Low-intensity pulsed ultrasound is associated with H3K4me3 remodeling, stress–associated transcriptional responses, and impaired clonogenic survival in cancer cells

Low-intensity pulsed ultrasound (LIPUS) is a non-ionizing biophysical stimulus with emerging therapeutic relevance, but its epigenomic effects in cancer remain incompletely understood. Here, we investigated whether LIPUS is associated with chromatin remodeling, transcriptional reprogramming, and stress–associated responses in non-small cell lung cancer (NSCLC) and oral squamous cell carcinoma (OSCC) models. A single LIPUS exposure delayed wound closure in NSCLC cells, modified transforming growth factor-β–associated EMT–like morphology, marker expression, and invasive behavior, and markedly suppressed long-term clonogenic survival in cancer cell lines. At the chromatin level, LIPUS induced context-dependent changes in global histone modification patterns and increased promoter-associated H3K4me3 enrichment in OC3 cells. Representative tumor suppressor–related genes and ER stress/ER homeostasis–associated genes, including CDKN1A, CBL, LATS2, SFN, ACSL3, ARF1, and HERPUD1, showed increased promoter-associated H3K4me3 enrichment and gene- or cell line-dependent transcriptional activation. Integrative analysis of H3K4me3 ChIP-seq and transcriptomic datasets further identified a heterogeneous but functionally structured set of LIPUS-responsive genes related to chromatin regulation, checkpoint signaling, immune/stress responses, apoptosis/proliferation regulation, and cancer-associated pathways. LIPUS also increased ER stress-associated protein markers, including PERK, BiP/GRP78, ATF4, and CHOP, and was accompanied by increased apoptosis and reduced colony formation. Notably, LIPUS did not significantly reduce colony formation in non-malignant BEAS-2B bronchial epithelial cells under the same conditions. Together, these findings support a model in which LIPUS acts as a tunable physical stimulus associated with chromatin-level remodeling, stress-associated transcriptional responses, and impaired clonogenic survival in cancer cells.