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SPACE: Surface Proteomics for AML-derived Cells Explores potential new targets and biomarkers through multi-omics strategy

Human Health Proteomics

Abstract #358 Posted on27 May 20253 June 2025 3 June 2025 12h57

Abstract

Acute Myeloid Leukemia (AML) is a highly heterogeneous disease, presenting significant challenges in treatment, with many patients lacking viable therapeutic options. In the pursuit of novel therapeutic targets, particularly for antibody drug conjugate and T-cell engagers, comprehensive mapping of the cell surface proteome is critical to differentiate between blasts and healthy cells.
This study outlines two innovative proteomic strategies developed to identify and quantify the cell surface proteome in patient-derived blasts. The first strategy involves membrane isolation through centrifugation, while the second employs non-transmembrane biotin labeling of surface proteins extracellular domain on living cells followed by streptavidin enrichment. Both methodologies proceed with the digestion of isolated membrane proteins into peptides, which are subsequently identified via state-of-the-art mass spectrometry coupled with liquid chromatography.
These approaches have successfully identified over 2000 membrane proteins, including 80 cluster dissociation (CD) proteins, in the OCI-AML-3 cell line, demonstrating the efficiency of the protocols. However, further refinements are needed to ensure effectiveness with low amounts of material and frozen samples. Once optimized, the protocol will be applied to AML patient samples to further elucidate the cell surface proteome profile in AML. It could also be used to investigate other cancer types. Additionally, samples' RNA will be sequenced, and proteomics and genomics data layers will be merged to provide a comprehensive mapping of the molecular landscape of AML. This method holds significant potential for uncovering new therapeutic targets, ultimately contributing to the development of more effective treatments for patients.

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Acute Myeloid Leukemia (AML) is a highly heterogeneous disease, presenting significant challenges in treatment, with many patients lacking viable therapeutic options. In the pursuit of novel therapeutic targets, particularly for antibody drug conjugate and T-cell engagers, comprehensive mapping of the cell surface proteome is critical to differentiate between blasts and healthy cells. 
This study outlines two innovative proteomic strategies developed to identify and quantify the cell surface proteome in patient-derived blasts. The first strategy involves membrane isolation through centrifugation, while the second employs non-transmembrane biotin labeling of surface proteins extracellular domain on living cells followed by streptavidin enrichment. Both methodologies proceed with the digestion of isolated membrane proteins into peptides, which are subsequently identified via state-of-the-art mass spectrometry coupled with liquid chromatography. 
These approaches have successfully identified over 2000 membrane proteins, including 80 cluster dissociation (CD) proteins, in the OCI-AML-3 cell line, demonstrating the efficiency of the protocols. However, further refinements are needed to ensure effectiveness with low amounts of material and frozen samples. Once optimized, the protocol will be applied to AML patient samples to further elucidate the cell surface proteome profile in AML. It could also be used to investigate other cancer types. Additionally, samples' RNA will be sequenced, and proteomics and genomics data layers will be merged to provide a comprehensive mapping of the molecular landscape of AML. This method holds significant potential for uncovering new therapeutic targets, ultimately contributing to the development of more effective treatments for patients.

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