Integrative analysis of proteomics and metabolomics reveals amino acid metabolism disorder in adriamycin-resistant acute myeloid leukemia cells

TL;DR

This study finds that amino acid metabolism is disrupted in leukemia cells resistant to adriamycin, suggesting new targets for treatment.

Contribution

The study integrates proteomics and metabolomics to reveal amino acid metabolism disruptions in adriamycin-resistant leukemia cells.

Findings

Differential expression of 3,241 proteins and 260 metabolites was observed in adriamycin-resistant HL60 cells.

Key amino acid metabolism pathways were altered, including alanine, aspartate, glutamate, cysteine, methionine, and glutathione metabolism.

Interfering with specific proteins (MAT2A, BCAT1, GCLM) increased apoptosis in resistant cells.

Abstract

Acute myeloid leukemia (AML) is a complex and aggressive hematopoietic malignancy. Clinically, adriamycin is an important therapeutic drug. However, drug resistance often leads to refractory or relapse of patients after anthracycline-based treatment, and the prognosis is poor. Despite extensive research, the molecular mechanisms underlying adriamycin resistance in AML remain elusive. 4D label-free quantitative proteomics and untargeted metabolomics techniques were used to quantify and analyze the protein and metabolic profiles of HL60 and adriamycin-resistant cell line HL60/R. A total of 3,241 proteins were differentially expressed, including 1,686 up-regulated and 1,555 down-regulated proteins, and 260 metabolites were differentially expressed with 79 up-regulated and 41 down-regulated under positive ion mode, and 77 up-regulated and 63 down-regulated under negative ion mode in HL60/R compared to HL60. Subsequently, bioinformatics analysis of the altered proteins showed that they were involved in many biological processes, particularly cAMP signaling pathway, HIF-1 signaling pathway and oxidative phosphorylation. Furthermore, an integrated analysis of proteome and metabolome showed that the significantly altered metabolism pathways were mainly involved in amino acid metabolism, such as alanine, aspartate and glutamate metabolism, cysteine and methionine metabolism and glutathione metabolism, which indicated that they may participated in the pathogenesis of drug resistance in HL60 cells. Finally, six significantly changed proteins including GOT1, GPX1, AHCY, MAT2A, BCAT1, GCLM in amino acid metabolism were further validated through western blot. MAT2A, BCAT1 and GCLM were selected for small interfering RNA experiments and the results exhibited that apoptosis rates significantly promoted in HL60/R when MAT2A, BCAT1 or GCLM were interfered. An integrative analysis of proteomic and metabolomic data revealed significant disruptions in amino acid metabolism in HL60/R cells, including the metabolic pathways of alanine, aspartate and glutamate, cysteine and methionine, as well as glutathione metabolism.

The online version contains supplementary material available at 10.1038/s41598-026-35675-3.

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