Biology subjects

Neumann, L.

Publications and source records attributed to Neumann, L..

5 recordsLinked to original sources

bioRxiv2026

Naloxone as mitochondrial phenotype rescuer in a 3D bioprinted LCHADD/VLCADD model

For patients diagnosed with long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (LCHADD) or very-long-chain acyl-CoA dehydrogenase deficiency (VLCADD), fasting episodes or high-energy demands remain life threatening. Due to the low incidence, clinical trials for novel LCHADD/VLCADD therapies are limited, and current mouse models recapitulate human symptoms only partially. Here, we report the use of mitochondrial morphology and 3D bioprinted, vascularized tissue models to establish a robust testing platform for dietary-based and experimental treatment approaches. Using this platform, we demonstrated that mitochondrial morphology is strictly regulated by NOX2-driven ROS formation. Treatment of LCHADD/VLCADD-derived fibroblasts with the NOX2-inhibitor naloxone led to the reassembly of mitochondrial structures controlled by DNM1L/MFN2. Using RNA transcriptomics, we identified a pro-fibrotic phenotype in LCHADD and VLCADD patient cells, which impaired vessel formation in fully 3D bioprinted human tissue equivalents. Metabolic supplementation with dietary approaches, which are used in standard therapy, partially improved vascularization. Naloxone induced the strongest improvement, restoring vessel length and network complexity to those of healthy controls, suggesting increased oxidative stress as main driver. Interestingly, naloxone had no effect on healthy fibroblasts, underscoring its safety. Taken together, these findings suggest the opioid antagonist naloxone as a potential rescue medication during LCHADD/VLCADD-driven metabolic crises.

molecular biology↗

bioRxiv2025

Optimised dissociation and multimodal profiling of prostate cancer stroma reveal fibromuscular cell heterogeneity with clinical correlates

BackgroundDynamic remodelling of the tumour microenvironment (TME) plays a central role in prostate cancer (PCa) progression, immune evasion and therapy resistance. However, the co-existence of both tumour-promoting and tumour-restraining stromal elements necessitates extensive characterisation of the TME for effective targeting. Fibromuscular cell heterogeneity in PCa remains poorly characterised, in part due to challenges in isolating cells embedded within the desmoplastic stroma. This study therefore aimed to better characterise fibroblast and smooth muscle cell (SMC) populations as the major tissue-resident stromal cell subtypes within the PCa TME. MethodsA PCa single-cell RNA sequencing (scRNA-seq) dataset was re-analysed to define fibromuscular subtypes. Due to low fibroblast yields, an optimised tissue dissociation protocol was developed and benchmarked against two commercial kits via flow cytometry, immunostaining of clinical specimens and ex vivo culture. Dimensionality reduction and clustering were applied to the CD31- stromal fraction using a multiparameter surface marker panel. Annotation of the resulting clusters based on their surface marker profile was supported by integrating scRNA-seq and immuno-histological findings. ResultsThe optimised protocol yielded over twice the viable cells/mg tissue compared to two commercial kits, preserved surface marker integrity, enhanced successful cultivation of mesenchymal cells and recovered diverse stromal subpopulations from benign and malignant samples. Dimensionality reduction and clustering of flow cytometry counts identified 11 distinct CD31- stromal populations. Integration with transcriptomic data and immunofluorescence of clinical specimens identified spatially- and prognostically-distinct fibroblast subtypes, including inflammatory and myofibroblastic cancer-associated fibroblasts, pericytes linked to poor prognosis and a novel SMC subset associated with stromal activation. ConclusionThis study presents a robust workflow for improved isolation and characterisation of fibromuscular stromal cells in PCa. The multimodal approach enabled refined characterisation of phenotypically distinct and clinically-relevant stromal subpopulations within their spatial context providing a foundation for future TME-targeted therapies.

cancer biology↗

bioRxiv2025

Unraveling the YAP1-TGFβ1 axis: a key driver of androgen receptor loss in prostate cancer-associated fibroblasts

Due to their pivotal roles in tumor progression and therapy resistance, cancer-associated fibroblasts (CAF) are considered key therapeutic targets with loss of stromal androgen receptor (AR) a poorly understood hallmark of aggressive prostate cancer (PCa). A paucity of pre-clinical models however has hampered functional studies of CAF heterogeneity. We demonstrate that our newly-generated CAF biobank contains three FAP+-fibroblast subtypes, each with unique molecular and functional traits. Cultures with an early-activated phenotype expressed the highest levels of AR and exhibited AR-dependent growth. Consistently, stromal cells expressing early-activation markers co-expressed nuclear AR in clinical specimens and were enriched in pre-neoplastic lesions/low-grade PCa. Conversely, myofibroblastic CAF (myCAF), which expressed low AR levels in vitro and in vivo and were proliferatively-insensitive to AR signaling modulation, constituted the predominant CAF subpopulation in stromogenic high-grade PCa and castration-resistant LACP9 patient-derived xenografts. Exacerbation of the myCAF state upon castration of LAPC9-bearing hosts underscored these findings. Mechanistically, AR loss in myCAF was driven by an NF{kappa}B-TGF{beta}1-YAP1 axis, whose combined targeting synergistically repressed myofibroblastic hallmarks and impaired autophagic flux, effects that were potentiated by enzalutamide resulting in myCAF cell death. Collectively, these findings provide a mechanistic rationale for adjuvant targeting of the YAP1-TGF{beta} signaling axis to improve patient outcomes.

cancer biology↗

bioRxiv2024

Trapped ion mobility spectrometry-guided molecular discrimination between plasmalogens and other ether lipids in lipidomics experiments

Trapped Ion Mobility Spectrometry (TIMS) has demonstrated promissing potential as a powerful discriminating method when coupled with mass spectrometry, enhancing the precision of feature annotation. Such a technique is particularly valuable for lipids, where a large number of isobaric but structurally distinct molecular species often coexist within the same sample matrix. In this study we explored the potential of ion mobility for ether lipid isomer differentiation. Mammalian ether phospholipids are characterized by a fatty alcohol residue at the sn-1 position of their glycerol backbone. Ether lipids can make up to 20% of the total phospholipid mass. They are present in a broad range of tissues where they are for example crucial for nervous system function, membrane homeostasis and inter-as well as intracellular signaling. Molecular ether lipid species are difficult to distinguish analytically, as they occur as 1-O-alkyl and 1-O-alkenyl subclasses, with the latter being also known as plasmalogens. Isomeric ether lipid pairs can be separated with reversed-phase chromatography. However, their precise identification remains challenging due to the lack of clear internal reference points, inherent to the nature of lipid profiles and the lack of sufficient commercially available standard substances. Here, we demonstrate - with focus on phosphatidylethanolamines - that ion mobility measurements allow to discriminate between the ether lipid subclasses through distinct differences in their gas phase geometries. This approach offers significant advantages as it does not depend on the variability of chromatography. However, the current resolution in the ion mobility dimension is not sufficient to baseline separate 1-O-alkyl and 1-O-alkenyl isobars, and the observed differences are not yet accurately represented in existing collision cross section databases. Despite these challenges, the predictable properties of the ion mobility behavior of ether lipid species can significantly support their accurate annotation and hold promise for future advancements in lipid research.

biochemistry↗

bioRxiv2021

Time grid-based isomer specific N-glycan analysis and detection of bisecting Lewis X in human brain

The importance of protein glycosylation in the biomedical field demands for methods capable of resolving and identifying isomeric structures of N-glycans. However, the unambiguous identification of isomeric structures from complex mixtures is currently not reasonably realized even by the most sophisticated approaches. Here we present a novel approach which uses stable isotope labelled reference N-glycans to establish a retention time grid (glyco-TiGr) on porous graphitized carbon. This furthermore enables retention as the primary criterion for the structural assignment of isomeric N-glycans. Moreover, we biosynthesized forty natural isomers of the fundamental N-glycan type consisting of five hexoses, four N-acetylhexosamines and one fucose residue. Nearly all of these isomers occupied unique positions on the retention time grid. Reference glycan assisted retention time determination with deci-minute accuracy narrowed the assignment space to very few, often only one possible glycan isomer. Application of the glyco-TiGr approach revealed yet undescribed isomers of Lewis x determinants in multimeric human IgA and hybrid type N-glycans in human brain with galactose and even fucose linked to the bisecting N-acetylglucosamine. Thus, the brain N-glycome displayed a degree of sophistication commensurate with this organs role.

biochemistry↗