Biology subjects

Swoboda, P.

Publications and source records attributed to Swoboda, P..

6 recordsLinked to original sources

bioRxiv2026

Supplementation via DAF-16 and pnk-1 driven pantothenate-coenzyme A flux improves disease related stress resistance in C. elegans

Metabolic pathways are increasingly recognized as tractable targets in aging and disease. Building on prior work demonstrating that supplementation with low-molecular weight metabolites (amino acids, vitamins, and their intermediates) can extend lifespan in Caenorhabditis elegans, we focused on pantothenate (vitamin B5), which is dysregulated in sarcopenic muscle and in several neurodegenerative and metabolic disorders. Pantothenate is the obligate precursor of coenzyme A through a short, highly conserved biosynthetic pathway in which loss-of-function mutations can cause neurodegeneration with brain iron accumulation. In C. elegans, the longevity curtailing transcription factor DAF-16/FOXO has a conserved binding element in the promoter region of pnk-1, encoding the first enzyme (PNK-1) in the coenzyme A pathway, and pnk-1 is markedly upregulated in long-lived daf-2 (insulin/-like receptor) mutants, implicating coenzyme A metabolism in longevity. Here, we demonstrate that CoA levels naturally increase during early life and decrease towards older age in C. elegans. Dietary pantothenate supplementation increases coenzyme A levels with minimal effects on lifespan but systemic effects on lipid metabolism, mitochondrial dynamics, and muscle structure under basal conditions. Under DAF-16-associated stress conditions, including heat and oxidative stress, pnk-1 expression is upregulated and pantothenate supplementation robustly extends lifespan and improves mobility. Finally, we demonstrate dysregulation of daf-16 and pnk-1 expression in amyotrophic lateral sclerosis (ALS) models, in which pantothenate supplementation confers both lifespan extension and cholinergic neuroprotection.

neuroscience↗

bioRxiv2026

Multi-layered regulatory networks driving human dopaminergic neuron differentiation

Neuronal differentiation requires coordinated regulation across chromatin organization, gene expression, protein abundance, and post-translational modifications. Using the LUHMES human dopaminergic neuronal differentiation model, we integrated proteome and phosphoproteome profiling with previously generated enhancer-promoter interaction maps from NET-CAGE and HiCap and transcriptomic analysis across three consecutive differentiation stages. Differentiation was accompanied by increased abundance and phosphorylation of proteins involved in axon guidance, cytoskeletal organization, and synaptic signaling, alongside repression of the cell cycle, DNA replication, and chromatin-associated programs. Phosphoproteome analysis further revealed extensive remodeling of signaling networks associated with neuronal maturation. Enhancer-promoter interaction analysis revealed substantially greater rewiring at enhancers than promoters and identified master and relay transcription factors regulated across multiple molecular layers. siRNA-mediated knockdown showed that transcription factors MYT1, ISL2, and NHLH2 are crucial for proper neuronal maturation, whereas LCOR acts as a negative regulator of differentiation. Integrative network reconstruction further nominated MEOX2 as a candidate enhancer-associated regulator of late dopaminergic maturation. Together, these findings provide a multi-layered view of regulatory networks governing human neuronal differentiation.

systems biology↗

bioRxiv2024

Metabolic analysis of sarcopenic muscle identifies positive modulators of longevity and health span in C. elegans

Sarcopenia is the age-related degeneration of skeletal muscle, resulting in loss of skeletal muscle tone, mass, and quality. Skeletal muscle is a source of systemic metabolites and macromolecules important for neuronal health, function and healthy neuronal aging. Age-related loss of skeletal muscle might result in decreased metabolite and macromolecule availability, resulting in reduced neuronal function or increased susceptibility to unhealthy aging and neurodegenerative diseases. We aimed to identify muscle metabolite candidates that regulate healthy aging. C57BL/6J mice were aged to young adult (4 months) and old age (25 months) and skeletal muscle was collected. Age related muscle loss was confirmed by reduced muscle mass, muscle fiber degeneration, reduced myosin intensity, in addition to a metabolic shift and increased DNA damage in skeletal muscle. Using a low molecular weight enriched metabolomics protocol, we assessed the metabolic profile of skeletal muscle from young adult and old mice and identified 20 metabolites that were significantly changed in aged muscle. These candidate metabolites were tested in C. elegans assays of lifespan, health span, muscle-, and mitochondrial morphology under normal and stressed conditions. We identified four candidate metabolites (beta-alanine, 4-guanidinobutanoic acid, 4-hydroxyproline, pantothenic acid) that when supplemented in C. elegans provided robust gero- and mitochondrial protection. These candidates also affected life-, and health span in C. elegans models of amyotrophic lateral sclerosis and Duchenne muscular dystrophy. Our findings support that aging muscle can be used to identify novel metabolite modulators of lifespan and health and may show promise for future treatments of neurodegenerative and neuromuscular disorders.

cell biology↗

bioRxiv2023

Primary cilia promote the differentiation of human neurons through the WNT signaling pathway

Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cells immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and a mutant with altered cilia (RFX2 -/-), we discovered an early-differentiation "ciliary time window" during which transient cilia promote axon outgrowth, branching and arborization. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in "mild" impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.

neuroscience↗

bioRxiv2021

The C. elegans DAF-19M module: a shift from general ciliogenesis to ciliary and behavioral specialization

In animals, cilia are important for the interaction with environments and the proper function of tissues and organs. Understanding the distinctive identities of each type of ciliated cell is essential for therapeutic solutions for ciliopathies, complex disorders with impairments of various organs caused by defective cilia development and function. Here, we report a regulatory module consisting of a cascade of transcription factors and their target genes that confer the cell type-specific ciliary identities on the IL2 ciliated neurons in C. elegans. We found that DAF-19M, isoform of the sole C. elegans RFX transcription factor DAF-19, through X-box promoter motif variants, heads a regulatory module in IL2 neurons, comprising the core target genes klp-6 (kinesin), osm-9 (TRP channel), and cwp-4 (novel); under the overall control of terminal selector proteins UNC-86 and CFI-1. Considering the conservation of this DAF-19M module in IL2 neurons for nictation, a dauer larva-specific behavior, and in male-specific neurons for mating behavior, we propose the existence of an evolutionarily adaptable, hard-wired genetic module for distinct behaviors that share the feature "recognizing the environment."

molecular biology↗

bioRxiv2020

Differentiation of ciliated human midbrain-derived LUHMES neurons

Many human cell types are ciliated, including neural progenitors and differentiated neurons. Ciliopathies are characterized by defective cilia and comprise various disease states, including brain phenotypes, where the underlying biological pathways are largely unknown. Our understanding of neuronal cilia is rudimentary and an easy-to-maintain, ciliated human neuronal cell model is missing. LUHMES is a ciliated neuronal cell line derived from human fetal mesencephalon. LUHMES cells can easily be maintained and differentiated into mature, functional neurons within one week. They have a single primary cilium as proliferating progenitor cells and as post-mitotic, differentiating neurons. These developmental stages are completely separable within one day of culture condition change. The Sonic Hedgehog (SHH) signaling pathway is active in differentiating LUHMES neurons. RNA-seq time course analyses reveal molecular pathways and gene-regulatory networks critical for ciliogenesis and axon outgrowth at the interface between progenitor cell proliferation, polarization and neuronal differentiation. Gene expression dynamics of cultured LUHMES neurons faithfully mimic the corresponding in vivo dynamics of human fetal midbrain. In LUHMES, neuronal cilia biology can be investigated along a complete timeline: from proliferation through differentiation to mature neurons. Summary StatementWith LUHMES, a ciliated human neuronal cell model, the underlying "neurobiology" of cilia and ciliopathies can be investigated along a complete time line: from proliferation through differentiation to mature neurons.

neuroscience↗