Evidence map›Paper›PMID 41266370›Full record

ArticleNature communications2025

Combinatorial protein engineering identifies potent CRISPR activators with reduced toxicity.

Marla Giddins, Alexander F Kratz, Mark B De Los Santos, Antoine Forget, Richa Tiwari, Gwendolyn Jang, Tomasz Blazejewski, Chuyan Qin, Yiming Huang, Yeh-Hsing Lao and 7 more

Abstract read
In one paragraph

Article in Nature communications, 2025. 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

17 authors.

Marla Giddins *Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-4416-4395
Alexander F Kratz *Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
Mark B De Los SantosDepartment of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-7195-5141
Antoine ForgetQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
Richa TiwariQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-3069-8510
Gwendolyn JangQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-7806-9874
Tomasz BlazejewskiDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
Chuyan QinDepartment of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.
Yiming HuangDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0003-1932-2803
Yeh-Hsing LaoDepartment of Biomedical Engineering, Columbia University, New York, NY, USA.ORCID http://orcid.org/0000-0002-7990-199X
Thomas FalconerDepartment of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.ORCID http://orcid.org/0000-0001-6904-1394
Kam W LeongDepartment of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
Nevan KroganQuantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0003-4902-337X
Max StallerDepartment of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-9094-5697
Harris WangDepartment of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
Lai WeiDepartment of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA. larrywei@health.ucsd.edu.ORCID http://orcid.org/0000-0002-2892-2977
Alejandro ChavezDepartment of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA. chavez2@health.ucsd.edu.ORCID http://orcid.org/0000-0001-5626-7140

Funding

Tumor Biology and Microenvironment ProgramP30CA013696 · NCI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI Anil K Rustgi · 1985 to 2026
$115.3M
The Cancer Cell Map Initiative v2.0U54CA274502 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Trey Ideker · 2022 to 2026
$14.2M
A high-performance and versatile technology for precision microbiome engineeringR01EB031935 · NIBIB · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI Samuel Henry Sternberg, Harris H Wang · 2021 to 2026
$3.3M
Methods to Rapidly Explore Combinatorial Diversity and Their Application to CRISPR-Cas9 SystemsDP2NS131566 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Alejandro Chavez · 2022 to 2026
$2.4M
BD Biosciences InfluxS10OD020056 · OD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI SNOECK, HANS-WILLEM E · 2015 to 2015
$600k
NCI NIH HHS P30 CA013696NCI NIH HHS U54 CA274502NIBIB NIH HHS R01 EB031935NIH HHS S10 OD020056NINDS NIH HHS DP2 NS131566United States Department of Defense | Defense Advanced Research Projects Agency (DARPA) HR0011-19-2-0009U.S. Department of Health & Human Services | National Institutes of Health (NIH) 1R01EB031935U.S. Department of Health & Human Services | National Institutes of Health (NIH) DP2NS131566-01
6 · The paper itself

Abstract

Current protein engineering methods are inadequate to explore the combinatorial potential offered by nature's vast repertoire of protein domains-limiting our ability to create optimal synthetic tools. To overcome this barrier, we develop an approach to create and test thousands of chimeric proteins and employ it to probe an expansive combinatorial landscape of over 15,000 multi-domain CRISPR activators. Our findings indicate that many activators produce substantial cellular toxicity, often unrelated to their capacity to regulate gene expression. We also explore the biochemical features of activation domains and determine how their combinatorial interactions shape activator behavior. Finally, we identify two potent CRISPR activators, MHV and MMH, and demonstrate their enhanced activity across diverse targets and cell types compared to the gold-standard MCP activator, synergistic activation mediator (SAM).

Indexed as

Clustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Cas SystemsProtein EngineeringAnimalsHEK293 CellsHumansProtein DomainsRecombinant Fusion ProteinsRecombinant Fusion Proteins

Identifiers

PMID41266370
PMCPMC12706070

What OpenQuestion holds

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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.