Evidence map›Paper›PMID 36452860›Full record

ArticleCell reports methods2022

Assessment of spatial transcriptomics for oncology discovery.

Anna Lyubetskaya, Brian Rabe, Andrew Fisher, Anne Lewin, Isaac Neuhaus, Constance Brett, Todd Brett, Ethel Pereira, Ryan Golhar, Sami Kebede and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell reports methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.

0numbers the graph read from it
0cells of the map it votes in
30citing 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

30 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Review
  9. Single-Cell Spatial Transcriptomic of Sjögren's Disease Salivary Glands.Methods in molecular biology (Clifton, N.J.) · 2026
    Article
  10. Article
  11. Review
  12. Article
  13. PLXDC1Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
    Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. 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

17 authors.

Anna LyubetskayaResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Brian RabeResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Andrew FisherResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Anne LewinResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Isaac NeuhausResearch and Early Development, Bristol Myers Squibb Company, Route 206 & Province Line Road, Princeton, NJ 08543, USA.
Constance BrettAggregate Genius, Inc., 560 Fulford-Ganges Road, Salt Spring Island, BC V8K 2K1, Canada.
Todd BrettAggregate Genius, Inc., 560 Fulford-Ganges Road, Salt Spring Island, BC V8K 2K1, Canada.
Ethel PereiraResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Ryan GolharResearch and Early Development, Bristol Myers Squibb Company, Route 206 & Province Line Road, Princeton, NJ 08543, USA.
Sami KebedeResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Alba Font-TelloResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Kathy MosureResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Nicholas Van WittenbergheResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Konstantinos J MavrakisResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Kenzie MacIsaacResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Benjamin J ChenResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.
Eugene DrokhlyanskyResearch and Early Development, Bristol Myers Squibb Company, 100 Binney Street, Cambridge, MA 02142, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Tumor heterogeneity is a major challenge for oncology drug discovery and development. Understanding of the spatial tumor landscape is key to identifying new targets and impactful model systems. Here, we test the utility of spatial transcriptomics (ST) for oncology discovery by profiling 40 tissue sections and 80,024 capture spots across a diverse set of tissue types, sample formats, and RNA capture chemistries. We verify the accuracy and fidelity of ST by leveraging matched pathology analysis, which provides a ground truth for tissue section composition. We then use spatial data to demonstrate the capture of key tumor depth features, identifying hypoxia, necrosis, vasculature, and extracellular matrix variation. We also leverage spatial context to identify relative cell-type locations showing the anti-correlation of tumor and immune cells in syngeneic cancer models. Lastly, we demonstrate target identification approaches in clinical pancreatic adenocarcinoma samples, highlighting tumor intrinsic biomarkers and paracrine signaling.

Indexed as

AdenocarcinomaPancreatic NeoplasmsBiomarkers, TumorGene Expression ProfilingHumansMedical OncologyTranscriptomeBiomarkers, Tumorbiomarkerscancer biologycancer genomicsdigital pathologygenomicsoncologypancreatic cancerspatial genomicsspatial transcriptomicstumors

Identifiers

PMID36452860
PMCPMC9701619

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.