Global proteomic analysis of pediatric T-cell acute lymphoblastic leukemia patient samples reveals distinct protein upregulation signature

Acute lymphoblastic leukemia (ALL) is one of the most frequently diagnosed pediatric cancers. Despite significant improvements in overall survival rates, children with T-cell ALL (T-ALL), accounting for approximately 15% of pediatric ALL cases, have worse outcomes than children with B-cell ALL, particularly upon relapse. Although T-ALL cases have been extensively profiled at the genomic and transcriptomic levels, the molecular mechanisms underlying poor therapeutic response remain unclear. To address this gap and identify novel putative therapies, we utilized mass spectrometry-based global proteomic profiling to reveal potential targetable features unique to this leukemia. In this study, we identified eight pediatric T-ALL patients treated at Children's Mercy with bone marrow aspirate samples collected at both diagnosis and remission banked in the Children's Mercy Biorepository. We generated global proteomic profiles for paired diagnosis and remission samples via data independent acquisition (DIA) using the timsTOF HT (Bruker). Data were searched in DIA-NN using the Bruker spectral library and human protein database downloaded from Uniprot on 05-05-2024. Downstream data analysis was performed in R 4.3.3 including differential expression analysis using limma 3.58.1 and pathway enrichment using gProfiler 0.2.3. Differential expression analysis identified 374 proteins more highly expressed at diagnosis and 434 proteins more highly expressed at remission (p < 0.05, |log2FC| > 1). Pathways upregulated at diagnosis include cell cycle processes, cellular senescence, and nucleoside triphosphate diphosphatase activity. A number of proteins including CD7, CD38, HDAC1, HDAC2, and IL3RA (CD123) show elevated expression at diagnosis compared to remission, consistent with prior flow cytometry and/or gene expression studies of T-ALL. Surprisingly, several tumor suppressors including PTEN and BRCA2 also show elevated expression at diagnosis. While constitutive expression of PTEN has previously been reported in leukemias, it has typically been associated with mutations in the PTEN gene, which were not observed in these patients. This cohort of T-ALL patients shows upregulation of several proteins at diagnosis which are not seen in our analyses of other leukemias including B-cell ALL and acute myeloid leukemia. Global proteomic analysis comparing paired T-ALL samples from diagnosis and remission recapitulates increased expression of known proliferation and T-cell specific markers at diagnosis, as well as unexpected elevation of tumor suppressor protein expression. Further investigation of kinase activity and validation of these findings may reveal novel therapeutic targets to improve outcomes for pediatric T-ALL patients.