Biology subjects

Wolters, J. C.

Publications and source records attributed to Wolters, J. C..

12 recordsLinked to original sources

bioRxiv2026

The COPI coatomer influences LDL receptor activity, hepatic lipid storage, and apoB secretion

BackgroundDecreased hepatic removal of low density lipoproteins (LDL) and increased apolipoprotein B (apoB) production cause hypercholesterolemia, a major causal risk factor of atherosclerotic cardiovascular disease (ASCVD). By a genome-wide siRNA screen, we previously identified subunits of the Coat protein I (COPI) complex to limit LDL uptake into Huh-7 hepatocarcinoma cells. MethodsThese findings were validated by targeted in vitro experiments as well as genetic association studies in humans and three mouse models with mutated or disrupted COPI genes. ResultsSilencing of COPA, COPB1, COPB2, ARCN1, COPG1, and COPZ1 in Huh-7 cells resulted in decreased uptake of LDL and aberrant glycosylation and altered cell surface abundance of the LDL receptor (LDLR) as well as increased apoB secretion and cellular lipid storage. Single nucleotide polymorphisms of ARCN1 were associated with lower ARCN1 expression and higher levels of LDL-cholesterol (LDL-C). Rare variants of COPA and COPG1 were enriched among patients with LDL-C > 5 mmol/L. Patients and mice carrying other rare immunopathogenic missense variants of COPA and COPG1 did not present with elevated plasma levels of LDL-C, while hepatic knockdown of murine Copg1 increased the concentrations of non-HDL-cholesterol in plasma and triglycerides in the liver. ConclusionsThe COPI coatomer regulates LDLR activity and apoB secretion as well as lipid content of liver cells. Loss of function of some variants of COPI genes are associated with higher LDL-C levels.

cell biology↗

bioRxiv2025

Decoding the Glycan Signature: Unraveling N-Glycosylation Alterations in Glycogen Storage Disease Ia and Ib

Glycogen storage disease (GSD) types Ia and Ib are rare inherited metabolic disorders caused by pathogenic variants in G6PC or SLC37A4, respectively. These defects disrupt glucose homeostasis and may affect protein glycosylation. We systematically profiled sera N-glycomes from retrospectively collected GSD Ia (n=17), GSD Ib (n=8), and control (n=21) samples. Derived traits analyses revealed distinct, subtype-specific, and shared glycomic alterations, including shifts from 2,3-to 2,6-sialylation in both subtypes. GSD Ia showed enhanced branching and reduced fucosylation, whereas GSD Ib displayed elevated fucosylation, bisection, and reduced branching. In GSD Ia patients with hepatocellular adenoma/carcinoma (HCA/HCC), further enrichment of oligomannosidic and 2,3-sialylation was observed. Several individual N-glycans showed strong discriminatory performance, supporting their potential as biomarkers for GSD I subtyping and HCA/HCC surveillance. This study provides the first comprehensive characterization of systemic N-glycans in GSD Ia and Ib, revealing glycomic remodeling as a potential biomarker of disease subtypes and tumor progression. Take-home message (synopsis) of the articleSerum/plasma N-glycomic profiling reveals distinct glycosylation signatures in GSD Ia and GSD Ib, including tumor-associated shifts in GSD Ia, highlighting novel biomarkers for disease subtyping and surveillance of hepatic complications.

biochemistry↗

bioRxiv2025

Proteomics profiling of serum and liver in GSD Ia and Ib patients: insights into complication mechanisms and circulation biomarkers

BackgroundGlycogen Storage Disease (GSD) Types Ia and Ib are rare metabolic diseases caused by gene variants in G6PC1 and SLC37A4, respectively. Although life-threatening fasting hypoglycemia can be controlled by a strict diet, patients often suffer from multiple metabolic abnormalities and severe long-term complications. However, the underlying mechanisms remain incompletely understood, and the lack of effective monitoring biomarkers makes it a challenge to treat patients. Therefore, the aims of this study are to investigate the pathological mechanisms of the disease and disease complications in GSD I and identify potential protein biomarkers. MethodsIn this study, we employed comprehensive untargeted proteomics on stored samples: 26 serum or plasma samples from 18 GSD Ia and 8 GSD Ib patients with 21 matched control sera, complemented by 4 liver samples from 2 GSD Ia patients who received liver transplantation (from the one patient with hepatocellular carcinoma we obtained tissue from both the carcinoma tissue and the adjacent non-carcinoma tissue), and 1 from a GSD Ib patient, compared to 10 donor liver samples. ResultsWe identified a total of 415 proteins in our analyses. Pathway analysis of the differentially regulated proteins revealed distinct changes in serum/plasma of GSD Ia and Ib. The coagulation pathway was the most significantly changed biological process in the GSD Ia patients. Immune response-associated proteins, especially a large number of immunoglobulins, were increased in GSD Ib specifically. Proteins related to liver injury, cholesterol, and amyloidosis were altered in two subtypes, though more pronounced in GSD Ia. Potential biomarkers with significant alterations both in the circulation as well as in the liver tissue were identified specifically for monitoring GSD I subtypes and prognosing liver deterioration, namely GSD Ia (COL163 and PROC), GSD Ib (F11 and CD163), and hepatocellular carcinoma (HCC) in GSD Ia patients (ALDOB and CFHR5). ConclusionsThese findings provide new insights into the differences between the two GSD I subtypes and the pathogenesis of GSD I-related complications, as well as highlighting the potential of protein circulating biomarkers for monitoring complication progression in GSD I and assessing HCC risk in GSD Ia patients. Trial registrationNot applicable. A concise 1 sentence take-home message (synopsis) of the articleThis comprehensive in-depth proteomics study on blood and liver GSD Ia and Ib patient samples provided novel insights into understanding of the disease subtypes as well as the the pathogenesis of GSD I-related complications, such as HCC risk in GSD Ia patients and identified potential biomarkers for the disease subtypes and complications.

systems biology↗

bioRxiv2024

Targeted detection of endogenous LINE-1 proteins and ORF2p interactions

BackgroundBoth the expression and activities of LINE-1 (L1) retrotransposons are known to occur in numerous cell-types and are implicated in pathobiological contexts such as aging-related inflammation, autoimmunity, and in cancers. L1s encode two proteins that are translated from bicistronic transcripts. The translation product of ORF1 (ORF1p) has been robustly detected by immunoassays and shotgun mass spectrometry (MS). Yet, more sensitive detection methods would enhance the use of ORF1p as a clinical biomarker. In contrast, until now, no direct evidence of endogenous L1 ORF2 translation to protein (ORF2p) has been shown. Instead, assays for ORF2p have been limited to ectopic L1 ORF over-expression contexts and to indirect detection of endogenous ORF2p enzymatic activity, such as by the sequencing of de novo genomic insertions. Immunoassays for endogenous ORF2p have been problematic, producing apparent false positives due to cross-reactivities, and shotgun MS has not yielded reliable evidence of ORF2p peptides in biological samples. ResultsHere we present targeted mass spectrometry assays, selected and parallel reaction monitoring (SRM and PRM, respectively) to detect and quantify L1 ORF1p and ORF2p at their endogenous abundances. We were able to quantify ORF1p and ORF2p present in our samples down to a range in the low attomoles. Confident in our ability to affinity enrich ORF2p, we describe an interactome associated with endogenous ORF2-containing macromolecular assemblies. ConclusionThis is the first assay to demonstrate sensitive and robust quantitation of endogenous ORF2p. The ability to assay ORF2p directly and quantitatively will improve our understanding of the developmental and diseased cell states where L1 expression and its activity naturally occur. The ability to simultaneously assay endogenous L1 ORF1p and ORF2p is an important step forward for L1 analytical biochemistry. Endogenous ORF2p interactomes can now be presented with confidence that ORF2p is among the enriched proteins.

molecular biology↗

bioRxiv2024

Fibroblast-derived osteoglycin promotes epithelial cell repair

There is an urgent need for innovative pharmacological treatments targeting defective epithelial repair in chronic diseases, such as chronic obstructive pulmonary disease. The mesenchymal niche is a critical regulator in epithelial stem cell activation during repair. We hypothesized that secreted factors in this interaction are potent drug targets. Utilizing a cutting-edge proteomics-guided drug discovery strategy, we explored the lung fibroblast secretome to uncover impactful drug targets. Our lung organoid assays identified several regenerative ligands, with the secreted matrix protein osteoglycin (OGN) surprisingly showing the most profound effects. Transcriptomic analyses revealed that OGN enhances alveolar progenitor cell differentiation, boosts reactive oxygen species detoxification, reduces cellular senescence, and strengthens fibroblast-epithelial crosstalk. Critically, OGN expression was diminished in COPD patients and smoke-exposed mice. An active fragment of OGN, encompassing leucine-rich repeat regions 4-7, demonstrated regenerative potential akin to full-length OGN. This fragment significantly ameliorated elastase-induced lung injury precision-cut lung slices and improved lung function in vivo. These findings highlight lung fibroblast-derived OGN as a pivotal secreted protein for alveolar epithelial growth, positioning its active fragment as a promising therapeutic for epithelial repair in individuals with accelerated lung tissue damage.

pharmacology and toxicology↗

bioRxiv2023

The Hansenula polymorpha Mitochondrial Carrier Family proteins Mir1 and Aac2 are dually localized at peroxisomes and mitochondria

Peroxisomes are ubiquitous cell organelles involved in various metabolic pathways. In order to properly function, several cofactors, substrates and products of peroxisomal enzymes need to pass the organellar membrane. So far only a few transporter proteins have been identified. We analysed peroxisomal membrane fractions purified from the yeast Hansenula polymorpha by untargeted label-free quantitation mass spectrometry. As expected, several known peroxisome-associated proteins were enriched in the peroxisomal membrane fraction. In addition, several other proteins were enriched, including mitochondrial transport proteins. Localization studies revealed that two of them, the mitochondrial carrier family proteins Aac2 and Mir1, have a dual localization on mitochondria and peroxisomes. To better understand the molecular mechanisms of dual sorting, we tested the localization of Mir1 in cells lacking Pex3 or Pex19, two peroxins that play a role in targeting of peroxisomal membrane proteins. In these cells Mir1 only localized to mitochondria, indicating that Pex3 and Pex19 are required to sort Mir1 to peroxisomes. Analysis of the localization of various truncated versions of Mir1 in wild-type H. polymorpha cells revealed that several localized to mitochondria, but only one, consisting of the transmembrane domains 3-6, was peroxisomal. Peroxisomal localization of this construct was lost in a MIR1 deletion strain, indicating that full length Mir1 was required for the localization of the truncated protein to peroxisomes. Our data suggest that only full length Mir1 sorts to peroxisomes, while Mir1 contains multiple regions with mitochondrial sorting information.

cell biology↗

bioRxiv2023

The endosomal sorting complex Retromer has a central role insystemic cholesterol homeostasis by controlling endo-lysosomal cholesterol transport in hepatocytes

BackgroundDisturbed hepatic cholesterol homeostasis is associated with multiple diseases, including atherosclerotic cardiovascular disease and metabolic dysfunction- associated steatotic liver disease. The endo-lysosomal system is essential for cholesterol uptake and intracellular distribution, yet the mechanisms governing these processes remain incompletely understood. Here, we investigated the impact of hepatic VPS35, a subunit of the endosomal sorting complex retromer, on hepatocellular and whole-body cholesterol homeostasis. MethodsWe generated a liver-specific Vps35 knockout mouse model (Vps35HepKO) and applied biochemical analyses, proteomics, and stable-isotope-labeled tracers to quantify critical processes of cholesterol metabolism. Human iPSC-derived liver organoids and CRISPR technology were used to translate our findings to humans. Mechanistic studies were performed in precision-cut liver slices from WT and Vps35HepKO mice. ResultsHepatic VPS35 deficiency led to an increase in endo-lysosomal degradative compartments and a marked reduction in specific lysosomal proteins, including lysosomal acid lipase (LAL), Scavenger Receptor Class B Member 2 (SCARB2), and Niemann-Pick type C1 (NPC1). Using pathway-specific inhibitors, we showed that VPS35 loss impairs the translation of SCABR2 and NPC1. Consistently, human iPSC-derived liver organoids lacking VPS35 also exhibited reduced expression of NPC1 and SCARB2 proteins. The decrease in these lysosomal proteins correlated with increased cholesterol levels in the plasma and liver of Vps35HepKO mice. This was likely explained by the disrupted cholesterol trafficking through the endo-lysosomal system, delayed plasma cholesterol turnover, and upregulated cholesterol biosynthesis. ConclusionThese findings uncover a previously unknown role for the hepatic retromer complex in maintaining systemic cholesterol homeostasis. Beyond its established function in endosomal cargo transport, we now demonstrate that retromer is also essential for lysosomal cholesterol handling. This role is mediated by regulating key lysosomal proteins involved in cholesterol metabolism, including LAL, NPC1, and SCARB2.

molecular biology↗

bioRxiv2023

Nucleoporin Nsp1 surveils the phase state of FG-Nups

Transport through the NPC relies on intrinsically disordered FG-Nups forming a selective barrier. Away from the NPC, FG-Nups readily form condensates and aggregates, and we address how this behavior is surveilled in cells. FG-Nups, including Nsp1, together with nuclear transport receptor Kap95, form a native cytosolic condensate in yeast. In aged cells this condensate disappears as cytosolic Nsp1 levels decline. Biochemical assays and modeling show that Nsp1 is a modulator of FG-Nup liquid-liquid phase separation, promoting a liquid-like state. Nsp1s presence in the cytosol and condensates is critical, as a reduction of cytosolic levels in young cells induces NPC assembly and transport defects and a general decline in protein quality control, all quantitatively mimicking aging phenotypes. Excitingly, these phenotypes can be rescued by cytosolic Nsp1. We conclude that Nsp1 is a phase state regulator that surveils FG-Nups and impacts general protein homeostasis. HighlightsO_LINups form native cytosolic condensates C_LIO_LINsp1 reduction mimics NPC aging phenotypes C_LIO_LINsp1 acts as phase state modulator of FG-Nups C_LIO_LINsp1 shares surveillance function with classical chaperones C_LI

cell biology↗

bioRxiv2023

Age and diet modulate the insulin-sensitizing effects of exercise: a tracer-based oral glucose tolerance test

Diet modulates the development of insulin resistance during aging. This includes tissue-specific alterations in insulin signaling and mitochondrial function, which ultimately affect glucose homeostasis. Exercise stimulates glucose clearance, mitochondrial lipid oxidation and enhances insulin sensitivity. It is not well known how exercise interacts with age and diet in the development of insulin resistance. To investigate this, oral glucose tolerance tests (OGTT) with a tracer were conducted in mice ranging from 4 to 21 months of age, fed a low- (LFD) or high-fat diet (HFD), with or without life-long voluntary access to a running wheel (RW). We developed a computational model to derive glucose fluxes, which were commensurate with independent values from steady-state tracer infusions. Both insulin sensitivity indices derived for peripheral tissues and liver (IS-P and IS-L, respectively) were steeply decreased by aging and a HFD. This preceded the age-dependent decline in the mitochondrial capacity to oxidize lipids. In LFD young animals, RW access enhanced the IS-P concomitantly with the muscle {beta}-oxidation capacity. Surprisingly, RW access completely prevented the age-dependent IS-L decrease, but only in LFD animals. This study indicates, therefore, that endurance exercise can improve the age-dependent decline in organ-specific IS mostly in the context of a healthy diet.

physiology↗

bioRxiv2022

Nuclear transport under stress phenocopies transport defects in models of C9Orf72 ALS

The nucleus is the hallmark of eukaryotic life and transport to and from the nucleus occurs through the nuclear pore complex (NPC). There is a multitude of data connecting the nuclear transport machinery - i.e. the NPCs and associated nuclear transport factors - to neurodegenerative diseases, but the mechanisms are not well understood. Using Saccharomyces cerevisiae, we systematically studied how the expression of polyPR and polyGA related to C9Orf72 amyotrophic lateral sclerosis impacts the nuclear transport machinery. We measured the abundance and localization of NPC components and transport factors, and assessed the kinetics of import and export by four transport receptors. PolyPR and polyGA cause distinct, and transport receptor dependent effects. We compared the specific changes in transport to those obtained when cells were exposed to different stress situations or mutations. This comparison showed similar patterns of transport defects in cells lacking specific NTRs and cells expressing polyPR. In contrast, polyGA expressing cells bear resemblance to stress conditions where energy maintenance is decreased. The similarity of the patterns of transport deficiencies suggests that polyPR has a direct effect on nuclear transport via NTRs, while polyGA impacts the energy state of the cell and subsequently changes transport.

cell biology↗

bioRxiv2021

Age-related susceptibility to insulin resistance is due to a combination of CPT1B decline and lipid overload

BACKGROUNDAdvanced age increases the susceptibility to diet-induced insulin resistance (IR). A key driver of this phenomenon is lipid accumulation in the skeletal muscle. It is debated, however, whether this is due to dietary lipid overload or decline of mitochondrial function. To address the interplay of diet and age in the flexibility of muscle lipid and glucose handling, we put young and aged mice on a low- or high-fat diet (HFD). RESULTSAs expected, aged mice were more susceptible to IR when given a HFD than young mice. The HFD induced intramuscular lipid accumulation specifically in aged mice, including C18:0-containing ceramides and diacylglycerols. This was reflected by the mitochondrial {beta}-oxidation capacity, which was upregulated by the HFD in young, but not in old mice. Conspicuously, most {beta}-oxidation proteins were upregulated by the HFD in both groups, but carnitine palmitoyltransferase 1B (CPT1B) declined in aged animals. Computational modelling traced the flux control mostly to CPT1B, suggesting a CPT1B-driven loss of flexibility to the HFD with age. Finally, in old animals glycolytic protein levels were reduced and less flexible to the diet. CONCLUSIONWe conclude that intramuscular lipid accumulation and decreased insulin sensitivity are not due to age-related mitochondrial dysfunction or nutritional overload alone, but rather to their interaction. Moreover, we identify CPT1B as a potential target to counteract age-dependent intramuscular lipid accumulation and thereby IR.

biochemistry↗

bioRxiv2019

Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease

Refsum disease is an inborn error of metabolism that is characterised by a defect in peroxisomal -oxidation of the branched-chain fatty acid phytanic acid. The disorder presents with late-onset progressive retinitis pigmentosa and polyneuropathy and can be diagnosed biochemically by elevated levels of phytanic acid in plasma and tissues of patients. To date, no cure exists for Refsum disease, but phytanic acid levels in patients can be reduced by plasmapheresis and a strict diet.\n\nIn this study, we reconstructed a fibroblast-specific genome-scale model based on the recently published, FAD-curated model, based on Recon3D reconstruction. We used transcriptomics (available via GEO database with identifier GSE138379), metabolomics, and proteomics data (available via ProteomeXchange with identifier PXD015518), which we obtained from healthy controls and Refsum disease patient fibroblasts incubated with phytol, a precursor of phytanic acid.\n\nOur model correctly represents the metabolism of phytanic acid and displays fibroblast-specific metabolic functions. Using this model, we investigated the metabolic phenotype of Refsum disease at the genome-scale, and we studied the effect of phytanic acid on cell metabolism. We identified 53 metabolites that were predicted to discriminate between Healthy and Refsum disease patients, several of which with a link to amino acid metabolism. Ultimately, these insights in metabolic changes may provide leads for pathophysiology and therapy.

systems biology↗