Biology subjects

Dudek, M.

Publications and source records attributed to Dudek, M..

9 recordsLinked to original sources

bioRxiv2026

Circadian transcriptome in cultured cells depends on synchronisation method and differs from in vivo condition

In vitro synchronisation is widely used to study circadian clocks in cells, but whether cultured cells recapitulate tissue-level rhythmic outputs remains unclear. Articular cartilage provides a useful model to address this because chondrocytes are the only resident cell type. Here, we compared circadian time series transcriptomes between primary mouse chondrocytes synchronised by heat shock, dexamethasone, or osmotic stress and in vivo cartilage tissue. All three stimuli robustly synchronised core clock gene rhythms but produced distinct circadian phases and markedly different rhythmic transcriptomes, depending on the synchronizer. Heat shock, dexamethasone, and osmotic stress yielded 5255, 2008, and 879 transcripts classified as rhythmic, respectively, in primary chondrocytes, yet only 64 genes were shared across the three in vitro datasets, and only 15 were shared when in vivo cartilage transcriptome was included. Pairwise comparisons between synchronizers revealed some statistically enriched overlaps, but only marginally above chance, and shared genes showed limited conservation of circadian phase. Functional enrichment analysis also revealed stimulus-dependent rhythmic programmes with modest pathway-level overlap. These findings indicate that circadian output in cultured cells is shaped by the synchronising cue and cellular microenvironment. We also present BodyClocks.org, an interactive resource implementing this comparative framework across a curated collection of circadian transcriptomic datasets.

genomics↗

bioRxiv2025

Single cell decomposition of multicellular aging programs associated with impaired lung regeneration

Aging impairs the regenerative capacity of mammalian organs and is a major risk factor for organ fibrosis. Mechanisms underlying persistent fibrosis after lung injury in old individuals remain unclear. We used longitudinal single-cell RNA-seq after lung injury and dissected aging effects computationally and experimentally at baseline and during repair. In old mice, sustained fibroblast activation in the resolution phase of fibrosis was associated with prolonged epithelial senescence and persistent epithelial-mesenchymal crosstalk. Single-cell interpretable tensor decomposition analysis revealed that aging most strongly affected T/B-lymphocytes and macrophages. Notably, we identified a Granzyme K-high CD8+ T cell state that was unique to aged mice, co-localized with epithelial progenitors, and its co-culture or Gzmk treatments in lung organoids impaired progenitor function by inducing stem cell senescence. In summary, our study highlights the effects of immune aging on epithelial progenitor function and provides a time-resolved high resolution map of lung regeneration in the context of aging.

cell biology↗

bioRxiv2025

Outer Kinetochore Proteins form Linear Elements to Regulate Vesicle Transport

During cell division, several key regulators of chromosome segregation play additional roles during vesicle trafficking required for cytokinesis. During anaphase I in C. elegans oocytes, chromosome segregation is coordinated with vesicle trafficking to support polar body extrusion and exocytosis of extracellular matrix material. Prior to anaphase, numerous outer kinetochore proteins localize to mysterious "linear element" structures throughout the cortex in addition to chromosomes, which has been observed in oocytes of multiple species. Linear elements initially form as puncta just before nuclear envelope breakdown and rapidly assemble into larger elongated structures. As linear elements grow, they form large clusters with secretory vesicles, initiating an elaborate transport mechanism that distributes vesicles throughout the cortex by anaphase I. Linear elements dynamically interact with microtubules and endoplasmic reticulum during this process. Microtubules are required for linear element assembly, motility, and clustering with vesicles. Knockdown of a plus end microtubule binding kinetochore component also inhibits linear element growth and vesicle clustering, but not the motility of linear element puncta. Depletion of several outer kinetochore proteins causes defects in extracellular matrix formation. Therefore, linear elements facilitate the microtubule-dependent transport of vesicles for their proper distribution in the cortex. We hypothesize that outer kinetochore complexes coordinate movements of chromosomes and cytoplasmic membranes to enhance the fidelity of cell division.

cell biology↗

bioRxiv2024

Modulation of circadian rhythms in articular cartilage by heat pulses

ObjectivePrior studies have shown that disruption of the circadian clock leads to cartilage degeneration in mice while shift work is associated with higher risk of osteoarthritis (OA) in humans. In this study we investigated the potential of heat pulses to restore dampened circadian rhythms in articular cartilage. MethodsFemoral head cartilage explants and primary chondrocytes were isolated from PER2::LUC mice. Human femoral condyle cartilage was obtained from osteoarthritic patients undergoing total knee replacement. Tissues and cells were exposed to heat shock at various temperatures (37-43 {degrees}C) and incubation lengths. Bioluminescence from explants and cells was recorded in real-time. RNA sequencing and qPCR were used to assess gene expression changes in response to heat. ResultsWe established that a 60-min pulse at 43 {degrees}C was sufficient to restore dampened PER2::LUC rhythms in mouse cartilage explants or in primary chondrocytes. Transcriptome analysis in mouse articular cartilage showed an up-regulation of genes encoding heat shock proteins and collagens, and a transient down-regulation of Sox9, Runx2, Per1, Clock and Cry2. Heat induced the expression of circadian clock genes in human osteoarthritic knee cartilage. Mechanistically, inhibition of HSP90 activity or perturbation of F-actin polymerisation blocked the heat-induced resynchronisation of circadian rhythms. ConclusionTogether, these data have contributed to a greater understanding of the multifaceted nature of the connections between circadian timekeeping, heat stress responses and homeostasis in articular cartilage. These findings also suggest that time-prescribed temperature increases could be developed into a non-invasive intervention to slow down tissue ageing and restore homeostasis in osteoarthritic joints by improving circadian oscillations of cartilage rhythmic pathways.

cell biology↗

bioRxiv2023

The clock transcription factor BMAL1 is a key regulator of extracellular matrix homeostasis and cell fate in the intervertebral disc

The circadian clock in mammals temporally coordinates physiological and behavioural processes to anticipate daily rhythmic changes in their environment. Chronic disruption to circadian rhythms (e.g., through ageing or shift work) is thought to contribute to a multitude of diseases, including degeneration of the musculoskeletal system. The intervertebral disc (IVD) in the spine contains circadian clocks which control [~]6% of the transcriptome in a rhythmic manner, including key genes involved in extracellular matrix (ECM) homeostasis. However, it remains largely unknown to what extent the local IVD molecular clock is required to drive rhythmic gene transcription and IVD physiology. In this work, we identified profound age-related changes of ECM microarchitecture and an endochondral ossification-like phenotype in the annulus fibrosus (AF) region of the IVD in the Col2a1-Bmal1 knockout mice. Circadian time series RNA-Seq of the whole IVD in Bmal1 knockout revealed loss of circadian patterns in gene expression, with an unexpected emergence of 12-hour ultradian rhythms, including FOXO transcription factors. Further RNA sequencing of the AF tissue identified region-specific changes in gene expression, evidencing a loss of AF phenotype markers and a dysregulation of ECM and FOXO pathways in Bmal1 knockout mice. Consistent with an up-regulation of FOXO1 mRNA and protein levels in Bmal1 knockout IVDs, inhibition of FOXO1 in AF cells suppressed their osteogenic differentiation. Collectively, these data highlight the importance of the local molecular clock mechanism in the maintenance of the cell fate and ECM homeostasis of the IVD. Further studies may identify potential new molecular targets for alleviating IVD degeneration.

physiology↗

bioRxiv2022

Increased glycolysis and functional mitochondria fuel acinar-ductal metaplasia in the pancreas

Reprogramming of the cellular metabolism is a hallmark of pancreatic cancer, yet it remains unclear at what stage during carcinogenesis it occurs. Here, we investigated the metabolic requirements for acinar-to-ductal metaplasia (ADM), the first step in pancreatic carcinogenesis. We detected increased glycolytic marker expression in human ADM suggesting that a metabolic switch occurs during ADM formation. We report that this switch was similarly required for ADM formation in different oncogenic mouse models (KRAS, PI3K, and MEK1) and in ligand-induced ADM in mouse wild-type acini. In addition, we show that a functional electron transport chain (ETC), but not mitochondrial ATP production, was essential to ADM formation. We conclude that the ETC provides NAD+ for the de novo synthesis of serine from glycolysis intermediates. Our findings demonstrate that metabolic programming is essential for the initiation of pancreatic carcinogenesis and thus identifies potential targets for metabolic intervention.

cancer biology↗

bioRxiv2021

Mechanical loading and hyperosmolarity as a daily resetting cue for skeletal circadian clocks

Daily rhythms in mammalian behaviour and physiology are generated by a multi-oscillator circadian system entrained through environmental cues (e.g. light). Presence of niche-dependent physiological time cues has been proposed, allowing local tissues flexibility of phase adjustment. However, to date, such stimuli have remained elusive. Here we show that cycles of mechanical loading and osmotic stimuli within physiological range drive rhythmic expression of clock genes and reset clock phase and amplitude in cartilage and intervertebral disc tissues. Hyperosmolarity (not hypo-osmolarity) resets clocks in young and ageing skeletal tissues through mTORC2-AKT-GSK3{beta} pathway, leading to genome-wide induction of rhythmic genes. These results advocate diurnal patterns of mechanical loading and consequent daily surges in osmolarity as a bona fide tissue niche-specific time cue to maintain skeletal circadian rhythms in sync. One-Sentence SummaryCircadian clocks in aneural skeletal tissues sense the passage of time through rhythmic patterns of loading and osmolarity

physiology↗

bioRxiv2019

The Ufm1 system is upregulated by ER stress during osteogenic differentiation

ObjectiveMutations in the catalytic site of the ubiquitin-fold modifier 1(UFM1)-specific peptidase 2 (UFSP2) gene have been identified to cause autosomal dominant Beukes hip dysplasia in a large multigenerational family and a novel form of autosomal dominant spondyloepimetaphyseal dysplasia in a second family. We investigated the expression of the UFSP2/UFM1 system during mouse joint development the connection to ER stress induced during osteogenic differentiation.\n\nMethodsThe pattern of expression of Ufsp2 was determined by radioactive RNA in situ hybridisation on mouse tissue sections. qPCR was used to monitor expression during in vitro osteogenic differentiation and chemically induced ER stress. Affinity purification and mass spectrometry was used for isolation and identification of Ufm1 conjugation targets. Luciferase reporter assay was used to investigate the activity of Ufm1 system genes promoters.\n\nResultsWe found that Ufsp2 was predominantly expressed in the bone and secondary ossification centres of 10-day old mice. The Ufm1 system was upregulated during in vitro osteogenic differentiation and in response to chemically induced ER stress. We identified unfolded protein response elements in the upstream sequences of Uba5, Ufl1, Ufm1and Lzap. We identified putative Ufm1 conjugation targets where conjugation was increased in response to ER stress.\n\nConclusionHigher expression of Ufsp2 in bone and secondary ossification centres as well as upregulation of components of the Ufm1system in response to ER stress suggests that the molecular pathway between the UFSP2 mutations and form of skeletal dysplasia may relate to abnormal ER stress responses during osteoblast differentiation.

cell biology↗

bioRxiv2019

Circadian time series proteomics reveals daily dynamics in cartilage physiology

ObjectivesArticular cartilage undergoes cyclical heavy loading and low load recovery during the 24-hour day/night cycle. We investigated the daily changes of protein abundance in mouse femoral head articular cartilage by performing 24-hour time-series proteomics study.\n\nMethodsTandem mass spectrometry analysis was used to quantify proteins extracted from mouse cartilage. Bioinformatics analysis was performed to quantify rhythmic changes in protein abundance. Primary chondrocytes were isolated and cultured for independent validation of selected rhythmic proteins.\n\nResults145 rhythmic proteins were detected. Among these were key cartilage molecules including CCN2, MATN1, PAI-1 and PLOD1 & 2. Pathway analysis revealed that proteins related to protein synthesis, cytoskeleton and glucose metabolism exhibited time-of-day dependent peaks in their abundance. Meta-analysis of published proteomics datasets from articular cartilage revealed that numerous rhythmic proteins were dysregulated in osteoarthritis and/or ageing.\n\nConclusionsOur circadian proteomics study revealed that articular cartilage is a much more dynamic tissue than previously thought. Chondrocytes exhibit circadian rhythms not only in gene expression but also in protein abundance. Our results clearly call for the consideration of circadian timing in understanding cartilage biology, osteoarthritis pathogenesis, treatment strategies and biomarker detection.

physiology↗