Abrahamson, S. | bioRxiv Science

bioRxiv2026

Mechanical Signaling Regulates DNA Methylation to Maintain Muscle Stem Cell Quiescence

Skeletal muscle stem cells (MuSCs) reside within a mechanically dynamic niche where they integrate biophysical and biochemical cues to maintain quiescence. Here, we show that substrate stiffness and RhoA-dependent signaling regulate MuSC fate. MuSCs cultured on soft matrices or depleted of RhoA exhibit altered morphology, diminished actomyosin organization, and undergo premature activation. Loss of RhoA reshapes the DNA methylation landscape, leading to widespread changes in gene expression and alternative splicing. Dnmt3a was among the genes transcriptionally downregulated following loss of RhoA signaling. Mechanistically, RhoA maintains Dnmt3a expression by promoting SP1 occupancy at its promoter. Importantly, loss of Dnmt3a in quiescent MuSCs is sufficient to drive activation, identifying Dnmt3a as a key epigenetic effector downstream of mechanical signaling. Together, these findings define a mechanotransduction-epigenetic axis in which RhoA maintains stem cell quiescence by preserving DNA methylation programs through Dnmt3A.

cell biology↗

bioRxiv2025

A Hotspot Phosphorylation Site on SHP2 Drives Oncoprotein Activation and Drug Resistance

SHP2 is a phosphatase and a critical mediator of receptor tyrosine kinase (RTK)-driven RAS/mitogen-activated protein kinase (MAPK) signaling. Despite promising preclinical data, SHP2 inhibitors have shown minimal clinical efficacy, with no defined clinical mechanisms of primary resistance. Here, we elucidate phosphorylation of SHP2 at tyrosine 62 (pY62) as a hotspot phosphorylation site in the proteome and RTK-driven tumor types in patients. We demonstrate that SRC family kinases directly phosphorylate SHP2 at Y62, downstream of but not directly phosphorylated by RTKs. Using biochemical and biophysical analyses, we show that SHP2 Y62D enforces an open, active conformation, resulting in constitutive phosphatase activation that is sufficient to activate MAPK signaling and confer resistance to allosteric SHP2 inhibitors. These findings establish that SHP2 pY62 is a phosphorylation hotspot phenocopying mutational activation, a mechanism of primary resistance to SHP2 inhibitors, and a cancer drug target distinct from wildtype SHP2. Statement of significanceThis study identifies phosphorylation of SHP2 at tyrosine 62 (pY62) as a conserved mechanism of resistance to allosteric SHP2 inhibitors. By stabilizing an open, active SHP2 conformation, pY62 phenocopies oncogenic PTPN11 mutations and sustains MAPK signaling across cancer types. These findings redefine SHP2 inhibitor resistance as a phosphorylation-driven, target-intrinsic process, nominate pY62 as a potential biomarker for therapeutic response, and propose phosphorylated SHP2 as a distinct drug target.

cancer biology↗