Evidence map›Paper›PMID 40081369›Full record

ArticleCell2025

Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits.

Loϊc Binan, Aiping Jiang, Serwah A Danquah, Vera Valakh, Brooke Simonton, Jon Bezney, Robert T Manguso, Kathleen B Yates, Ralda Nehme, Brian Cleary and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.

0numbers the graph read from it
0cells of the map it votes in
75citing 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

75 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
  4. Review
  5. Review
  6. A meta-interaction basis for cell-cell communication in tissues.bioRxiv : the preprint server for biology · 2026
    Article
  7. Article
  8. Article
  9. Review
  10. Review
  11. Review
  12. Article
  13. Review
  14. Review
  15. Review
  16. Review
  17. Bridging maternal effects and epitranscriptomics: A novel perspective in developmental biology.Developmental dynamics : an official publication of the American Association of Anatomists · 2026
    Review
  18. Review
  19. Article
  20. Article

15 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Loϊc BinanSpatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Aiping JiangCancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02144, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
Serwah A DanquahSpatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Vera ValakhSpatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Brooke SimontonKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Jon BezneyKlarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Robert T MangusoCancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02144, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
Kathleen B YatesCancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02144, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
Ralda NehmeStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Brian ClearyFaculty of Computing and Data Sciences, Boston University, Boston, MA 02215, USA; Department of Biology, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Program in Bioinformatics, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA. Electronic address: bcleary@bu.edu.
Samouil L FarhiSpatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: sfarhi@broadinstitute.org.

Funding

Unraveling the Genetic Programs Engaged in ASD Neurons Through Coupled Transcriptomic and Phenotypic ReadoutsR01MH128366 · NIMH · BROAD INSTITUTE, INC. · PI Samouil Farhi, Ralda Nehme · 2022 to 2026
$3.7M
Scaling up spatial RNA profiling with compressed sensingRF1MH121289 · NIMH · BROAD INSTITUTE, INC. · PI CHEN, FEI, ELDAR, YONINA · 2019 to 2019
$1.6M
NIMH NIH HHS R01 MH128366NIMH NIH HHS RF1 MH121289
6 · The paper itself

Abstract

Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but they have not yet leveraged the power of highly plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present a combination of imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs (Perturb-FISH). Perturb-FISH recovers intracellular effects that are consistent with single-cell RNA-sequencing-based readouts of perturbation effects (Perturb-seq) in a screen of lipopolysaccharide response in cultured monocytes, and it uncovers intercellular and density-dependent regulation of the innate immune response. Similarly, in three-dimensional xenograft models, Perturb-FISH identifies tumor-immune interactions altered by genetic knockout. When paired with a functional readout in a separate screen of autism spectrum disorder risk genes in human-induced pluripotent stem cell (hIPSC) astrocytes, Perturb-FISH shows common calcium activity phenotypes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a general method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.

Indexed as

Clustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Cas SystemsGene Regulatory NetworksTranscriptomeAnimalsAstrocytesAutism Spectrum DisorderGene Expression ProfilingHumansImmunity, InnateInduced Pluripotent Stem CellsLipopolysaccharidesMiceMonocytesSingle-Cell AnalysisLipopolysaccharidesmultimodal screeningpooled CRISPR screenpooled optical profilingsingle-cell perturbationsspatial transcriptomics

Identifiers

PMID40081369
PMCPMC12135205

What OpenQuestion 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 OpenQuestion graph.