bims-mepmim 2024-10-06 papers

bims-mepmim

Biomed News

on Metabolites in pathological microenvironments and immunometabolism

Issue of 2024–10–06
23 papers selected by
Erika Mariana Palmieri, NIH/NCI Laboratory of Cancer ImmunoMetabolism

Small molecules targeting selective PCK1 and PGC-1α lysine acetylation cause anti-diabetic action through increased lactate oxidation.
MDM2 induces pro-inflammatory and glycolytic responses in M1 macrophages by integrating iNOS-nitric oxide and HIF-1α pathways in mice.
Cancer cell-intrinsic biosynthesis of itaconate promotes tumor immunogenicity.
Differential Mobility Spectrometry-Based Cardiolipin Analysis.
Cysteamine dioxygenase (ADO) governs cancer cell mitochondrial redox homeostasis through proline metabolism.
Distinctive CD39+CD9+ lung interstitial macrophages suppress IL-23/Th17-mediated neutrophilic asthma by inhibiting NETosis.
SUMOylation of MFF coordinates fission complexes to promote stress-induced mitochondrial fragmentation.
Deletion of CD38 mitigates the severity of NEC in experimental settings by modulating macrophage-mediated inflammation.
Temporal alterations of the nascent proteome in response to mitochondrial stress.
Caspase-1-dependent spatiality in triple-negative breast cancer and response to immunotherapy.
Activation of NOD1 on tumor-associated macrophages augments CD8+ T cell-mediated antitumor immunity in hepatocellular carcinoma.
GLP-1 programs the neurovascular landscape.
Immunoresponsive Gene 1 Facilitates TLR4-agonist-Induced Augmentation of Innate Antimicrobial Immunity.
NMR-Based Stable Isotope Tracing of Cancer Metabolism.
Identifying metabolic limitations in the tumor microenvironment.
ARF1 compartments direct cargo flow via maturation into recycling endosomes.
Intracellular biliverdin dynamics during ferroptosis.
Crosstalk of T cells within the ovarian cancer microenvironment.
An iron-rich subset of macrophages promotes tumor growth through a Bach1-Ednrb axis.
Intrinsic temperature increase drives lipid metabolism towards ferroptosis evasion and chemotherapy resistance in pancreatic cancer.
Ironing out MAFLD: Therapeutic targeting of liver ferroptosis.
Oxidised phosphatidylcholine induces sarcolemmal ceramide accumulation and insulin resistance in skeletal muscle.
Getting in the zone: Metabolite transport across liver zones.

Cell Chem Biol. 2024 Sep 26. pii: S2451-9456(24)00393-3. [Epub ahead of print]

Small molecules targeting selective PCK1 and PGC-1α lysine acetylation cause anti-diabetic action through increased lactate oxidation.

Beste Mutlu, Kfir Sharabi, Jee Hyung Sohn, Bo Yuan, Pedro Latorre-Muro, Xin Qin, Jin-Seon Yook, Hua Lin, Deyang Yu, João Paulo G Camporez, Shingo Kajimura, Gerald I Shulman, Sheng Hui, Theodore M Kamenecka, Patrick R Griffin, Pere Puigserver.

Small molecules selectively inducing peroxisome proliferator-activated receptor-gamma coactivator (PGC)-1α acetylation and inhibiting glucagon-dependent gluconeogenesis causing anti-diabetic effects have been identified. However, how these small molecules selectively suppress the conversion of gluconeogenic metabolites into glucose without interfering with lipogenesis is unknown. Here, we show that a small molecule SR18292 inhibits hepatic glucose production by increasing lactate and glucose oxidation. SR18292 increases phosphoenolpyruvate carboxykinase 1 (PCK1) acetylation, which reverses its gluconeogenic reaction and favors oxaloacetate (OAA) synthesis from phosphoenolpyruvate. PCK1 reverse catalytic reaction induced by SR18292 supplies OAA to tricarboxylic acid (TCA) cycle and is required for increasing glucose and lactate oxidation and suppressing gluconeogenesis. Acetylation mimetic mutant PCK1 K91Q favors anaplerotic reaction and mimics the metabolic effects of SR18292 in hepatocytes. Liver-specific expression of PCK1 K91Q mutant ameliorates hyperglycemia in obese mice. Thus, SR18292 blocks gluconeogenesis by enhancing gluconeogenic substrate oxidation through PCK1 lysine acetylation, supporting the anti-diabetic effects of these small molecules.

DOI: https://doi.org/10.1016/j.chembiol.2024.09.001
Nat Commun. 2024 Oct 04. 15(1): 8624

MDM2 induces pro-inflammatory and glycolytic responses in M1 macrophages by integrating iNOS-nitric oxide and HIF-1α pathways in mice.

Kelvin Ka-Lok Wu, Xiaofan Xu, Manyin Wu, Xiaomu Li, Moinul Hoque, Gloria Hoi Yee Li, Qizhou Lian, Kekao Long, Tongxi Zhou, Hailong Piao, Aimin Xu, Hannah Xiaoyan Hui, Kenneth King-Yip Cheng.

M1 macrophages induce protective immunity against infection, but also contribute to metabolic and inflammatory diseases. Here we show that the E3 ubiquitin ligase, MDM2, promotes the glycolytic and inflammatory activities of M1 macrophage by increasing the production of IL-1β, MCP-1 and nitric oxide (NO). Mechanistically, MDM2 triggers the ubiquitination and degradation of E3 ligase, SPSB2, to stabilize iNOS and increases production of NO, which s-nitrosylates and activates HIF-1α for triggering the glycolytic and pro-inflammatory programs in M1 macrophages. Myeloid-specific haplodeletion of MDM2 in mice not only blunts LPS-induced endotoxemia and NO production, but also alleviates obesity-induced adipose tissue-resident macrophage inflammation. By contrast, MDM2 haplodeletion induces higher mortality, tissue damage and bacterial burden, and also suppresses M1 macrophage response, in the cecal ligation and puncture-induced sepsis mouse model. Our findings thus identify MDM2 as an activator of glycolytic and inflammatory responses in M1 macrophages by connecting the iNOS-NO and HIF-1α pathways.

DOI: https://doi.org/10.1038/s41467-024-53006-w
EMBO J. 2024 Sep 30.

Cancer cell-intrinsic biosynthesis of itaconate promotes tumor immunogenicity.

Zining Wang, Lei Cui, Yanxun Lin, Bitao Huo, Hongxia Zhang, Chunyuan Xie, Huanling Zhang, Yongxiang Liu, Huan Jin, Hui Guo, Mengyun Li, Xiaojuan Wang, Penghui Zhou, Peng Huang, Jinyun Liu, Xiaojun Xia.

  The Krebs cycle byproduct itaconate has recently emerged as an important metabolite regulating macrophage immune functions, but its role in tumor cells remains unknown. Here, we show that increased tumor-intrinsic cis-aconitate decarboxylase (ACOD1 or CAD, encoded by immune-responsive gene 1, Irg1) expression and itaconate production promote tumor immunogenicity and anti-tumor immune responses. Furthermore, we identify thimerosal, a vaccine preservative, as a specific inducer of IRG1 expression in tumor cells but not in macrophages, thereby enhancing tumor immunogenicity. Mechanistically, thimerosal induces itaconate production through a ROS-RIPK3-IRF1 signaling axis in tumor cells. Further, increased IRG1/itaconate upregulates antigen presentation-related gene expression via promoting TFEB nuclear translocation. Intratumoral injection of thimerosal induced itaconate production, activated the tumor immune microenvironment, and inhibited tumor growth in a T cell-dependent manner. Importantly, IRG1 deficiency markedly impaired tumor response to thimerosal treatment. Furthermore, itaconate induction by thimerosal potentiates the anti-tumor efficacy of adoptive T-cell therapy and anti-PD1 therapy in a mouse lymphoma model. Hence, our findings identify a new role for tumor intrinsic IRG1/itaconate in promoting tumor immunogenicity and provide a translational means to increase immunotherapy efficacy.

Keywords:  Immunogenicity; Immunotherapy; Itaconate; Thimerosal

DOI:  https://doi.org/10.1038/s44318-024-00217-y
Methods Mol Biol. 2025 ;2855 373-385

Differential Mobility Spectrometry-Based Cardiolipin Analysis.

Fabien Riols, Michael Witting, Mark Haid.

  Cardiolipins (CL) are special lipids in many respects. First of all, CL are composed of four fatty acids linked by two phosphatidic acids, which provide CL a unique molecular structure. Secondly, in eukaryotic cells they are specific to a single organelle, mitochondria, where they are also synthetized. CL are one of the most abundant lipid classes in mitochondria, mainly localized in the inner membrane. They are key determinants of mitochondrial health and homeostasis by modulating membrane integrity and fluidity, mitochondrial shapes, and metabolic pathways. Disturbances in mitochondrial CL composition can lead to tissue malfunction and diseases. It is therefore important to develop analytical tools to study the mitochondrial lipidome, and more particularly the CL. The method described here allows the quantification of cardiolipins at the sum composition level in isolated mitochondria or in liver tissue by flow injection analysis coupled to differential mobility spectrometry (FIA-DMS), also known as DMS-based shotgun lipidomics.

Keywords:  Cardiolipins; Differential mobility spectrometry; Flow injection analysis; Mass spectrometry; Mitochondria

DOI:  https://doi.org/10.1007/978-1-0716-4116-3_22
Sci Adv. 2024 Oct 04. 10(40): eadq0355

Cysteamine dioxygenase (ADO) governs cancer cell mitochondrial redox homeostasis through proline metabolism.

Sandy Che-Eun S Lee, Andrea Hye An Pyo, Helia Mohammadi, Ji Zhang, Anna Dvorkin-Gheva, Lucie Malbeteau, Stephen Chung, Shahbaz Khan, M Teresa Ciudad, Vincent Rondeau, Rob A Cairns, Thomas Kislinger, Tracy L McGaha, Bradly G Wouters, Julie A Reisz, Rachel Culp-Hill, Angelo D'Alessandro, Courtney L Jones, Marianne Koritzinsky.

2-Aminoethanethiol dioxygenase (ADO) is a thiol dioxygenase that sulfinylates cysteamine and amino-terminal cysteines in polypeptides. The pathophysiological roles of ADO remain largely unknown. Here, we demonstrate that ADO expression represents a vulnerability in cancer cells, as ADO depletion led to loss of proliferative capacity and survival in cancer cells and reduced xenograft growth. In contrast, generation of the ADO knockout mouse revealed high tolerance for ADO depletion in adult tissues. To understand the mechanism underlying ADO's essentiality in cancer cells, we characterized the cell proteome and metabolome following depletion of ADO. This revealed that ADO depletion leads to toxic levels of polyamines which can be driven by ADO's substrate cysteamine. Polyamine accumulation in turn stimulated expression of proline dehydrogenase (PRODH) which resulted in mitochondrial hyperactivity and ROS production, culminating in cell toxicity. This work identifies ADO as a unique vulnerability in cancer cells, due to its essential role in maintenance of redox homeostasis through restraining polyamine levels and proline catabolism.

DOI: https://doi.org/10.1126/sciadv.adq0355
Nat Commun. 2024 Oct 04. 15(1): 8628

Distinctive CD39+CD9+ lung interstitial macrophages suppress IL-23/Th17-mediated neutrophilic asthma by inhibiting NETosis.

Seunghan Han, Bomin Kim, Do Young Hyeon, Daeun Jeong, Jaechan Ryu, Jae-Sung Nam, Yoon Ha Choi, Bo-Ram Kim, Sang Chul Park, Youn Wook Chung, Sung Jae Shin, June-Yong Lee, Jong Kyoung Kim, Jihye Park, Sei Won Lee, Tae-Bum Kim, Jae Hee Cheon, Hyung-Ju Cho, Chang-Hoon Kim, Joo-Heon Yoon, Daehee Hwang, Ji-Hwan Ryu.

The IL-23-Th17 axis is responsible for neutrophilic inflammation in various inflammatory diseases. Here, we discover a potential pathway to inhibit neutrophilic asthma. In our neutrophil-dominant asthma (NDA) model, single-cell RNA-seq analysis identifies a subpopulation of CD39+CD9+ interstitial macrophages (IMs) suppressed by IL-23 in NDA conditions but increased by an IL-23 inhibitor αIL-23p19. Adoptively transferred CD39+CD9+ IMs suppress neutrophil extracellular trap formation (NETosis), a representative phenotype of NDA, and also Th17 cell activation and neutrophilic inflammation. CD39+CD9+ IMs first attach to neutrophils in a CD9-dependent manner, and then remove ATP near neutrophils that contribute to NETosis in a CD39-dependent manner. Transcriptomic data from asthmatic patients finally show decreased CD39+CD9+ IMs in severe asthma than mild/moderate asthma. Our results suggest that CD39+CD9+ IMs function as a potent negative regulator of neutrophilic inflammation by suppressing NETosis in the IL-23-Th17 axis and can thus serve as a potential therapeutic target for IL-23-Th17-mediated neutrophilic asthma.

DOI: https://doi.org/10.1038/s41467-024-53038-2
Sci Adv. 2024 Oct 04. 10(40): eadq6223

SUMOylation of MFF coordinates fission complexes to promote stress-induced mitochondrial fragmentation.

Richard Seager, Nitheyaa Shree Ramesh, Stephen Cross, Chun Guo, Kevin A Wilkinson, Jeremy M Henley.

Mitochondria undergo fragmentation in response to bioenergetic stress, mediated by dynamin-related protein 1 (DRP1) recruitment to the mitochondria. The major pro-fission DRP1 receptor is mitochondrial fission factor (MFF), and mitochondrial dynamics proteins of 49 and 51 kilodaltons (MiD49/51), which can sequester inactive DRP1. Together, they form a trimeric DRP1-MiD-MFF complex. Adenosine monophosphate-activated protein kinase (AMPK)-mediated phosphorylation of MFF is necessary for mitochondrial fragmentation, but the molecular mechanisms are unclear. Here, we identify MFF as a target of small ubiquitin-like modifier (SUMO) at Lys151, MFF SUMOylation is enhanced following AMPK-mediated phosphorylation and that MFF SUMOylation regulates the level of MiD binding to MFF. The mitochondrial stressor carbonyl cyanide 3-chlorophenylhydrazone (CCCP) promotes MFF SUMOylation and mitochondrial fragmentation. However, CCCP-induced fragmentation is impaired in MFF-knockout mouse embryonic fibroblasts expressing non-SUMOylatable MFF K151R. These data suggest that the AMPK-MFF SUMOylation axis dynamically controls stress-induced mitochondrial fragmentation by regulating the levels of MiD in trimeric fission complexes.

DOI: https://doi.org/10.1126/sciadv.adq6223
Redox Biol. 2024 Sep 19. pii: S2213-2317(24)00314-8. [Epub ahead of print]77 103336

Deletion of CD38 mitigates the severity of NEC in experimental settings by modulating macrophage-mediated inflammation.

Yue Ma, Yunfei Zhang, Xinli Liu, Xinyi Yang, Hongjie Guo, Xionghui Ding, Cuilian Ye, Chunbao Guo.

  Necrotizing enterocolitis (NEC) is a form of potentially lethal gastrointestinal inflammation that primarily affects preterm neonates. It is crucial to recognize that, while the disease carries significant risks, timely and effective medical intervention can greatly enhance the chances of survival. Additionally, NEC is closely linked to the activation of macrophages, highlighting the complex interplay between the immune response and disease progression. CD38, acting as an ectoenzyme, catalyzes the hydrolysis of NAD+ to produce cyclic ADP-ribose (cADPR), a reaction critical for modulating cellular redox balance and energy homeostasis. This enzymatic activity is particularly pertinent in the context of necrotizing enterocolitis (NEC). In this research, we investigated whether CD38 deletion can elevate NAD+ levels to reduce macrophage-mediated inflammation and improve NEC severity. We show that NEC patients was associated with the increased CD38 expression in intestine and blood. These results were also observed in NEC mice, and CD38 deletion ameliorated NEC intestinal injury. Mechanistically, CD38 deletion elevated NAD+ levels that reduced oxidative stress and intestinal inflammation. Furthermore, CD38 deletion promoted M2 macrophage polarization, inhibited macrophage activation and phagocytosis ability. Thus, our results reveal a critical role for CD38 as an intracellular immune regulator for regulating macrophage activation and intestinal inflammation in NEC. Targeting CD38 and NAD+ signal maybe a promising strategy for treatment of NEC.

Keywords:  CD38; Inflammation; Macrophage; Necrotizing enterocolitis; Nicotinamide adenine dinucleotide; Phagocytosis; Reactive oxygen species

DOI:  https://doi.org/10.1016/j.redox.2024.103336
Cell Rep. 2024 Oct 02. pii: S2211-1247(24)01154-9. [Epub ahead of print]43(10): 114803

Temporal alterations of the nascent proteome in response to mitochondrial stress.

Tomasz M Stępkowski, Vanessa Linke, Dorota Stadnik, Maciej Zakrzewski, Anna E Zawada, Remigiusz A Serwa, Agnieszka Chacinska.

  Under stress, protein synthesis is attenuated to preserve energy and mitigate challenges to protein homeostasis. Here, we describe, with high temporal resolution, the dynamic landscape of changes in the abundance of proteins synthesized upon stress from transient mitochondrial inner membrane depolarization. This nascent proteome was altered when global translation was attenuated by stress and began to normalize as translation was recovering. This transition was associated with a transient desynchronization of cytosolic and mitochondrial translation and recovery of cytosolic and mitochondrial ribosomal proteins. Further, the elongation factor EEF1A1 was downregulated upon mitochondrial stress, and its silencing mimicked the stress-induced nascent proteome remodeling, including alterations in the nascent respiratory chain proteins. Unexpectedly, the stress-induced alterations in the nascent proteome were independent of physiological protein abundance and turnover. In summary, we provide insights into the physiological and pathological consequences of mitochondrial function and dysfunction.

Keywords:  CP: Cell biology; CP: Metabolism; EEF1A; EEF1A1; cellular stress; elongation factor; mass spectrometry; mitochondria; nascent chain; protein synthesis; proteomics; translation

DOI:  https://doi.org/10.1016/j.celrep.2024.114803
Nat Commun. 2024 Oct 01. 15(1): 8514

Caspase-1-dependent spatiality in triple-negative breast cancer and response to immunotherapy.

Weiyue Zheng, Wanda Marini, Kiichi Murakami, Valentin Sotov, Marcus Butler, Chiara Gorrini, Pamela S Ohashi, Michael Reedijk.

Tumor immune microenvironment (TIME) spatial organization predicts outcome and therapy response in triple-negative breast cancer (TNBC). An immunosuppressive TIME containing elevated tumor-associated macrophages (TAM) and scarce CD8+ T cells is associated with poor outcome, but the regulatory mechanisms are poorly understood. Here we show that ETS1-driven caspase-1 expression, required for IL1β processing and TAM recruitment, is negatively regulated by estrogen receptors alpha (ERα) and a defining feature of TNBC. Elevated tumoral caspase-1 is associated with a distinct TIME characterized by increased pro-tumoral TAMs and CD8+ T cell exclusion from tumor nests. Mouse models prove the functional importance of ERα, ETS1, caspase-1 and IL1β in TIME conformation. Caspase-1 inhibition induces an immunoreactive TIME and reverses resistance to immune checkpoint blockade, identifying a therapeutically targetable mechanism that governs TNBC spatial organization.

DOI: https://doi.org/10.1038/s41467-024-52553-6
Sci Adv. 2024 Oct 04. 10(40): eadp8266

Activation of NOD1 on tumor-associated macrophages augments CD8+ T cell-mediated antitumor immunity in hepatocellular carcinoma.

Feng Zhang, Qiuyu Jiang, Jialiang Cai, Fansheng Meng, Wenqing Tang, Zhiyong Liu, Xiahui Lin, Wenfeng Liu, Yi Zhou, Xizhong Shen, Ruyi Xue, Ling Dong, Si Zhang.

The efficacy of immunotherapy targeting the PD-1/PD-L1 pathway in hepatocellular carcinoma (HCC) is limited. NOD-like receptors (NLRs) comprise a highly evolutionarily conserved family of cytosolic bacterial sensors, yet their impact on antitumor immunity against HCC remains unclear. In this study, we uncovered that NOD1, a well-studied member of NLR family, exhibits predominant expression in tumor-associated macrophages (TAMs) and correlates positively with improved prognosis and responses to anti-PD-1 treatments in patients with HCC. Activation of NOD1 in vivo augments antitumor immunity and enhances the effectiveness of anti-PD-1 therapy. Mechanistically, NOD1 activation resulted in diminished expression of perilipin 5, thereby hindering fatty acid oxidation and inducing free fatty acid accumulation in TAMs. This metabolic alteration promoted membrane localization of the costimulatory molecule OX40L in a lipid modification-dependent manner, thereby activating CD8+ T cells. These findings unveil a previously unrecognized role for NOD1 in fortifying antitumor T cell immunity in HCC, potentially advancing cancer immunotherapy.

DOI: https://doi.org/10.1126/sciadv.adp8266
Cell Metab. 2024 Oct 01. pii: S1550-4131(24)00367-X. [Epub ahead of print]36(10): 2173-2189

GLP-1 programs the neurovascular landscape.

Bandy Chen, Xiaofei Yu, Claudia Horvath-Diano, María José Ortuño, Matthias H Tschöp, Ania M Jastreboff, Marc Schneeberger.

  Readily available nutrient-rich foods exploit our inherent drive to overconsume, creating an environment of overnutrition. This transformative setting has led to persistent health issues, such as obesity and metabolic syndrome. The development of glucagon-like peptide-1 receptor (GLP-1R) agonists reveals our ability to pharmacologically manage weight and address metabolic conditions. Obesity is directly linked to chronic low-grade inflammation, connecting our metabolic environment to neurodegenerative diseases. GLP-1R agonism in curbing obesity, achieved by impacting appetite and addressing associated metabolic defects, is revealing additional benefits extending beyond weight loss. Whether GLP-1R agonism directly impacts brain health or does so indirectly through improved metabolic health remains to be elucidated. In exploring the intricate connection between obesity and neurological conditions, recent literature suggests that GLP-1R agonism may have the capacity to shape the neurovascular landscape. Thus, GLP-1R agonism emerges as a promising strategy for addressing the complex interplay between metabolic health and cognitive well-being.

Keywords:  GLP-1; blood-brain barrier; cerebral blood flow; cerebral vasculature; cerebrospinal fluid; metabolic syndrome; myelination; neurodegeneration; neurovascular coupling; obesity

DOI:  https://doi.org/10.1016/j.cmet.2024.09.003
J Leukoc Biol. 2024 Oct 01. pii: qiae198. [Epub ahead of print]

Immunoresponsive Gene 1 Facilitates TLR4-agonist-Induced Augmentation of Innate Antimicrobial Immunity.

Margaret A McBride, Katherine R Caja, Tazeen K Patil, Allison M Owen, Liming Luan, Julia K Bohannon, Antonio Hernandez, Cody L Stothers, Irina A Trenary, Mohsin Rahim, Jamey D Young, M Wade Calcutt, Victoria R Stephens, Xenia Davis, Mary A Oliver, Dan Hao, Clara Si, Malik McRae, Kenny K Nguyen, Nicholas S Davis, Jingbin Wang, Naeem K Patil, Edward R Sherwood.

  Treatment with the toll-like receptor (TLR) 4 agonist monophosphoryl lipid A (MPLA) conditions innate immunocytes to respond robustly to subsequent infection, a phenotype termed innate immune memory. Our published studies show that metabolic reprogramming of macrophages is a prominent feature of the memory phenotype. We undertook studies to define the functional contributions of tricarboxylic acid (TCA) cycle reprogramming to innate immune memory. We observed that priming of wild type (WT) mice with MPLA potently facilitated accumulation of the TCA cycle metabolite itaconate at sites of infection and enhanced microbial clearance. Augmentation of itaconate accumulation and microbial clearance was ablated in immuneresponsive gene 1 (Irg1) -deficient mice. We further observed that MPLA potently induces expression of Irg1 and accumulation of itaconate in macrophages. Compared to WT macrophages, the ability of Irg1-deficient macrophages to kill Pseudomonas aeruginosa was impaired. We further observed that itaconate is directly antimicrobial against P. aeruginosa at pH 5, which is characteristic of the phagolysosome, and is facilitated by reactive oxygen species. MPLA-induced augmentation of glycolysis, oxidative phosphorylation and accumulation of the TCA cycle metabolites succinate and malate was decreased in Irg1 KO macrophages compared to WT controls. RNA sequencing revealed suppressed transcription of genes associated with phagolysosome function and increased expression of genes associated with cytokine production and chemotaxis in Irg1 deficient macrophages. This study identifies a contribution of itaconate to MPLA-induced augmentation of innate antimicrobial immunity via facilitation of microbial killing as well as impact on metabolic and transcriptional adaptations.

Keywords:  Immune Responsive Gene; Innate Immune Memory; Itaconate; Macrophages; Monophosphoryl Lipid A

DOI:  https://doi.org/10.1093/jleuko/qiae198
Methods Mol Biol. 2025 ;2855 457-504

NMR-Based Stable Isotope Tracing of Cancer Metabolism.

Penghui Lin, Andrew N Lane, Teresa W-M Fan.

  NMR is widely used for metabolite profiling (metabolomics, metabonomics) particularly of various readily obtainable biofluids such as plasma and urine. It is especially valuable for stable isotope tracer studies to track metabolic pathways under control or perturbed conditions in a wide range of cell models as well as animal models and human subjects. NMR has unique properties for utilizing stable isotopes to edit or simplify otherwise complex spectra acquired in vitro and in vivo, while quantifying the level of enrichment at specific atomic positions in various metabolites (i.e., isotopomer distribution analysis).In this protocol, we give an overview with specific protocols for NMR-based stable isotope-resolved metabolomics, or SIRM, with a workflow from administration of isotope-enriched precursors, via sample preparation through to NMR data collection and reduction. We focus on indirect detection of common NMR-active stable isotopes including 13C, 15N, 31P, and 2H, using a variety of 1H-based two-dimensional experiments. We also include the application and analyses of multiplex tracer experiments.

Keywords:  Isotopomer distribution analysis; NMRNuclear magnetic resonance (NMR); Spectral editing; Stable isotope-resolved metabolomics

DOI:  https://doi.org/10.1007/978-1-0716-4116-3_26
Sci Adv. 2024 Oct 04. 10(40): eadq7305

Identifying metabolic limitations in the tumor microenvironment.

Guillaume Cognet, Alexander Muir.

Solid tumors are characterized by dysfunctional vasculature that limits perfusion and delivery of nutrients to the tumor microenvironment. Limited perfusion coupled with the high metabolic demand of growing tumors has led to the hypothesis that many tumors experience metabolic stress driven by limited availability of nutrients such as glucose, oxygen, and amino acids in the tumor. Such metabolic stress has important implications for the biology of cells in the microenvironment, affecting both disease progression and response to therapies. Recently, techniques have been developed to identify limiting nutrients and resulting metabolic stresses in solid tumors. These techniques have greatly expanded our understanding of the metabolic limitations in tumors. This review will discuss these experimental tools and the emerging picture of metabolic limitations in tumors arising from recent studies using these approaches.

DOI: https://doi.org/10.1126/sciadv.adq7305
Nat Cell Biol. 2024 Oct 04.

ARF1 compartments direct cargo flow via maturation into recycling endosomes.

Alexander Stockhammer, Petia Adarska, Vini Natalia, Anja Heuhsen, Antonia Klemt, Gresy Bregu, Shelly Harel, Carmen Rodilla-Ramirez, Carissa Spalt, Ece Özsoy, Paula Leupold, Alica Grindel, Eleanor Fox, Joy Orezimena Mejedo, Amin Zehtabian, Helge Ewers, Dmytro Puchkov, Volker Haucke, Francesca Bottanelli.

Cellular membrane homoeostasis is maintained via a tightly regulated membrane and cargo flow between organelles of the endocytic and secretory pathways. Adaptor protein complexes (APs), which are recruited to membranes by the small GTPase ARF1, facilitate cargo selection and incorporation into trafficking intermediates. According to the classical model, small vesicles would facilitate bi-directional long-range transport between the Golgi, endosomes and plasma membrane. Here we revisit the intracellular organization of the vesicular transport machinery using a combination of CRISPR-Cas9 gene editing, live-cell high temporal (fast confocal) or spatial (stimulated emission depletion) microscopy as well as correlative light and electron microscopy. We characterize tubulo-vesicular ARF1 compartments that harbour clathrin and different APs. Our findings reveal two functionally different classes of ARF1 compartments, each decorated by a different combination of APs. Perinuclear ARF1 compartments facilitate Golgi export of secretory cargo, while peripheral ARF1 compartments are involved in endocytic recycling downstream of early endosomes. Contrary to the classical model of long-range vesicle shuttling, we observe that ARF1 compartments shed ARF1 and mature into recycling endosomes. This maturation process is impaired in the absence of AP-1 and results in trafficking defects. Collectively, these data highlight a crucial role for ARF1 compartments in post-Golgi sorting.

DOI: https://doi.org/10.1038/s41556-024-01518-4
J Biochem. 2024 Sep 28. pii: mvae067. [Epub ahead of print]

Intracellular biliverdin dynamics during ferroptosis.

Kazuma Nakajima, Hironari Nishizawa, Guan Chen, Shunichi Tsuge, Mie Yamanaka, Machi Kiyohara, Riko Irikura, Mitsuyo Matsumoto, Kozo Tanaka, Rei Narikawa, Kazuhiko Igarashi.

  Ferroptosis is a cell death mechanism mediated by iron-dependent lipid peroxidation. Although ferroptosis has garnered attention as a cancer-suppressing mechanism, there are still limited markers available for identifying ferroptotic cells or assessing their sensitivity to ferroptosis. The study focused on biliverdin, an endogenous reducing substance in cells, and examined the dynamics of intracellular biliverdin during ferroptosis using a biliverdin-binding cyanobacteriochrome. It was found that intracellular biliverdin decreases during ferroptosis and that this decrease is specific to ferroptosis among different forms of cell death. Furthermore, the feasibility of predicting sensitivity to ferroptosis by measuring intracellular biliverdin was demonstrated using a ferroptosis model induced by the re-expression of the transcription factor BACH1. These findings provide further insight into ferroptosis research and are expected to contribute to the development of cancer therapies that exploit ferroptosis.

Keywords:  BACH1; Biliverdin; Cyanobacteriochrome; Ferroptosis; Heme

DOI:  https://doi.org/10.1093/jb/mvae067
Trends Cancer. 2024 Sep 27. pii: S2405-8033(24)00190-0. [Epub ahead of print]

Crosstalk of T cells within the ovarian cancer microenvironment.

Bovannak S Chap, Nicolas Rayroux, Alizée J Grimm, Eleonora Ghisoni, Denarda Dangaj Laniti.

  Ovarian cancer (OC) represents ecosystems of highly diverse tumor microenvironments (TMEs). The presence of tumor-infiltrating lymphocytes (TILs) is linked to enhanced immune responses and long-term survival. In this review we present emerging evidence suggesting that cellular crosstalk tightly regulates the distribution of TILs within the TME, underscoring the need to better understand key cellular networks that promote or impede T cell infiltration in OC. We also capture the emergent methodologies and computational techniques that enable the dissection of cell-cell crosstalk. Finally, we present innovative ex vivo TME models that can be leveraged to map and perturb cellular communications to enhance T cell infiltration and immune reactivity.

Keywords:  3D tumor models; T cell; cellular crosstalk; ovarian cancer; spatial omics; tumor microenvironment

DOI:  https://doi.org/10.1016/j.trecan.2024.09.001
J Exp Med. 2024 Oct 07. pii: e20230420. [Epub ahead of print]221(10):

An iron-rich subset of macrophages promotes tumor growth through a Bach1-Ednrb axis.

Ian W Folkert, William A Molina Arocho, Tsun Ki Jerrick To, Samir Devalaraja, Irene S Molina, Jason Shoush, Hesham Mohei, Li Zhai, Md Naushad Akhtar, Veena Kochat, Emre Arslan, Alexander J Lazar, Khalida Wani, William P Israel, Zhan Zhang, Venkata S Chaluvadi, Robert J Norgard, Ying Liu, Ashley M Fuller, Mai T Dang, Robert E Roses, Giorgos C Karakousis, John T Miura, Douglas L Fraker, T S Karin Eisinger-Mathason, M Celeste Simon, Kristy Weber, Kai Tan, Yi Fan, Kunal Rai, Malay Haldar.

We define a subset of macrophages in the tumor microenvironment characterized by high intracellular iron and enrichment of heme and iron metabolism genes. These iron-rich tumor-associated macrophages (iTAMs) supported angiogenesis and immunosuppression in the tumor microenvironment and were conserved between mice and humans. iTAMs comprise two additional subsets based on gene expression profile and location-perivascular (pviTAM) and stromal (stiTAM). We identified the endothelin receptor type B (Ednrb) as a specific marker of iTAMs and found myeloid-specific deletion of Ednrb to reduce tumor growth and vascular density. Further studies identified the transcription factor Bach1 as a repressor of the iTAM transcriptional program, including Ednrb expression. Heme is a known inhibitor of Bach1, and, correspondingly, heme exposure induced Ednrb and iTAM signature genes in macrophages. Thus, iTAMs are a distinct macrophage subset regulated by the transcription factor Bach1 and characterized by Ednrb-mediated immunosuppressive and angiogenic functions.

DOI: https://doi.org/10.1084/jem.20230420
Nat Commun. 2024 Oct 02. 15(1): 8540

Intrinsic temperature increase drives lipid metabolism towards ferroptosis evasion and chemotherapy resistance in pancreatic cancer.

Vincent de Laat, Halit Topal, Xander Spotbeen, Ali Talebi, Jonas Dehairs, Jakub Idkowiak, Frank Vanderhoydonc, Tessa Ostyn, Peihua Zhao, Maarten Jacquemyn, Michele Wölk, Anna Sablina, Koen Augustyns, Tom Vanden Berghe, Tania Roskams, Dirk Daelemans, Maria Fedorova, Baki Topal, Johannes V Swinnen.

A spontaneously occurring temperature increase in solid tumors has been reported sporadically, but is largely overlooked in terms of cancer biology. Here we show that temperature is increased in tumors of patients with pancreatic ductal adenocarcinoma (PDAC) and explore how this could affect therapy response. By mimicking this observation in PDAC cell lines, we demonstrate that through adaptive changes in lipid metabolism, the temperature increase found in human PDAC confers protection to lipid peroxidation and contributes to gemcitabine resistance. Consistent with the recently uncovered role of p38 MAPK in ferroptotic cell death, we find that the reduction in lipid peroxidation potential following adaptation to tumoral temperature allows for p38 MAPK inhibition, conferring chemoresistance. As an increase in tumoral temperature is observed in several other tumor types, our findings warrant taking tumoral temperature into account in subsequent studies related to ferroptosis and therapy resistance. More broadly, our findings indicate that tumoral temperature affects cancer biology.

DOI: https://doi.org/10.1038/s41467-024-52978-z
Cell Metab. 2024 Oct 01. pii: S1550-4131(24)00369-3. [Epub ahead of print]36(10): 2167-2169

Ironing out MAFLD: Therapeutic targeting of liver ferroptosis.

Tuo Shao, Raymond T Chung.

Metabolic dysfunction-associated fatty liver disease (MAFLD) is associated with iron metabolism disorders and ferroptosis, but the mechanisms underlying this association remain unclear. Fudi Wang's group1 used animal models, human cohorts, and multi-omics data to demonstrate the role of iron imbalance in MAFLD and the therapeutic potential of the iron chelator FerroTerminator 1 (FOT1).

DOI: https://doi.org/10.1016/j.cmet.2024.09.005
Diabetologia. 2024 Sep 30.

Oxidised phosphatidylcholine induces sarcolemmal ceramide accumulation and insulin resistance in skeletal muscle.

Karin A Zemski Berry, Amanda Garfield, Purevsuren Jambal, Simona Zarini, Leigh Perreault, Bryan C Bergman.

   AIMS/HYPOTHESIS: Intracellular ceramide accumulation in specific cellular compartments is a potential mechanism explaining muscle insulin resistance in the pathogenesis of type 2 diabetes. Muscle sarcolemmal ceramide accumulation negatively impacts insulin sensitivity in humans, but the mechanism explaining this localised accumulation is unknown. Previous reports revealed that circulating oxidised LDL is elevated in serum of individuals with obesity and type 2 diabetes. Oxidised phosphatidylcholine, which is present in oxidised LDL, has previously been linked to ceramide pathway activation, and could contribute to localised ceramide accumulation in skeletal muscle. We hypothesised that oxidised phosphatidylcholine inversely correlates with insulin sensitivity in serum, and induces sarcolemmal ceramide accumulation and decreases insulin sensitivity in muscle.
METHODS: We used LC-MS/MS to quantify specific oxidised phosphatidylcholine species in serum from a cross-sectional study of 58 well-characterised individuals spanning the physiological range of insulin sensitivity. We also performed in vitro experiments in rat L6 myotubes interrogating the role of specific oxidised phosphatidylcholine species in promoting sarcolemmal ceramide accumulation, inflammation and insulin resistance in skeletal muscle cells.
RESULTS: Human serum oxidised phosphatidylcholine levels are elevated in individuals with obesity and type 2 diabetes, inversely correlated with insulin sensitivity, and positively correlated with sarcolemmal C18:0 ceramide levels in skeletal muscle. Specific oxidised phosphatidylcholine species, particularly 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphocholine (POVPC), increase total ceramide and dihydroceramide and decrease total sphingomyelin in the sarcolemma of L6 myotubes by de novo ceramide synthesis and sphingomyelinase activation. POVPC also increases inflammatory signalling and causes insulin resistance in L6 myotubes.
CONCLUSIONS/INTERPRETATION: These data suggest that circulating oxidised phosphatidylcholine species promote ceramide accumulation and decrease insulin sensitivity in muscle, help explain localised sphingolipid accumulation and muscle inflammatory response, and highlight oxidised phosphatidylcholine species as potential targets to combat insulin resistance.

Keywords:  Ceramide; Inflammation; Insulin resistance; Obesity; Type 2 diabetes

DOI:  https://doi.org/10.1007/s00125-024-06280-8
Acta Physiol (Oxf). 2024 Oct 04. e14239

Getting in the zone: Metabolite transport across liver zones.

Stan F J van de Graaf, Coen C Paulusma, Wietse In Het Panhuis.

  The liver has many functions including the regulation of nutrient and metabolite levels in the systemic circulation through efficient transport into and out of hepatocytes. To sustain these functions, hepatocytes display large functional heterogeneity. This heterogeneity is reflected by zonation of metabolic processes that take place in different zones of the liver lobule, where nutrient-rich blood enters the liver in the periportal zone and flows through the mid-zone prior to drainage by a central vein in the pericentral zone. Metabolite transport plays a pivotal role in the division of labor across liver zones, being either transport into the hepatocyte or transport between hepatocytes through the blood. Signaling pathways that regulate zonation, such as Wnt/β-catenin, have been shown to play a causal role in the development of metabolic dysfunction-associated steatohepatitis (MASH) progression, but the (patho)physiological regulation of metabolite transport remains enigmatic. Despite the practical challenges to separately study individual liver zones, technological advancements in the recent years have greatly improved insight in spatially divided metabolite transport. This review summarizes the theories behind the regulation of zonation, diurnal rhythms and their effect on metabolic zonation, contemporary techniques used to study zonation and current technological challenges, and discusses the current view on spatial and temporal metabolite transport.

Keywords:  circadian rhythms; liver; metabolic dysfunction‐associated steatotic liver disease; metabolic zonation; nutrient/metabolite transport

DOI:  https://doi.org/10.1111/apha.14239