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Updated: Sep 15, 2025
Characterization of Neuronal Lysosome Interactome with Proximity Labeling Proteomics
Published on: June 23, 2022
Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants
Anne E van Vlimmeren1,2, Lauren C Tang2, Ziyuan Jiang1
1Department of Chemistry, Columbia University, New York, NY 10027.
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 revealed mutation- and inhibitor-dependent alterations in the SHP2 interactome, with several mutations also changing localization. Some mutants had increased mitochondrial localization and impacted 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.
Insights
Missense mutations in PTPN11 (protein tyrosine phosphatase SHP2) impact signaling in developmental disorders and cancers. Proximity-labeling proteomics revealed mutation-specific changes in SHP2 interactions and localization, offering new disease insights.
Area of Science:
- Biochemistry
- Molecular Biology
- Genetics
Background:
- Missense mutations in PTPN11, encoding SHP2, are linked to developmental disorders and cancers.
- These mutations can hyperactivate SHP2 or alter its function through mechanisms beyond catalytic activity, such as changes in protein interactions or cellular localization.
Purpose of the Study:
- To comprehensively map the interaction networks and localization patterns of wild-type SHP2, clinically relevant mutants, and an auto-inhibited SHP2 state.
- To investigate how missense mutations and inhibitor binding affect SHP2's molecular interactions and subcellular distribution.
- To explore the functional consequences of mutation-induced alterations in SHP2 signaling.
Main Methods:
- Proximity-labeling proteomics was utilized to identify SHP2 interacting proteins in cells expressing wild-type SHP2, ten distinct PTPN11 mutants, and SHP2 stabilized in an auto-inhibited conformation by an inhibitor.
- Cellular localization studies were performed to assess the impact of mutations on SHP2 distribution.
Main Results:
- The study identified distinct alterations in the SHP2 interactome that were dependent on specific mutations and inhibitor treatment.
- Several PTPN11 mutations led to altered SHP2 localization, including increased presence in mitochondria.
- Mutations causing mitochondrial mislocalization were found to impact mitochondrial function.
Conclusions:
- Missense mutations in PTPN11 can drive disease pathogenesis by modifying SHP2's interaction network and subcellular localization, independent of changes in catalytic activity.
- Proximity-labeling proteomics is a powerful tool for dissecting the complex effects of missense mutations on protein behavior.
- This research provides a valuable resource and novel insights into the molecular mechanisms underlying SHP2-associated diseases.
