Biology subjects

Cox, J.

Publications and source records attributed to Cox, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Induction and regulation of a reversible form of suspended animation in C. elegans

Suspended animation, a state of extreme quiescence with microscopically invisible movement and development, is a remarkable yet poorly understood stress resilience strategy in animals. Here, we describe a newly discovered form of suspended animation inducible by high-population density in isosmotic liquids in C. elegans throughout larval development and adulthood. Transcriptomic, metabolomic and live-cell activity reporter imaging analyses reveal striking molecular and cellular landscape changes by such liquid-induced suspended animation (LISA), including remodeling of gene expression programs, energy metabolites, lysosomal and mitochondrial morphology. Genetic screens identify mutants with altered stress responses and survival against LISA. While key endo-lysosomal regulators promote survival during LISA, organelle remodeling and a neuronal axis via downstream neuropeptide and cAMP/PKA signaling orchestrate behavioral awakening from LISA. Our findings define a facile paradigm for reversible SA, providing a powerful model system to uncover key molecular and cellular mechanisms governing an extreme case of reversible life arrest and dormancy.

developmental biology↗

bioRxiv2025

STING and VDAC inhibitors attenuate inflammation and ineffective erythropoiesis caused by an altered metabolome in the Nan (EKLF/E339D) mouse model of neonatal anemia

Erythroid Kruppel-like factor (EKLF/KLF1) is an essential transcriptional regulator of all aspects of erythropoiesis. The mouse neonatal anemia (Nan) mutation is driven by a semi-dominant mutation in one allele of the EKLF second Zn-finger at position E339D. RNA-seq analysis of Nan/+ erythroid cells showed that expression of numerous enzymes associated with metabolic pathways are changed as a result. We assessed and analyzed the effects of this dysregulation by mass spectrometry of embryonic and adult material. Our results show that mono-allelic expression of Nan-EKLF has profound impacts on erythroid cell metabolism: levels of amino acids, nucleotides, and metabolites are altered, more energy is needed for survival and proliferation, and glucose is taken up more rapidly. As a result, mitochondrial morphology is distorted, leading to VDAC1 oligomerization and mtDNA release to the cytosol. This activates the cGAS-STING signaling pathway and induces a type-I IFN response that drives inflammation. Use of STING or VDAC inhibitors alleviates these conditions both ex vivo and in vivo. Mechanistically, treatment restores normal erythroid cell divisions and differentiation, and decreases inflammatory pathways in the bone marrow. Our findings are likely directly relevant to the dyserythropoiesis observed in CDA type IV patients that carry a similar mutation.

molecular biology↗

bioRxiv2025

pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

The increasing scale and complexity of proteomics data demand robust, scalable, and interpretable quality control (QC) frameworks to ensure data reliability and reproducibility. Here, we present pmultiqc, an open-source Python package that standardizes and generates web-based QC reports across multiple proteomics data analysis platforms. Built on top of the widely adopted MultiQC framework, pmultiqc offers specialized modules tailored to mass spectrometry workflows, with full initial support for quantms, DIA-NN, MaxQuant/MaxDIA, and mzIdentML/mzML-based pipelines. The package computes a wide range of QC metrics, including raw intensity distributions, identification rates, retention time consistency, and missing value patterns, and presents them in interactive, publication-ready reports. By leveraging sample metadata in the SDRF format, pmultiqc enables metadata-aware QC and introduces, for the first time in proteomics, QC reports and metrics guided by standardized sample metadata. Its modular architecture allows easy extension to new workflows and formats. Alongside comprehensive documentation and examples for running pmultiqc locally or integrated into existing workflows, we offer a cloud-based service that enables users to generate QC reports from their own data or public PRIDE datasets.

bioinformatics↗

bioRxiv2025

Improved peptide search for identification of SUMO and sequence-based modifications, in MaxSBM

Post-translational modifications (PTMs), such as SUMOylation and ubiquitination, regulate key cellular processes by covalently attaching to lysine residues. While mass spectrometry allows site-specific identification of PTMs, most existing search engines are optimized for small, non-fragmenting modifications and struggle to detect large, fragmenting protein-based modifiers. We refer to these as Sequence-Based Modifiers (SBMs). To overcome this limitation, we developed an SBM-specific search strategy within MaxQuant that accounts for the fragmentation behavior of SBMs during peptide identification. Using publicly available datasets, we validated our approach for SUMO2/3. Our analysis identified distinct diagnostic features and characteristic mass shifts associated with SBM fragmentation, referred to in this study as d-ions (diagnostic ions) and p-ions. By leveraging these features, our method improved the identification of SUMOylated peptides from human cell lines by 13%, SUMOylation sites in mouse embryonic cells by 18%, and in mouse adipocytes by 25%. Our search method improved spectral annotation of SBMs by up to 9% increase in the median Andromeda score. Taken together, we highlight the potential of our SBM search to enhance the discovery of protein-based modifications. HighlightsO_LIDevelopment of a MaxQuant module tailored for identifying Sequence-Based Modifiers (SBMs), including SUMO2/3 C_LIO_LIIncorporation of SBM-specific fragmentation patterns into search algorithms C_LIO_LIEnhanced biological discovery through improved PTM identification from mass spectrometry datasets C_LI In BriefHere, we introduce MaxSBM, an optimized framework for interpreting complex sequence-based modifiers (SBMs), particularly SUMO, within MaxQuant. Our approach incorporates SBM-specific d- and p-ion series into peptide scoring and annotation. By extending the theoretical spectral space to include fragments bearing partial SUMO (or other SBM) peptide remnants, MaxSBM provides a more comprehensive spectral annotation which enhances peptide scoring, resulting in increased identification rates at a higher confidence. Beyond methodological refinement, we validated MaxSBM via reanalysis of several physiological SUMO datasets, ultimately unlocking new insights via mapping of previously obscured modification sites.

bioinformatics↗

bioRxiv2025

Lean breast adipocytes secrete an oxylipin that suppresses breast cancer via ferroptosis

Obesity is predicted to become the largest modifiable risk factor for breast cancer in postmenopausal women, yet the mechanisms underlying this association are unclear. We identified a novel role for the endogenous oxylipin 9S-HODE, secreted by lean adipocytes, to induce ferroptosis in breast cancer cells while sparing normal breast epithelial cells. Obese adipocytes fail to secrete 9S-HODE, suggesting that the loss of ferroptosis induction significantly contributes to the acceleration of obesity-associated breast cancer. Consequently, the inhibition of ferroptosis accelerates breast cancer in lean, but not obese, mice. Further, 9S-HODE inhibits the growth of patient-derived breast cancer organoids, and supplementing 9S-HODE into tumors in obese mice is sufficient to reduce tumor burden, underscoring its potential as a therapeutic agent.

cancer biology↗

bioRxiv2025

Facilitating Analysis and Dissemination of Proteomics data through Metadata Integration in MaxQuant

Metadata plays an essential role in the analysis and dissemination of proteomics data. It annotates sample information for output tables from library searches and displays sample information from data files in public repositories. However, integrating metadata into data analysis can be time-consuming and is not well standardized. Then inconsistent metadata formats in public repositories would make it even more difficult for other researchers to reproduce and reuse these public datasets. Here we present the metadata integration in MaxQuant, which provides a user-friendly way to export metadata as SDRF, the standard format that maps sample properties to proteomics data files. We have also implemented the annotation of output tables with the SDRF file, enabling users to perform seamless downstream data analysis with annotated output tables. These new features provide a simple and standardized approach to creating and leveraging standardized metadata. They will greatly facilitate data analysis and improve the reusability and reproducibility of public proteomics datasets.

bioinformatics↗

bioRxiv2025

Bimodal peptide collision cross section distribution reflects two stable conformations in the gas phase

Recent high throughput applications to shotgun proteomics have shown great benefits of coupling ion mobility spectrometry (IMS) to mass spectrometry. IMS adds a separation dimension by differentiating biomolecules by their size and shape. We (and others) find that the distribution of peptide collision cross section (CCS) is often bimodal, which limits the utility of current machine learning predictions for peptide identification. Molecular dynamics simulations indicate that the peptides in the drift tube can adopt multiple stable conformations and that the two modes correspond to predominantly extended (mostly helical) and more compact (globular and less ordered) conformations. Most peptides have a charge-dependent strong preference for one of the two conformations, while some can adapt both, as evidenced by a simple geometric model of the CCS data. We suggest a novel two-valued CCS predictor allowing for multiple peptide conformations. Its integration into data-independent acquisition proteomics increases identification rates of peptides compared to single-value predictors.

bioinformatics↗

bioRxiv2025

CD200R1 is required for the development of γδ 17 T cells

{gamma}{delta} T cells are enriched at barrier sites such as skin, gut and lung, where they protect against cancer and infections and promote healing. They detect diverse ligands in T cell receptor-dependent or independent manners, producing large quantities of pro-inflammatory cytokines. {gamma}{delta} T cells develop in foetal thymi in temporally controlled waves where, unlike {beta} T cells, many {gamma}{delta} T cells adopt their effector fate, becoming either IFN{gamma} or IL-17A-producers ({gamma}{delta}17 T cells). CD200R1 suppresses myeloid cell activity but has also been shown to promote innate lymphoid cell IL-17A production, enhancing psoriasis-like skin inflammation. {gamma}{delta}17 T cells are potent IL-17A producers in skin therefore, the effect of CD200R1 on IL-17A production by {gamma}{delta}17 T cells was investigated. CD200R1 was found to promote IL-17A production by {gamma}{delta} T cells by supporting the development of {gamma}{delta}17 T cells, enhancing IL-17-producing and ROR{gamma}t+ {gamma}{delta} T cell numbers in foetal thymic organ cultures. To fulfil this role, CD200R1 acts either directly on developing {gamma}{delta} T cells, or indirectly on thymic stromal cells. This identifies CD200R1 as a critical novel regulator of {gamma}{delta}17 T cell development in early life, a key process for ensuring immunity, particularly at barrier sites.

immunology↗

bioRxiv2025

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. We identify that glioblastoma heterogeneity is driven by spatially-patterned transitions of cancer cells from developmental-like states towards those defined by a glial injury response and hypoxia. This cellular trajectory regionalises tumours into distinct tissue niches and manifests in a molecularly conserved manner across tumours as well as genetically distinct tumour subclones. Moreover, using a new deep learning framework to map cancer cell states jointly with clones in situ, we show that tumour subclones are finely spatially intermixed through glioblastoma tissue niches. Finally, we show that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments. Our findings define a stereotyped trajectory of cancer cells in glioblastoma and unify glioblastoma tumour heterogeneity into a tractable cellular and tissue framework.

cancer biology↗

bioRxiv2025

Schistosoma mansoni antigen induced innate immune memory features mitochondrial biogenesis and can be inhibited by ovarian produced hormones

We have previously identified that S. mansoni infection induces a unique form of myeloid training that protects male but not female mice from high fat diet induced disease. Here we demonstrate that ovarian derived hormones account for this sex specific difference. Ovariectomy of females prior to infection permits metabolic reprogramming of the myeloid lineage, with BMDM exhibiting carbon source flexibility for cellular respiration, and mice protected from systemic metabolic disease. The innate training phenotype of infection can be replicated by in vivo injection of SEA, and by exposure of bone marrow to SEA in culture prior to macrophage differentiation (Day 0). This protective phenotype is linked to increased chromatin accessibility of lipid and mitochondrial pathways in BMDM including Nrf1 and Tfam, as well as mitochondrial biogenesis. This work provides evidence that S. mansoni antigens induce a unique form of innate training inhibited by ovarian-derived hormones in females.

immunology↗

bioRxiv2024

ProteoPlotter: an executable proteomics visualization tool compatible with Perseus

Mass spectrometry-based proteomics experiments produce complex datasets requiring robust statistical testing and effective visualization tools to ensure meaningful conclusions are drawn. The publicly-available proteomics data analysis platform, Perseus, is extensively used to perform such tasks, but opportunities to enhance visualization tools and promote accessibility of the data exist. In this study, we developed ProteoPlotter, a user-friendly, executable tool to complement Perseus for visualization of proteomics datasets. ProteoPlotter is built on the Shiny framework for R programming and enables illustration of multi-dimensional proteomics data. ProteoPlotter provides mapping of one-dimensional enrichment analyses, enhanced adaptability of volcano plots through incorporation of Gene Ontology terminology, visualization of 95% confidence intervals in principal component analysis plots using data ellipses, and customizable features. ProteoPlotter is designed for intuitive use by biological and computational researchers alike, providing descriptive instructions (i.e., Help Guide) for preparing and uploading Perseus output files. Herein, we demonstrate the application of ProteoPlotter towards microbial proteome remodeling under altered nutrient conditions and highlight the diversity of visualizations enabled with the platform for improved biological characterization. Through its comprehensive data visualization capabilities, linked to the power of Perseus data handling and statistical analyses, ProteoPlotter facilitates a deeper understanding of proteomics data to drive new biological discoveries.

bioinformatics↗

bioRxiv2024

Semaglutide-induced weight loss improves mitochondrial energy efficiency in skeletal muscle

ObjectiveGlucagon-like peptide 1 receptor agonists (e.g. semaglutide) potently induce weight loss and thereby reducing obesity-related complications. However, weight regain occurs when treatment is discontinued. An increase in skeletal muscle oxidative phosphorylation (OXPHOS) efficiency upon diet-mediated weight loss has been described, which may contribute to reduced systemic energy expenditure and weight regain. We set out to determine the unknown effect of semaglutide on muscle OXPHOS efficiency. MethodsC57BL/6J mice were fed a high-fat diet for 12 weeks before receiving semaglutide or vehicle for 1 or 3 weeks. The rate of ATP production and O2 consumption were measured by a high-resolution respirometry and fluorometry to determine OXPHOS efficiency in skeletal muscle at these 2 timepoints. ResultsSemaglutide treatment led to significant reductions in fat and lean mass. Semaglutide improved skeletal muscle OXPHOS efficiency, measured as ATP produced per O2 consumed (P/O) in permeabilized muscle fibers. Mitochondrial proteomic analysis revealed changes restricted to two proteins linked to complex III assembly (Lyrm7 and Ttc1, p <0.05 without multiple corrections) without substantial changes in the abundance of OXPHOS subunits. ConclusionsThese data indicate that weight loss with semaglutide treatment increases skeletal muscle mitochondrial efficiency. Future studies could test whether it contributes to weight regain.

physiology↗

bioRxiv2024

Isobaric labeling update in MaxQuant

We present an update of the MaxQuant software for isobaric labeling data and evaluate its performance on benchmark datasets. Impurity correction factors can be applied to labels mixing C- and N-type reporter ions, such as TMT Pro. Application to a single-cell multi-species mixture benchmark shows high accuracy of the impurity-corrected results. TMT data recorded with FAIMS separation can be analyzed directly in MaxQuant without splitting the raw data into separate files per FAIMS voltage. Weighted median normalization, is applied to several datasets, including large-scale human body atlas data. In the benchmark datasets the weighted median normalization either removes or strongly reduces the batch effects between different TMT plexes and results in clustering by biology. In datasets including reference channels, we find that weighted median normalization performs as well or better when the reference channels are ignored and only the sample channel intensities are used, suggesting that the measurement of reference channels is unnecessary when using weighted median normalization in MaxQuant. We demonstrate that MaxQuant including the weighted median normalization performs well on multi-notch MS3 data, as well as on phosphorylation data. MaxQuant is freely available for any purpose and can be downloaded from https://www.maxquant.org/.

bioinformatics↗

bioRxiv2024

Tesorai Search: Large pretrained model boosts identifications in mass spectrometry proteomics without the need for Percolator.

The original mass spectrometry search engines used simple algorithms for peptide identification. Recent tools improved accuracy by adding several extra components such as fragment ion intensities or retention times prediction and training target-decoy classifiers on-the-fly, leading to sometimes inconsistent results. Our study explores the impact of replacing those extra components with a deep-learning pretrained model that directly learns the complex relationship between the full spectra and associated peptide sequence, without using decoys. This simplified workflow has fewer parameters to tweak, making it easier to use and perform robustly on data from instruments and use-cases never seen during training. Surprisingly, our approach consistently identifies more peptides than FragPipe, PEAKS, and Proteome Discoverer (12%, 9%, and 21% more, respectively, across a range of datasets). Tesorai Search is also fast - 250 immunopeptidomics searches in 45 minutes - and free for academics, available as a webserver at console.tesorai.com.

bioinformatics↗

bioRxiv2024

HAF Prevents Hepatocyte Apoptosis and Hepatocellular Carcinoma through Transcriptional Regulation of the NF-κB pathway.

BackgroundHepatocellular carcinoma (HCC) incidence is increasing worldwide due to the obesity epidemic, which drives metabolic dysfunction-associated steatohepatitis (MASH) that can lead to HCC. However, the molecular pathways that lead to MASH-HCC are poorly understood. We have previously reported that male mice with global haploinsufficiency of hypoxia-associated factor, HAF (SART1+/-) spontaneously develop MASH/HCC. However, the cell type(s) responsible for HCC associated with HAF loss are unclear. ResultsSART1-floxed mice were crossed with mice expressing Cre-recombinase within hepatocytes (Alb-Cre; hepS-/-) or macrophages (LysM-Cre, macS-/-). Only hepS-/- mice (both male and female) developed HCC suggesting that HAF protects against HCC primarily within hepatocytes. HAF-deficient macrophages showed decreased P-p65 and P-p50 and in many major components of the NF-{kappa}B pathway, which was recapitulated using HAF siRNA in vitro. HAF depletion increased apoptosis both in vitro and in vivo, suggesting that HAF mediates a tumor suppressor role by suppressing hepatocyte apoptosis. We show that HAF regulates NF-{kappa}B activity by controlling transcription of TRADD and RIPK1. Mice fed a high-fat diet (HFD) showed marked suppression of HAF, P-p65 and TRADD within their livers after 26 weeks, but manifest profound upregulation of HAF, P-65 and TRADD within their livers after 40 weeks of HFD, implicating deregulation of the HAF-NF-{kappa}B axis in the progression to MASH. In humans, HAF was significantly decreased in livers with simple steatosis but significantly increased in HCC compared to normal liver. ConclusionsHAF is novel transcriptional regulator of the NF-{kappa}B pathway that protects against hepatocyte apoptosis and is a key determinant of cell fate during progression to MASH and MASH-HCC.

cancer biology↗

bioRxiv2023

Phospholipid isotope tracing reveals β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma

Background and AimsActivating mutations in the CTNNB1 gene encoding {beta}-catenin are among the most frequently observed oncogenic alterations in hepatocellular carcinoma (HCC). HCC with CTNNB1 mutations show profound alterations in lipid metabolism including increases in fatty acid oxidation and transformation of the phospholipidome, but it is unclear how these changes arise and whether they contribute to the oncogenic program in HCC. MethodsWe employed untargeted lipidomics and targeted isotope tracing to quantify phospholipid production fluxes in an inducible human liver cell line expressing mutant {beta}-catenin, as well as in transgenic zebrafish with activated {beta}-catenin-driven HCC. ResultsIn both models, activated {beta}-catenin expression was associated with large changes in the lipidome including conserved increases in acylcarnitines and ceramides and decreases in triglycerides. Lipid flux analysis in human cells revealed a large reduction in phosphatidylcholine (PC) production rates as assayed by choline tracer incorporation. We developed isotope tracing lipid flux analysis for zebrafish and observed similar reductions in phosphatidylcholine synthesis flux accomplished by sex-specific mechanisms. ConclusionsThe integration of isotope tracing with lipid abundances highlights specific lipid class transformations downstream of {beta}-catenin signaling in HCC and suggests future HCC-specific lipid metabolic targets. SynopsisIn this work, we show by lipid specific isotope tracing that mutations in the oncogene CTNNB1 leads to conserved changes in lipid metabolism in hepatocellular carcinoma. These include the stimulation of fatty acid oxidation and a suppression of phosphorylcholine synthesis.

cancer biology↗

bioRxiv2023

Enamel proteins reveal biological sex and genetic variability within southern African Paranthropus

The evolutionary relationships among extinct African hominin taxa are highly debated and largely unresolved, due in part to a lack of molecular data. Even within taxa, it is not always clear, based on morphology alone, whether ranges of variation are due to sexual dimorphism versus potentially undescribed taxonomic diversity. For Paranthropus robustus, a Pleistocene hominin found only in South Africa, both phylogenetic relationships to other taxa 1,2 and the nature of intraspecific variation 3-6 are still disputed. Here we report the mass spectrometric (MS) sequencing of enamel proteomes from four ca. 2 million year (Ma) old dental specimens attributed morphologically to P. robustus, from the site of Swartkrans. The identification of AMELY-specific peptides and semi-quantitative MS data analysis enabled us to determine the biological sex of all the specimens. Our combined molecular and morphometric data also provide compelling evidence of a significant degree of variation within southern African Paranthropus, as previously suggested based on morphology alone 6. Finally, the molecular data also confirm the taxonomic placement of Paranthropus within the hominin clade. This study demonstrates the feasibility of recovering informative Early Pleistocene hominin enamel proteins from Africa. Crucially, it also shows how the analysis of these proteins can contribute to understanding whether hominin morphological variation is due to sexual dimorphism or to taxonomic differences. We anticipate that this approach can be widely applied to geologically-comparable sites within South Africa, and possibly more broadly across the continent.

evolutionary biology↗

bioRxiv2022

Design and validation of an exposure system for efficient inter-animal SARS-CoV-2 airborne transmission in Syrian hamsters

SARS-CoV-2 is a highly transmissible respiratory pathogen whose main transmission route is airborne. Development of an animal model and exposure system that recapitulates airborne transmission of SARS-CoV-2 is integral for understanding the dynamics of SARS-CoV-2 spread in individuals and populations. Here we designed, built, and characterized a hamster transmission caging and exposure system that allows for efficient SARS-CoV-2 airborne transmission from an infected index animal to naive recipients under unidirectional airflow, without contribution from fomite or direct contact transmission. To validate our system, we assessed a 1:1 or 1:4 ratio of infected index to naive recipient hamsters and compared their virological and clinical measurements after eight hours of airborne exposure. Airborne exposure concentrations and pulmonary deposited dose of SARS-CoV-2 in index and naive hamsters, respectively, were similar in both groups. Daily nasal viral RNA levels, and terminal (day 5) lung viral RNA and infectious virus, and fecal viral RNA levels were statistically similar among 1:1 and 1:4 naive animals. However, virological measurements in the 1:4 naive animals were more variable than the 1:1 naive animals, likely due to hamster piling behavior creating uneven SARS-CoV-2 exposure during the grouped 1:4 airborne exposure. This resulted in slight, but not statistically significant, changes in daily body weights between the 1:1 and 1:4 naive groups. Our report describes a multi-chamber caging and exposure system that allowed for efficient SARS-CoV-2 airborne transmission in single and grouped hamsters. This system can be used to better define airborne transmission dynamics and test transmission-blocking therapeutic strategies against SARS-CoV-2. ImportanceThe main route of SARS-CoV-2 transmission is airborne. However, there are few experimental systems that can assess airborne transmission dynamics of SARS-CoV-2 in vivo. Here, we designed, built, and characterized a hamster transmission caging and exposure system that allows for efficient SARS-CoV-2 airborne transmission in Syrian hamsters, without contributions from fomite or direct contact transmission. We successfully measured SARS-CoV-2 viral RNA in aerosols and demonstrated that SARS-CoV-2 is transmitted efficiently at either a 1:1 or 1:4 infected index to naive recipient hamster ratio. This is meaningful as a 1:4 infected index to naive hamster ratio would allow for simultaneous comparisons of various interventions in naive animals to determine their susceptibility of infection by aerosol transmission of SARS-CoV-2. Our SARS-CoV-2 exposure system allows for testing viral airborne transmission dynamics and transmission-blocking therapeutic strategies against SARS-CoV-2 in Syrian hamsters.

microbiology↗