NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES · PI THOMAS, CRAIG · 2023 to 2025
$1.1M
Cancer Research UK 15601Cancer Research UK 22905Intramural NIH HHS Z99 TR999999NIGMS NIH HHS T32 GM007753Wellcome Trust
6 · The paper itself

Abstract

Single-cell RNA sequencing (scRNA-seq) is a powerful technique for describing cell states. Identifying the spatial arrangement of these states in tissues remains challenging, with the existing methods requiring niche methodologies and expertise. Here, we describe segmentation by exogenous perfusion (SEEP), a rapid and integrated method to link surface proximity and environment accessibility to transcriptional identity within three-dimensional (3D) disease models. The method utilizes the steady-state diffusion kinetics of a fluorescent dye to establish a gradient along the radial axis of disease models. Classification of sample layers based on dye accessibility enables dissociated and sorted cells to be characterized by transcriptomic and regional identities. Using SEEP, we analyze spheroid, organoid, and in vivo tumor models of high-grade serous ovarian cancer (HGSOC). The results validate long-standing beliefs about the relationship between cell state and position while revealing new concepts regarding how spatially unique microenvironments influence the identity of individual cells within tumors.

Indexed as

Gene Expression ProfilingTranscriptomeKineticsOrganoidsPhysicsgenomicsoncologyovarian cancerRNA sequencingscRNA-seqsingle-cell transcriptomicsspatially resolved transcriptomicsspatial transcriptomics

Identifiers

PMID37348462
PMCPMC10424188
OpenAlexW4381549576

What OpenQuestion holds

Textmetadata
LicenceTDM
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 OpenQuestion graph.