Proteomics reveals COX7B as a prognostically relevant oxphos-linked protein in pediatric AML

Abstract Introduction: Acute myeloid leukemia (AML) is a complex and highly heterogeneous hematologic malignancy with poor clinical outcomes. Despite improvements in supportive care, the standard treatment for AML has remained largely unchanged since the 1970s through use of cytarabine in combination with anthracyclines. The approval of only a limited number of new antileukemic agents since 2017 highlights the urgent need for innovative approaches to identify factors contributing to relapse, drug resistance, and therapeutic failure. This study aims to elucidate the prognostic and therapeutic relevance of proteomics in AML. Methods: Global proteomic analysis of leukemic cells obtained at diagnosis from 97 pediatric patients treated in the St. Jude AML02 clinical trial was performed using Tandem Mass Tag (TMT) labeling followed by two-dimensional Liquid Chromatography (LC/LC) and Tandem Mass Spectroscopy (MS/MS). Data were preprocessed with median normalization and log transformation and batch correction. Proteomic signatures were compared across patient subgroups, clinical characteristics, and AML-linked genetic alterations and with survival outcomes as event free survival (EFS), overall survival (OS) and measurable residual disease after induction 1 (MRD1). Results: Among the most significantly expressed proteins (p < 0.001), 25 proteins were associated with poor clinical outcomes and 16 proteins were associated with superior outcomes. Among the proteins predictive of poor outcome significant enrichment was observed in metabolic pathways. COX7B (cytochrome C oxidase subunit 7B), a component of mitochondrial complex IV involved in the oxidative phosphorylation involved in oxidative phosphorylation (OXPHOS) pathway was strongly associated with adverse prognosis (EFS, HR=2.6; OS, HR=3.8, both p<0.001). Given that leukemic stem cells (LSCs) depend on OXPHOS for survival making it a potential therapeutic target. These findings are consistent with previous reports showing that elevated mRNA levels of mitochondrial/OXPHOS genes to be associated with poor outcome in AML. SLC25A15, a mitochondrial amino acid and proton transport, was also associated with poor prognosis (EFS, HR=3.5, OS, HR=5.3 both p<0.001 and MRD1, OR=4.2, p=0.03). SCL25A15 is frequently upregulated in cancers and contributes to cancer progression and poor prognosis. Among other metabolic pathway enzymes associated with poor prognosis included fumarate hydratase with role in TCA cycle, lysophospholipase (shown to modulate LSCs response), 3-ketodihydrosphingosine reductase, dehydrogenase/reductase 13, mitochondrialaspartyl-tRNA synthetase 2, protein O-glucosyltransferase 1, protein O-fucosyltransferase 1 and glucosidase. Other proteins associated with poor prognosis included ODR4, belonging to G protein coupled receptor signaling (p < 0.001, EFS and OS) and NLE, involved in Notch signaling pathway with a role in hematopoietic stem cell homoeostasis. Among proteins predictive of better clinical outcome included GRB10, a growth factor receptor bound protein 10, ALOX5AP, Creatinine kinase B, microtubule associated protein, deoxyribonucleae etc. Conclusions: This study represents one of the first and most comprehensive global proteome profiling of diagnostic bone marrow samples from pediatric AML patients. We report several metabolic enzymes that are predictive of poor outcome and specifically COX7B and its role in OXPHOS pathway is highly relevant as LSC survival is dependent on OXPHOS highlighting its therapeutic potential. Understanding the molecular mechanisms behind these distinct protein patterns may guide the development of precision therapies as well as identify novel drug targets in AML. Our ongoing study is in the process of expanding this analysis to a full cohort of 448 patient samples across multiple clinical trials.