Bone marrow-based highly sensitive proteomics profiling reveals valuable biomarkers for pediatric B-cell acute lymphoblastic leukemia

Genomic analyses have revolutionized risk stratification and clinical management of pediatric B-cell acute lymphoblastic leukemia (B-ALL), but these methods are time-consuming and costly. To address this gap, we employed highly sensitive and specific Olink proteomics analysis of bone marrow plasma samples from pediatric B-ALL patients and B-ALL patients with complete molecular remission (CMR) as controls. Fifty pediatric B-ALL patients and 43 controls were randomly divided into a “discovery” cohort (30 B-ALL patients, 26 CMR controls), and a “validation” cohort (20 B-ALL patients and 17 CMR controls). The Olink Target 96 Oncology Response protein panel was used. Normalized log2-scale protein expression values revealed 37 differentially expressed proteins (DEPs) between pediatric B-ALL and CMR control groups. LASSO regression analysis showed nine of these DEPs, including CXCL13, NCR1, ADA, IL6, HO-1, CCL3, CCL4, CD27, and ADGRG1, to be significant in differentiating between patients with B-ALL and CMR controls (validation AUC = 0.98). We further strengthened the study by validating key Olink-identified proteins using independent assays, including ELISA in patient bone marrow plasma and immunohistochemistry in patient-derived xenograft tissues, which confirmed some Olink proteomic findings, such as CCL3, CCL4, and CD27. In addition, we found that higher levels of DEPs, such as CD27, TNF, CCL3, CCL4, IL12RB1, PDCD1, and GZMB, in patients with genetic alterations associated with poor prognosis. Our Olink proteomics analysis identified nine key proteins that were differentially expressed between the pediatric B-ALL and control groups, which may contribute to the diagnosis and/or risk stratification of pediatric B-ALL.