Evidence map›Paper›PMID 41429940›Full record

ArticleEMBO reports2026

Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants.

Anne E van Vlimmeren, Lauren C Tang, Ziyuan Jiang, Abhishek Iyer, Rashmi Voleti, Konstantin Krismer, Jellert T Gaublomme, Marko Jovanovic, Neel H Shah

Abstract read
In one paragraph

Article in EMBO reports, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Anne E van VlimmerenDepartment of Chemistry, Columbia University, New York, NY, 10027, USA.ORCID 0000-0003-0379-4945
Lauren C TangDepartment of Biological Sciences, Columbia University, New York, NY, 10027, USA.
Ziyuan JiangDepartment of Chemistry, Columbia University, New York, NY, 10027, USA.
Abhishek IyerDepartment of Biological Sciences, Columbia University, New York, NY, 10027, USA.
Rashmi VoletiDepartment of Chemistry, Columbia University, New York, NY, 10027, USA.
Konstantin KrismerKoch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.ORCID 0000-0001-8994-3416
Jellert T GaublommeDepartment of Biological Sciences, Columbia University, New York, NY, 10027, USA.ORCID 0000-0002-1266-052X
Marko JovanovicDepartment of Biological Sciences, Columbia University, New York, NY, 10027, USA.ORCID 0000-0001-9707-3377
Neel H ShahDepartment of Chemistry, Columbia University, New York, NY, 10027, USA. neel.shah@columbia.edu.ORCID 0000-0002-1186-0626

Funding

SPATIALLY MAPPING OF POOLED IN VIVO CRISPR SCREENS IN THE TUMOR MICROENVIRONMENTDP2CA281605 · NCI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI GAUBLOMME, JELLERT · 2022 to 2025
$2.5M
Probing tyrosine phosphatase structure and functionR35GM138014 · NIGMS · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI SHAH, NEEL H · 2020 to 2024
$2.3M
How dynamic molecular interactions of RNA Binding Proteins drive post-transcriptional gene expression changesR35GM152258 · NIGMS · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI Marko Jovanovic · 2024 to 2026
$1.6M
HHS | NIH | National Cancer Institute (NCI) 1DP2CA281605HHS | NIH | National Institute of General Medical Sciences (NIGMS) R35GM138014HHS | NIH | National Institute of General Medical Sciences (NIGMS) R35GM152258NCI NIH HHS DP2 CA281605NIGMS NIH HHS R35 GM138014NIGMS NIH HHS R35 GM152258NSF | National Science Foundation Graduate Research Fellowship Program (GRFP) 2036197
6 · The paper itself

Abstract

Missense mutations in PTPN11, which encodes the protein tyrosine phosphatase SHP2, are common in several developmental disorders and cancers. While many mutations disrupt auto-inhibition and hyperactivate SHP2, several do not enhance catalytic activity. Both activating and non-activating mutations could potentially drive pathogenic signaling by altering SHP2 interactions or localization. We employed proximity-labeling proteomics to map the interaction networks of wild-type SHP2, ten clinically relevant mutants, and SHP2 bound to an inhibitor that stabilizes its auto-inhibited state. Our analyses reveal mutation- and inhibitor-dependent alterations in the SHP2 interactome, with several mutations also changing localization. Some mutants show increased mitochondrial localization and impact mitochondrial function. This study provides a resource for exploring SHP2 signaling and offers new insights into the molecular basis of SHP2-driven diseases. Furthermore, this work highlights the capacity for proximity-labeling proteomics to detect missense-mutation-dependent changes in protein interactions and localization.

Indexed as

Protein Tyrosine Phosphatase, Non-Receptor Type 11ProteomicsHEK293 CellsHumansMitochondriaMutation, MissenseProtein BindingProtein Interaction MappingProtein Interaction MapsSignal TransductionProtein Tyrosine Phosphatase, Non-Receptor Type 11PTPN11 protein, humanMitochondriaProtein-Protein InteractionPTPN11TurboIDTyrosine Phosphatase

Identifiers

PMID41429940
PMCPMC12894930

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Registered trials

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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.