Identification of Differentially Expressed Proteins As Potential Biomarkers for Diagnosis and Prognosis of Acute Myeloid Leukemia
Authors: Al-Amrani Safa , Al-Zadjali Fahad , Jeelani Yasir , Al-Jabri Zaeema , Al Bulushi Mahdiya Pir , Al-Rawahi Mohammed , Al-Zaabi Adhari , AlShekaili Jalila , Al-Huneini Mohammed , Al-Khabori Murtadha 
Published: December 2024

Understanding the biology of Acute Myeloid Leukemia (AML) has significantly advanced with the development of proteomic profiling. This study aimed to identify differentially expressed proteins (DEPs) in AML patients using a global proteomics approach, providing insights into potential biomarkers for diagnosis, prognosis, and treatment outcomes.

The study included peripheral blood (PB) and bone marrow (BM) samples from 15 adult AML patients and PB samples from three healthy controls. Patients with a confirmed diagnosis of AML who completed the induction therapy and were alive at the time of remission assessment were included. Informed consent was obtained from all participants, and ethical approval was granted by the Medical Research Ethics Committee (MREC#1999) at Sultan Qaboos University. A total of 43 samples were analyzed, including 14 PB samples at diagnosis, 10 PB samples at remission, 12 BM samples at diagnosis, and 9 BM samples at remission.

Proteins were extracted from cryopreserved mononuclear cells and analyzed using liquid chromatography-mass spectrometry (LC-MS) at the Clinical Proteomics Mass Spectrometry Laboratory Karolinska Institute in Sweden. The study employed a modified SP3 protein clean-up and digestion technique, followed by TMTpro 16-plex labeling for peptide quantification. Data analysis was conducted using Bioconductor packages in R. DEPs were identified through differential expression analysis and further examined using principal component analysis (PCA) and protein-protein interaction (PPI) network analysis.

The study identified and quantified 10,302 proteins per sample. When comparing control samples to PB of patients at diagnosis (PBD), 119 DEPs were identified, with significant involvement in KEGG pathways, including “Spliceosome,” “Nucleotide excision repair,” and “Ribosome.” Comparing PBD and PB at remission (PBR), 818 DEPs were identified, all upregulated in PBD. These DEPs were associated with KEGG pathways including “Insulin resistance” and “vascular smooth muscle contraction.”

Functional enrichment analysis revealed significant associations between DEPs and various biological processes, molecular functions, and cellular components. These include HMGA1, HNRNPU, HMGN2, H1-2, RCC1, H3-2, and H1-5, which were significantly upregulated in PBD compared to controls, suggesting their potential role in AML pathogenesis. The PPI network analysis confirmed significant interactions among DEPs, indicating a complex interplay of proteins in AML.

This comprehensive proteomic analysis provides valuable insights into the molecular underpinnings of AML. The identified DEPs and their associated pathways offer potential biomarkers for AML diagnosis and prognosis and may guide the development of targeted therapies. Future studies should focus on validating these biomarkers in larger cohorts and exploring their functional roles in AML pathogenesis.