Evidence map›Paper›PMID 39960754›Full record

ArticleeLife2025

Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning.

Gabriella O Estevam, Edmond Linossi, Jingyou Rao, Christian B Macdonald, Ashraya Ravikumar, Karson M Chrispens, John A Capra, Willow Coyote-Maestas, Harold Pimentel, Eric A Collisson and 2 more

Abstract read
In one paragraph

Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing 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

11 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors.

Gabriella O EstevamDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0002-9142-7805
Edmond LinossiCardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0002-8039-573X
Jingyou RaoDepartment of Computer Science, University of California, Los Angeles, Los Angeles, United States.
Christian B MacdonaldDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0002-0201-8832
Ashraya RavikumarDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.
Karson M ChrispensDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.
John A CapraBakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0001-9743-1795
Willow Coyote-MaestasDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0001-9614-5340
Harold PimentelDepartment of Computer Science, University of California, Los Angeles, Los Angeles, United States.
Eric A CollissonHuman Biology, Fred Hutchinson Cancer Center, Seattle, United States.ORCID https://orcid.org/0000-0001-8037-9388
Natalia JuraCardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0001-5129-641X
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.ORCID https://orcid.org/0000-0002-5080-2859

Funding

Equipment for Discovering and Manipulating Macromolecular Conformational EnsemblesR35GM145238 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James Solomon Fraser · 2022 to 2026
$3.1M
Optimizing Treatment Approaches to Lung Cancers Harboring MET Exon 14 mutationsR01CA239604 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI COLLISSON, ERIC · 2019 to 2023
$2.0M
Personalized Structural Biology: Enabling Exome Interpretation in Undiagnosed DiseasesR01LM013434 · NLM · VANDERBILT UNIVERSITY · PI CAPRA, JOHN ANTHONY, MEILER, JENS · 2021 to 2024
$1.4M
Illumina NovaSeq 6000 Sequencing SystemS10OD028511 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHOW, ERIC D · 2020 to 2020
$583k
NCI NIH HHS CA239604NCI NIH HHS R01 CA239604NIGMS NIH HHS GM145238NIGMS NIH HHS R35 GM145238NIH HHS LM013434NIH HHS S10 OD028511NLM NIH HHS R01 LM013434
6 · The paper itself

Abstract

Mutations in the kinase and juxtamembrane domains of the MET Receptor Tyrosine Kinase are responsible for oncogenesis in various cancers and can drive resistance to MET-directed treatments. Determining the most effective inhibitor for each mutational profile is a major challenge for MET-driven cancer treatment in precision medicine. Here, we used a deep mutational scan (DMS) of ~5764 MET kinase domain variants to profile the growth of each mutation against a panel of 11 inhibitors that are reported to target the MET kinase domain. We validate previously identified resistance mutations, pinpoint common resistance sites across type I, type II, and type I ½ inhibitors, unveil unique resistance and sensitizing mutations for each inhibitor, and verify non-cross-resistant sensitivities for type I and type II inhibitor pairs. We augment a protein language model with biophysical and chemical features to improve the predictive performance for inhibitor-treated datasets. Together, our study demonstrates a pooled experimental pipeline for identifying resistance mutations, provides a reference dictionary for mutations that are sensitized to specific therapies, and offers insights for future drug development.

Indexed as

Drug Resistance, NeoplasmMutationProtein Kinase InhibitorsProto-Oncogene Proteins c-metHumansProtein DomainsMET protein, humanProtein Kinase InhibitorsProto-Oncogene Proteins c-metbiochemistrychemical biologydrug discoveryhumanmutagenesisprotein kinase

Identifiers

PMID39960754
PMCPMC11832172

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.