UQCRC2 lactylation-mediated mitophagy orchestrates colorectal cancer cell metabolism to establish a drug-tolerant state during chemotherapy

Drug-tolerant persister (DTP) cells survive anticancer therapy through reversible adaptive states and can contribute to tumor regrowth. However, how colorectal cancer (CRC) DTP cells preserve mitochondrial fitness during chemotherapy remains unclear. We investigated the metabolic and post-translational mechanisms underlying the FOLFOXIRI-induced DTP state. FOLFOXIRI-induced DTP–regrowth models were established using CRC patient-derived xenografts, PDX-derived organoids, cell lines, and cell line-derived xenografts. Whole-exome sequencing and transcriptomic, proteomic, metabolomic, and lactylomic analyses (global mass-spectrometry-based profiling of lysine lactylation sites) were integrated with genetic and pharmacological perturbations, metabolic and mitochondrial assays, protein-stability and ubiquitination analyses, and a cell-free delactylation assay, assessing the enzymatic removal of lysine lactylation. Clinical relevance was evaluated in chemotherapy-exposed CRC tissues and circulating tumor cells (CTCs). FOLFOXIRI-surviving CRC cells exhibited reduced proliferation without increased apoptosis, resumed growth after drug withdrawal, retained FOLFOXIRI sensitivity upon regrowth, and showed reversible molecular and metabolic remodeling. DTP cells displayed suppressed glycolytic activity, reduced lactate production, and increased reliance on oxidative phosphorylation, accompanied by activation of mitophagy. The mitochondrial complex III subunit UQCRC2 accumulated in DTP cells and supported Parkin (PRKN)/SQSTM1-associated mitophagy and residual-cell survival. Reduced lactate production was accompanied by decreased global lysine lactylation and reduced UQCRC2 lactylation at lysine 430 (UQCRC2-K430la). Increased UQCRC2-K430la promoted K48-linked ubiquitination and proteasome-dependent degradation of UQCRC2. SIRT1 directly delactylated UQCRC2 at K430 in an NAD + -dependent manner, thereby reducing K48-linked ubiquitination and stabilizing UQCRC2. Depletion of PINK1 or UQCRC2 and genetic or pharmacological inhibition of SIRT1 reduced residual DTP-cell survival and delayed regrowth. Among chemotherapy-responsive patients with advanced CRC, low tumor UQCRC2-K430la expression remained associated with poorer overall survival after multivariable adjustment. In paired CTC samples, increased SIRT1 or decreased UQCRC2-K430la expression after chemotherapy was associated with shorter progression-free survival. These findings identify a low-lactate/SIRT1–UQCRC2-K430la mechanism that couples glycolytic suppression to mitophagy-associated mitochondrial quality control and enables reversible chemotherapy tolerance in CRC. This pathway represents a candidate therapeutic vulnerability and supports further evaluation of UQCRC2-K430la as a biomarker of chemotherapy-associated residual disease.