Dataset Information

Optimized Method for Cell Surface Protein Identification on Primary B-Cell Precursor Acute Lymphoblastic Leukemia Cells

ABSTRACT: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is caused by abnormal expansion of immature B cells. Genetic alterations can be identified in most of the BCP-ALL cases, however, some specific lesions including rearrangements of the mixed lineage leukemia (MLL) gene encoding lysine methyltransferase 2A (KMT2A) are associated with particularly poor prognosis. This MLL-rearranged subtype of leukemia poorly responds to conventional treatment and frequently undergoes a lymphoid-to-myeloid lineage switch in response to CD19-directed immunotherapy with consequent loss of B cell-specific targets for immunotherapy. Therefore, there is an urgent need to identify new targets for treatment of relapsed/refractory MLLr-BCP-ALL. Attractive targets may be found in a cell surfaceome, as membrane proteins are often expressed abnormally on cancer cells and are more accessible for therapeutics. Membrane proteins also play key roles in mediating external signaling and interactions with the microenvironment, thus being essential for cancer cell survival. RNA-based data may not always correlate with plasma membrane protein levels. Therefore, we performed the analysis of the BCP-ALL cell surfaceome by biotin labeling of plasma membrane proteins followed by tandem mass spectrometry (LC-MS/MS). This method requires high cell input and therefore was previously applied mainly to cell lines. However, the cell lines often do not fully represent primary samples due to genetic modifications and culture conditions. We have optimized the protocol of plasma membrane protein isolation and LC-MS/MS identification of patient-derived xenografts (PDXs) BCP-ALL cells. We confirmed the LC-MS/MS results by flow cytometry. Additionally, we compared the surfaceomes of PDXs BCP-ALL cells with BCP-ALL cell lines. We profiled six BCP-ALL PDXs and one cell line SEM, all with MLL translocations. In BCP-ALL PDXs we identified 1409 membrane-associated proteins, 945 of which were present in at least 3 samples. Tissue specificity analysis demonstrated that 93 of these proteins are specific for lymphoid cells, including already reported promising immunotherapeutic targets CD19, CD22, CD38, CD70, CD72, CD79A, and CD79B. The expression of selected proteins was confirmed by flow cytometry and compared to the expression on B-ALL cell lines with MLL translocation. Moreover, we identified an additional subset of proteins with potential therapeutic significance, including CD48, IL7R, ITGB7, LAIR1, LILRB1. Importantly, we observed profound differences between surfaceomes of BCP-ALL cell lines and PDX cells.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B-cell Lymphoma/leukemia 11b

DISEASE(S): B-cell Acute Lymphoblastic Leukemia

SUBMITTER: Agata Malinowska

LAB HEAD: Malgorzata Firczuk

PROVIDER: PXD058992 | Pride | 2025-06-09

REPOSITORIES: Pride

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			Action	DRS
	20210706fir_OBL9NB1_b.raw	Raw
	20210707fir_OBL9NB2_b.raw	Raw
	20210708fir_OBL9biot1_b.raw	Raw
	20210709fir_OBL9biot2_b.raw	Raw
	20210710fir_OBL9biot3_b.raw	Raw

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Publications

LILRB1-directed CAR-T cells for the treatment of hematological malignancies.

Marhelava Katsiaryna K Fidyt Klaudyna K Pepek Monika M Krawczyk Marta M Forcados Christopher C Malinowska Agata A Swiderska Bianka B Fernandez-Fuentes Narcis N Czerwik Natalia N Baranowska Iwona I Krzywdzinska Agnieszka A Sedek Lukasz L Slota Lukasz L Perkowski Bartosz B Villatoro Alicia A Leray Thibault T Lech-Maranda Ewa E Menendez Pablo P Inderberg Else Marit EM Wälchli Sébastien S Winiarska Magdalena M Firczuk Malgorzata M

Leukemia 20250405 6

CD19 CAR-T cells have established a new standard for relapsed/refractory B-cell malignancies. However, the treatment fails in 50% of patients, often due to CD19 antigen loss. Alternative immunotherapies targeting other antigens are being tested but show limited efficacy, especially in cases of lineage switching or loss of B-cell phenotype, highlighting the need for novel targets. Herein, we identified leukocyte-immunoglobulin-like-receptor-B1 (LILRB1, CD85j) as a novel target for CAR-T cells thr ...[more]

PMID: 40186066

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