Biology subjects

Patti, G. J.

Publications and source records attributed to Patti, G. J..

At least 19 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

A genetically encoded redox bottleneck constrains human developmental rate

The intrinsically slow pace of human development poses challenges for regenerative medicine and disease modeling. This trait is attributed to low metabolic rates, yet the endogenous mechanisms determining species-specific metabolic flux remain unknown. Here, we identify coupling between glycolytic NADH production and mitochondrial oxidation through the glycerol-3-phosphate (G3P) shuttle as a genetic bottleneck constraining human developmental tempo. Using stem cell-derived models of the segmentation clock, an oscillator whose period reflects developmental rate, we show that low expression of the G3P shuttle enzyme GPD1L limits NADH oxidation in human progenitors compared to mouse. Overexpressing GPD1L boosts metabolic flux, accelerating the segmentation clock, cell cycle, and differentiation across germ layers. G3P-mediated redox coupling is thus a genetically encoded, rate-limiting mechanism that sets the tempo of human development.

developmental biology↗

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

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↗

bioRxiv2026

MassID provides near complete annotation of metabolomics data with identification probabilities

Liquid chromatography coupled to mass spectrometry (LC/MS) is a powerful tool in metabolomics research, generating tens-of-thousands of signals from a single biological sample. However, current software solutions for unbiased assessment of metabolomics data analysis are limited by complex sources of noise and non-quantitative metabolite identifications that make results difficult to interpret. Here, we present MassID, a cloud-based untargeted metabolomics pipeline that aims to overcome the innate challenges of unbiased metabolite analysis and perform end-to-end data processing, transforming raw spectra to normalized and identified metabolite profiles. MassID incorporates a suite of software functionalities, including deep learning-based peak detection and comprehensive noise filtering. In addition, with MassID we introduce a novel software module: DecoID2 that enables probabilistic metabolite identification for false discovery rate (FDR)-controlled metabolomics. When applied to a human plasma dataset, MassID results in near-complete signal annotation, identification of >4,000 metabolites (including >1,200 compounds at an FDR <5%) across four complementary LC/MS runs, and enables integrated downstream analyses to understand biochemical dysregulation at both the molecular and pathway level. When compared to the Metabolomics Standards Initiative (MSI) confidence levels, identification probability generally correlated with MSI levels. However, only 356/418 of MSI Level 1 compounds were identified with <5% FDR and the remaining 884 FDR < 5% compounds were identified from MSI L2-L3 compounds, highlighting the enhanced specificity and discovery potential achieved by MassID.

bioinformatics↗

bioRxiv2025

Cell type diversification and phenotype convergence underlying white fin-ornamentation of cyprinid fishes

Neural crest derived cells offer valuable opportunities to dissect mechanisms of cell fate specification and differentiation within individual ontogenies and the underpinnings of cell type diversification over evolutionary time. Particularly useful for such analyses are pigment cells of ectothermic vertebrates that arise from neural crest cells, or via latent neural crest derived stem cells, and comprise several classes with cell-type specific pigmentary phenotypes. Among these are white cells, "leucophores," present in a variety of species that contribute to patterns on the body or ornamentation on the fins. To better understand developmental and evolutionary origins of these cells we have examined leucophores harboring deposits of yellow/orange carotenoids, "xantholeucophores," of zebrafish and leucophores of white cloud minnow, within the same family Cyprinidae. We show that white phenotypes of both cell types require sepiapterin reductase that promotes accumulation of pale and colorless pteridines. We further demonstrate that xantholeucophores develop directly from yellow sepiapterin rich xanthophore-like cells and that this transition requires both gap junctional activity and permeability of the aquaglyceroporin / peroxiporin channel Aquaporin 3. These findings identify these white cells as distinct developmentally, genetically, and biochemically from another type of white cell in zebrafish and other white cells present across phylogenetic lineages. Our results highlight remarkable convergences and parallelisms in the acquisition of white cell phenotypes within and between species and identify this as a rich system for enquiries into the evolutionary individuation of novel cell types. SignificanceUnderstanding how cell types arise is fundamental to explaining animal complexity. Pigment cells offer opportunities to address this question because they display striking variation. We show that white pigment cells comprise multiple classes with independent origins. In zebrafish, white cells on one fin develop from melanophores whereas white cells on another fin develop from yellow precursors that convert their pigments to colorless ones. White cells of a related minnow require the same colorless pigments yet differ in other ways. These findings illuminate remarkable convergence: white cells have arisen repeatedly from different progenitor cell lineages by different mechanisms. This diversity--even within and between closely related species--identifies a powerful model for understanding the evolution of cell types with distinct identities and functions.

developmental biology↗

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

Adipose Tissue Overexpression of Nicotinamide Phosphoribosyltransferase Prevents Metabolic Dysfunction in Obese Mice

Nicotinamide adenine dinucleotide (NAD+) is a vital coenzyme and a central factor in energy metabolism. Nicotinamide phosphoribosyltransferase (NAMPT) maintains the cellular NAD+ pool by synthesizing the NAD+ precursor, nicotinamide mononucleotide (NMN), and diminished adipocyte NAMPT activity has been implicated in aging- and obesity-related metabolic dysfunction. Herein, we examined the effects of overexpressing or knocking out NAMPT in adipocytes on metabolic dysfunction and interorgan communication in mice. We generated new adipocyte-specific NAMPT overexpressing(ANOV) mice model. Male ANOV mice are protected from diet-induced metabolic dysfunction including adipose tissue inflammation, glucose intolerance, and insulin resistance. In contrast female ANOV mice were less protected from metabolic dysfunction, possibly due to higher endogenous expression of NAMPT in WT female mice. Livers of ANOV mice showed improved insulin signaling, increased NAD content, and reduced steatosis, suggesting that NAMPT regulates interorgan communication between adipocytes and hepatocytes. Extracellular vesicles (EV) isolated from ANOV mice enhanced insulin signaling in HepG2 cells and improved glucose tolerance in WT obese mice. In contrast, EV from ANKO mice suppressed HepG2 insulin signaling and inhibition of EV release improved glucose tolerance in ANKO female mice. Collectively, these data highlight a novel mechanism by which adipocyte NAD+ metabolism regulates systemic metabolic dysfunction via EVs.

physiology↗

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↗

bioRxiv2024

Ketone Body Metabolism is Not Required for Improvement of Heart Failure by Ketogenic Diet in Mice

Failing hearts increasingly metabolize ketone bodies, and enhancing ketosis improves heart failure (HF) remodeling. Circulating ketones are elevated by fasting/starvation, which is mimicked with a high-fat, low-carbohydrate "ketogenic diet" (KD). While speculated that KD improves HF through increased ketone oxidation, some evidence suggests KD paradoxically downregulates cardiac ketone oxidation despite increased ketone delivery. We sought to clarify the significance of cardiac ketone metabolism during KD in HF. Mice were subjected to transverse aortic constriction with apical myocardial infarction (TAC-MI) and fed either low-fat (LF) control or KD. Cardiac-specific mitochondrial pyruvate carrier 2 (csMPC2-/-) mice were used as a second model of heart failure. In both mice, feeding a KD improved HF, determined by echocardiography, heart weights, and gene expression analyses. Although KD increases plasma ketone bodies, gene expression for ketone metabolic genes is decreased in the hearts of KD-fed mice. Cardiac-specific {beta}-hydroxybutyrate dehydrogenase 1 (csBDH1-/-), the first enzyme in ketone catabolism, mice were also studied and crossed with the csMPC2-/-mice to create double knockout (DKO) mice. These mice were aged to 16 weeks and switched to LF or KD, and KD was able to completely normalize the hearts of both csMPC2-/- and DKO mice, suggesting that ketone metabolism is unnecessary for improving heart failure with ketogenic diet. These studies were then repeated, and mice injected with U-13C-{beta}-hydroxybutyrate to evaluate ketone metabolism. KD feeding significantly decreased the enrichment of the TCA cycle from ketone body carbons, as did the BDH1-deletion in DKO mice. Gene expression and respirometry suggests that KD instead increases cardiac fat oxidation. In conclusion, these results suggest that ketogenic diet decreases cardiac ketone metabolism and does not require ketone metabolism to improve heart failure.

physiology↗

bioRxiv2024

Introducing identification probability for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence - the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate approaches to communicate compound identification confidence also have been developed based on identification points schema. However, neither qualitative levels of identification confidence nor quantitative scoring systems address the degree of ambiguity in compound identifications in context of the chemical space being considered, are easily automated, or are transferable between analytical platforms. In this perspective, we propose that the metabolomics and related communities consider identification probability as an approach for automated and transferable assessment of compound identification and ambiguity in metabolomics and related studies. Identification probability is defined simply as 1/N, where N is the number of compounds in a reference library or chemical space that match to an experimentally measured molecule within user-defined measurement precision(s), for example mass measurement or retention time accuracy, etc. We demonstrate the utility of identification probability in an in silico analysis of multi-property reference libraries constructed from the Human Metabolome Database and computational property predictions, provide guidance to the community in transparent implementation of the concept, and invite the community to further evaluate this concept in parallel with their current preferred methods for assessing metabolite identification confidence.

biochemistry↗

bioRxiv2024

Loss of mitochondrial pyruvate transport initiates cardiac glycogen accumulation and heart failure

Heart failure involves metabolic alterations including increased glycolysis despite unchanged or decreased glucose oxidation. The mitochondrial pyruvate carrier (MPC) regulates pyruvate entry into the mitochondrial matrix, and cardiac deletion of the MPC in mice causes heart failure. How MPC deletion results in heart failure is unknown. We performed targeted metabolomics and isotope tracing in wildtype (fl/fl) and cardiac-specific Mpc2-/- (CS-Mpc2-/-) hearts after in vivo injection of U-13C-glucose. Failing CS-Mpc2-/- hearts contained normal levels of ATP and phosphocreatine, yet these hearts displayed increased enrichment from U-13C-glucose and increased glycolytic metabolite pool sizes. 13C enrichment and pool size was also increased for the glycogen intermediate UDP-glucose, as well as increased enrichment of the glycogen pool. Glycogen levels were increased [~]6-fold in the failing CS-Mpc2-/- hearts, and glycogen granules were easily detected by electron microscopy. In young, non-failing CS-Mpc2-/- hearts, increased glycolytic 13C enrichment occurred, but glycogen levels remained low and unchanged compared to fl/fl hearts. Inhibiting glycogen synthase with MZ-101 reduced cardiac glycogen levels and improved heart failure. Feeding a ketogenic diet to CS-Mpc2-/- mice reversed the heart failure and normalized the cardiac glycogen and glycolytic metabolite accumulation. Cardiac glycogen levels were also elevated in mice infused with angiotensin-II, and both the cardiac hypertrophy and glycogen levels were improved by ketogenic diet. Thus, loss of MPC in the heart causes glycogen accumulation and heart failure, while inhibition of glycogen synthesis or a ketogenic diet can reverse both the glycogen accumulation and heart failure.

physiology↗

bioRxiv2024

Dihydroceramide desaturase governs endoplasmic reticulum and lipid droplet homeostasis to promote glial function in the nervous system

Dihydroceramide desaturases convert dihydroceramides to ceramides, the precursors of all complex sphingolipids. Reduction of DEGS1 dihydroceramide desaturase function causes pediatric neurodegenerative disorder hypomyelinating leukodystrophy-18 (HLD-18). We discovered that infertile crescent (ifc), the Drosophila DEGS1 homolog, is expressed primarily in glial cells to promote CNS development by guarding against neurodegeneration. Loss of ifc causes massive dihydroceramide accumulation and severe morphological defects in cortex glia, including endoplasmic reticulum (ER) expansion, failure of neuronal ensheathment, and lipid droplet depletion. RNAi knockdown of the upstream ceramide synthase schlank in glia of ifc mutants rescues ER expansion, suggesting dihydroceramide accumulation in the ER drives this phenotype. RNAi knockdown of ifc in glia but not neurons drives neuronal cell death, suggesting that ifc function in glia promotes neuronal survival. Our work identifies glia as the primary site of disease progression in HLD-18 and may inform on juvenile forms of ALS, which also feature elevated dihydroceramide levels.

developmental biology↗

bioRxiv2023

Circadian regulation of MGMT expression and promoter methylation underlies daily rhythms in TMZ sensitivity in glioblastoma

BackgroundGlioblastoma (GBM) is the most common primary brain tumor in adults. Despite extensive research and clinical trials, median survival post-treatment remains at 15 months. Thus, all opportunities to optimize current treatments and improve patient outcomes should be considered. A recent retrospective clinical study found that taking TMZ in the morning compared to the evening was associated with a 6-month increase in median survival in patients with MGMT-methylated GBM. Here, we hypothesized that TMZ efficacy depends on time-of-day and O6-Methylguanine-DNA Methyltransferase (MGMT) activity in murine and human models of GBM. Methods and ResultsIn vitro recordings using real-time bioluminescence reporters revealed that GBM cells have intrinsic circadian rhythms in the expression of the core circadian clock genes Bmal1 and Per2, as well as in the DNA repair enzyme, MGMT. Independent measures of MGMT transcript levels and promoter methylation also showed daily rhythms intrinsic to GBM cells. These cells were more susceptible to TMZ when delivered at the daily peak of Bmal1 transcription. We found that in vivo morning administration of TMZ also decreased tumor size and increased body weight compared to evening drug delivery in mice bearing GBM xenografts. Finally, inhibition of MGMT activity with O6-Benzylguanine abrogated the daily rhythm in sensitivity to TMZ in vitro by increasing sensitivity at both the peak and trough of Bmal1 expression. ConclusionWe conclude that chemotherapy with TMZ can be dramatically enhanced by delivering at the daily maximum of tumor Bmal1 expression and minimum of MGMT activity. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC="FIGDIR/small/557630v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@2e9058org.highwire.dtl.DTLVardef@1069917org.highwire.dtl.DTLVardef@2cf000org.highwire.dtl.DTLVardef@40abc9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Effects of hepatic mitochondrial pyruvate carrier deficiency on de novo lipogenesis and glycerol-mediated gluconeogenesis in mice

The liver coordinates the systemic response to nutrient deprivation and availability by producing glucose from gluconeogenesis during fasting and synthesizing lipids via de novo lipogenesis (DNL) when carbohydrates are abundant. Mitochondrial pyruvate metabolism is thought to play important roles in both gluconeogenesis and DNL. We examined the effects of hepatocyte-specific mitochondrial pyruvate carrier (MPC) deletion on the fasting-refeeding response. Rates of DNL during refeeding were impaired by liver MPC deletion, but this did not reduce intrahepatic lipid content. During fasting, glycerol is converted to glucose by two pathways; a direct cytosolic pathway essentially reversing glycolysis and an indirect mitochondrial pathway requiring the MPC. MPC deletion reduced the incorporation of 13C-glycerol into TCA cycle metabolites but not into newly synthesized glucose. However, suppression of glycerol metabolism did not affect glucose concentrations in fasted hepatocyte-specific MPC-deficient mice. Thus, glucose production by kidney and intestine may compensate for MPC deficiency in hepatocytes.

physiology↗

bioRxiv2023

Adipocyte lipin 1 is positively associated with metabolic health in humans and regulates systemic metabolism in mice.

Dysfunctional adipose tissue is believed to promote the development of hepatic steatosis and systemic insulin resistance, but many of the mechanisms involved are still unclear. Lipin 1 catalyzes the conversion of phosphatidic acid to diacylglycerol (DAG), the penultimate step of triglyceride synthesis, which is essential for lipid storage. Herein we found that adipose tissue LPIN1 expression is decreased in people with obesity compared to lean subjects and low LPIN1 expression correlated with multi-tissue insulin resistance and increased rates of hepatic de novo lipogenesis. Comprehensive metabolic and multi-omic phenotyping demonstrated that adipocyte-specific Lpin1-/- mice had a metabolically-unhealthy phenotype, including liver and skeletal muscle insulin resistance, hepatic steatosis, increased hepatic de novo lipogenesis, and transcriptomic signatures of nonalcoholic steatohepatitis that was exacerbated by high-fat diets. We conclude that adipocyte lipin 1-mediated lipid storage is vital for preserving adipose tissue and systemic metabolic health and its loss predisposes mice to nonalcoholic steatohepatitis.

physiology↗