Biology subjects

Shriver, L. P.

Publications and source records attributed to Shriver, L. P..

9 recordsLinked to original sources

bioRxiv2026

Using XCiMS to Quantify the Benefits of Ion Mobility Spectrometry for Untargeted Metabolomics

Integrating ion mobility spectrometry (IMS) with liquid chromatography-mass spectrometry (LC-MS) has the potential to improve untargeted metabolomics workflows, but assessing the benefits of IMS has been challenging due to a paucity of software solutions to process raw LC-IMS-MS data in a manner that enables direct comparison with LC-MS data. We developed the XCiMS software to collapse 4D data into pseudo-3D data. Peak detection is then performed in the pseudo-3D space, followed by targeted extraction of 4D signals from 3D-guided regions of interest. Here, we applied XCiMS to estimate the potential of IMS for untargeted metabolomics when analyzing human plasma. First, we assessed the number of metabolites that are uniquely resolved by LC-IMS-MS but not LC-MS. Although as many as 50% of 3D peaks produce multiple 4D peaks when using high-resolution IMS, few represent newly resolved structural isomers. We found that the increase in features due to IMS was mostly caused by charge isomers and ion clusters. Second, we investigated the impact of IMS on metabolite identification. When using a 16-minute chromatographic separation, we found that IMS can decrease the frequency of chimeric MS/MS by about half. We conclude that while IMS adds considerable complexity to untargeted metabolomics data without resolving a large number of additional structural isomers relative to a standard LC-MS experiment, it does facilitate metabolite identification by decreasing chimeric spectra and providing CCS values for library searching.

bioinformatics↗

bioRxiv2026

Sustained loss of Pptc7 triggers variable skeletal muscle dysfunction and diminished body mass through dysregulation of BNIP3

The mitochondrial phosphatase PPTC7 is required to sustain mammalian metabolism, as its global knockout (KO) triggers hypoketotic hypoglycemia and perinatal lethality in mice. However, the extent to which the loss of Pptc7 manifests pathology beyond the perinatal transition is unknown. Furthermore, PPTC7 was recently identified as dual functional, regulating mitochondrial protein phosphorylation and receptor mediated mitophagy, rendering it unclear which function(s) may influence in vivo physiology. Here, we find that sustained, inducible Pptc7 KO decreased lean mass, compromised whole body oxygen consumption, and altered circulating metabolites in adult male mice. We hypothesized that these phenotypes stemmed from skeletal muscle dysfunction and found lower mass and fiber cross-sectional area with shifts in fiber type distribution in select muscles of the hindlimb in Pptc7 KO animals. Loss of PPTC7 increased BNIP3 protein levels and decreased mitochondrial content in skeletal muscle, suggesting elevated mitophagy may drive pathology. Consistently, KO of Bnip3 rescued the lower body weight and lean mass seen in inducible Pptc7 KO adult animals and partially rescued perinatal lethality in global Pptc7 KO mice. These data demonstrate that loss of PPTC7 incites surprisingly variable dysfunction across physiological contexts that at least partially stems from dysregulated BNIP3.

physiology↗

bioRxiv2026

Cell-specific isotope labeling identifies myo-inositol transfer between neurons and oligodendroglia to support myelin repair

Neurons and glial cells are biochemically coupled through the exchange of nutrients, but our knowledge of which metabolites are transferred between them remains limited due to technical challenges. Here, we introduce a strategy to label specific cell types with isotopic tracers so that metabolite transfer can be measured directly in the intact brain. By engineering neurons in mice to metabolize 13C-labeled cellobiose, a glucose dimer that wild-type cells cannot catabolize, we selectively track neuron-derived metabolites by using mass spectrometry-based metabolomics. Applying this approach enabled us to identify myo-inositol as a critical metabolite synthesized by neurons and transferred to oligodendrocyte progenitor cells (OPCs) via the SLC5A3 transporter. The transfer of myo-inositol from neurons to OPCs promotes OPC proliferation and differentiation by enhancing phosphatidylinositol synthesis and upregulating expression of myelin-associated genes. During demyelination, deficient nutrient transfer can be rescued by dietary supplementation of myo-inositol, which accelerates myelin repair. These findings establish a generalizable technology for tracing intercellular metabolite transfer in vivo and identify a previously unrecognized mechanism of myo-inositol transfer from neurons to glial cells in support of CNS regeneration, revealing a potential metabolic target for therapeutic intervention in neurodegenerative disease.

biochemistry↗

bioRxiv2026

Metabolites from plasma-like medium fuel nitrogen metabolism and influence proliferation in Leptospira interrogans

Leptospirosis, caused by pathogenic Leptospira spp. such as L. interrogans, is a bacterial zoonosis of increasing prevalence with no consistently effective treatments in severe cases. We sought to characterize metabolic mechanisms that support L. interrogans infection in the host setting, with the ultimate goal of revealing unexplored therapeutic opportunities. We first established and validated a culture medium, which we refer to as supplemented Human Plasma-Like Medium (sHPLM). sHPLM more closely resembles the physiological environment of the human host than standard culture media, such as the EMJH (Ellinghausen-McCullough-Johnson-Harris) medium typically used for Leptospira culture. To better understand bacterial metabolism, we pioneered metabolomics in sHPLM-cultured Leptospira. Specifically, we developed a liquid chromatography mass spectrometry (LC/MS) metabolomics-based workflow for both medium analysis and stable isotope tracing with L. interrogans cultures. The application of these innovations revealed that the amino acid glutamine is a major nitrogen source for L. interrogans. A small-molecule inhibitor blocking glutamine utilization, JHU-083, effectively impaired the proliferation of sHPLM cultures. Further, adding glutamine to non-physiological EMJH medium rapidly induced a short-term proliferative boost in L. interrogans and increased biofilm formation. RNA-sequencing after glutamine exposure revealed transcriptional trends for increases in biosynthesis to support these phenotypes. Although ammonium has long been thought to be the sole nitrogen source for L. interrogans, our results demonstrate that glutamine provides a second source of nitrogen for biosynthesis and may act as a metabolite signal to alter L. interrogans physiology in ways that could influence infection. This work highlights that studying L. interrogans under physiological conditions is key to understanding mechanisms supporting infection and points to nitrogen assimilation as a potential target for therapies. Author SummaryLeptospirosis is a potentially fatal disease transmitted through water and soil contaminated with pathogenic Leptospira bacteria. Much research is currently focused on the idea that an improved understanding of how Leptospira infects hosts and causes disease may inspire the development of improved therapeutics, which are urgently needed. Focusing on Leptospira interrogans, a clinically important pathogenic species, we determined that conventional growth media are inadequate for understanding how the bacterium behaves when inside hosts. Instead, we designed an optimized formulation to mimic human blood, and we applied an underutilized technique for measuring the biochemical reactions that enable pathogen survival. These two innovations revealed that L. interrogans uses glutamine, an abundant nutrient in host blood and tissues, as a source of nitrogen for the production of biomolecules that are required for replication and infection. This discovery is notable as nitrogen demands were previously thought to be met using ammonium. Treating L. interrogans with inhibitors of both glutamine and ammonium metabolism blocked bacterial replication. We also discovered that L. interrogans increases its growth rate, upregulates its expression of biosynthetic pathways when exposed to glutamine, and increases its formation of biofilm. Our results reveal the importance of glutamine in supporting the lifecycle of leptospirosis-causing bacteria.

microbiology↗

bioRxiv2025

Preoptic activation induces a torpor-like hypothermic and hypometabolic state that is cerebroprotective

Therapeutic hypothermia for stroke has been limited by shivering, increased metabolic demand, and poor patient tolerance. Engaging endogenous thermoregulatory circuits to lower body temperature may overcome these limitations and modulate metabolism, offering an integrated approach to cerebroprotection. Here, we show that chemogenetic activation of neurons in the preoptic area (POA) elicits a torpor-like state in mice, characterized by sustained hypothermia and hypometabolism. In an animal stroke model, this endogenous hypothermic state significantly reduced infarct volume and improved motor outcomes compared to controls, whereas maintaining normothermia attenuated these protective effects. To explore metabolic mechanisms contributing to this state, we performed untargeted metabolomic profiling 30 minutes after POA activation and identified coordinated shifts in nucleotide, phospholipid, and sphingolipid pathways. These rapid, temperature-dependent changes indicate a metabolically reprogrammed state that may enhance neuronal resilience during ischemic stress. Together, our findings suggest that POA-driven hypothermia confers cerebroprotection through specific metabolic adaptations with translational potential.

neuroscience↗

bioRxiv2025

Construction of Multi-Modal Transcriptome-Small Molecule Interaction Networks from High-Throughput Measurements to Study Human Complex Traits

We present Gene-Embedded Multi-modal Networks (GEM-Net), a semi-supervised framework for constructing multi-modal networks centered on genes. GEM-Net uses gene-level modules and selectively incorporates heterogeneous omics profiles using a correlated meta-analysis strategy that accounts for scale imbalance, missingness, and intra-modular correlation. Prior to network inference, we developed a harmonized data processing protocol that adjusts each omic layer independently through a shared mathematical workflow involving transformation, dimensionality reduction, and regression-based covariate adjustment. GEM-Net modules were inferred and benchmarked against unsupervised methods using transcriptomic, metabolomic, and lipidomic data from the Long Life Family Study (LLFS), a unique cohort enriched for exceptional familial longevity and health. GEM-Net modules were more diverse and biologically interpretable, with stronger support from protein- protein interactions, transcriptional regulation, and metabolic annotations. Applying GEM-Net to metabolic health in LLFS revealed an axis between the microbiome-derived metabolite N-acetylglycine and immune genes (FCER1A, HDC, CPA3, MS4A2) associated with improved insulin sensitivity and reduced inflammation in healthy older individuals. GEM-Nets offer a reusable reference from a long-lived population and a generalizable framework for multi-omics discovery. https://doi.org/10.5281/zenodo.15003731.

systems biology↗

bioRxiv2025

ADAR1 Regulates Lipid Remodeling through MDM2 to Dictate Ferroptosis Sensitivity

Triple-negative breast cancer (TNBC), defined by the lack of estrogen, progesterone, and HER2 receptor expressions, is aggressive and lacks targeted treatment options. Adenosine deaminase acting on RNA 1 (ADAR1) has been shown to contribute to TNBC tumorigenesis by modulating an innate immune response. However, little is known about its role in the regulation of metabolic fitness of TNBC. We tested the hypothesis that ferroptosis is an ADAR1-protected vulnerability by showing that ADAR1 knockdown sensitizes TNBC cells to ferroptosis inducers. Lipidomic analyses showed that ADAR1 loss increased the abundance of phospholipids enriched with polyunsaturated fatty acids (PUFA), of which peroxidation is the main driver of ferroptosis. Transcriptomic analyses discovered that the proto-oncogene MDM2 contributes to the lipid remodeling phenotype. A ferroptosis-focused drug screen identified FDA-approved cobimetinib as a drug-repurposing candidate to synergize with ADAR1 loss. This finding supports further basic, pre-clinical, and clinical studies to develop novel therapeutic strategies for TNBC through ADAR1-mediated metabolic regulation.

cancer biology↗

bioRxiv2024

Agouti and BMP signaling drive a naturally occurring fate conversion of melanophores to leucophores in zebrafish

The often-prominent pigment patterns of vertebrates are varied in form and function and depend on several types of pigment cells derived from embryonic neural crest or latent stem cells of neural crest origin. These cells and the patterns they produce have been useful for uncovering features of differentiation and morphogenesis that underlie adult phenotypes, and they offer opportunities to discover how patterns and the cell types themselves have diversified. In zebrafish, a body pattern of stripes arises by self organizing interactions among three types of pigment cells. Yet these fish also exhibit white ornamentation on their fins that depends on the transdifferentiation of black melanophores to white cells, "melanoleucophores." To identify mechanisms underlying this conversion we used ultrastructural, transcriptomic, mutational and other approaches. We show that melanophore- melanoleucophore transition depends on regional BMP signals transduced through non-canonical receptors (Rgmb-Neo1a-Lrig2) as well as BMP-dependent signaling by Agouti genes, asip1 and asip2b. These signals lead to expression of transcription factor genes including foxd3 and runx3 that are necessary to induce loss of melanin by an autophagy-like process, curtail new melanin production, and deploy a pathway for accumulating guanine crystals that, together, confer a white phenotype. These analyses uncover an important role for positional information in specifying ornamentation in zebrafish and show how tissue environmental cues and a novel gene regulatory program have allowed terminal addition of a distinct phenotype to a pre-existing cell type. SignificanceFish often have striking color patterns with important functions in behavior. In zebrafish, the familiar striped pattern forms through self-organizing interactions between pigment cells, yet the white highlights on their fins arise differently--through the transformation of black pigment cells into white ones. This study reveals how this dramatic cell transformation happens: signals from the surrounding tissue, specifically BMP and Agouti proteins, instruct black cells to change their fate. These signals trigger expression of specific genes that cause the cells to break down their black pigment while acquiring white, crystal-like structures. This work shows how local signals in tissues can drive the development of ornamental features and provides insights into how new cell types evolve.

developmental biology↗

bioRxiv2020

Imaging Cuprizone-Induced Mitochondrial Dysfunction

Cuprizone is a copper chelator that induces mitochondrial dysfunction in myelin-producing oligodendrocytes and hepatic cells. Inhibition of oxidative phosphorylation has been proposed as a potential mechanism, but the exact relationship between shape changes and metabolic alterations is not well-understood. Here we explore how mitochondrial shape influences oxidative phosphorylation rates by performing simultaneous imaging and respiration measurements within intact cells. We observed that MO3.13 cells exposed to cuprizone undergo an initial increase in respiration followed by mitochondrial dysfunction and genetic dysregulation within 8 hours. Oxygen consumption was measured within 30 minutes of treatment and found to be elevated. This increase was followed by swelling of mitochondria over the first 8 hours, but preceded cell death by 24 hours. A transcriptomic analysis of early changes in cellular gene expression identified alterations within the electron transport chain, stress response pathways, and mitochondrial dynamics compared to control cells. These results suggest that pathological mitochondrial swelling is associated with increased oxygen consumption rates leading to transcriptional changes in respiratory complexes and ultimately mitochondrial failure.

biochemistry↗