Biology subjects

Bauer, C.

Publications and source records attributed to Bauer, C..

11 recordsLinked to original sources

bioRxiv2026

Photocrosslinkable silk fibroin-hyaluronic acid hybrid hydrogels enable chondrocyte-driven matrix deposition and mechanical maturation for cartilage tissue engineering

Articular cartilage has limited self-repair capacity, and current treatments fail to fully restore its structure and function. 3D hydrogels that support chondrocyte viability and extracellular matrix (ECM) deposition offer a promising strategy for cartilage regeneration. Here, we developed a photo-crosslinkable silk fibroin-hyaluronic acid hydrogel for 3D encapsulation of primary human chondrocytes. Hydrogels were formulated with varying silk fibroin methacrylate (SilMA, 10-20% w/v) and hyaluronic acid methacrylate (HAMA, 1-2% w/v) concentrations and characterized for rheological, mechanical, and morphological properties. All SilMA-HAMA hydrogel formulations exhibited shear-thinning behavior and rapidly gelled (<20 s) under UV irradiation while maintaining high porosity, thereby ensuring injectability and efficient nutrient diffusion. Notably, the Youngs modulus of the cell-laden scaffolds increased from [~]18 kPa to [~]1200 kPa over culture, indicating mechanical maturation driven by chondrocyte-mediated matrix deposition. This maturation was further confirmed by histological analysis and qPCR, which demonstrated enhanced ECM production and chondrogenic gene expression. Taken together, these results highlight SilMA-HAMA hydrogels as a promising biomimetic platform that couples mechanical reinforcement with biological functionality for cartilage tissue engineering.

bioengineering↗

bioRxiv2026

Leukemia stem cell expansion cultures reveal clonal drivers of leukemogenesis and therapy response

Leukemia stem cells (LSCs) contain the highest capacity for leukemia-reinitiation and therapy-resistance across all leukemic cells, but our understanding of their molecular and cellular properties remains limited due to their relative rarity and ineffective cell culture systems to maintain their purity at scale. Here, we develop Polymer-based Leukemic STem-cell Cultures (PLSTCs) and demonstrate their capacity to derive and propagate large numbers of Npm1cA/Flt3ITD acute myeloid leukemia (AML) stem cells at high purities. Compared to traditional cultures, PLSTCs show more than 1000-fold enrichment in functional LSCs based on single-cell gene expression signatures and leukemia-initiating assays. Tracing LSC clones with genomic LARRY barcodes during ex vivo expansion, we reveal that PLSTCs can sustain a diversity of self-renewing LSC states with stable, heritable transcriptional programs. Using dynamic state-fate analysis, we characterize clonal programs that are linked with enhanced ex vivo self-renewal, in vivo leukemia initiation, and therapeutic response to induction chemotherapy. LSC clones primed to resist treatment were enriched for a rare cell state that underwent a fate-switch and produced megakaryocytic-erythroid-like leukemic cells that expanded in the spleen. Targeting LSC programs through pooled CRISPR and single-cell sequencing (CROPseq) in PLSTCs, we reveal that chondroitin-sulfate synthesis is required to maintain a primitive LSC state and leukemic recovery from chemotherapy. In sum, our studies showcase the powerful application of scalable leukemic stem-cell expansion cultures and dynamic state-fate analysis of AML LSCs. We anticipate these systems will accelerate our understanding and interception of stem cell plasticity in cancer.

cancer biology↗

bioRxiv2025

DNA Methylation Ageing Atlas Across 17 Human Tissues

Aging involves widespread epigenetic remodeling across tissues, yet the nature and consistency of these changes remain unclear. We conducted a meta-analysis of more than 15,000 human methylomes spanning 17 tissues, identifying both conserved and tissue-specific aging signatures. We examined linear changes via differentially methylated positions, variability shifts via variably methylated positions, and Shannon-entropy to capture methylation disorder. Network analysis revealed fragile co-methylation modules largely resistant to beneficial perturbation. Key disruptors, including PCDHGA1, MEST, HDAC4, and HOX genes, exacerbated aging signals across tissues. Notably, a resilient module enriched for NAD{square} salvage metabolism supports therapeutic targeting of NAD{square} in aging. PCDHGA1 emerged as a conserved cross-tissue driver, suggesting protocadherin-mediated adhesion plays a broader role in maintaining structural and signaling stability in multiple organ systems. Our open-access atlas provides a foundational resource for dissecting the molecular architecture of human aging and identifying testable targets for intervention, biomarkers, and translational epigenetic therapies.

bioinformatics↗

bioRxiv2025

TET dioxygenases localize at splicing speckles and promote RNA splicing

The dynamic regulation of RNA metabolism plays a crucial part in cellular function, with emerging evidence suggesting an important role for RNA modifications in this process. This study explores the relationship between RNA splicing and the TET dioxygenase activity, shedding light on the role of hm5C (RNA 5-hydroxymethylcytosine), and TET proteins, in RNA metabolism. Integrating data from mass spectrometry, AlphaFold structural modeling, microscopic analysis, and different functional assays including in vitro splicing, TET proteins were found to regulate splicing. We show that TET1, TET2, and TET3 interact with the splicing factors U2AF1 and U2AF2. Interestingly, TET dioxygenases localize in splicing speckles in mammalian and Drosophila cells. TET speckles association is RNA dependent, as it is TET interaction with splicing factors. Furthermore, in vitro splicing assays revealed that all three TET proteins promote splicing efficiency, and the oxidation of m5C to hm5C can restore splicing efficiency in vitro. The latter highlights the regulatory role of cytosine modifications in RNA metabolism. These findings provide insights into the complex interplay between RNA modifications and splicing, suggesting a multifaceted role for TET proteins in RNA metabolism beyond its canonical DNA demethylation function. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/641893v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1a304bborg.highwire.dtl.DTLVardef@18b91d3org.highwire.dtl.DTLVardef@12efeforg.highwire.dtl.DTLVardef@1464355_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- TET1 localizes in splicing speckles in an RNA-dependent manner - TET proteins, especially TET1, interact with the splicing factors U2AF1 and U2AF2 - TET proteins increase splicing efficiency, independent of their catalytic activity - RNA 5-methylcytosine (m5C) oxidation to 5-hydroxymethylcytosine (hm5C) restores splicing efficiently in vitro

cell biology↗

bioRxiv2024

Hampered AMPK-ULK1 cascade in Alzheimer disease (AD) instigates mitochondria dysfunctions and AD-related alterations that are alleviated by metformin

BackgroundMitochondrial structure and function alterations are key pathological features in Alzheimers disease (AD) brains. The adenosine monophosphate-activated protein kinase (AMPK) and its downstream effector Unc-51 like autophagy activating kinase 1 (ULK1) represent a key node controlling mitochondria health, the alteration of which likely contribute to AD development. MethodsWe designed this study to investigate AMPK-ULK1 activation state in post-mortem human sporadic AD brains, in 3xTgAD mice that recapitulate most of human AD features, and in neuronal cells expressing the amyloid precursor protein with the familial Swedish mutation (APPswe). We examined the impact of the pharmacological and genetic modulation of AMPK-ULK1 cascade on mitochondria structure and functions in APPswe cells. We evaluated the potential beneficial impact of AMPK-ULK1 activation by Metformin (Met) on mitochondria defects, as well as on early- and late-stage AD-related alterations in vivo and ex vivo. ResultsAt first, we show that AMPK-ULK1 cascade is defective in murine and human AD brains as well as in APPswe cells. We then report that Met administration to 3xTgAD mice alleviates the alterations of neuronal mitochondria structure and function and we consolidate these results in cells using both pharmacological and genetic tools to modulate AMPK-ULK1 cascade. In mice brains, Met reduces the early accumulation of APP C-terminal fragments (APP-CTFs) as well as the amyloid beta (A{beta}) burden present in aged mice. Mechanistically, we show that Met increases the localization of APP-CTFs within cathepsin D-positive lysosomal compartments in vivo and enhances cathepsin D activity in vitro. The reduction of A{beta} load by Met occurs through an increased recruitment of Iba1+ cells to A{beta} plaques and an enhancement of the phagocytic activity of microglia. Accordingly, in symptomatic 3xTgAD mice, Met alleviates microgliosis and astrogliosis, modulates microglia morphology, reduces peripheral proinflammatory cytokines levels, and regulates the expression of a set of inflammatory genes. In addition, Met normalizes dendritic spines shape in organotypic hippocampal slice cultures modeling AD and improves learning performance of 3xTgAD mice. ConclusionsOur study demonstrates potential therapeutic benefits of targeting AMPK-ULK1 cascade to reverse both early and late AD-related alterations, deserving further investigation in fundamental research and in human clinical studies.

neuroscience↗

bioRxiv2024

Molecular Landscape of Modality-Specific Exercise Adaptation in Human Skeletal Muscle through Large-Scale Multi-OMICs Integration

We conducted a large-scale, statistically powered, meta-analysis of exercise adaptations in human skeletal muscles, integrating epigenetic, transcriptomic, transcription factors, and proteomic data across 12 independent cohorts comprising over 1000 participants and 2340 human muscle samples. Our study identified distinctive signatures associated with maximal oxygen consumption (VO2max), and identified five genes robustly intersecting multi-OMIC layers. Notably, transcription factors predominantly functioned as activators across these layers, regulating expression of target genes irrespective of whether DNA methylation levels were low or high, indicating a synergistic effect between TFs and the methylome. Analysis of distinct exercise modalities (aerobic and resistance exercise) revealed unique gene pathways, contrasting with patterns observed in inactivity (muscle disuse) studies. These findings offer a comprehensive understanding of exercise and modality-specific adaptations, shedding light on muscle health and the molecular mechanisms associated with cardiorespiratory fitness, aging, and disease prevention.

molecular biology↗

bioRxiv2021

Single cell RNA-seq uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19

The systemic immune response to viral infection is shaped by master transcription factors such as NF{kappa}B or PU.1. Although long non-coding RNAs (lncRNAs) have been suggested as important regulators of transcription factor activity, their contributions to the systemic immunopathologies observed during SARS-CoV-2 infection have remained unknown. Here, we employed a targeted single-cell RNA-seq approach to reveal lncRNAs differentially expressed in blood leukocytes during severe COVID-19. Our results uncover the lncRNA PIRAT as a major PU.1 feedback-regulator in monocytes, governing the production of the alarmins S100A8/A9 - key drivers of COVID-19 pathogenesis. Knockout and transgene expression, combined with chromatin-occupancy profiling characterized PIRAT as a nuclear decoy RNA, diverting the PU.1 transcription factor from alarmin promoters to dead-end pseudogenes in naive monocytes. NF{kappa}B-dependent PIRAT down-regulation during COVID-19 consequently releases a transcriptional brake, fueling alarmin production. Our results suggest a major role of nuclear noncoding RNA circuits in systemic antiviral responses to SARS-CoV-2 in humans.

immunology↗

bioRxiv2019

Sex-associated differences in cytomegalovirus prevention: Prophylactic strategy is associated with a strong kidney function impairment in female renal transplant patients

Post-transplantation cytomegalovirus (CMV) syndrome can be prevented using the antiviral drug (val)ganciclovir. (Val)ganciclovir is typically administered following a prophylactic or a pre-emptive strategy. The prophylactic strategy entails early universal administration, the pre-emptive strategy, early treatment in case of infection. However, it is not clear which strategy is superior with respect to transplantation outcome; sex-specific effects of these prevention strategies are not known. We have retrospectively analysed 540 patients from the multi-centre Harmony study along eight pre-defined visits: 308 were treated according to a prophylactic, 232 according to a pre-emptive strategy. As expected, we observed an association of prophylactic strategy with lower incidence of CMV syndrome, delayed onset and lower viral loads compared to the pre-emptive strategy. However, in female patients, the prophylactic strategy was associated with a strong impairment of glomerular filtration rate one year post-transplant (difference: -12.0{+/-}4.2 mL{middle dot}min-1{middle dot}1.73m-2, P=0.005). Additionally, we observed a tendency of higher incidence of acute rejection and severe BK virus reactivation in the prophylactic strategy group. While the prophylactic strategy was more effective for preventing CMV syndrome, our results suggest for the first time that the prophylactic strategy might lead to inferior transplantation outcomes in female patients, providing evidence for a strong association with sex.

pharmacology and toxicology↗

bioRxiv2019

The Hsp70/Hsp90 Co-Chaperone Hop/Stip1 Shifts the Proteostatic Balance from Folding Towards Degradation

Hop/Stip1/Sti1 is thought to be essential as a co-chaperone to facilitate substrate transfer between the Hsp70 and Hsp90 molecular chaperones. Despite this proposed key function for protein folding and maturation, it is not essential in a number of eukaryotes and bacteria lack an ortholog. We set out to identify and to characterize its eukaryote-specific function. Human cell lines and the budding yeast with deletions of the Hop/Sti1 gene display reduced proteasome activity due to inefficient capping of the core particle with regulatory particles. Unexpectedly, knock-out cells are more proficient at preventing protein aggregation and at promoting protein refolding. Without the restraint by Hop, a more efficient folding activity of the prokaryote-like Hsp70/Hsp90 complex, which can also be demonstrated in vitro, compensates for the proteasomal defect and ensures an alternate proteostatic equilibrium. Thus, cells may act on Hop to shift the proteostatic balance between folding and degradation.

cell biology↗

bioRxiv2019

Free water in white matter differentiates MCI and AD from control subjects

Recent evidence show that neuroinflammation plays a role in many neurological diseases including mild cognitive impairment (MCI) and Alzheimers disease (AD), and that free water (FW) modeling from clinically acquired diffusion MRI (DTI-like acquisitions) can be sensitive to this phenomenon. This FW index measures the fraction of the diffusion signal explained by isotropically unconstrained water, as estimated from a bi-tensor model. In this study, we developed a simple FW processing pipeline that uses a safe white matter (WM) mask without gray matter (GM)/CSF partial volume contamination (WMsafe) near ventricles and sulci. We investigated if FW inside the WMsafe mask, including and excluding areas of white matter damage such as white matter hyperintensities (WMHs) as shown on T2 FLAIR, computed across the whole white matter could be indicative of diagnostic grouping along the AD continuum. After careful quality control, 81 cognitively normal controls (NC), 103 subjects with MCI and 42 with AD were selected from the ADNIGO and ADNI2 databases. We show that MCI and AD have significantly higher FW measures even after removing all partial volume contamination. We also show, for the first time, that when WMHs are removed from the masks, the significant results are maintained, which demonstrates that the FW measures are not just a byproduct of WMHs. Our new and simple FW measures can be used to increase our understanding of the role of inflammation-associated edema in AD and may aid in the differentiation of healthy subjects from MCI and AD patients.

neuroscience↗

bioRxiv2018

A novel approach reveals that HLA class 1 single antigen bead-signatures provide a means of high-accuracy pre-transplant risk assessment of acute cellular rejection

Acute cellular rejection (ACR) is associated with complications after kidney transplantation, such as graft dysfunction and graft loss. Early risk assessment is therefore critical for the improvement of transplantation outcomes. In this work, we retrospectively analyzed a pre-transplant HLA antigen bead assay data set that was acquired by the e:KID consortium as part of a systems medicine approach. The data set included single antigen bead (SAB) reactivity profiles of 52 low-risk graft recipients (negative complement dependent cytotoxicity crossmatch, PRA<30%) who showed detectable pre-transplant anti-HLA 1 antibodies. To assess whether the reactivity profiles provide a means for ACR risk assessment, we established a novel approach which differs from standard approaches in two aspects: the use of quantitative continuous data and the use of a multiparameter classification method. Remarkably, it achieved significant prediction of the 38 graft recipients who experienced ACR with a balanced accuracy of 82.7% (sensitivity=76.5%, specificity= 88.9%). The resultant classifier achieved one of the highest prediction accuracies in the literature for pre-transplant risk assessment of ACR. Importantly, it can facilitate risk assessment in non-sensitized patients who lack donor-specific antibodies. As the classifier is based on continuous data and includes weak signals, our results emphasize that not only strong but also weak binding interactions of antibodies and HLA 1 antigens contain predictive information.

immunology↗