Biology subjects

Weinberg, J.

Publications and source records attributed to Weinberg, J..

8 recordsLinked to original sources

bioRxiv2026

Lactococcus lactis subsp. cremoris Reprograms the Gut-Liver Axis and Protects Against Liver Injury

Metabolic diseases are increasingly linked to dysregulation of the gut-liver axis, highlighting the therapeutic potential of probiotics. Lactococcus lactis subsp. cremoris (LLC) protects against experimental hepatic steatosis, but the mechanisms underlying its benefits remain poorly understood. Here, we integrated untargeted metabolomics, gnotobiotic mouse models, targeted bile acid profiling, and liver injury paradigms to systematically define LLC-mediated metabolic reprogramming. LLC extensively remodeled serum and hepatic metabolomes in Western diet-fed mice, enriching pathways associated with lipid metabolism, xenobiotic biotransformation, and redox homeostasis. LLC attenuated ethanol-induced steatosis and acetaminophen-induced liver injury, accompanied by activation of Nrf2-dependent antioxidant programs and FXR signaling. LLC monocolonization was sufficient to reprogram the hepatic metabolome, revealing direct host metabolic effects. Reduced intestinal bile acid conjugation emerged as a prominent LLC-associated phenotype. Together, these findings identify LLC as a probiotic that reprograms the gut-liver metabolic axis to enhance metabolic resilience and hepatoprotection.

microbiology↗

bioRxiv2026

Anti-psychotic therapeutics modify gut microbial metabolism and modulate susceptibility to gastrointestinal infection in mice

Antipsychotic medications are widely prescribed and associated with increased infection risk, but underlying mechanisms remain unclear. We examined if antipsychotic-induced microbiome and metabolome alterations impair colonization resistance. Using a murine model, we evaluated haloperidol, olanzapine, risperidone, and quetiapine through longitudinal microbiome profiling, untargeted metabolomic fingerprinting, behavioral testing, and enteric infection challenge. Antipsychotic exposure induced persistent behavioral changes and increased susceptibility to Citrobacter rodentium, with quetiapine and olanzapine producing the greatest weight loss. Microbiome sequencing revealed treatment-specific shifts in beta diversity without consistent alpha diversity changes, while untargeted metabolomic analysis demonstrated robust, drug-specific metabolic reprogramming, particularly in lipid and sterol pathways. Although microbial compositional changes did not fully account for functional outcomes, their integration with metabolomics data revealed disrupted bacterial taxa-metabolite networks and loss of homeostatic metabolic modules. These results provide a potential mechanistic link between the disruptive effects of antipsychotics on the microbiome and impaired colonization resistance.

microbiology↗

bioRxiv2026

MSMICA: computational metabolite identification in untargeted metabolomics by integrating MS, retention time, and biological evidence

Mass Spectrometry Metabolomics Identification Connection Algorithm (MSMICA) is an algorithm for automated metabolite identification in untargeted liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analyses. Limitations in metabolite identification can occur due to the availability and cost of standards and prevent recognition of metabolic factors impacting human health and disease. MSMICA performs mass-to-charge-ratio matching with chemical structures and clusters of LC-HRMS features for adduct and isotope forms. A local optimization is then used to integrate retention time prediction, metabolite precursor-product and transporter correlations, and biospecimen-specific abundance information for metabolite identification. Applying MSMICA to various internal and external mammalian datasets, validation results showed a 96.2 +- 5.1% correct rate of metabolite identification. When multiple LC-HRMS datasets were used, MSMICA enabled greater metabolite identifications, expanded metabolic pathway coverage, and data harmonization. Thus, MSMICA applies multiple pieces of evidence to substantially improve metabolite identification coverage and accuracy for known metabolites.

bioinformatics↗

bioRxiv2026

Microbiome-Derived Metabolites Shape CD4⁺ T-Cell Differentiations and Immune Aging in Chronic HIV-1 Infection

The role of aromatic gut-derived bacterial metabolites (GDBMs) in shaping immune cell metabolism and function remains poorly explored. Using ex vivo metabolomic profiling of paired plasma and CD4 T-cells from people living with HIV-1 (PLWH), we identified a network of aromatic GDBMs whose cell-associated abundance, rather than systemic levels, was linked to broad alterations in CD4 T-cell metabolic and functional states. Among these metabolites, p-cresol sulfate (PCS) emerged as a mechanistic prototype investigated in depth. Ex vivo flow cytometry and single-cell RNA sequencing of CD4 T-cells stratified by cell-associated PCS levels revealed dose-dependent enrichment of transcriptional programs associated with impaired differentiation capacity, regulatory-like identity, and cellular senescence. Consistently, in vitro transcriptomic and proteomic analyses of PCS-exposed CD4 T cells demonstrated induction of cell-cycle arrest, mitochondrial dysfunction, and senescence-associated programs, including upregulation of p16 and p21. Integration of these immunometabolic features with measurements of HIV-1 reservoir size in PLWH revealed that CD4 T-cell states defined by cell-associated GDBMs track with intact proviral DNA levels in vivo. Together, these findings define a microbiome-derived axis that reshapes CD4 T-cell metabolism and fate and promotes immune aging-associated states in PLWH. Our data suggest that cell-associated GDBMs may foster immunometabolic CD4 T-cell states previously linked to long-term HIV-1 reservoir persistence in vivo. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/699280v1_figa1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@faf44aorg.highwire.dtl.DTLVardef@1bc590aorg.highwire.dtl.DTLVardef@79c557org.highwire.dtl.DTLVardef@8b0a64_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO PCS-driven metabolic reprogramming and senescence promoting CD4+ T-cell immune cell aging.Dietary proteins are metabolized by proteolytic gut microbiota into p-cresol, which is absorbed and converted in the liver to PCS. Circulating PCS accumulates in CD4 T-cells, where it activates the aryl hydrocarbon receptor (AhR). AhR signaling reduces glycolysis and mTOR activity, while enhancing TGF-, Wnt/-catenin, and TCF7 pathways, driving a regulatory-like and stem-like transcriptional program. These changes are associated with increased expression of p16 and p21, leading to cell cycle arrest and cellular senescence promoting CD4+ T-cell immune cell aging. C_FIG

systems biology↗

bioRxiv2025

Genes govern metabolism-Enzymes define pathways and metabolic relationships

Gene-centric pathway mapping tools, widely used to interpret untargeted liquid chromatography mass spectrometry (LC-MS) metabolomics data, may underperform because a single metabolite can generate multiple spectral features, inflating false positive rates. Classic enzymology, which established metabolite flow before gene sequencing, offers experimentally validated precursor-product relationships that could overcome these ambiguities. We evaluated whether enzymology-defined precursor-product correlations are consistently detectable in human plasma LC-MS data. We detected amino acids, carnitine-related, TCA cycle, and pentose phosphate pathway metabolites in one individual sampled eight times over five years and in 50 adults sampled 6 to 8 times each. In the single participant repeated measures, strong positive correlations were observed for most direct precursor-product pairs. The longitudinal and cross-sectional analyses reproduced these patterns. Precursor-product proportionality, a fundamental principle of enzymology, is detectable in LC-MS datasets and remains consistent across studies. Applying these correlations to metabolomics workflows can improve pathway analysis, help metabolite identification, and reveal how genetic variations, diets, therapeutic drugs, and environmental exposures jointly impact metabolic pathways.

systems biology↗

bioRxiv2025

Integrated single cell spatial multi-omics landscape of WHO grades 2-4 diffuse gliomas identifies locoregional metabolomic regulators of glioma growth

Diffuse infiltrating gliomas are aggressive tumors of the central nervous system driven by intra-tumoral heterogeneity and aberrant normal-tumor cell-cell interactions. Grade specific and locoregional metabolic dependencies driving aberrant cell-states linked to treatment resistance, seizures and infiltration of gliomas remain elusive. Here, we applied spatial transcriptomics (stRNAseq), imaging mass cytometry (IMC) and mass spectrometry imaging (MSI; metabolites, peptides and glycans) to the core and edge tumor tissue from patients with World Health Organization (WHO) grades 2-4 diffuse infiltrating gliomas including isocitrate dehydrogenase (IDH) mutant oligodendrogliomas (WHO Grades 2 and 3) and IDH wildtype astrocytomas including anaplastic astrocytoma (prior 2016 WHO histological grade 3) and glioblastoma (GBM, WHO grade 4) stRNAseq identified regions-specific differentially expressed genes with significant overall survival implications particularly in IDH wildtype GBM. Integration of stRNA seq and MSI-derived metabolite expression demonstrated enrichment of L-glutamine in SOX4+ Neural progenitor-like (NPC-like) cells and DL-dopamine in GPNMB+ Mesenchymal-like (MES-like) GBM cells at the tumor edge relative to the core. Our results uncover clinically relevant and locoregional cell state-specific metabolites that may contribute to GBM proliferation, infiltration and seizures. This comprehensive pan-diffuse infiltrating glioma multi-omics study could serve as a resource for uncovering region-specific metabolic vulnerabilities encompassing metabolites, glycans and peptides within transcriptionally defined cell states across WHO 2-4 diffuse glioma.

cancer biology↗

bioRxiv2023

Heterotypic responses against nsp12/nsp13 from prior SARS-CoV-2 infection associates with lower subsequent endemic coronavirus incidence

Immune responses from prior SARS-CoV-2 infection and COVID-19 vaccination do not prevent re-infections and may not protect against future novel coronaviruses (CoVs). We examined the incidence of and immune differences against human endemic CoVs (eCoV) as a proxy for response against future emerging CoVs. Assessment was among those with known SARS-CoV-2 infection, COVID-19 vaccination but no documented SARS-CoV-2 infection, or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not COVID-19 vaccination alone, protects against subsequent symptomatic eCoV infection. CD8+ T cell responses to the non-structural eCoV proteins, nsp12 and nsp13, were significantly higher in individuals with previous SARS-CoV-2 infection as compared to the other groups. The three groups had similar cellular responses against the eCoV spike and nucleocapsid, and those with prior spike exposure had lower eCoV-directed neutralizing antibodies. Incorporation of non-structural viral antigens in a future pan-CoV vaccine may improve protection against future heterologous CoV infections.

immunology↗

bioRxiv2018

Early and Late Effects of Maternal Experience on Hippocampal Neurogenesis, Microglia, and the Circulating Cytokine Milieu

The maternal brain displays considerable plasticity, and motherhood is associated with changes in affective and cognitive function. Motherhood can alter the trajectory of brain ageing, including modifications to neuroplasticity and cognition. Here, we investigated the short- and long-term effects of motherhood on hippocampal neurogenesis, microglial density and morphology, and circulating cytokines, domains known to be altered with age and implicated in cognition and mood. Female rats were bred then euthanized during gestation or at various postpartum timepoints, culminating in middle age, and nulliparous rats served as age-matched controls. Hippocampal neurogenesis was significantly suppressed during gestation and the postpartum period. Interestingly, neurogenesis declined significantly in middle-aged nulliparous rats, but increased in primiparous rats across the same period. Transient postpartum adaptations to the neuroimmune environment of the hippocampus were evidenced, as Iba-1-immunoreactive microglia assumed a de-ramified morphology followed by increased density. Intriguingly, ageing-related changes in circulating cytokines were dependent on parity. These adaptations in neurogenic and immune processes may have ramifications for maternal mood and cognition across the peripartum period and beyond.

neuroscience↗