RNA-seq analysis of NHE1 knockdown in human T-cell acute lymphoblastic leukemia cells

ABSTRACT: T-cell acute lymphoblastic leukemia (T-ALL) remains incurable for many patients who relapse, largely because conventional chemotherapy fails to eradicate leukemia stem cells (LSCs). To uncover druggable LSC dependencies, we leveraged an LSC-enriched transgenic zebrafish T-ALL model to screen 773 FDA-approved compounds in >2,500 animals, identifying amiloride as a top hit. Amiloride reduced the proportion of leukemia-positive fish, lowered functional LSC frequency >4-fold in limiting dilution transplants (p = 0.0026), and selectively suppressed the colony formation ability of human T-ALL cells in vitro without overt toxicity. Amiloride targets the sodium-hydrogen exchanger NHE1, which is upregulated in T-ALL relapses and associated with poorer overall survival event-free survival (hazard ratio = 2.308, p = 0.0089). shRNA-mediated inhibition of NHE1 reproduced the drug's effects: clonogenicity of T-ALL cells was reduced by 70%, expression of self-renewal genes decreased, and cells accumulated in G1. The pharmacologic and genetic inhibition of NHE1 also resulted in impaired mitochondrial function and morphology. Transcriptomics, proteomics, and untargeted metabolomics profiling of NHE1 knockdown cells revealed coordinated downregulation of oxidative phosphorylation, tricarboxylic acid cycle, and mitochondrial biosynthesis pathways, consistent with impaired mitochondrial function. In mouse xenograft models, NHE1-deficient T-ALL cells had significantly reduced bone marrow engraftment (p < 0.0001) and increased apoptosis, suggesting a functional LSC defect in vivo. These data establish NHE1 as a previously unrecognized regulator of T-ALL LSC self-renewal, mitochondrial metabolism, and bone marrow homing, and suggest readily available NHE1 inhibitors as possible candidates for relapse-directed therapy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE341718 | GEO | 2026/10/11

REPOSITORIES: GEO