Biology subjects

Zimmermann, J.

Publications and source records attributed to Zimmermann, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Predatory bacteria as members of human microbiomes and their impact on gut diversity and homeostasis

BackgroundBdellovibrio and like organisms (BALOs) are obligate bacterial predators that shape microbial communities by promoting species diversity, yet they have long been considered irrelevant to the human gut due to their presumed obligate aerobic lifestyle. Here, we challenge this view through a combined meta-analytic, experimental, and conceptual investigation of BALOs in human microbiomes. ResultsReanalyzing 168,000 consistently processed samples from the Human Microbiome Compendium spanning 482 studies, we detected BALOs in more than 80 studies and across multiple body sites worldwide, with a gut prevalence of 2.4%, a finding confirmed by reanalysis of the PRIME database for 16S rRNA microbiome data. Strikingly, BALO presence was consistently associated with higher microbial alpha-diversity across body sites and disease contexts. Biopsy-derived samples showed a substantially higher prevalence than fecal samples, suggesting a mucosa-proximal niche. Our laboratory experiments showed that multiple Bdellovibrio strains can delay the loss of microbial diversity in vitro and remain active under gut-relevant conditions, including 37{degrees}C, pH 6.5, and in the presence of mucus. Genomic analyses further revealed terminal reductases, including nitrite reductases, in several BALO genomes, indicating the capacity for anaerobic or microaerobic respiration, consistent with persistence in mucosal microenvironments. Notably, the metabolic and ecological profiles of cultured BALOs closely match those of facultative anaerobes, which constitute their preferred prey and are central drivers of dysbiosis in inflammatory bowel disease, diabetes, colorectal cancer, and chronic kidney disease. ConclusionBuilding on these findings, we propose a conceptual framework in which BALOs contribute to gut homeostasis by controlling the expansion of facultative anaerobes under inflammatory conditions, thereby facilitating the restoration of fermentative, butyrate-producing communities. Together, our results establish BALOs as consistent, functionally relevant members of the human microbiome and a promising natural candidate for therapeutic strategies targeting chronic gut disease.

microbiology↗

bioRxiv2026

Predatory bacteria impact C. elegans life-history traits by modulating microbiota community dynamics and thereby vitamin B12 availability

Predatory bacteria such as Bdellovibrio are emerging as ecological modulators in microbial communities by restructuring community composition, yet their roles in host-associated microbiomes remain poorly understood. Using Caenorhabditis elegans as model host and its defined microbiota, we investigated how two Bdellovibrio strains with distinct prey ranges (B. tiberii MYbb2 and B. krueschi MYbb4) affect microbial community composition and host life-history traits. Both strains consistently altered microbiome composition, with MYbb4 causing more pronounced alpha-diversity shifts and MYbb2 selectively enriching strains of the genus Ochrobactrum which coincided with higher host median lifespan. Genome-based predictions indicate that de novo vitamin B12 synthesis by Ochrobactrum underlies the observed host phenotype, which was confirmed through quantitative measurements of the vitamin in mono-cell cultures. Employing the acdh-1p::GFP transcriptional reporter strain, we confirmed that a diet of B12-producing bacteria suppresses the B12-independent propionate detoxification pathway in the host, demonstrating that bacterially produced B12 is bioavailable to C. elegans. Exogenous B12 supplementation assays further confirmed the lifespan-extending effect. Together, these results suggest that predation-driven enrichment of B12-producing bacteria maintains B12 levels sufficient to detoxify propionyl-CoA via the B12-dependent pathway, preventing the accumulation of toxic metabolic byproducts that would otherwise arise under B12-limiting conditions and reduce host lifespan. Our findings demonstrate that predatory bacteria are important drivers of microbiome structure with direct consequences for host physiology, representing an underappreciated ecological mechanism for microbiome modulation.

ecology↗

bioRxiv2026

Scaling up polarization-sensitive optical coherence tomography to image the whole macaque brain

Polarization-sensitive optical coherence tomography (PS-OCT) is a label-free imaging technique that exploits birefringence to visualize myelinated axons at micrometer resolution. However, serial PS-OCT imaging has been limited to small volumes, including tissue blocks from larger species, owing to constraints in acquisition speed, system stability, and data processing. These limitations have prevented its application to whole-brain mapping in large mammals. Here we present a scalable PS-OCT acquisition system and computational pipeline for whole-brain imaging in the rhesus macaque. The framework integrates high-throughput serial imaging with automated reconstruction and processing, enabling volumetric imaging at micrometer-scale resolution across decimeter-scale brain volumes. Using this approach, we acquired two complete macaque brains at a voxel size of 5.5 x 5.5 x 3.4 m and an effective resolution of approximately 10 x 10 x 5.5 m, generating multi-terabyte datasets consisting of multiple contrasts including fiber orientation information. The datasets and associated processing tools are made publicly available. This platform establishes a method for large-scale, high-resolution mapping of white matter architecture in primate brains. The resulting datasets provide a reference for validating MRI models and support the development of neurotechnological applications, including deep brain stimulation, where accurate characterization of axonal organization is required.

neuroscience↗

bioRxiv2026

Temporal multi-omic profiling of immune, gut, and microbiome responses to ischemic stroke reveals convergence of host and microbial perturbations one week after brain injury

Ischemic stroke poses a significant medical challenge with limited therapy options, therefore detailed understanding of stroke-associated pathophysiological processes across systems and organs is crucial for further research and identification of novel therapeutic targets. In this manuscript, we provide parallel multi-omic host and gut microbiome characterization on several timepoints (day 1, 7 and 14) in the mouse experimental stroke model (middle cerebral artery occlusion, MCAo). Expanding existing host-derived datasets, we profiled transcriptomes from microglia, brain-infiltrating leukocytes and peripheral leukocytes using single cell RNA sequencing. Our data deliver time-resolved characterization of microglial subtypes and highlight heterogeneous dendritic cell populations as main interaction partners of microglia on all timepoints. In peripheral blood, we did not observe large transcriptomic differences when comparing the immune subsets from MCAo and sham-operated control animals. Here, the neutrophils exhibited most transcriptomic changes on day 1 among all blood leukocytes. Parallel proteomic analysis of 5 intestinal segments (duodenum, jejunum, ileum, caecum and colon) and mesenteric lymph nodes highlighted day 7 as the most important timepoint for changes in the gut-related metabolic pathways especially in the jejunum and colon. Specific hypothesis testing revealed compartmentalized regulation of gut-related immune pathways and proteins related to gut permeability. Finally, gut microbiome analyses (longitudinal metatranscriptomics including day -1, 3, 7, 14, and metagenomics from day 14) highlighted temporally matched changes in microbial gene expression (with day 7 emerging again as the most relevant timepoint), larger overall community perturbations when compared to baseline from day -1 in stroke animals and expansion of facultative anaerobes on day 7. Graphical abstractWe performed longitudinal multi-omic host and gut microbiota profiling from experimental stroke and sham control mice. Our data indicate marked differences in brain-infiltrating leukocytes and microglia already on early timepoints after surgery, whereas stroke-specific changes in gut proteomics, bacterial gene expression and community structure emerge on day 7 after middle cerebral artery occlusion/sham surgery. Created in https://BioRender.com O_FIG O_LINKSMALLFIG WIDTH=169 HEIGHT=200 SRC="FIGDIR/small/727504v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@129eff8org.highwire.dtl.DTLVardef@49c401org.highwire.dtl.DTLVardef@e32b22org.highwire.dtl.DTLVardef@24f6df_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

A retinotopic wiring principle of the human brain

Summary paragraphA central challenge in neuroscience is to understand how anatomical connectivity links neural representations to behavior. In sensory systems, cortical areas encode structured maps of the external world, yet it remains unclear whether and how this representational geometry constrains long-range connectivity in the living human brain. Here, we show that structural connectivity in the human visual cortex preserves retinotopic organization, revealing a retinotopic wiring principle; cortical regions representing the same locations in visual space preferentially connect. Across more than 1,700 participants spanning ages 2 to 88 years, we further show that well-known perceptual asymmetries correspond to systematic asymmetries in connectivity within early visual cortex, but not in connections linking visual cortex to the rest of the brain. We introduce a scalable approach to map retinotopic connectivity when tractography alone is unreliable. Together, these findings demonstrate that anatomical connectivity preserves the geometry of neural representations, providing a general principle linking brain structure, function, and behavior.

neuroscience↗

bioRxiv2026

Title: Optogenetic WNT signaling drives germ layer self-organization in a human gastruloid model

In vitro stem cell models of human gastrulation have been an advance for developmental biology, though elucidating mechanisms of germ layer formation remains challenging. While investigating whether spatially-patterned signaling is required for germ layer formation, we tested a "salt-and-pepper" signaling strategy in which WNT was optogenetically activated in a subset of human pluripotent stem cells (hPSC) uniformly mixed into an aggregate. Following mesendodermal specification, WNT-activated cells spatially segregated into a hemisphere, then underwent further differentiation and organization into mesoderm and endoderm. RNAseq-based lineage analysis revealed that WNT activation non-autonomously induced TGF{beta}/BMP signaling, leading to robust emergence of an anterior visceral endoderm-like population that patterned adjacent neural and mesendodermal fates. Transcriptional profiles and trajectories closely mirrored those observed during human gastrulation. Moreover, TGF{beta} or cadherin perturbation disrupted germ layer formation or spatial organization, respectively. This simple model thus enables mechanistic dissection of complex human lineage specifications and organization during gastrulation.

bioengineering↗

bioRxiv2026

eDNA metabarcoding provides scalable and continuous biodiversity monitoring across the tree of life

Environmental DNA (eDNA) metabarcoding has the potential to substantially expand our knowledge of global biodiversity beyond that provided by conventional approaches. However, the degree to which eDNA data provides real ecological insight, rather than primarily reflecting environmental factors that affect eDNA shedding and degradation, remains unclear. Additional uncertainties arise in terms of cost-effectiveness and whether the price is worth any extra biodiversity information that is gleaned. Here, we established a high-resolution, bi-weekly eDNA time-series in Germany across aquatic and riparian habitats to quantify seasonal biodiversity dynamics, to relate eDNA to different potential environmental drivers, and to parametrize cost estimates. Over one year, eDNA metabarcoding detected more than 1,000 species across multiple trophic levels and primarily revealed real, taxon-specific seasonal patterns, in addition to some relationships to water temperature, discharge, and conductivity. Compared to historical records dating back to 1891, year-round eDNA monitoring increased reported species numbers by 2.4-fold for invertebrates, 2.2-fold for mammals, 1.7-fold for diatoms, 1.2-fold for fish and lamprey, and 1.03-fold for birds. Cumulative biodiversity estimates increased strongly with sampling frequency, demonstrating the value of eDNA for high-frequency time-series monitoring. Moreover, eDNA monitoring was highly cost-effective, providing more than twice the biodiversity information of many conventional surveys for one-sixth the cost, enabling scalable, high-resolution freshwater biodiversity assessments.

ecology↗

bioRxiv2025

10.5 Tesla High-Resolution Macaque Brain MRI for Connectivity Studies

Mapping brain connectivity in primates remains a major challenge due to difficulties in resolving microscopic white matter architecture, while maintaining whole-brain coverage. Increasing imaging spatial resolution is key for disambiguating fibre configurations within smaller anatomical volumes. Here, we present novel developments that allow high-resolution diffusion MRI of the macaque brain using one of the world's highest-field human MRI scanners operating at 10.5 Tesla, allowing both in vivo and ex vivo macaque brain imaging. Our approach achieves very high spatial resolution across both tissue states, (up to 580 m)3 in vivo and (300 m)3 ex vivo, with diffusion weighting up to b = 6000 s/mm2. We detail methodological advances in data acquisition, image reconstruction, processing and whole-brain tractography that overcome critical challenges associated with ultra-high-field imaging. This work establishes a new framework for high-resolution in vivo and ex vivo neuroimaging of the NHP brain at 10.5 T using a human bore scanner, paving the way for subsequent analyses of brain connectivity across species and tissue states at unprecedented detail. The dataset, along with all processing pipelines, containerised workflows, and reusable web services, is openly shared to support reproducibility and future integration with microscopy for studying white matter microstructure and connections at the mesoscale.

neuroscience↗

bioRxiv2025

Diffusion-weighted steady-state free precession imaging in the ex vivo macaque brain on a 10.5T human MRI scanner

Diffusion MRI provides a non-invasive probe of local fibre bundles and long-range anatomical connections to characterise the structural connectome. One way to achieve very high spatial resolution diffusion MRI data for connectivity investigations is to scan ex-vivo brains over many hours or days, ideally at ultra-high field strength to boost signal levels. However, conventional diffusion MRI acquisition techniques do not generally deliver good data quality for the challenging conditions of ex-vivo tissue, characterised by reduced diffusivities and relaxation times when compared to in vivo. In this work, we investigate the potential of the diffusion-weighted steady-state free precession (DW-SSFP) sequence for ex vivo diffusion imaging of the macaque brain using a 10.5 T human MRI scanner with a conventional (Gmax = 70 mT/m) gradient set. SNR-efficiency optimisations incorporating experimental relaxation times demonstrate that the DW-SSFP sequence is predicted to achieve improved or similar SNR efficiency compared to a diffusion-weighted spin- and stimulated-echo sequence. Importantly, DW-SSFP can achieve this with the additional benefit of negligible geometric distortions, unlike conventional diffusion MRI using an echo-planar imaging readout. Using optimised DW-SSFP sequence parameters, we propose a protocol at 0.4 mm isotropic resolution using a two-shell multi-orientation protocol (effective b-values of 3200 s/mm2 and 5600 s/mm2). We fit the data using Tensor, Ball and 3-Sticks and Constrained Spherical Deconvolution signal representations. The results demonstrate high-quality diffusivity estimates across the entire brain with the ability to resolve multiple fibre populations in challenging crossing-fibre regions. The data will be made fully open source and multimodal as part of the Center for Mesoscale Connectomics, providing a resource for future connectivity investigations.

neuroscience↗

bioRxiv2025

An RF coil array system for in vivo & ex vivo non-human primate brain studies at 10.5 Tesla

PurposeWe aimed to develop an innovative RF coil toolset for high resolution in vivo and ex vivo non-human primate neuroimaging applications at 10.5T MRI. The main goal was to improve our multimodal neural connectivity pipeline through the improved SNR, CNR, and spatial resolution that result from utilizing high-density RF coil arrays in combination with ultra-high field MRI. MethodsTwo RF coil arrays, both comprising 8 transmit and 40 receive channels, were designed and built for in vivo and ex vivo NHP imaging at 10.5 T. Experimental data was collected on multiple in vivo and ex vivo specimens, showing the utility UHF MRI for NHP neuroscience. ResultsExperimental results demonstrate uniform whole-brain coverage within both in vivo--which included the cerebellar, and spinal cord regions--and ex vivo specimens. High spatial resolutions (in vivo: 0.1x0.1x0.5 mm, ex vivo: 120 micron isotropic) were achieved, revealing detailed anatomical structures throughout. High temporal stability allowed for EPI and dMRI applications. ConclusionAn RF coil toolset comprising two 8ch transmit/40ch receive arrays was successfully designed for both in vivo and ex vivo NHP brain applications at 10.5 T. Both high-density RF coil arrays coupled with the SNR and CNR benefits available at UHF supported unmatched anatomical, functional, and diffusion applications at some of the highest spatial resolutions to date. Additionally, the combined capability of both in vivo and ex vivo MRI with the same brain specimen allows for tighter control for experimental-paradigm multistage studies examining translation between in vivo and ex vivo methodologies.

neuroscience↗

bioRxiv2025

LigHTS: Massively Parallel Biomimetic Photo-Functionalization for Imaging-Based Ultra-High-Throughput Screening

Imaging-based ultra-high-throughput screening (UHTS) in pharma and biotech still runs on 384/1536-well plates whose stiff, flat substrates limit biological fidelity and screening efficiency. Highly biomimetic organs-on-chips and organoids improve relevance but lack reproducibility and plate-scale throughput. Biomimetic hydrogel scaffolds can be produced at scale through photopolymerization, which yet uses focused optics to define micrometer-resolved geometries, constraining scalability. To address the technical challenge of truly scalable biomimetic substrates featuring anisotropies, this study presents LigHTS, an all-optical, in-well method that replaces focused with collimated illumination to photofabricate structured hydrogels in standard 384/1536-well plates. Adding food dye tartrazine to gelatin-methacrylate (GelMA) solutions increases hydrogel thickness sensitivity to UV dose by [~]10x, allowing uniform control of film thickness without lenses. Entire plates are functionalized in parallel with soft hydrogels ([~]1-10 kPa) whose thickness is tunable from 10 to 100 {micro}m. Simultaneously, simply interposing film photomasks encoding anisotropies enables orthogonal control of thickness and topography at UHTS throughput. Biological effect is demonstrated with mechanosensitive HT1080 cells, which display stiffness- and topography-dependent spreading and contact-guided migration on LigHTS-produced grooved substrates. Geometric uniformity across the plate (coefficient of variation <20%) meets HTS reproducibility standards, providing a readily available solution with enhanced biomimicry for imaging-based UTHS pipelines.

bioengineering↗

bioRxiv2025

Context-Dependent Metabolic Adaptation in Microbial Communities: From Monocultures to Complex Ecological Interactions

Microbial communities perform myriad functions in various environments, including the mammalian gut. These functions are largely based on the metabolic activity of microbial communities, which arises from the individual members contributions and their interactions. However, microbial functions and interactions are often inferred from simplified systems such as pure or pairwise cultures. Larger communities, in particular, are mainly analysed by metagenomics and the activity is deduced from the genetic potential of their community members. Although these approaches allow detailed insights into compositions, pairwise interactions and potential functions, they neglect the complexities of microbial communities, as evident in higher-order relationships, competition outcomes and the regulatory influence of environmental factors and other community members. Here, we study a mouse gut community along a gradient of complexity - from monocultures, to in vitro communities, to the mouse gut, to probe how bacteria adapt metabolically to their biotic and abiotic environments. Using metaproteomics to analyze realized bacterial niches and metabolic modeling to infer community interactions, we found that bacteria substantially modify their carbon source usage, biosynthetic activities, and protein allocation when grown in communities versus isolation. Furthermore, communities themselves adapted to their growth environment, changing in functionality as well as in the metabolic network between members. Host-associated communities isolated from the mouse gut invested in resource acquisition and utilized a broader spectrum of carbon sources, resulting in a large increase of predicted interactions between them. Our findings demonstrate the remarkable adaptability of microbes and microbial communities across environmental contexts. This underscores the critical need to study microbiomes under near-natural conditions and incorporate context-specific data into functional analyses.

systems biology↗

bioRxiv2025

Cerebrospinal fluid flow and clearance driven by lateral ventricle volume oscillations

In the human brain, substance clearance is intimately connected to the cerebrospinal fluid (CSF) and its flow. CSF extends from the lateral ventricles (LVs) to the parenchymas perivascular spaces. Macroscopic undulating CSF flow is present during both wakefulness and sleep and can be experimentally induced. However, the mechanisms generating this flow and its contribution to brain clearance remain unclear. Using fMRI and PET across various conditions, we demonstrate that LV-volume oscillations drive undulating CSF flow in the ventricles and subarachnoid basal cisternae. LV oscillations are driven by cortical blood-volume changes induced by neuronal activity, heartbeat and respiration. LV oscillations amplitudes determine PET-tracer clearance from the LVs. Conclusively, induced by extra- and intracranial physiological drivers and mediated by cortical blood-volume changes, LV-volume oscillations drive macroscopic CSF flow and clearance.

neuroscience↗

bioRxiv2025

Bioimage analysis for multiplexed FUCCI acquisitions powered by deep learning

The FUCCI sensor fluorescently labels cell cycle phases, which is essential to assess normal and abnormal cell-cycle progression in physiological and pathological conditions of developing organisms. However, accurate cell-cycle decoding is challenging in the low signal-to-noise conditions typical of multiplexed live cell imaging. To address this challenge, we developed deep learning networks that integrate FUCCI signals with a cytoplasmic alpha-tubulin fluorescent reporter. Our approach outperforms existing methods for both segmenting and classifying FUCCI nuclei, even in low signal-to-noise conditions. The resulting high-accuracy segmentation enables robust automated tracking. We leverage this to introduce a dynamic time warping analysis that determines cell cycle pseudotime from incomplete tracks and can detect cell cycle arrest. We provide pre-trained networks for multichannel FUCCI analysis, offering a powerful tool for studies in cancer research, development, and mechanobiology.

bioengineering↗

bioRxiv2025

Vertically Integrated System for Tracking and Assessing cell-cycle aware phenotypes under confinement

Quantitative cell biology often studies migration and the cell-cycle (CC) in separate assays, limiting mechanistic insights, particularly under geometric confinement. Here, we introduce a vertically integrated platform for simultaneously tracking single-cell migration and assessing CC under confinement. Our system integrates cell engineering via multiplexed sensors for cell-cycle, actin, and tubulin, as well as photopatterned engineered extracellular matrix (ECM) islands of defined sizes. It also features an automated, high-throughput pattern-aware imaging pipeline (Fab2Mic) that enables on-pattern, joint migration-CC assessment in the same live cells. Since the local microenvironment plays a critical role in metastasis by constraining cell behaviors within spatial boundaries, we used an HT1080 fibrosarcoma model as an illustrative case. Where static phenotyping yielded 40% G1 and 60% S/G2/M, with larger cell areas and tubulin spread in the S/G2/M phase, dynamic phenotyping via live-cell imaging confirmed CC-linked motility, with faster instantaneous velocities in G1, exemplifying the CC-migration correlations. These phenotypes were modulated by the spatial confinement imposed by the engineered ECM islands. Stronger confinement reduced cell area and tubulin spread and increased the frequency of abnormal CC events, particularly Long G1 states on smaller engineered ECM islands. It also induced a confinement-specific S/G2/M-G1 mitotic slippage, observed only under our confined conditions. Together, this vertically integrated system suggests that confinement may continuously tune migration-CC coupling and provides a deployable pipeline for CC-aware mechanobiology and screening. Moreover, we stress how dynamic imaging provides access to variables that are difficult or impossible to infer from static snapshots, including velocity and CC timing.

bioengineering↗

bioRxiv2025

Convergent and divergent neural and behavioral responses to chronic cocaine use in macaques

Chronic cocaine use leads to physical dependence, psychological addiction, and various health problems such as cardiovascular issues and cognitive impairments. This condition continues to be extremely difficult to treat, as we grapple with its neural and behavioral complexities. What we are missing is a comprehensive account on how naive brains react to occasional and chronic cocaine use, abstinence and re-exposure within subject. We tracked naive macaques using precision functional mapping before, during and after chronic cocaine self-administration over a period of nine months. We analyzed the entire brain to illustrate the pervasive impact of chronic cocaine use on overall function. Although we set out to map the "addiction" connectome, we found that the neural correlates of chronic drug use and recovery are more complex that can be captured by a singular, canonical connectome. We provide a preclinical model that maps the progression of the macaque functional connectome from a naive state through chronic cocaine use, recovery and re-exposure. We demonstrate that the "addiction" connectome is dynamic and is characterized by the interaction of subject by drug by time. Occasional cocaine use, whether initial or re-exposure, overrides individual differences, leading to a strong homogenous effect across subjects, or convergence. However, the brains response to prolonged cocaine use becomes more individualized, resulting in the divergence of effects across subjects. This can be explained by heterogeneity in cocaine-induced effects and in their associated timescales. Abstinence-induced neural alterations converged across subjects after 1-month, but by 2 months, individual trajectories revealed heterogeneity, possibly indicating differences in recovery.

neuroscience↗

bioRxiv2025

Differential alterations in peripheral tryptophan pathways in methamphetamine versus MDMA users are linked to their contrasting psychiatric symptoms

Methamphetamine (METH, "Crystal Meth") and 3,4-methylenedioxymethamphetamine (MDMA, "Ecstasy") are two types of substituted amphetamines that share structural-chemical similarities but exhibit contrasting acute and chronic effects including addictive liability. Tryptophan (TRY) pathways are involved in pleiotropic physiological functions at the interface of brain-body connections. Preclinical evidence suggests that amphetamines may modulate these pathways and, thus, indirectly influence brain functions via persistent alterations of peripheral metabolites. However, little is known about alterations of TRY-related metabolites in the blood and their clinical implications in chronic users of MDMA and METH. Hence, we characterized serum levels of TRY-related metabolites in a comparative cross-sectional study including n=36 chronic MDMA users, n=33 chronic METH users, and n=71 sex-matched, stimulant-naive healthy controls (Ntotal=140). An ultra- high performance liquid chromatography-mass spectrometry method was used to determine TRY metabolites. Combining metabolite levels, metabolic ratios, and network analysis we found robust evidence of divergent pathway alterations between METH and MDMA users. Chronic METH use was particularly associated with a depletion of serum TRY and serotonin levels, and a general activation of kynurenine pathways, while chronic MDMA use was linked to a selective activation of the OH-kynurenine metabolic branch. Metabolite changes were associated with the severity of psychopathology in the depression and psychosis domains across groups. Altogether, our findings demonstrate differential changes of serum TRY pathways in chronic MDMA and METH users. Persistent alterations of these pathways might contribute to the contrasting clinical profile of the substances and constitute a peripheral dimension of neurochemical plasticity with relevant implications for therapeutic targets.

biochemistry↗

bioRxiv2025

Pharmacological inhibition of CXCR4 increases the anti-tumor activity of conventional and targeted therapies in B-cell lymphoma models

BackgroundCXCR4 is a chemokine receptor frequently implicated in the pathogenesis and treatment resistance of B-cell lymphomas and other tumor types. Thus, CXCR4 targeting is explored using various approaches, including small molecules, antibodies, and short peptides. Here, we investigated the antitumor effects of the CXCR4 pharmacological inhibition with the synthetic peptides SPX5551 and balixafortide, as single agents and in combination, in various B-cell lymphoma models. MethodsBinding modalities were assessed via molecular docking and simulation. In vitro assays evaluated single-agent and combinatorial effects of CXCR4 antagonists with BTK, PI3K, and conventional therapies across 20 lymphoma cell lines, including models with acquired resistance. Transcriptomic analyses and mechanistic studies elucidated the pathways modulated by combined CXCR4 and BTK inhibition. ResultsStructural modeling confirmed similar CXCR4 binding modes for SPX5551 and balixafortide. SPX5551 displayed minimal single-agent activity but restored sensitivity to BTK and PI3K inhibitors in resistant marginal zone lymphoma (MZL) models. Across mantle cell lymphoma (MCL), chronic lymphocytic leukemia (CLL), and diffuse large B-cell lymphoma (DLBCL) models, SPX5551 enhanced the efficacy and/or potency of ibrutinib, copanlisib, rituximab, and R-CHOP. In MCL, co-treatment with SPX5551 and ibrutinib synergistically induced apoptosis, inhibited NF-{kappa}B and AKT signaling, and led to broader transcriptomic repression of tumor-promoting pathways compared to either agent alone. ConclusionsAlthough CXCR4 inhibitors alone show limited cytotoxicity, their combination with standard and targeted therapies significantly enhances anti-lymphoma effects, particularly in drug-resistant settings. These findings provide a strong rationale for clinical evaluation of CXCR4 blockade as a combinatorial strategy in B-cell lymphomas.

cancer biology↗