Cell Metabolism

Brown adipose tissue (BAT) is a mitochondria-rich thermogenic organ whose function depends on high oxidative capacity, yet how primary mitochondrial dysfunction remodels BAT identity and metabolism remains poorly defined. Using the Deletor mouse model of progressive mtDNA deletion disease, we identify a pseudohypoxiairon-NAD+ axis as a central organiser of BAT pathology. Deletor BAT underwent profound structural, transcriptional and metabolic remodelling, characterised by mitochondrial ultrastructural damage, loss of thermogenic identity, PHD3/HIF associated pseudohypoxic signalling, iron dysregulation and NAD+/NADH redox imbalance. Indirect calorimetry confirmed that this molecular disease program translates to functional thermogenic failure under physiological demand. Deletor mice showed significantly reduced heat production under acute cold challenge and failed to switch to fatty acid oxidation Metabolomic profiling revealed altered TCA cycle intermediates, glycolytic rewiring and selective amino acid accumulation. Pharmacological perturbation showed that the PHD inhibitor roxadustat worsened disease-associated features, whereas HIF-1 suppression with PX-478 attenuated the integrated stress response, indicating that pseudohypoxic signalling is maladaptive in this setting. Nicotinamide riboside broadly attenuated the disease metabolome and transcriptome, restoring NAD+/NADH balance, suppressing ISRmt, iron-stress and pseudohypoxic gene programs, and correcting selective carnitine and acylcarnitine abnormalities consistent with impaired fatty-acid handling. These findings define a therapeutically tractable pseudohypoxia-iron-NAD+ axis as a core determinant of BAT dysfunction in mitochondrial disease.

Hematopoietic stem cell (HSC) aging is associated with epigenetic remodeling, yet the molecular mechanisms driving these changes, their overlap with stress-induced alterations, and whether this course can be durably reset remain incompletely understood. Here, we show that transient induction of the Yamanaka factors OCT4, SOX2, KLF4, and MYC in young mice durably delays and partially reverses physiological and LPS-driven HSC aging in mice. Transient reprogramming improved hematopoietic reconstitution, reduced myeloid bias, and limited DNA damage. Multi-omic analyses revealed reduced chromatin accessibility at AP-1-enriched regulatory regions, attenuated age-associated AP-1 transcriptional programs, and repression of transposable elements (TEs). Pharmacological AP-1 inhibition prevented LPS-induced TE activation and loss of HSC clonogenicity. Reverse transcriptase inhibition in aged mice reduced DNA damage and improved HSC function, demonstrating a functional contribution of TE activity to HSC decline. Together, these findings identify AP-1-associated chromatin remodeling as a candidate mechanism linking inflammatory stress, TE activation and HSC aging.

Clonal hematopoiesis (CH) increases with age, but whether different somatic clones represent an ageing phenotype or exert distinct systemic effects is unclear. In 450,587 UK Biobank participants, including 46,324 with plasma proteomics, we compared clonal hematopoiesis of indeterminate potential (CHIP) and mosaic loss of chromosome Y (mLOY) or X (mLOX) across biological ageing, incident disease, and circulating proteins. Despite shared age dependence, these alterations showed distinct disease spectra: non-DNMT3A CHIP was associated with broad multisystem disease burden, mLOY with a more focused respiratory, musculoskeletal and cardiovascular profile, whereas mLOX lacked broad age-related disease associations. Clone burden mapped to distinct proteomic programs: mLOY to neutrophil degranulation and extracellular-matrix remodeling, non-DNMT3A CHIP to myeloid immune regulation, and mLOX unexpectedly to cytotoxic lymphocyte/NK-cell responses. Mendelian randomization supported selected protein-disease relationships. Thus, age-related hematopoietic clones are not interchangeable markers of ageing but define alteration-specific systemic programs associated with distinct disease vulnerabilities.

Background: India has a rising incidence of chronic non-communicable diseases, making it a major healthcare burden today. Growing evidence suggests that chronic low-grade inflammation links ageing with cardiometabolic disorders, captured by the emerging concept of inflammaging. However, most evidence on biological ageing comes from Western populations, with no similar models developed for the Indian population. Given the country's distinctive genetic makeup, unique exposome, and heterogeneous NCD presentation, Western models may not capture inflammaging and its effects in the Indian population. Methods: We analysed baseline data from 4,240 adults in the Phenome India CSIR Health Cohort Knowledgebase (PI CheCK), a nationwide multi-centre cohort. Participants were stratified into eight cardiometabolic phenotype groups by BMI (Asian cut off), blood pressure and HbA1c status. We trained a Super Learner ensemble to predict chronological age in the lean normotensive-normoglycaemic reference group (n=615) using 44 plasma cytokines, sex, haemoglobin, and bioimpedance-derived visceral fat area, per cent body fat, and total body water. Performance was assessed by repeated five-fold cross-validation and in a held-out healthy test set. Calibrated biological age acceleration was then estimated in the remaining 3,625 participants. Results: Median age was 51.0 years (IQR 41.0 to 62.0) and 49.4% were female. The Super Learner outperformed elastic net and XGBoost comparators. Permutation importance identified visceral fat area, per cent body fat, CTACK, SDF1a, haemoglobin and sex as leading contributors, with body composition measures accounting for the largest share, indicating an immune-metabolic rather than cytokine-only signal. Biological age acceleration was concentrated in overweight/obese phenotypes. Lean phenotypes showed acceleration close to the reference (0.32 0.50 years). Conclusions: Cytokine and body composition measures capture a quantifiable immunometabolic ageing signal in a South Asian cohort, with acceleration driven predominantly by adiposity. External validation and longitudinal follow up are required.

Tissue regeneration requires careful allocation of metabolic resources, yet how organisms adjust this allocation in response to varying amounts of tissue loss remains poorly understood. Here, we show that the regenerative metabolic response is not fixed: the size of an injury regulates how glucose is allocated at both local and organism-wide levels. We first demonstrate that tail regeneration requires glucose metabolism in the axolotl (Ambystoma mexicanum), a salamander capable of regenerating centimetre-scale tissues. We then mapped glucose uptake in axolotls regenerating from small or large tail injuries using positron emission tomography/magnetic resonance imaging (PET/MRI) and the radiolabelled glucose analogue [18F]FDG. Glucose uptake was elevated in regenerating tails compared to uninjured tails. During early regeneration, larger injuries induced higher glucose uptake than smaller injuries, correlating with faster regenerative outgrowth. Larger injuries also increased glucose uptake in distant organs, indicating a systemic metabolic response. Together, our findings suggest that metabolic responses tuned to injury size underlie faithful tissue regeneration and establish PET/MRI as a powerful approach for studying whole-body metabolic dynamics in large regenerating vertebrates.

Antral CCK2R+ stem cells are regulated by gastrin, but how endocrine and neural cues integrate under chronic injury remains unclear. Here we show that inducible hypogastrinemia shifts from asymmetric renewal to symmetric expansion of CCK2R+ stem cells. With carcinogenic stress, these cells acquire a cycling, injury responsive progenitor state revealed by single-cell RNA profiling. Acute gastrin loss activates a CCK2R+ nodose DMV vagal reflex that increases acetylcholine release, NGF production, cholinergic innervation, and Chrm3 expression, driving ERK and YAP signaling in CCK2R+ stem cells. Vagotomy, Trk inhibition, or Chrm3 deletion each suppressed stem cell expansion. In H. pylori and MNU injury models, hypogastrinemia amplified inflammation, dysplasia, and CCK2R+ clone expansion, whereas gastrin suppressed these responses. Human scRNA seq and spatial profiling confirmed G cell depletion and progenitor state enrichment. These findings define an endocrine neural epithelial axis in which gastrin loss boosts vagal M3R signaling to initiate antral preneoplasia, highlighting this pathway for early interception.

Hyperglycaemia is a hallmark of diabetes and a major risk factor for diabetic kidney disease (DKD). However, the molecular consequences of long-term cumulative hyperglycaemia (CH) remain unclear. As a stable epigenetic modification, DNA methylation may capture past glycaemic exposure. Here, we assessed CH-associated DNA methylation in 1,245 participants with type 1 diabetes (T1D) from Finland and the United Kingdom-Republic of Ireland cohorts. We identified 17 CH-associated CpGs, with the strongest association at cg19693031 (TXNIP). Longitudinal analyses demonstrate that these CH-associated DNA methylation levels remain stable despite short-term glycaemic fluctuations, suggesting lasting epigenetic imprints of earlier metabolic control. Integrative analyses combining genomic, epigenetic, and proteomic data characterized these CpGs and potential target proteins. Mendelian randomization suggested a causal association between cg20853880 (KLF11) and DKD, supported by chromatin accessibility and kidney KLF11 expression. Our findings suggest that epigenetic changes contribute to metabolic memory and may mediate the effects of hyperglycaemia on DKD.

The Mediator complex, a vital transcriptional coregulator in eukaryotes, partners with transcription factors to orchestrate gene transcription and in turn many developmental and physiological processes. Mediator subunit MED15 is required for the pre-natal development and post-natal maturation of pancreatic {beta}-cells in mice. However, whether MED15 plays a role in {beta}-cell function after initial development and throughout adulthood is unknown. To investigate the role of MED15 in {beta}-cells post-maturation, we induced a {beta}-cell specific Med15 knockout at six weeks age in male and female mice. This post-developmental Med15 ablation led to glucose intolerance and impaired insulin secretion. RNA-sequencing revealed downregulation of {beta}-cell maturation markers, indicating that MED15 is continuously required to maintain {beta}-cell functionality. Further, we implanted insulin pellets into Med15 knockout mice to lower blood glucose and used RNA-seq to validate that the transcriptional changes we observed are a direct consequence of Med15 loss and not an indirect effect of hyperglycemia arising in the knockout mice. In sum, our study shows that MED15 is continuously required after weaning to maintain functional {beta}-cell maturity.

Obesity is a significant public health concern. Early-onset obesity in the context of rare disease can reflect genetically-mediated pathology or elevated susceptibility through indirect mechanisms. Mapping the diverse characteristics and needs of young people with obesity in the rare disease population is a first step toward mechanistic and translational research. We carried out a retrospective comparative analysis of demographic, genotypic, phenotypic and health service utilisation data for young people with obesity (cases: n=500) and without obesity (controls: n=11,444) from the UK 100,000 Genomes Project rare disease cohort. Cases and controls were recruited prior to genomic diagnosis, across clinical disorder categories. We observed significant association between socioeconomic deprivation and obesity risk. Young people with obesity had significantly higher utilisations of acute care and mental health services, indicating an overall higher health burden. A curated panel of 519 candidate obesity-associated genes demonstrated aggregate association with obesity, although no single gene reached significance. Phenotypic comparison between cases and controls highlighted increased multi-organ and neurological system involvement, highlighting the overlap between neurodevelopmental and obesity risks. Within the case group, we conducted cluster analysis to identify early-onset obesity groups with different phenotypic profiles, potentially arising from different causal pathways - this identified six obesity subgroups of interest, with differing involvement of neurodevelopmental and other systems. Our study confirms that obesity co-occurs with a wide range of factors within the rare disease population, and is associated with significant physical and mental health needs, requiring holistic lifelong care.

Background Ageing clocks are promising non-invasive tools to assess biological ageing, but they generally cannot guide intervention. We aimed to develop a urinary peptidomic ageing clock, expected to react to intervention, and to test whether the resulting age acceleration predicts all-cause mortality and adverse health outcomes. Methods In this retrospective multi-cohort study, urinary peptides were measured by capillary electrophoresis-mass spectrometry (CE-MS). An unconditioned clock (UPBioAge) was developed in a kidney function-preserved derivation cohort (n = 1,811), then conditioned on estimated glomerular filtration rate (eGFR) and urinary albumin-to-creatinine ratio (UACR) by Filtrate-Aware Calibration (FAC) fitted in an independent kidney-diverse cohort (n = 7,798), resulting in k-UPBioAge. Age prediction accuracy was evaluated in three cohorts independent of model development. Kidney-conditioned age acceleration (k-UPBioAgeAcc) was related to all-cause mortality and incident disease in a clinically enriched follow-up cohort (n = 7,469; 625 deaths; median follow-up 3.95 years) using Cox models adjusted for age, sex, comorbidities, body-mass index, mean arterial pressure and eGFR. Findings After standard age-bias correction, k-UPBioAge estimated chronological age with a calibrated holdout mean absolute error of 4.91 years (r = 0.945), and 5.43-5.47 years in two validation cohorts (one population cohort and the other samples analysed in an external site). Each SD increment in k-UPBioAgeAcc was associated with all-cause mortality (HR 1.48, 95% CI 1.35-1.63), incident coronary artery disease (1.44, 1.27-1.63), heart failure (1.27, 1.14-1.42) and chronic kidney disease progression (1.35, 1.05-1.73). The association did not differ by sex (P for interaction = 0.33), and none of four comorbidity interactions survived correction for multiple testing (adjusted P = 0.65-0.72), but no association was evident in participants with an eGFR of 15-29 mL/min/1.73 m2 (n = 433, 84 deaths) or macroalbuminuria (n = 92, 34 deaths). Interpretation Multiple urinary peptides are significantly associated with ageing, enabling the establishment of a robust biological ageing clock. As urine is generated in the kidney, a urinary ageing clock is affected by kidney function, mandating correction. The corrected urinary peptide-based biological ageing clock is affected by disease, and may warrant evaluation for monitoring or guiding personalised interventions.

Post-COVID-19 syndrome (PCS) is characterized by fatigue, neurological impairment and systemic symptoms. This heterogeneity of symptoms hinders biomarker development. Here, we profiled extracellular-vesicle (EV) surface markers in plasma and CSF from 61 participants with PCS (COVIDpost), 80 recovered controls (COVIDreco), and 10 participants with non-SARS-CoV-2 post-viral syndromes. EVs were analysed by bead-based multiplex flow cytometry using tetraspanin-directed (TSPN) and phosphatidylserine-directed lactadherin (PS) detection. Amongst 37 targets covering tetraspanins and vasculature-, immunity- and stemness-associated markers, none met a 1% false-discovery-rate threshold. However, L1-regularized logistic regression under fully nested 5x5 cross-validation identified a distributed plasma EV profile, with mean out-of-fold areas under the receiver operating characteristic curve (AUCs) of 0.788 (95% CI 0.715 - 0.852) for TSPN and 0.716 (95% CI 0.636 - 0.792) for PS detection. Across the pooled COVIDpost and COVIDreco population, EV classification scores covaried with clinical group differences, but did not track clinical severity within either cohort. These PCS-EV classification scores decreased at one-year follow-up in COVIDpost participants. Our findings identify an internally cross-validated multivariable EV surface profile associated with COVIDpost versus COVIDreco status and support independent validation and exploration of EV-based biomarkers in post-viral fatigue syndromes.

Service members with traumatic brain injury are at approximately two- to four-fold higher risk of Alzheimer's disease or related dementias than those without such an injury, with risk increasing with injury severity. The amyloid/tau/neurodegeneration biomarker framework treats amyloid, tau, and neurodegeneration as independent axes but omits astroglial injury, despite evidence that reactive astrogliosis (indexed by glial fibrillary acidic protein, GFAP) must be elevated for cognitive decline to occur in amyloid-positive individuals. Total GFAP immunoassays aggregate intact protein with multiple calpain- and caspase-cleaved proteoforms, blurring the biological signal. We compared a calpain-cleaved GFAP neoepitope, the glial fibrillary acidic protein neoepitope (neoGFAP), against total GFAP across the full traumatic brain injury--mild cognitive impairment--Alzheimer's disease continuum in Veterans using a two-stage plasma-to-cerebrospinal-fluid biomarker approach. A plasma triage gate combining phosphorylated tau 217 and amyloid beta 42 was applied to 367 unique subjects; a cerebrospinal-fluid benchmarking cohort of 57 subjects (controls, chronic blast traumatic brain injury, mild cognitive impairment, and Alzheimer's disease) received head-to-head neoGFAP and total GFAP measurement. In the whole benchmarking cohort, neoGFAP discriminated mild cognitive impairment plus Alzheimer's disease from non-Alzheimer subjects with an area under the receiver-operating-characteristic curve of 0.81 versus 0.73 for total GFAP, a trend-level advantage that did not reach nominal significance. Within the gate-positive, amyloid-committed subset of 23 subjects, neoGFAP dominance became significant by McNemar's exact test (six discordant subjects favored neoGFAP, none the reverse). Across diagnostic contrasts, neoGFAP outperformed total GFAP for Alzheimer's disease versus control and, importantly for Veterans, for mild cognitive impairment versus chronic blast-exposed Veterans without cognitive impairment. In chronic blast injury, neoGFAP was paradoxically depleted relative to controls, consistent with tissue sequestration of aggregated proteoform fragments. Unbiased proteomic profiling confirmed coordinated elevation across astrocytic, neuronal, mitochondrial, and microglial compartments. An exploratory subject-level reclassification improved accuracy from 71.1 percent using plasma alone to 79.5 percent with added cerebrospinal-fluid markers and age. In a same-cohort ProQuantum replication (n=57), CSF neoGFAP preserved its discrimination advantage over total GFAP for MCI+AD versus non-AD (AUROC 0.76 vs 0.72; cross-platform Spearman {rho}=0.84), while plasma neoGFAP achieved AUROC 0.90, comparable to pTau217 (0.92) and exceeding A{beta}42/40 (0.84). In this small sample, neoGFAP is a superior proteoform-resolved diagnostic and prognostic biomarker across the continuum and supports adding an astroglial-proteoform axis to amyloid/tau/neurodegeneration biomarker frameworks in high-risk populations.

Vaccine responses vary across individuals due to differences in ageing and health status. Using transcriptomic profiling, we analyzed early gene expression profiles after influenza (QIV) followed by pneumococcal (PCV13) vaccination in 148 participants spanning young, middle-aged, and older adults. The two vaccines induced distinct immune signatures: QIV elicited innate and interferon immune activation, while PCV13 triggered inflammation-based responses. Older adults showed weaker but similar transcriptomic profiles compared to young adults. Among older adults, frailty, in addition to age, was strongly associated with reduced innate responses. In addition, we identified associations between early-stage transcriptomic profiles and later-stage antibody responses for QIV; however, no such associations were observed for PCV13. Importantly, observed group differences arose not from altered immune modules but from differences in the magnitude of gene expression, paving the way for immune-boosting interventions to enhance early gene expression in at-risk populations.

O-linked {beta}-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is the sole writer for intracellular O-GlcNAcylation. It catalyzes O-GlcNAcylation of thousands of protein substrates, but relatively less is known about the post-translational modifications that occur on OGT itself. Herein, we demonstrate that OGT is S-palmitoylated at Cys-472 and Cys-477, which is mediated by the S-acyltransferase Zinc Finger DHHC-Type Palmitoyl transferase 14 (zDHHC14) and removed by acyl protein thioesterase 2 (APT2). S-Palmitoylation stabilizes OGT by shunting it away from the lysosomal chaperone-mediated autophagy (CMA) pathway, as S-palmitoylation decreases the interaction between OGT and heat shock cognate 70 kDa protein (HSC70), the CMA chaperone. Via label-free quantitative mass spectrometry, we find that S- palmitoylation elevates the affinity between OGT and protein phosphatase 1 catalytic subunit gamma (PPP1CC), but not PPP1CB. We further demonstrate that S-palmitoylation of OGT augments binding with Yes-associated protein-1 (YAP), a protein that associates with PPP1CC, and subsequently enhances YAP O-GlcNAcylation. Our work unearths S-palmitoylation of OGT and CMA-mediated degradation of lysosomal OGT, the orchestration of which finetunes the activity of key OGT complexes, such as OGT-PPP1CC, and contributes to OGT substrate selectivity.

Metabolic dysfunction-associated steatotic liver disease (MASLD), the leading cause of chronic liver pathologies worldwide, represents a growing clinical burden. Its diagnosis remains reliant on liver biopsy that limits early detection and the ability to capture molecular changes across disease progression. A systematic understanding of stage-dependent gene expression changes is essential to identify biomarkers and effectively characterize disease mechanisms. Therefore recent studies provided databases for searching genes as well as prediction of multi-gene signatures for disease progression. However, there is still a need for interactive and comprehensive meta-analysis of datasets of MASLD patients with available histological metadata. Herein, we performed a meta-analysis of RNA-seq datasets using NAFLD Activity Score (NAS; n = 897) and fibrosis stage (n = 856) upon conducting pairwise comparisons across histological stages and identified differentially expressed genes associated with disease progression. Most importantly, we provide our findings via a dedicated web server, the MASLD-META NETWORK (https://masld.scilicium.com), enabling users to interactively explore meta-analysis results across diverse network modalities. In addition, we characterized gene expression dynamics across increasing disease stages to identify consistent progression-associated pathways using Louvain clustering. Network-based parameters such as centrality in combination with meta-analysis scores further highlighted central genes and pathways implicated in disease mechanisms. Accordingly, MASLD-META NETWORK enabled an integrative reassessment of recently published gene signatures, identifying COL1A1, COL3A1, THBS2, FBLN5, and PDGFA as the most central genes, and SULF2, MMP14, IL32, GPNMB, and COL3A1 as candidate markers of earlier transcriptional alterations. Network analysis of MASLD associated biological modules further identified LAMA2 and LAMA3 as previously unrecognized central candidate targets.

Apoptosis-inducing factor is a mitochondrial flavoprotein that links redox metabolism to mitochondrial homeostasis through its interaction with the disulfide relay protein CHCHD4. Although NADH-dependent AIF dimerization has been proposed as the activated state mediating CHCHD4 engagement, whether it is strictly required for productive AIF-CHCHD4 function remains unclear. Here, combining cellular, biochemical and biophysical approaches, we show that disruption of the AIF dimer interface compromises oxidative phosphorylation, respiratory-chain organization and CHCHD4-dependent mitochondrial homeostasis, yet preserves partial AIF function. Our data reveal that the AIF-CHCHD4 system operates as a conformational dynamic redox module in which distinct AIF oligomeric and redox states sustain CHCHD4 activity with different efficiencies. Mechanistically, dimerization is coupled to NADH-dependent conformational changes that regulate coenzyme binding, charge-transfer complex stabilization and catalytic efficiency. In turn, CHCHD4 binding remodels AIF conformational and redox properties, partially compensating for defects in dimer stabilization or redox coupling. Consistently, a peptide derived from the CHCHD4 N-terminus partially restores redox function in a pathogenic AIF variant defective in dimer stabilization, supporting partner-assisted allosteric regulation as a potential therapeutic strategy.

Biological aging occurs heterogeneously across individuals and organs. However, current measures of biological age incompletely capture organ-specific differences in health and disease risk. Because chest CT visualizes multiple thoracic organs, it offers an opportunity to quantify structural aging across organ systems. Here, we developed MOSAIC-Age, a framework characterizing eight organ-specific aging clocks on chest CT. The clocks were developed and validated using 9,971 CT scans from CT-RATE and MIDRC, and subsequently locked and applied to two independent prospective cohorts with 35,293 participants from the National Lung Screening Trial and Genetic Epidemiology of COPD study. CT-derived biological age gaps (BAGs) were examined in relation to lifestyle and socioeconomic factors, prevalent comorbidities, incident chronic diseases, and all-cause and cause-specific mortality. Higher BAGs, indicating organs that appeared older on CT than expected for their chronological age, were broadly associated with adverse health characteristics, chronic disease burden, and increased mortality risk. Multiple disease outcomes were associated with aging across several organs, whereas in multivariable analyses including all eight organ-specific BAGs, the remaining associations were more organ specific. A greater number of markedly older-appearing organs and a faster pace of aging were each associated with higher mortality. Together, these findings demonstrate that routine chest CT captures both shared and organ-specific patterns of biological aging and establish CT-derived organ aging as a quantitative imaging biomarker for assessing multi-organ health and long-term disease risk.

Pancreatic ductal adenocarcinoma (PDAC) exhibits profound metabolic rewiring and strong resistance to DNA-damaging therapies, yet how metabolic pathways regulate genome maintenance remains poorly understood. The hexosamine biosynthetic pathway (HBP) integrates nutrient availability with protein glycosylation through production of UDP-GlcNAc, but its role in DNA damage response (DDR) regulation is unclear. Here we show that inhibition of the HBP enzyme phosphoglucomutase-3 (PGM3) reduces DNA repair capacity in pancreatic cancer cells. Transcriptomic and functional analyses reveal that the selective PGM3 inhibitor FR054 amplifies gemcitabine-induced replication stress, disrupts ATR-CHK1 and ATM-CHK2 checkpoint signaling, and selectively impairs homologous recombination. Glycoproteomic profiling identifies the AAA+ ATPase RUVBL2 as a key metabolic-DDR node. Gemcitabine increases RUVBL2 O-GlcNAcylation, with Thr81 identified as a modified residue within the Walker A nucleotide-binding motif. Structural modelling predicts that Thr81 O-GlcNAcylation stabilizes the RUVBL1-RUVBL2 complex without compromising ATP-Mg engagement. PGM3 inhibition and Thr81 mutation similarly reduced ATR and ATM abundance and promoted persistent DNA damage, supporting a role for RUVBL2 Thr81 O-GlcNAcylation in sustaining checkpoint signalling and genome stability. Consequently, PGM3 inhibition induces a BRCAness-like state that sensitizes pancreatic cancer cells to PARP inhibition, both in vitro and in vivo, as well as to ionizing radiation. These findings reveal a nutrient-sensitive mechanism linking protein glycosylation to genome maintenance and identify HBP-dependent DNA repair as a potentially actionable vulnerability in pancreatic cancer.

KRAS is one of the most frequently mutated oncoproteins in cancer. Its ability to induce malignant transformation relies on metabolic reprogramming that causes cells to become dependent on aerobic glycolysis as a primary source of energy and for generating biological building blocks. Thus far, the signaling mechanism used by oncogenic KRAS to promote these changes in cancer cell metabolism has not been fully elucidated. However, through studies in pancreatic ductal adenocarcinoma (PDAC) cell lines and patient-derived organoids, we now demonstrate how oncogenic KRAS triggers an increase in glycolytic activity and identify Survivin as a newly discovered and critical KRAS-signaling partner essential for promoting these metabolic changes. We show that oncogenic KRAS potently upregulates the expression of Survivin in PDAC cells and patient-derived organoids undergoing increased glycolysis, whereas depleting Survivin expression inhibits their glycolytic activity and growth. Through a combination of cellular, biochemical, and imaging approaches, we further show that Survivin promotes the formation of unique microtubule-based structures that resemble invadosome rosettes, allowing for the recruitment of the glycolytic enzymes triose phosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) to these super-structures which drives the increases in glycolysis. These findings demonstrate that by directing the assembly of a microtubule-based complex of metabolic enzymes, Survivin serves as a vital link in a KRAS signaling pathway responsible for promoting the metabolic changes necessary for the accelerated growth of PDAC cells, and thus potentially highlight new therapeutic strategies for treating KRAS-dependent cancers.

Lysine acylations, including lactylation (Klac), are pivotal regulators of cellular physiology. However, their analysis is currently bottlenecked by antibody enrichment strategies that suffer from sequence bias and require milligram-scale protein inputs, severely precluding the profiling of scarce clinical biopsies and rare cell populations. Here we present ChemIntelligence, an acyl-NHS chemistry-empowered derivatization strategy that rapidly generates unprecedented acylation-specific spectral libraries, exemplified by over 2.5x10^9 human Klac peptides, enabling cross-species reference atlases. Integrated with Prosit-based rescoring, these libraries substantially increase Klac identifications across diverse proteomic datasets. Leveraging this spectral resource, we devised ChemIntelligence Scope, a reproducible, multiplexed parallel reaction monitoring (PRM) platform that quantifies hundreds of Klac peptides per injection from as little as ~200 ng of cell lysates, clinical biopsies, and even true single cells - revealing functional Klac signatures inaccessible to conventional methods. The ChemIntelligence pipeline also extends seamlessly to lysine nicotinylation, underscoring its broad adaptability for discovering and profiling new acylations. Together, these chemical and computational advances establish a scalable, antibody-free framework for acyl-proteome mapping that overcomes input constraints and enables deep functional insights from otherwise intractable biological samples.