Evidence map›Paper›PMID 39574586›Full record

ArticlebioRxiv : the preprint server for biology2024

A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS.

Sami Nourreddine, Yesh Doctor, Amir Dailamy, Antoine Forget, Yi-Hung Lee, Becky Chinn, Hammza Khaliq, Benjamin Polacco, Monita Muralidharan, Emily Pan and 13 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

5 · Who and what money

Authors and funding

23 authors.

Sami NourreddineDepartment of Bioengineering, University of California San Diego, CA, USA.
Yesh DoctorDepartment of Bioengineering, University of California San Diego, CA, USA.
Amir DailamyDepartment of Bioengineering, University of California San Diego, CA, USA.
Antoine ForgetQuantitative Biosciences Institute (QBI), University of California San Francisco, CA, USA.
Yi-Hung LeeDepartment of Bioengineering, University of California San Diego, CA, USA.
Becky ChinnDepartment of Bioengineering, University of California San Diego, CA, USA.
Hammza KhaliqDepartment of Bioengineering, University of California San Diego, CA, USA.
Benjamin PolaccoQuantitative Biosciences Institute (QBI), University of California San Francisco, CA, USA.
Monita MuralidharanQuantitative Biosciences Institute (QBI), University of California San Francisco, CA, USA.
Emily PanDepartment of Bioengineering, University of California San Diego, CA, USA.
Yifan ZhangDepartment of Bioengineering, University of California San Diego, CA, USA.
Alina SigaevaDivision of Cellular and Clinical Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden.
Jan Niklas HansenDepartment of Bioengineering, Stanford University, CA, USA.
Jiahao GaoSchool of Medicine, University of California San Diego, CA, USA.
Jillian A ParkerSchool of Medicine, University of California San Diego, CA, USA.
Kirsten ObernierGladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
Timothy ClarkDepartment of Medicine, University of Virginia, VA, USA.
Jake Y ChenDepartment of Computer Science, The University of Alabama at Birmingham, VA, USA.
Christian MetalloDepartment of Bioengineering, University of California San Diego, CA, USA.
Emma LundbergDepartment of Bioengineering, Stanford University, CA, USA.
Trey IdekerDepartment of Bioengineering, University of California San Diego, CA, USA.
Nevan KroganQuantitative Biosciences Institute (QBI), University of California San Francisco, CA, USA.
Prashant MaliDepartment of Bioengineering, University of California San Diego, CA, USA.

Funding

VIRAL MALIGNANCYP30CA023100 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Dwayne G. Stupack · 1985 to 2026
$124.9M
Bridge2AI: Cell Maps for AI (CM4AI) Data Generation ProjectOT2OD032742 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Jean-Christophe Bélisle-Pipon, TIMOTHY W CLARK · 2022 to 2026
$21.5M
The Cancer Cell Map Initiative v2.0U54CA274502 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Emma Lundberg · 2022 to 2026
$14.2M
Next generation massively multiplexed combinatorial genetic screensR01HG012351 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Trey Ideker, Prashant Mali · 2023 to 2026
$2.7M
NEURAXIAL AAVS TARGETING DRG CHANNELS INVOLVED IN CHRONIC POST INFLAMMATORY PAINR01NS131560 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI TONY L. YAKSH · 2024 to 2026
$1.8M
Illumina NovaSeq 6000 Sequencing SystemS10OD026929 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEPSEN, KRISTEN LYNN · 2019 to 2019
$600k
NCI NIH HHS P30 CA023100NCI NIH HHS U54 CA274502NHGRI NIH HHS R01 HG012351NIH HHS OT2 OD032742NIH HHS S10 OD026929NINDS NIH HHS R01 NS131560
6 · The paper itself

Abstract

Towards comprehensively investigating the genotype-phenotype relationships governing the human pluripotent stem cell state, we generated an expressed genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J human induced pluripotent stem cells (hiPSCs) mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes. Using the transcriptional phenotypes, we created a minimum distortion embedding map of the pluripotent state, demonstrating rich recapitulation of protein complexes, such as strong co-clustering of MRPL, BAF, SAGA, and Ragulator family members. Additionally, we uncovered transcriptional regulators that are uncoupled from cell fitness, discovering potential novel pluripotency (JOSD1, RNF7) and metabolic factors (ZBTB41). We validated these findings via phenotypic, protein-interaction, and metabolic tracing assays. Finally, we propose a contrastive human-cell engineering framework (CHEF), a machine learning architecture that learns from perturbation cell atlases to predict perturbation recipes that achieve desired transcriptional states. Taken together, our study presents a comprehensive resource for interrogating the regulatory networks governing pluripotency.

Identifiers

PMID39574586
PMCPMC11580897

What Socratic 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 Socratic graph.