Biology subjects

Thomas, C.

Publications and source records attributed to Thomas, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Molecular and structural remodeling of stress granules in slowly and rapidly progressive Alzheimer's disease

Stress granules (SGs) are dynamic ribonucleoprotein condensates that modulate RNA metabolism during cellular stress. Although SG dysfunction has been increasingly linked to neurodegenerative diseases, their structural and molecular remodeling in Alzheimers disease (AD), particularly rapidly progressive AD (rpAD), remains poorly understood. Here, we present a comprehensive multi-omics characterization of SGs from postmortem frontal cortex tissues of control, slowly progressive AD (spAD), and rpAD subjects. SGs were immunoprecipitated using Anti-TIAR antibodies and analyzed via transmission electron microscopy (TEM), LCMS/MS-based proteomics, and RNA sequencing. Key protein findings were validated in human cortical brain homogenates and a 3xTg mouse model of A{beta} and tau pathology. TEM revealed disease-specific SG morphologies: small spherical granules in controls; moderate clustering in spAD; and large, amorphous aggregates in rpAD. Proteomic profiling identified 1,667 high-confidence SG-associated proteins, including RNA-binding proteins and disease-linked proteins such as MAPT, APP, and SNCA. SGs in rpAD were significantly enriched for pathways involved in MAPK signaling, proteostasis, and neuroinflammation, while showing reduced abundance of key cytoskeletal and translational regulators, such as TUBA1B and EEF1A2. Transcriptome analysis revealed widespread depletion of long, GC-rich, protein coding RNAs in rpAD SGs. Notably dynamic dysregulation of TUBA1B was also observed in the 3xTg mouse model and human cortical tissues, highlighting cytoskeletal vulnerability during disease progression. Together, these findings uncover profound structural and molecular remodeling of SGs in AD, with rpAD exhibiting a distinctive shift towards pathological SG composition and function. Our results highlight a link between SG alterations and aggressive AD subtypes, providing new mechanistic insights and suggesting new potential targets for therapeutic intervention.

neuroscience↗

bioRxiv2025

Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland

The subsurface biosphere remains poorly characterized, with many resident microorganisms uncultured and lacking genomic references. Despite the growing accessibility of shotgun metagenomics, 16S rRNA gene sequencing remains a standard tool for microbial community profiling, often relying on sequence similarity to reference databases such as SILVA to infer taxonomy and potential function. However, in environments with low biomass and high proportions of unknown lineages, such as deeper sedimentary environments, the accuracy of these inferences and our ability to capture rare taxa remain uncertain. A better inference of these rare taxa may now be possible with the advent of accurate long-read applications that have recently become available. Here we provide a comparison of long-read (PacBio) and short-read (Illumina NextSeq) 16S rRNA approaches for microbial communities from a sediment core of Lake Arnon (Switzerland). We compared community composition in environmental samples and mock controls to evaluate the strengths and limitations of each method. While sequencing technology significantly influenced observed community structure, sediment depth had an even stronger effect. Taxonomic profiles were broadly consistent across methods for most bacterial groups, but archaeal diversity was underrepresented in the long-read data, likely due to primer mismatch. When detected, long-read sequencing offered more accurate taxonomic resolution, often down to the species level, enabling better inference of metabolic potential. Beta diversity patterns were similar at broad taxonomic levels between methods, though more detailed metrics such as species contributions to beta diversity (SCBD) and co-occurrence networks showed enhanced resolution and specificity in long-read datasets. Our results highlight the critical importance of primer design, in particular for capturing archaeal taxa that play important roles in the deep biosphere. With improved primer coverage and continued cost reductions, long-read sequencing holds strong potential for advancing our understanding of subsurface microbial identity, structure and function.

ecology↗

bioRxiv2025

Klotho deficiency promotes skeletal muscle weakness and is associated with impaired motor unit connectivity

Muscle wasting and weakness are important clinical problems that impact quality of life and health span by restricting mobility and independence, and by increasing the risk for physical disability. The molecular basis for this has not been fully determined. Klotho expression is downregulated in conditions associated with muscle wasting, including aging, chronic kidney disease, and myopathy. The objective of this study was to investigate a mechanistic role for Klotho in regulating muscle wasting and weakness. Body weight, lean mass, muscle mass, and myofiber caliber were reduced in Klotho-deficient mice. In the tibialis anterior muscle of Klotho null mice, type IIa myofibers were resistant to changes in size, and muscle composition differed with a higher concentration of type IIb fibers to the detriment of type IIx fibers. Glycolytic enzymatic activity also increased. The composition of the soleus muscle was unaffected and myofiber caliber was reduced comparably in type I, IIa, and IIx fibers. Muscle contractile function declined in Klotho-deficient mice, as evidenced by reduced absolute twitch and torque, and decreased rates of contraction and relaxation. RNA-sequencing analysis identified increased transcriptional expression of synaptic and fetal sarcomeric genes, which prompted us to test effects on muscle innervation. Klotho-deficiency induced morphological remodeling of the neuromuscular junction, myofiber denervation, and a functional loss of motor units. Loss of motor units correlated with absolute torque. Collectively, our findings have uncovered a novel mechanism through which Klotho-deficiency leads to alterations to the muscle synapse affecting motor unit connectivity that likely influences muscle wasting and weakness. Key points summaryO_LIMaintaining skeletal muscle mass and function is critical to preserve physical capacity and independence. Clinical observations implicate longevity factor Klotho as a key regulator of muscle mass and weakness. Low Klotho levels are reported to correlate with muscle weakness and frailty. C_LIO_LIUsing Klotho null mice, our study shows that Klotho-deficiency promotes skeletal muscle weakness and impaired motor unit connectivity. C_LIO_LIRNA-sequencing analysis identified altered expression of sarcomeric and synaptic genes suggesting changes to the muscle synapse in Klotho-deficient mice. C_LIO_LIHistopathological analyses revealed Klotho-deficiency is associated with reduced myofiber caliber, altered muscle composition, and increased prevalence of NCAM+ denervated fibers. Imaging of the NMJ further showed morphological changes and reduced area of synaptic contact. C_LIO_LIOverall, our findings show that Klotho regulates the structure and function of the NMJ affecting motor unit connectivity which may have an important role in the pathogenesis of muscle wasting and weakness. C_LI

physiology↗

bioRxiv2025

Amazon biodiversity is at risk from metal contamination due to mining activity

The Amazon basin hosts the most biodiverse and intact ecosystems on Earth, yet human activities are an increasing threat. Metal contamination due to mining constitutes one of these major threats, but its impacts remain poorly quantified. We provide the first quantitative assessment of biodiversity exposure to mining-associated metals--mercury [Hg], arsenic [As], copper [Cu], Zinc [Zn], and lead [Pb]--across the Amazon. Around 66% of the Amazons 38,890 species of birds, plants, mammals, reptiles, amphibians, and fishes are exposed to metal contamination, including biodiversity hotspots and Indigenous territories. Safeguarding the Amazons role as a global reservoir of biodiversity, ecosystem function, and cultural heritage requires addressing metal contamination not only as a localized issue, but as a pervasive threat to global biodiversity.

ecology↗

bioRxiv2025

Long-Term Ecological Baselines and Critical Thresholds in Ombrotrophic Peatlands of Europe: Implications for Restoration Strategies

Maintaining appropriate peatland hydration, particularly through the regulation of the depth to the water table (DWT), is crucial for peatland conservation, restoration, and the mitigation of greenhouse gas emissions. In this study, we assess the long-term ecological impact of hydrological changes, primarily induced by drainage, on ombrotrophic peatlands across Europe. Our analysis is based on novel palaeoecological data from seven peat cores collected from sites that have experienced varying degrees of anthropogenic disturbance. We reconstructed historical DWT fluctuations using plant macrofossil and testate amoeba analyses at high resolution. By applying Threshold Indicator Taxa Analysis (TITAN), we identified species-specific and community-level response thresholds to changes in water level. This approach revealed two distinct change points: the first, at approximately 7 cm DWT, corresponds to hydrological conditions favourable for moisture-dependent Sphagnum species, while the second, near 22 cm DWT, is associated with more drought-adapted taxa and signals ecosystem degradation. The interval between these points represents a transition zone between optimal and suboptimal conditions for peatland functioning. An additional TITAN analysis aimed at identifying the timing of the most significant ecological changes indicates that peatland degradation intensified over the past two centuries and has accelerated in recent decades. Our findings also show that even after hydrological restoration, microbial and plant communities often remain distinct from those in undisturbed peatlands. This underscores the importance of preserving sites that still retain near-natural conditions. Based on our results (and consistent with previous studies) we recommend maintaining a DWT of approximately 10 cm below the surface as an optimal target for both peatland conservation and restoration. Such conditions not only support ecological integrity but are also associated with reduced greenhouse gas emissions and higher peat accumulation rates, reinforcing the role of ombrotrophic peatlands as long-term carbon sinks.

ecology↗

bioRxiv2025

Structure of YbbAP-TesA: a Type VII ABC transporter lipid-hydrolase complex

Type VII ABC transporters are ATP-powered membrane protein complexes that drive key biological processes in the bacterial cell envelope. In E. coli, three of the four Type VII ABC systems have been extensively characterised including: the FtsEX-EnvC cell division complex, the LolCDE-LolA lipoprotein trafficking machinery and the MacAB-TolC efflux pump. Here we describe a fourth E. coli Type VII ABC system, YbbAP-TesA, which combines a Type VII ABC transporter with a multifunctional hydrolytic enzyme. Structures of the complete YbbAP-TesA complex, and of YbbAP with and without bound ATP analogues, capture the long-range transmembrane conformational changes that are the hallmark of this ABC superfamilys mechanotransmission mechanism. We further show that YbbAP-TesA can hydrolyse a variety of ester and thioester substrates and experimentally confirm a constellation of active site residues in TesA. Our data suggests YbbAP has a role in extracting hydrophobic molecules from the inner membrane and presenting these to TesA for hydrolysis. The work extends collective knowledge of the remarkable diversity of the ABC superfamily and establishes a new function for Type VII ABC transporters in bacterial cells. Significance StatementType VII ABC transporters are unique to bacteria and play important roles in bacterial physiology including cell division, antibiotic resistance, siderophore secretion, antibiotic sensing, toxin secretion, biofilm regulation and lipoprotein trafficking. Here we identify a complex that combines an atypical Type VII ABC transporter (YbbAP) with a periplasmic lipid hydrolase (TesA). The YbbAP-TesA complex is structurally and functionally distinct from all known Type VII ABC transporter systems including FtsEX-EnvC, LolCDE-LolA, BceAB-BceS and MacAB-TolC. Structures suggest that YbbAP-TesA uses ATP-driven mechanotransmission to extract substrates from the inner membrane and hydrolyse them in the periplasmic space. The discovery and characterisation of YbbAP-TesA highlights the structural and functional diversity of Type VII ABC transporter complexes and suggests a new function for these proteins in the bacterial cell envelope.

microbiology↗

bioRxiv2025

12/15-Lipoxygenase orchestrates murine wound healing via PPARg-activating oxylipins acting holistically to dampen inflammation.

12/15-lipoxygenase (12/15-LOX, Alox15) generates bioactive oxygenated lipids during inflammation, however its homeostatic role(s) in normal healing are unclear. Here, the role of 12/15-LOX in resolving skin wounds was elucidated, focusing on how its lipids act together in physiologically relevant amounts. In mice, wounding caused acute appearance of 12/15-LOX-expressing macrophages and stem cells, coupled to early generation of [~]12 monohydroxy-oxylipins and enzymatically oxygenated phospholipids (eoxPL). Alox15 deletion increased -smooth muscle actin, collagen deposition, stem cell/fibroblast proliferation, IL6/pSTAT3, pSMAD3, and IFN-{gamma} levels. Conversely, CD206 expression, F480+ cells, MMP9 and MMP2 activities were reduced. Alox15-/- skin was deficient in PPAR{gamma}/adiponectin activity. Furthermore, while pro-inflammatory genes were upregulated as normal during wounding, many including Il6, Il1b, ccl4, Cd14, Cd274, Clec4d, Clec4e, Csf3, and Cxcl2 failed to revert to baseline during healing, indicating disruption of an anti-inflammatory brake. Reconstituting Alox15-/- wounds with a physiological mixture of Alox15-derived primary oxylipins generated by healing wounds restored MMP and dampened collagen deposition. The oxylipin mixture activated PPAR{gamma} in vitro, while in vivo, the PPAR{gamma} co-activator, Helz2, was significantly upregulated. Additional inflammatory and proliferative gene networks impacted by Alox15-/-included Elf4, Cebpb and Tcf3, with many of their associated genes significantly dysregulated. In summary, the impact of 12/15-LOX is ascribed to the deficiency of abundantly generated monohydroxy oxylipins acting together via PPAR{gamma}/adiponectin. The identification of multiple gene alterations reveals several new targets for treatment of non-healing wounds. Our studies demonstrate that abundant 12/15-LOX oxylipins act together, dampening inflammation in vivo, revealing a need to consider lipid signaling holistically. Significance statementDefective wound healing is a significant global clinical problem. Macrophage 12/15-lipoxygenase (12/15-LOX, Alox15) generates abundant lipid mediators termed oxylipins during inflammation. However, its physiological role during resolving wound healing is unclear, with studies so far assessing the bioactivity of individual lipids pharmacologically, rather than holistically in physiological amounts. Here, we report that Alox15 deficiency in mice caused a fibrotic response with failure to dampen inflammation, due to a dysregulated PPAR{gamma}/adiponectin axis. Treatment of Alox15-/- wounds with physiological mixtures of PPAR{gamma}-activating 12/15-LOX primary monohydroxy products restored the phenotype. Several transcriptional networks (Elf4, Cebpb and Tcf3) controlled by Alox15 were uncovered, identifying new targets for promoting physiological wound healing.

pharmacology and toxicology↗

bioRxiv2025

Saccadic Suppression Enhances Saliency of Prey-Like Stimuli in the Optic Tectum

Saccadic suppression, a reduction in visual sensitivity around the time of rapid eye movements, is well-documented in primate psychophysics but its mechanisms and functions remain debated. Here, we use zebrafish to trace the origins of saccadic suppression and we demonstrate how saccadic suppression selectively enhances the visual salience of ecologically relevant stimuli. Saccadic suppression thus contributes to more than just compensation for rapid saccade-induced image shifts. We first established a behavioral correlate of saccadic suppression in larval zebrafish escape behavior. Then, using electrophysiology, we show that retinal ganglion cells jumpstart saccadic suppression in a spatial frequency dependent manner. Calcium imaging, combined with 360{degrees} visual stimulation and behavioral tracking, revealed that motor signals enhance peri-saccadic suppression strength in the optic tectum, where suppression lasts for more than 3000 ms. Notably, saccadic suppression is much weaker and more short-lived for stimuli related to hunting or escape behavior than for behaviorally less relevant global flashes. This unequal attenuation effectively increases the salience of the ecologically relevant stimuli in the optic tectum after saccades. Our results demonstrate that saccadic suppression integrates visual and motor signals to optimize sensory processing within neural constraints, and they provide insights into evolutionarily conserved visual strategies.

neuroscience↗

bioRxiv2025

Cancer cells suppress NK activity by actin-driven polarisation of inhibitory ligands at the synapse

Natural killer (NK) cells engage target cells via the immunological synapse, where inhibitory and activating signals determine whether NK cell cytotoxicity is suppressed or activated. We report that cancer cells can rapidly remodel their actin cytoskeleton upon NK cell engagement, leading to F-actin accumulation at the synapse. This process inhibits NK cell activation as indicated by impaired MTOC and lytic granule polarization. Exploring the underlying mechanism, we found that actin remodelling drives the recruitment of inhibitory ligands, such as HLA-A, -B, and -C, to the synapse. Disrupting HLA interaction with their cognate inhibitory receptors KIRs restored NK cell activation. Using NK cells expressing inhibitory KIR receptors, matched or unmatched to HLA molecules on cancer cells, we show that synaptic F-actin accumulation and matching KIR-HLA interactions jointly suppress NK cell cytotoxicity. Our findings reveal a novel immune evasion strategy in which cancer cells impair NK cell activation by altering synaptic signalling through actin cytoskeleton-driven recruitment of inhibitory signals to the immunological synapse.

cancer biology↗

bioRxiv2025

Securin and cyclin B1-CDK1, but not SGO2, regulate separase activity during meiosis I in mouse oocytes

During meiosis I in oocytes, anaphase is triggered by deactivation of cyclin B1-CDK1 and activation of separase. Active separase plays an essential role in cleaving cohesin rings that hold homologous chromosomes together. Critically, separase must be inhibited until all chromosomes are aligned and the cell is prepared for anaphase I. Inhibition can be mediated through the binding of separase to either securin or cyclin B1-CDK1. The relative contribution of each inhibitory pathway varies depending on cell type. Recently, shugoshin-2 (SGO2) has also been shown to inhibit separase in mitotic cells. Here, we used a separase biosensor and perturbed the three inhibitory pathways during meiosis I in mouse oocytes. We show that inhibition mediated by either securin or cyclin B1-CDK1, but not SGO2, is independently sufficient to suppress separase activity. However, when both the securin and cyclin B1-CDK1 inhibitory pathways are perturbed together, separase activity begins prematurely, resulting in gross segregation defects. Furthermore, we characterised shugoshin-2 destruction dynamics and conclude that it is not an essential separase inhibitor in mouse oocytes. The existence of multiple separase inhibitory pathways highlights the critical importance of tightly regulated separase activity during this unique and challenging cell division.

cell biology↗

bioRxiv2024

Multi-omic characterization of human sural nerves acrosspolyneuropathies

Diseases of peripheral nerves termed polyneuropathies (PNPs) are common, mechanistically heterogeneous, and challenging to diagnose. Here, we integrated single nuclei transcriptomics of peripheral nerves from 33 human PNP patients and four controls (365,708 nuclei) with subcellular spatial transcriptomics. We identified novel and human-specific nerve cell type markers including unexpectedly heterogeneous perineurial fibroblasts. All PNPs shared a loss of myelinating and an increase in repair Schwann cells and endoneurial lipid-associated macrophages. Transcriptional changes affected multiple cells outside of the endoneurium across PNPs, suggesting PNPs as pan-nerve diseases. Spatially, PNPs showed a previously unknown perineurial hyperplasia and fibrotic dispersion and this was most pronounced in immune-mediated PNPs. Single cell transcriptomics supported the differential diagnosis of PNPs with potential for future unbiased diagnostic classification. One-sentence summaryThe first large-scale integrated single cell and spatial transcriptomic characterization of human peripheral nerves identifies novel cell markers and unexpected heterogeneity of perineurial cells, reveals polyneuropathies as pan-nerve diseases, and shows that single cell transcriptomics hold potential for unbiased nerve disease classification.

neuroscience↗

bioRxiv2024

A new spatial multi-omics approach to deeply characterize human cancer tissue using a single tissue section

In the ever-changing world of digital pathology, being able to extract a maximum amount of information from a patient tissue sample is of paramount importance for better diagnosis, disease characterization, and therapeutic strategies. Recent technologies such as multiplex immunofluorescence imaging and spatial transcriptomic now enable a deep analysis of protein and gene expression while retaining the spatial context of the tissue. Here, we describe an innovative approach combining a 34-protein Phenocycler panel and transcriptome analysis using Visium on a single head and neck squamous cell carcinoma section. While protein analysis reveals the complexity of the immune phenotypes involved in the disease, transcriptome analysis reveals the intricate cellular states of cancer cells that coexist within the patients tumor. Finally, integrating both omics modalities, we uncover unique comparison of gene and protein expression of spatially resolved cellular subspaces.

cancer biology↗

bioRxiv2024

Zebrafish Pol-Theta and Human Pol-Theta, Orthologues with Homologous Function

DNA Polymerase Theta (Pol {theta}) is a conserved an A-family polymerase that plays an essential role in repairing double strand breaks, through micro-homology end joining, and bypassing DNA lesions, through translesion synthesis, to protect genome integrity. Despite its essential role in DNA repair, Pol {theta} is inherently error-prone. Recently, key loop regions were identified to play an important role in key functions of Pol {theta}. Here we present a comparative structure-function study of the polymerase domain of zebrafish and human Pol {theta}. We show that these two proteins share a large amount of sequence and structural homology. However, we identify differences in the amino acid composition within the key loop areas shown to drive characteristic Pol {theta} functions. Despite these differences zebrafish Pol {theta} still displays characteristics identify in human Pol {theta}, including DNA template extension in the presence of different divalent metals, microhomology-mediated end joining, and translesion synthesis. These results will support future studies looking to gain insight into Pol {theta} function on the basis of evolutionarily conserved features.

molecular biology↗

bioRxiv2024

Blood-based detection of MMP11 as a marker of prostate cancer progression regulated by the ALDH1A1-TGF-β1 signaling mechanism

BackgroundProstate cancer (PCa) is the second most common type of tumor diagnosed in men and the fifth leading cause of cancer-related death in male patients. The response of metastatic disease to standard treatment is heterogeneous. As for now, there is no curative treatment option available for metastatic PCa, and the clinical tests capable of predicting metastatic dissemination and metastatic response to the therapies are lacking. Our recent study identifies aldehyde dehydrogenases ALDH1A1 and ALDH1A3 as critical regulators of PCa metastases. Still, the exact mechanisms mediating the role of these proteins in PCa metastatic dissemination remain not fully understood, and plasma-based biomarkers of these metastatic mechanisms are also not available. MethodsGenetic silencing, gene overexpression, or treatment with different doses of the retinoic acid (RA) isomers, which are the products of ALDH catalytic activity, were used to modulate the interplay between retinoic acid receptors (RARs) and androgen receptor (AR). RNA sequencing (RNAseq), reporter assays, and chromatin immunoprecipitation (ChIP) analysis were employed to validate the role of RARs and AR in the regulation of the transforming growth factor-beta 1 (TGFB1) expression. Gene expression levels of ALDH1A1, ALDH1A3, and the matrix metalloproteinase 11 (MMP11) and their correlation with pathological parameters and clinical outcomes were analyzed by mining several publicly available patient datasets as well as our multi-center transcriptomic dataset from patients with high-risk and locally advanced PCa. The levels of MMP11 protein were analyzed by enzyme-linked immunosorbent assay (ELISA) in independent cohorts of plasma samples from patients with localized or metastatic PCa and healthy donors, while plasma proteome profiles were obtained for selected subsets of PCa patients. ResultsWe could show that ALDH1A1 and ALDH1A3 genes differently regulate TGFB1 expression in a RAR-and AR-dependent manner. We further observed that the TGF-{beta}1 pathway contributes to the regulation of the MMPs, including MMP11. We have confirmed the relevance of MMP11 as a promising clinical marker for PCa using several independent gene expression datasets. Further, we have validated plasma MMP11 levels as a prognostic biomarker in patients with metastatic PCa. Finally, we proposed a hypothetical ALDH1A1/MMP11-related plasma proteome-based prognostic signature. ConclusionsTGFB1/MMP11 signaling contributes to the ALDH1A1-driven PCa metastases. MMP11 is a promising blood-based biomarker of PCa progression.

cancer biology↗

bioRxiv2024

Astrocytes adopt a progenitor-like migratory strategy for regeneration in adult brain

Mature astrocytes become activated upon non-specific tissue damage and contribute to glial scar formation. Proliferation and migration of adult reactive astrocytes after injury is considered very limited. However, the regenerative behavior of individual astrocytes following selective astroglial loss, as seen in astrocytopathies, such as neuromyelitis optica spectrum disorder, remains unexplored. Here, we performed longitudinal in vivo imaging of cortical astrocytes after focal astrocyte ablation in mice. We discovered that perilesional astrocytes develop a remarkable plasticity for efficient lesion repopulation. A subset of mature astrocytes transforms into reactive progenitor-like (REPL) astrocytes that not only undergo multiple asymmetric divisions but also remain in a multinucleated interstage. This regenerative response facilitates efficient migration of newly formed daughter cell nuclei towards unoccupied astrocyte territories. Our findings define the cellular principles of astrocyte plasticity upon focal lesion, unravelling the REPL phenotype as a fundamental regenerative strategy of mature astrocytes to restore astrocytic networks in the adult mammalian brain. Promoting this regenerative phenotype bears therapeutic potential for neurological conditions involving glial dysfunction.

neuroscience↗

bioRxiv2024

A protective role for B-1 cells and oxidation-specific epitope IgM in lung fibrosis

Idiopathic pulmonary fibrosis (IPF) is a morbid fibrotic lung disease with limited treatment options. The pathophysiology of IPF remains poorly understood, and elucidation of the cellular and molecular mechanisms of IPF pathogenesis is key to the development of new therapeutics. B-1 cells are an innate B cell population which play an important role linking innate and adaptive immunity. B-1 cells spontaneously secrete natural IgM and prevent inflammation in several disease states. One class of these IgM recognize oxidation-specific epitopes (OSE), which have been shown to be generated in lung injury and to promote fibrosis. A main B-1 cell reservoir is the pleural space, adjacent to the typical distribution of fibrosis in IPF. In this study, we demonstrate that B-1 cells are recruited to the lung during injury where they secrete IgM to OSE (IgMOSE). We also show that the pleural B-1 cell reservoir responds to lung injury through regulation of the chemokine receptor CXCR4. Mechanistically we show that the transcription factor Id3 is a novel negative regulator of CXCR4 expression. Using mice with B-cell specific Id3 deficiency, a model of increased B-1b cells, we demonstrate decreased bleomycin-induced fibrosis compared to littermate controls. Furthermore, we show that mice deficient in secretory IgM (sIgM-/-) have higher mortality in response to bleomycin-induced lung injury, which is partially mitigated through airway delivery of the IgMOSE E06. Additionally, we provide insight into potential mechanisms of IgM in attenuation of fibrosis through RNA sequencing and pathway analysis, highlighting complement activation and extracellular matrix deposition as key differentially regulated pathways.

immunology↗

bioRxiv2024

The effects of clay minerals on bacterial community composition during arthropod decay

Fossilization, or the transition of an organism from the biosphere to the geosphere, is a complex mechanism involving numerous biological and geological variables. Bacteria are one of the most significant biotic players to decompose organic matter in natural environments, early on during fossilization. However, bacterial processes are difficult to characterize as many different abiotic conditions can influence bacterial efficiency in degrading tissues. One potentially important variable is the composition and nature of the sediment on which a carcass is deposited after death. We experimentally examined this by decaying the marine shrimp Palaemon varians underwater on three different clay sediments. Samples were then analyzed using 16S ribosomal RNA sequencing to identify the bacterial communities associated with each clay system. Results show that samples decaying on the surface of kaolinite have a lower bacterial diversity than those decaying on the surface of bentonite and montmorillonite, which could explain the limited decay of carcasses deposited on this clay. However, this is not the only role played by kaolinite, as a greater proportion of gram-negative over gram-positive bacteria is observed in this system. Gram-positive bacteria are generally thought to be more efficient at recycling complex polysaccharides such as those forming the body walls of arthropods. This is the first experimental evidence of sediments shaping an entire bacterial community. Such interaction between sediments and bacteria might have contributed to arthropods exquisite preservation and prevalence in kaolinite-rich Lagerstatten of the Cambrian Explosion.

paleontology↗

bioRxiv2023

Melanoma-derived DNA polymerase theta variants exhibit altered DNA polymerase activity

DNA Polymerase {theta} (Pol {theta} or POLQ) is primarily involved in repairing double-stranded breaks in DNA through the alternative pathway known as microhomology-mediated end joining (MMEJ) or theta-mediated end joining (TMEJ). Unlike other DNA repair polymerases, Pol {theta} is thought to be highly error prone, yet critical for cell survival. We have identified several mutations in the POLQ gene from human melanoma tumors. Through biochemical analysis, we have demonstrated that all three cancer-associated variants experienced altered DNA polymerase activity including a propensity for incorrect nucleotide selection and reduced polymerization rates compared to WT Pol {theta}. Moreover, the variants are 30 fold less efficient at incorporating a nucleotide during repair and up to 70 fold less accurate at selecting the correct nucleotide opposite a templating base. Taken together, this suggests that aberrant Pol {theta} has reduced DNA repair capabilities and may also contribute to increased mutagenesis. While this may be beneficial to normal cell survival, the variants were identified in established tumors suggesting that cancer cells may use this promiscuous polymerase to its advantage to promote metastasis and drug resistance.

biochemistry↗