Netherlands Metabolomics Centre

Abstract Microtubule networks are major determinants of cell architecture and logistics. Microtubule organization and density are regulated by severing enzymes, which cut microtubule lattices or affect their growth and shortening. These activities can lead to microtubule amplification or disassembly, depending on the presence of microtubule stabilizers or destabilizers, but the interplay between these factors is poorly understood. Here, we reconstituted in vitro the activity of microtubule severase katanin together with microtubule minus-end stabilizers CAMSAPs, their binding partner WDR47 and microtubule depolymerase kinesin-13/MCAK. We confirmed that katanin can amplify or destroy microtubules in a concentration-dependent manner. CAMSAPs recruit katanin to microtubules and reduce katanin concentration needed for both amplification and destruction, whereas kinesin-13 completely abolishes microtubule amplification. WDR47 binds to microtubules decorated by CAMSAPs and suppresses katanin binding and severing. In addition, both katanin and WDR47 inhibit polymerization of CAMSAP-decorated microtubule minus ends. These data explain how these proteins act together to fine-tune microtubule minus-end stability without strongly increasing microtubule abundance. Abstract Figure Graphical abstract

Most human invasive infections caused by extraintestinal pathogenic Escherichia coli (ExPEC) are associated with a limited number of O-serotypes and O-serogroups, including O101/O162. Here, we examined E. coli O101/O162 O-serogroup epidemiology among bacteremia isolates and performed genetic, biochemical and structural analyses. We demonstrate that the O101/O162 O-serogroup is globally widespread and highly associated with multidrug resistance (MDR). Dominant lineages belonged to clonal complex 10, including the high-risk clone ST167. Most O101/O162 ExPEC isolates contained an unusual O101 rfb locus previously identified as Onovel32, of which 30% harbored disruptions in the methyltransferase (MT) encoding gene. These disruptions resulted in alteration of the polysaccharide composition, and we identified two major O101 variants. Additionally, we found that an intact MT is a prerequisite for O-methylation of the polysaccharide, indicating terminal capping. Our data supports a model of a co-polymeric O101 O-antigen structure, which is unique for E. coli. Finally, we established that the two clinically relevant O101 O-antigen variant structures are highly immunogenic as polysaccharide-protein conjugates but differ in their ability to elicit opsonophagocytic antibodies. Altogether, our data provides important insights into O-serotype epidemiology and O-polysaccharide variation within E. coli O101/O162 isolates associated with bacteremia.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-026-45688-7.

Breast cancer cells undergo metabolic reprogramming to support proliferation and metastasis, but these alterations are heterogeneous. To systematically assess this heterogeneity under controlled conditions, we profiled 31 intracellular polar metabolites and 50 amines, together with exchange rates of 57 amines, in a panel of 51 breast cancer cell lines spanning diverse phenotypes. These data were integrated with lipidomics and transcriptomics. Multi-omics factor analysis identified metabolic signatures linked to proliferation and to differences between luminal, HER2-positive, basal A, and basal B cell lines, overlapping with an epithelial-to-mesenchymal transition phenotype. Fast-proliferating, aggressive cell lines showed increased uptake of essential amino acids and altered nucleotide levels, while heterogeneity in glutamine metabolism was mainly driven the subtype. This was partially associated with heterogeneous expression of metabolite transporters. To test the functional relevance, 67 metabolic genes were silenced in Hs578T using siRNA, and effects on proliferation and migration were measured by a sulforhodamine B assay, live-cell imaging, and a random cell migration assay. This resulted in 34 knockdowns that reduced proliferation and 20 reduced migration, with strong effects for the glycosyltransferases EXT1 and EXT2, nucleotide metabolism genes GART and HPRT1, and metabolite transporters SLC7A1, SLC7A11, and SLC16A3. These findings highlight phenotype-specific metabolic dependencies and identify candidate drug targets in aggressive breast cancer.

Cancer patients have an eleven-fold increased risk of venous thromboembolism (VTE) compared to the general population. In this hypothesis-generating study we investigated plasma protein levels in colorectal cancer patients with and without thrombosis using targeted absolute quantification of 269 plasma proteins. We included samples from 142 patients with stage III/IV colorectal cancer from MICA - a multinational prospective cohort study, and from 98 patients from CATS - a prospective cohort study with stage III/IV colorectal cancer. The primary outcome was objectively confirmed symptomatic or incidental deep vein thrombosis or pulmonary embolism during a 6-month follow-up period. In MICA, 11 (7.7%) developed VTE; in CATS 6 patients (6.1%) developed VTE within 6months, and 10 (10.2%) within 2years. Six differentially abundant proteins (DAPs) were identified in MICA: APOB100, CD5L, IGHG1, IGHM, PRG4, and TF. A model using these six proteins achieved a c-statistic of 0.687 (95% CI: 0.658-0.717) by internal cross-validation with 100 repeats and random 80% training sets. The optimism-corrected c-statistics was 0.675 (95% CI: 0.648-0.701). Using any subset of the DAPs yielded a c-statistics >0.67, with the best model reaching 0.768 (95% CI: 0.746-0.790). This outperformed the Khorana, modified-Vienna, PROTECHT, and CONKO models. The six DAPs had also predictive value in CATS with c-statistics at 0.70 (95% CI:0.671-0.728) for the 6-month, and 0.73 (95% CI:0.702-0.728) for 2-year follow-up. Two proteins showed inverted patterns between cohorts, likely due to chemotherapy. Our findings call for further investigation into the proteins identified, warranting further validation in larger, standardized studies.

ABSTRACTGlycogen storage disease type Ia (GSD Ia) is a rare autosomal recessive inherited disorder of carbohydrate metabolism, caused by a deficiency in glucose 6‐phosphatase‐α (G6PC1). Patients primarily suffer from failure to thrive, hepatomegaly, and severe fasting intolerance, biochemically characterized by hypoketotic, hypoglycemia, and hyperlipidemia. Because of clinical and biochemical heterogeneity, identifying biomarkers is imperative for prognosis and monitoring. An untargeted proteomics workflow was employed for identifying protein changes in liver and plasma from hepatocyte‐specific G6pc knockout mice under fed and fasted conditions. This links the effect of hepatic G6Pase/G6pc deficiency to circulating protein biomarkers and allows assessment of the relationship with different clinical circumstances and long‐term complications. In the liver, the main differences between hepatic GSD Ia mice versus controls were observed in proteins related to carbohydrate and lipid metabolism, proteasome, ribosome, NAD+ metabolism, and mitochondria. In GSD Ia mouse plasma, proteins were mainly down‐regulated in the complement and coagulation cascades. Effects in hepatic GSD Ia mice were in general more pronounced under fasting conditions. Several potential biomarkers that showed significant alterations in both liver and plasma were identified. These include proteins involved in carbohydrate and lipid metabolism (e.g., UGP2, ALDOB, and FASN), complement and coagulation cascades (SERPINA1E, C8b, and MBL2), 20S proteasome subunits (PSMA4, PSMA7, and PSMB5), and the electron transport chain (SDHA). Their consistent changes observed in both the liver and circulation indicate their potential as circulating biomarkers reflecting liver condition. Together with their reported associations with liver diseases, we hypothesize that they could monitor hepatic complications.

Mevalonate kinase deficiency (MKD) is a rare monogenic autoinflammatory disorder characterized by recurrent fever episodes driven by dysregulated IL-1β secretion. Mutations in the MVK gene cause enzymatic defects resulting in a shortage of geranylgeranyl pyrophosphate, leading to a lowering of the threshold for pyrin inflammasome activation. A cellular model of MKD was established to discover novel inflammatory pathways contributing to disease pathogenesis, with a focus on IL-18 and IFN-γ signaling. Using CRISPR/Cas9 gene editing, we generated a THP1 monocyte cell line harboring homozygous MVK I268T mutations, a pathogenic variant observed in patients with MKD. Functional assays were conducted to assess inflammasome activation and cytokine responses after stimulation with the pyrin agonist etiocholanolone. Experiments using MKD patient-derived peripheral blood mononuclear cells were performed to validate in vitro findings. MVKI268T/I268T THP1 cells exhibited impaired isoprenoid biosynthesis, consistent with the metabolic defect observed in MKD. Activation of the pyrin inflammasome in MVKI268T/I268T THP1 cells induced robust secretion of IL-1β and IL-18, which was attenuated by supplementation with geranylgeranyl pyrophosphate. MKD peripheral blood mononuclear cells hypersecreted IL-18 in response to pyrin inflammasome activation, reflected by elevated IL-18 levels in plasma of MKD patients. Specifically, MKD T and natural killer cells were characterized by enhanced IL-18-driven IFN-γ production. Elevated IFN-γ and IL-18 binding protein levels in MKD plasma as well as transcriptomic data of MKD peripheral blood mononuclear cells further confirmed the presence of an IFN-γ signature in MKD. A pyrin inflammasome-driven IL-18/IFN-γ axis is a key signaling module of MKD-associated inflammation. This pathway may represent a novel target for therapeutic intervention in MKD.

Inflammatory responses often involve metabolic rewiring within immune cells to support effector functions. Targeting metabolic pathways in immune cells therefore represents a promising strategy to modulate inflammatory diseases and improve therapeutic outcomes. Acyl-CoA synthesis by fatty acid transporter 2 (FATP2/SLC27A2) facilitates the transport of long-chain fatty acids into the cell. It represents a key step in fatty acid metabolism and the subsequent production of bioactive lipid mediators (LMs) with immunoregulatory functions. While the FATP2 inhibitor Lipofermata is currently evaluated for lipid-lowering therapies in metabolic diseases, and to revert the suppressive nature of myeloid cells in cancer, its effect on inflammatory responses in human macrophages remains elusive. Here, we show that Lipofermata reduced LPS-induced inflammatory responses in whole blood and human monocytes. This anti-inflammatory effect was paralleled by a decreased biosynthesis of arachidonic acid-derived inflammatory LMs, including prostaglandin E2 (PGE2) and thromboxane 2 (TxB2). These findings suggest an anti-inflammatory effect mediated by Lipofermata-mediated redirection of lipid metabolism in monocytes. Conversely, in mature human monocyte-derived macrophages, Lipofermata treatment enhanced LPS-induced cytokine production and induced cell death, likely through inflammasome activation. Together, these results underscore the cell type-specific effects of FATP2 inhibition and highlight the dual role of Lipofermata in modulating inflammatory immune responses. As such, targeting lipid metabolism with Lipofermata could have therapeutic potential with both anti- and pro-inflammatory applications, depending on the target cell type and context.

Cell cycle-inhibiting chemotherapeutics are widely used in cancer treatment. Although the primary aim is to block tumor cell proliferation, their clinical efficacy also involves specific effector CD8+ T cells that undergo synchronized proliferation and differentiation. How CD8+ T cells are programmed when these processes are uncoupled, as occurs during cell cycle inhibition, is unclear. Here, we show that activated CD8+ T cells arrested in their cell cycle can still undergo effector differentiation. Cell cycle-arrested CD8+ T cells become metabolically reprogrammed into a highly energized state, enabling rapid and enhanced proliferation upon release from arrest. This metabolic imprinting is driven by increased nutrient uptake, storage and processing, leading to enhanced glycolysis in cell cycle-arrested cells. The nutrient sensible mTORC1 pathway, however, was not crucial. Instead, elevated interleukin-2 production during arrest activates STAT5 signaling, which supports expansion of the energized CD8+ T cells following arrest. Transient arrest in vivo enables superior CD8+ T cell-mediated tumor control across models of immune checkpoint blockade, adoptive cell transfer and therapeutic vaccination. Thus, transient uncoupling of CD8+ T cell differentiation from cell cycle progression programs a favorable metabolic state that supports the efficacy of effector T cell-mediated immunotherapies.

ObjectivesThe early development of humoral immunity is important for long‐term protection of the newborn. Here, we set out to discern these infant‐produced antibodies from the vast background of maternal antibodies, which is challenging but essential to shed light on the infant‐produced repertoire.MethodsUsing IgA1 and IgG1 antibody clonal repertoire analysis by mass spectrometry, we compared matched maternal serum, maternal milk, and infant serum samples, both at birth (T1) and at 7–11 weeks after delivery (T2) in four mother–infant dyads.ResultsWe observed for both IgA1 and IgG1 unique infant‐produced antibody repertoires at T2. For IgA1 at T2, no substantial clonal overlap was found between infant serum and breastmilk. The serum IgG1 clonal repertoires were highly alike at birth for mother and infant, but at T2, the contribution of the maternal clonal population in the infant had been drastically reduced, and a large portion of the T2 IgG1 repertoire originated from the infant.ConclusionsNewborns produce their own antibody repertoires as early as a few months after birth. From this small study, no convincing evidence is found for transfer of milk antibodies into the infant circulation.

SummaryAltered microglial lipid metabolism is heavily implicated in Alzheimer’s disease (AD) and aging. Recently, protocols were developed to generate human induced pluripotent stem cell-derived microglia-like cells (iMGL) to study microglial function in vitro, including embryoid body-based methods and induced transcription factor (iTF)-dependent approaches. Here, we performed comparative lipidomics on iMGL from these methods and report major differences in multiple lipid classes, including triglycerides (TGs), a storage form of fatty acids implicated in microglial reactivity. TGs are strongly increased in iTF microglia due to the absence of a media supplement (B-27). Supplementing iTF microglia with B-27, or its component L-carnitine, reduces TGs and promotes a homeostatic state. B-27 also renders iTF microglia metabolically responsive to immune stimuli. Overall, our data show that iMGL differentiation methods have a major impact on microglial lipidomes and warrant attention when studying AD and neuroinflammatory processes involving lipids.