bims-mepmim Biomed News
on Metabolites in pathological microenvironments and immunometabolism
Issue of 2024–07–07
eightteen papers selected by
Erika Mariana Palmieri, NIH/NCI Laboratory of Cancer ImmunoMetabolism
  1. PAQR4 regulates adipocyte function and systemic metabolic health by mediating ceramide levels.
  2. Functional multi-organelle units control inflammatory lipid metabolism of macrophages.
  3. IFNγ-IL12 axis regulates intercellular crosstalk in metabolic dysfunction-associated steatotic liver disease.
  4. TRIM2 promotes metabolic adaptation to glutamine deprivation via enhancement of CPT1A activity.
  5. Pro-survival signaling regulates lipophagy essential for multiple myeloma resistance to stress-induced death.
  6. Proteomic predictors of individualized nutrient-specific insulin secretion in health and disease.
  7. Lipid-associated macrophages reshape BAT cell identity in obesity.
  8. ER-to-lysosome Ca2+ refilling followed by K+ efflux-coupled store-operated Ca2+ entry in inflammasome activation and metabolic inflammation.
  9. Moderate-intensity aerobic exercise training improves CD8+ tumor-infiltrating lymphocytes effector function by reducing mitochondrial loss.
  10. Significance and Amplification Methods of the Purine Salvage Pathway in Human Brain Cells.
  11. Adenosine signalling to astrocytes coordinates brain metabolism and function.
  12. Hepatocyte vitamin D receptor functions as a nutrient sensor that regulates energy storage and tissue growth in zebrafish.
  13. High-dimensional single-cell analysis of human natural killer cell heterogeneity.
  14. Protocol for detecting mitochondria extracellular vesicles of brown adipose tissue in mice.
  15. Dietary fiber alleviates alcoholic liver injury via Bacteroides acidifaciens and subsequent ammonia detoxification.
  16. GTPBP8 plays a role in mitoribosome formation in human mitochondria.
  17. Cardiomyocyte PANX1 Controls Glycolysis and Neutrophil Recruitment in Hypertrophy.
  18. IRF5 suppresses metastasis through the regulation of tumor-derived extracellular vesicles and pre-metastatic niche formation.
  1. Nat Metab. 2024 Jul 03.
    PAQR4 regulates adipocyte function and systemic metabolic health by mediating ceramide levels.
    Qingzhang Zhu, Shiuhwei Chen, Jan-Bernd Funcke, Leon G Straub, Qian Lin, Shangang Zhao, Chanmin Joung, Zhuzhen Zhang, Dae-Seok Kim, Na Li, Christy M Gliniak, Charlotte Lee, Alberto Cebrian-Serrano, Line Pedersen, Nils Halberg, Ruth Gordillo, Christine M Kusminski, Philipp E Scherer.
      PAQR4 is an orphan receptor in the PAQR family with an unknown function in metabolism. Here, we identify a critical role of PAQR4 in maintaining adipose tissue function and whole-body metabolic health. We demonstrate that expression of Paqr4 specifically in adipocytes, in an inducible and reversible fashion, leads to partial lipodystrophy, hyperglycaemia and hyperinsulinaemia, which is ameliorated by wild-type adipose tissue transplants or leptin treatment. By contrast, deletion of Paqr4 in adipocytes improves healthy adipose remodelling and glucose homoeostasis in diet-induced obesity. Mechanistically, PAQR4 regulates ceramide levels by mediating the stability of ceramide synthases (CERS2 and CERS5) and, thus, their activities. Overactivation of the PQAR4-CERS axis causes ceramide accumulation and impairs adipose tissue function through suppressing adipogenesis and triggering adipocyte de-differentiation. Blocking de novo ceramide biosynthesis rescues PAQR4-induced metabolic defects. Collectively, our findings suggest a critical function of PAQR4 in regulating cellular ceramide homoeostasis and targeting PAQR4 offers an approach for the treatment of metabolic disorders.
    DOI:  https://doi.org/10.1038/s42255-024-01078-9
  2. Nat Cell Biol. 2024 Jul 05.
    Functional multi-organelle units control inflammatory lipid metabolism of macrophages.
    Julia A Zimmermann, Kerstin Lucht, Manuel Stecher, Chahat Badhan, Katharina M Glaser, Maximilian W Epple, Lena R Koch, Ward Deboutte, Thomas Manke, Klaus Ebnet, Frauke Brinkmann, Olesja Fehler, Thomas Vogl, Ev-Marie Schuster, Anna Bremser, Joerg M Buescher, Angelika S Rambold.
      Eukaryotic cells contain several membrane-separated organelles to compartmentalize distinct metabolic reactions. However, it has remained unclear how these organelle systems are coordinated when cells adapt metabolic pathways to support their development, survival or effector functions. Here we present OrgaPlexing, a multi-spectral organelle imaging approach for the comprehensive mapping of six key metabolic organelles and their interactions. We use this analysis on macrophages, immune cells that undergo rapid metabolic switches upon sensing bacterial and inflammatory stimuli. Our results identify lipid droplets (LDs) as primary inflammatory responder organelle, which forms three- and four-way interactions with other organelles. While clusters with endoplasmic reticulum (ER) and mitochondria (mitochondria-ER-LD unit) help supply fatty acids for LD growth, the additional recruitment of peroxisomes (mitochondria-ER-peroxisome-LD unit) supports fatty acid efflux from LDs. Interference with individual components of these units has direct functional consequences for inflammatory lipid mediator synthesis. Together, we show that macrophages form functional multi-organellar units to support metabolic adaptation and provide an experimental strategy to identify organelle-metabolic signalling hubs.
    DOI:  https://doi.org/10.1038/s41556-024-01457-0
  3. Nat Commun. 2024 Jun 29. 15(1): 5506
    IFNγ-IL12 axis regulates intercellular crosstalk in metabolic dysfunction-associated steatotic liver disease.
    Randall H Friedline, Hye Lim Noh, Sujin Suk, Mahaa Albusharif, Sezin Dagdeviren, Suchaorn Saengnipanthkul, Bukyung Kim, Allison M Kim, Lauren H Kim, Lauren A Tauer, Natalie M Baez Torres, Stephanie Choi, Bo-Yeon Kim, Suryateja D Rao, Kaushal Kasina, Cheng Sun, Benjamin J Toles, Chan Zhou, Zixiu Li, Vivian M Benoit, Payal R Patel, Doris X T Zheng, Kunikazu Inashima, Annika Beaverson, Xiaodi Hu, Duy A Tran, Werner Muller, Dale L Greiner, Alan C Mullen, Ki Won Lee, Jason K Kim.
      Obesity is a major cause of metabolic dysfunction-associated steatohepatitis (MASH) and is characterized by inflammation and insulin resistance. Interferon-γ (IFNγ) is a pro-inflammatory cytokine elevated in obesity and modulating macrophage functions. Here, we show that male mice with loss of IFNγ signaling in myeloid cells (Lyz-IFNγR2-/-) are protected from diet-induced insulin resistance despite fatty liver. Obesity-mediated liver inflammation is also attenuated with reduced interleukin (IL)-12, a cytokine primarily released by macrophages, and IL-12 treatment in vivo causes insulin resistance by impairing hepatic insulin signaling. Following MASH diets, Lyz-IFNγR2-/- mice are rescued from developing liver fibrosis, which is associated with reduced fibroblast growth factor (FGF) 21 levels. These results indicate critical roles for IFNγ signaling in macrophages and their release of IL-12 in modulating obesity-mediated insulin resistance and fatty liver progression to MASH. In this work, we identify the IFNγ-IL12 axis in regulating intercellular crosstalk in the liver and as potential therapeutic targets to treat MASH.
    DOI:  https://doi.org/10.1038/s41467-024-49633-y
  4. FEBS J. 2024 Jul 01.
    TRIM2 promotes metabolic adaptation to glutamine deprivation via enhancement of CPT1A activity.
    Kaimin Liao, Kaiyue Liu, Zhongyu Wang, Kailiang Zhao, Yide Mei.
      Cancer cells undergo metabolic adaptation to promote their survival and growth under energy stress conditions, yet the underlying mechanisms remain largely unclear. Here, we report that tripartite motif-containing protein 2 (TRIM2) is upregulated in response to glutamine deprivation by the transcription factor cyclic AMP-dependent transcription factor (ATF4). TRIM2 is shown to specifically interact with carnitine O-palmitoyltransferase 1 (CPT1A), a rate-limiting enzyme of fatty acid oxidation. Via this interaction, TRIM2 enhances the enzymatic activity of CPT1A, thereby regulating intracellular lipid levels and protecting cells from glutamine deprivation-induced apoptosis. Furthermore, TRIM2 is able to promote both in vitro cell proliferation and in vivo xenograft tumor growth via CPT1A. Together, these findings establish TRIM2 as an important regulator of the metabolic adaptation of cancer cells to glutamine deprivation and implicate TRIM2 as a potential therapeutic target for cancer.
    Keywords:  CPT1A; TRIM2; glutamine deprivation; metabolic adaptation
    DOI:  https://doi.org/10.1111/febs.17218
  5. Cell Rep. 2024 Jul 03. pii: S2211-1247(24)00774-5. [Epub ahead of print]43(7): 114445
    Pro-survival signaling regulates lipophagy essential for multiple myeloma resistance to stress-induced death.
    Peng Peng, Colin Chavel, Wensheng Liu, Louise M Carlson, Sha Cao, Adam Utley, Scott H Olejniczak, Kelvin P Lee.
      Pro-survival metabolic adaptations to stress in tumorigenesis remain less well defined. We find that multiple myeloma (MM) is unexpectedly dependent on beta-oxidation of long-chain fatty acids (FAs) for survival under both basal and stress conditions. However, under stress conditions, a second pro-survival signal is required to sustain FA oxidation (FAO). We previously found that CD28 is expressed on MM cells and transduces a significant pro-survival/chemotherapy resistance signal. We now find that CD28 signaling regulates autophagy/lipophagy that involves activation of the Ca2+→AMPK→ULK1 axis and regulates the translation of ATG5 through HuR, resulting in sustained lipophagy, increased FAO, and enhanced MM survival. Conversely, blocking autophagy/lipophagy sensitizes MM to chemotherapy in vivo. Our findings link a pro-survival signal to FA availability needed to sustain the FAO required for cancer cell survival under stress conditions and identify lipophagy as a therapeutic target to overcome treatment resistance in MM.
    Keywords:  CD28; CP: Cancer; CP: Metabolism; autophagy; fatty acid metabolism; fatty acid oxidation; lipid droplets; lipophagy; multiple myeloma; pro-survival regulation
    DOI:  https://doi.org/10.1016/j.celrep.2024.114445
  6. Cell Metab. 2024 Jul 02. pii: S1550-4131(24)00226-2. [Epub ahead of print]36(7): 1619-1633.e5
    Proteomic predictors of individualized nutrient-specific insulin secretion in health and disease.
    Jelena Kolic, WenQing Grace Sun, Haoning Howard Cen, Jessica D Ewald, Jason C Rogalski, Shugo Sasaki, Han Sun, Varsha Rajesh, Yi Han Xia, Renata Moravcova, Søs Skovsø, Aliya F Spigelman, Jocelyn E Manning Fox, James Lyon, Leanne Beet, Jianguo Xia, Francis C Lynn, Anna L Gloyn, Leonard J Foster, Patrick E MacDonald, James D Johnson.
      Population-level variation and mechanisms behind insulin secretion in response to carbohydrate, protein, and fat remain uncharacterized. We defined prototypical insulin secretion responses to three macronutrients in islets from 140 cadaveric donors, including those with type 2 diabetes. The majority of donors' islets exhibited the highest insulin response to glucose, moderate response to amino acid, and minimal response to fatty acid. However, 9% of donors' islets had amino acid responses, and 8% had fatty acid responses that were larger than their glucose-stimulated insulin responses. We leveraged this heterogeneity and used multi-omics to identify molecular correlates of nutrient responsiveness, as well as proteins and mRNAs altered in type 2 diabetes. We also examined nutrient-stimulated insulin release from stem cell-derived islets and observed responsiveness to fat but not carbohydrate or protein-potentially a hallmark of immaturity. Understanding the diversity of insulin responses to carbohydrate, protein, and fat lays the groundwork for personalized nutrition.
    Keywords:  RNA-seq; human islets; insulin secretion; macronutrients; proteomics; stem cell-derived islets; type 2 diabetes
    DOI:  https://doi.org/10.1016/j.cmet.2024.06.001
  7. Cell Rep. 2024 Jul 03. pii: S2211-1247(24)00776-9. [Epub ahead of print]43(7): 114447
    Lipid-associated macrophages reshape BAT cell identity in obesity.
    Francesca Sciarretta, Andrea Ninni, Fabio Zaccaria, Valerio Chiurchiù, Adeline Bertola, Keaton Karlinsey, Wentong Jia, Veronica Ceci, Claudia Di Biagio, Ziyan Xu, Francesco Gaudioso, Flavia Tortolici, Marta Tiberi, Jiabi Zhang, Simone Carotti, Sihem Boudina, Paolo Grumati, Beiyan Zhou, Jonathan R Brestoff, Stoyan Ivanov, Katia Aquilano, Daniele Lettieri-Barbato.
      Obesity and type 2 diabetes cause a loss in brown adipose tissue (BAT) activity, but the molecular mechanisms that drive BAT cell remodeling remain largely unexplored. Using a multilayered approach, we comprehensively mapped a reorganization in BAT cells. We uncovered a subset of macrophages as lipid-associated macrophages (LAMs), which were massively increased in genetic and dietary model of BAT expansion. LAMs participate in this scenario by capturing extracellular vesicles carrying damaged lipids and mitochondria released from metabolically stressed brown adipocytes. CD36 scavenger receptor drove LAM phenotype, and CD36-deficient LAMs were able to increase brown fat genes in adipocytes. LAMs released transforming growth factor β1 (TGF-β1), which promoted the loss of brown adipocyte identity through aldehyde dehydrogenase 1 family member A1 (Aldh1a1) induction. These findings unfold cell dynamic changes in BAT during obesity and identify LAMs as key responders to tissue metabolic stress and drivers of loss of brown adipocyte identity.
    Keywords:  CP: Metabolism; adipocytes; extracellular mitochondria; immunometabolism; metabolism; mitochondria; single-cell RNA sequencing; thermogenesis; type 2 diabetes
    DOI:  https://doi.org/10.1016/j.celrep.2024.114447
  8. Elife. 2024 Jul 02. pii: RP87561. [Epub ahead of print]12
    ER-to-lysosome Ca2+ refilling followed by K+ efflux-coupled store-operated Ca2+ entry in inflammasome activation and metabolic inflammation.
    Hyereen Kang, Seong Woo Choi, Joo Young Kim, Soo-Jin Oh, Sung Joon Kim, Myung-Shik Lee.
      We studied lysosomal Ca2+ in inflammasome. Lipopolysaccharide (LPS) + palmitic acid (PA) decreased lysosomal Ca2+ ([Ca2+]Lys) and increased [Ca2+]i through mitochondrial ROS, which was suppressed in Trpm2-KO macrophages. Inflammasome activation and metabolic inflammation in adipose tissue of high-fat diet (HFD)-fed mice were ameliorated by Trpm2 KO. ER→lysosome Ca2+ refilling occurred after lysosomal Ca2+ release whose blockade attenuated LPS + PA-induced inflammasome. Subsequently, store-operated Ca2+entry (SOCE) was activated whose inhibition suppressed inflammasome. SOCE was coupled with K+ efflux whose inhibition reduced ER Ca2+ content ([Ca2+]ER) and impaired [Ca2+]Lys recovery. LPS + PA activated KCa3.1 channel, a Ca2+-activated K+ channel. Inhibitors of KCa3.1 channel or Kcnn4 KO reduced [Ca2+]ER, attenuated increase of [Ca2+]i or inflammasome activation by LPS + PA, and ameliorated HFD-induced inflammasome or metabolic inflammation. Lysosomal Ca2+ release induced delayed JNK and ASC phosphorylation through CAMKII-ASK1. These results suggest a novel role of lysosomal Ca2+ release sustained by ER→lysosome Ca2+ refilling and K+ efflux through KCa3.1 channel in inflammasome activation and metabolic inflammation.
    Keywords:  diabetes; immunology; inflammation; lipid; lysosome; mouse
    DOI:  https://doi.org/10.7554/eLife.87561
  9. iScience. 2024 Jun 21. 27(6): 110121
    Moderate-intensity aerobic exercise training improves CD8+ tumor-infiltrating lymphocytes effector function by reducing mitochondrial loss.
    Vanessa Azevedo Voltarelli, Mariane Tami Amano, Gabriel Cardial Tobias, Gabriela Silva Borges, Ailma Oliveira da Paixão, Marcelo Gomes Pereira, Niels Olsen Saraiva Câmara, Waldir Caldeira, Alberto Freitas Ribeiro, Leo Edmond Otterbein, Carlos Eduardo Negrão, James Edward Turner, Patricia Chakur Brum, Anamaria Aranha Camargo.
      Aerobic exercise training (AET) has emerged as a strategy to reduce cancer mortality, however, the mechanisms explaining AET on tumor development remain unclear. Tumors escape immune detection by generating immunosuppressive microenvironments and impaired T cell function, which is associated with T cell mitochondrial loss. AET improves mitochondrial content and function, thus we tested whether AET would modulate mitochondrial metabolism in tumor-infiltrating lymphocytes (TIL). Balb/c mice were subjected to a treadmill AET protocol prior to CT26 colon carcinoma cells injection and until tumor harvest. Tissue hypoxia, TIL infiltration and effector function, and mitochondrial content, morphology and function were evaluated. AET reduced tumor growth, improved survival, and decreased tumor hypoxia. An increased CD8+ TIL infiltration, IFN-γ and ATP production promoted by AET was correlated with reduced mitochondrial loss in these cells. Collectively, AET decreases tumor growth partially by increasing CD8+ TIL effector function through an improvement in their mitochondrial content and function.
    Keywords:  Biochemistry; Biological sciences; Cancer systems biology; Immunology; Natural sciences; Physiology; Systems biology
    DOI:  https://doi.org/10.1016/j.isci.2024.110121
  10. J Biol Chem. 2024 Jul 01. pii: S0021-9258(24)02025-8. [Epub ahead of print] 107524
    Significance and Amplification Methods of the Purine Salvage Pathway in Human Brain Cells.
    Mai Sekine, Megumi Fujiwara, Ken Okamoto, Kimiyoshi Ichida, Koji Nagata, Russ Hille, Takeshi Nishino.
      Previous studies suggest that uric acid or reactive oxygen species, products of xanthine oxidoreductase (XOR), may associate with neurodegenerative diseases. However, neither relationship has ever been firmly established. Here, we analyzed human brain samples, obtained under protocols approved by research ethics committees, and found no expression of XOR and only low levels of uric acid in various regions of the brain. In the absence of XOR, hypoxanthine will be preserved and available for incorporation into the purine salvage pathway. To clarify the importance of salvage in the brain, we tested using human induced pluripotent stem cell-derived neuronal cells. Stable isotope analyses showed that the purine salvage pathway was more effective for ATP synthesis than purine de novo synthesis. Blood uric acid levels were related to the intracellular adenylate pool (ATP + ADP + AMP), and reduced levels of this pool result in lower uric acid levels. XOR inhibitors are related to extracellular hypoxanthine levels available for uptake into the purine salvage pathway by inhibiting the oxidation of hypoxanthine to xanthine and uric acid in various organs where XOR is present and can prevent further decreases in the intracellular adenylate pool under stress. Furthermore, adding precursors of the pentose phosphate pathway enhanced hypoxanthine uptake, indicating that purine salvage is activated by PRPP replenishment. These findings resolve previous contradictions regarding XOR products and provide new insights into clinical studies. It is suggested that therapeutic strategies maximizing maintenance of intracellular adenylate levels may effectively treat pathological conditions associated with ischemia and energy depletion.
    Keywords:  HPRT; XOR; brain; pentose phosphate pathway; purine metabolism; salvage
    DOI:  https://doi.org/10.1016/j.jbc.2024.107524
  11. Nature. 2024 Jul 03.
    Adenosine signalling to astrocytes coordinates brain metabolism and function.
    Shefeeq M Theparambil, Olga Kopach, Alice Braga, Shereen Nizari, Patrick S Hosford, Virag Sagi-Kiss, Anna Hadjihambi, Christos Konstantinou, Noemi Esteras, Ana Gutierrez Del Arroyo, Gareth L Ackland, Anja G Teschemacher, Nicholas Dale, Tobias Eckle, Petros Andrikopoulos, Dmitri A Rusakov, Sergey Kasparov, Alexander V Gourine.
      Brain computation performed by billions of nerve cells relies on a sufficient and uninterrupted nutrient and oxygen supply1,2. Astrocytes, the ubiquitous glial neighbours of neurons, govern brain glucose uptake and metabolism3,4, but the exact mechanisms of metabolic coupling between neurons and astrocytes that ensure on-demand support of neuronal energy needs are not fully understood5,6. Here we show, using experimental in vitro and in vivo animal models, that neuronal activity-dependent metabolic activation of astrocytes is mediated by neuromodulator adenosine acting on astrocytic A2B receptors. Stimulation of A2B receptors recruits the canonical cyclic adenosine 3',5'-monophosphate-protein kinase A signalling pathway, leading to rapid activation of astrocyte glucose metabolism and the release of lactate, which supplements the extracellular pool of readily available energy substrates. Experimental mouse models involving conditional deletion of the gene encoding A2B receptors in astrocytes showed that adenosine-mediated metabolic signalling is essential for maintaining synaptic function, especially under conditions of high energy demand or reduced energy supply. Knockdown of A2B receptor expression in astrocytes led to a major reprogramming of brain energy metabolism, prevented synaptic plasticity in the hippocampus, severely impaired recognition memory and disrupted sleep. These data identify the adenosine A2B receptor as an astrocytic sensor of neuronal activity and show that cAMP signalling in astrocytes tunes brain energy metabolism to support its fundamental functions such as sleep and memory.
    DOI:  https://doi.org/10.1038/s41586-024-07611-w
  12. Cell Rep. 2024 Jun 28. pii: S2211-1247(24)00721-6. [Epub ahead of print]43(7): 114393
    Hepatocyte vitamin D receptor functions as a nutrient sensor that regulates energy storage and tissue growth in zebrafish.
    Scott H Freeburg, Arkadi Shwartz, Lajos V Kemény, Colton J Smith, Olivia Weeks, Bess M Miller, Nadia PenkoffLidbeck, David E Fisher, Kimberley J Evason, Wolfram Goessling.
      Vitamin D receptor (VDR) has been implicated in fatty liver pathogenesis, but its role in the regulation of organismal energy usage remains unclear. Here, we illuminate the evolutionary function of VDR by demonstrating that zebrafish Vdr coordinates hepatic and organismal energy homeostasis through antagonistic regulation of nutrient storage and tissue growth. Hepatocyte-specific Vdr impairment increases hepatic lipid storage, partially through acsl4a induction, while simultaneously diminishing fatty acid oxidation and liver growth. Importantly, Vdr impairment exacerbates the starvation-induced hepatic storage of systemic fatty acids, indicating that loss of Vdr signaling elicits hepatocellular energy deficiency. Strikingly, hepatocyte Vdr impairment diminishes diet-induced systemic growth while increasing hepatic and visceral fat in adult fish, revealing that hepatic Vdr signaling is required for complete adaptation to food availability. These data establish hepatocyte Vdr as a regulator of organismal energy expenditure and define an evolutionary function for VDR as a transcriptional effector of environmental nutrient supply.
    Keywords:  CP: Metabolism; evolution; liver; metabolism; nuclear hormone receptors; vitamin D; zebrafish
    DOI:  https://doi.org/10.1016/j.celrep.2024.114393
  13. Nat Immunol. 2024 Jul 02.
    High-dimensional single-cell analysis of human natural killer cell heterogeneity.
    Lucas Rebuffet, Janine E Melsen, Bertrand Escalière, Daniela Basurto-Lozada, Avinash Bhandoola, Niklas K Björkström, Yenan T Bryceson, Roberta Castriconi, Frank Cichocki, Marco Colonna, Daniel M Davis, Andreas Diefenbach, Yi Ding, Muzlifah Haniffa, Amir Horowitz, Lewis L Lanier, Karl-Johan Malmberg, Jeffrey S Miller, Lorenzo Moretta, Emilie Narni-Mancinelli, Luke A J O'Neill, Chiara Romagnani, Dylan G Ryan, Simona Sivori, Dan Sun, Constance Vagne, Eric Vivier.
      Natural killer (NK) cells are innate lymphoid cells (ILCs) contributing to immune responses to microbes and tumors. Historically, their classification hinged on a limited array of surface protein markers. Here, we used single-cell RNA sequencing (scRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to dissect the heterogeneity of NK cells. We identified three prominent NK cell subsets in healthy human blood: NK1, NK2 and NK3, further differentiated into six distinct subgroups. Our findings delineate the molecular characteristics, key transcription factors, biological functions, metabolic traits and cytokine responses of each subgroup. These data also suggest two separate ontogenetic origins for NK cells, leading to divergent transcriptional trajectories. Furthermore, we analyzed the distribution of NK cell subsets in the lung, tonsils and intraepithelial lymphocytes isolated from healthy individuals and in 22 tumor types. This standardized terminology aims at fostering clarity and consistency in future research, thereby improving cross-study comparisons.
    DOI:  https://doi.org/10.1038/s41590-024-01883-0
  14. STAR Protoc. 2024 Jun 27. pii: S2666-1667(24)00326-5. [Epub ahead of print]5(3): 103161
    Protocol for detecting mitochondria extracellular vesicles of brown adipose tissue in mice.
    Flavia Tortolici, Claudia Di Biagio, Daniele Lettieri-Barbato, Katia Aquilano.
      Brown adipose tissue (BAT) is mitochondria rich, enabling high oxidative metabolism for non-shivering thermogenesis. The release of large/small extracellular vesicles (EVs) containing mitochondria or mitochondrial fragments, termed mito-EVs, may support mitochondrial quality control or intercellular communication. We present a protocol to isolate and characterize mito-EVs. We detail steps for BAT processing, cell debris removal, differential centrifugation (dC), and mito-EV analysis by flow cytometry and immunoblotting assays. For complete details on the use and execution of this protocol, please refer to Rosina et al.1.
    Keywords:  Cell Biology; Cell Membrane; Cell culture; Flow Cytometry; Metabolism; Molecular Biology; Protein Biochemistry
    DOI:  https://doi.org/10.1016/j.xpro.2024.103161
  15. Cell Host Microbe. 2024 Jun 25. pii: S1931-3128(24)00226-9. [Epub ahead of print]
    Dietary fiber alleviates alcoholic liver injury via Bacteroides acidifaciens and subsequent ammonia detoxification.
    Haiyuan Shen, Liangliang Zhou, Hao Zhang, Yuanru Yang, Ling Jiang, Dongqing Wu, Hang Shu, Hejiao Zhang, Linxi Xie, Kaichen Zhou, Chen Cheng, Lei Yang, Jiali Jiang, Siya Wang, Yiran Han, Jiayi Zhu, Long Xu, Zhihua Liu, Hua Wang, Shi Yin.
      The gut microbiota and diet-induced changes in microbiome composition have been linked to various liver diseases, although the specific microbes and mechanisms remain understudied. Alcohol-related liver disease (ALD) is one such disease with limited therapeutic options due to its complex pathogenesis. We demonstrate that a diet rich in soluble dietary fiber increases the abundance of Bacteroides acidifaciens (B. acidifaciens) and alleviates alcohol-induced liver injury in mice. B. acidifaciens treatment alone ameliorates liver injury through a bile salt hydrolase that generates unconjugated bile acids to activate intestinal farnesoid X receptor (FXR) and its downstream target, fibroblast growth factor-15 (FGF15). FGF15 promotes hepatocyte expression of ornithine aminotransferase (OAT), which facilitates the metabolism of accumulated ornithine in the liver into glutamate, thereby providing sufficient glutamate for ammonia detoxification via the glutamine synthesis pathway. Collectively, these findings uncover a potential therapeutic strategy for ALD involving dietary fiber supplementation and B. acidifaciens.
    Keywords:  alcohol-related liver disease; ammonia detoxification; dietary fiber; gut microbiota; ornithine aminotransferase
    DOI:  https://doi.org/10.1016/j.chom.2024.06.008
  16. Nat Commun. 2024 Jul 05. 15(1): 5664
    GTPBP8 plays a role in mitoribosome formation in human mitochondria.
    Miriam Cipullo, Genís Valentín Gesé, Shreekara Gopalakrishna, Annika Krueger, Vivian Lobo, Maria A Pirozhkova, James Marks, Petra Páleníková, Dmitrii Shiriaev, Yong Liu, Jelena Misic, Yu Cai, Minh Duc Nguyen, Abubakar Abdelbagi, Xinping Li, Michal Minczuk, Markus Hafner, Daniel Benhalevy, Aishe A Sarshad, Ilian Atanassov, B Martin Hällberg, Joanna Rorbach.
      Mitochondrial gene expression relies on mitoribosomes to translate mitochondrial mRNAs. The biogenesis of mitoribosomes is an intricate process involving multiple assembly factors. Among these factors, GTP-binding proteins (GTPBPs) play important roles. In bacterial systems, numerous GTPBPs are required for ribosome subunit maturation, with EngB being a GTPBP involved in the ribosomal large subunit assembly. In this study, we focus on exploring the function of GTPBP8, the human homolog of EngB. We find that ablation of GTPBP8 leads to the inhibition of mitochondrial translation, resulting in significant impairment of oxidative phosphorylation. Structural analysis of mitoribosomes from GTPBP8 knock-out cells shows the accumulation of mitoribosomal large subunit assembly intermediates that are incapable of forming functional monosomes. Furthermore, fPAR-CLIP analysis reveals that GTPBP8 is an RNA-binding protein that interacts specifically with the mitochondrial ribosome large subunit 16 S rRNA. Our study highlights the role of GTPBP8 as a component of the mitochondrial gene expression machinery involved in mitochondrial large subunit maturation.
    DOI:  https://doi.org/10.1038/s41467-024-50011-x
  17. Circ Res. 2024 Jul 03.
    Cardiomyocyte PANX1 Controls Glycolysis and Neutrophil Recruitment in Hypertrophy.
    Caitlin M Pavelec, Alexander P Young, Hannah L Luviano, Emily E Orrell, Anna Szagdaj, Nabin Poudel, Abigail G Wolpe, Samantha H Thomas, Scott Yeudall, Clint M Upchurch, Mark D Okusa, Brant E Isakson, Matthew J Wolf, Norbert Leitinger.
       BACKGROUND: PANX1 (pannexin 1), a ubiquitously expressed ATP release membrane channel, has been shown to play a role in inflammation, blood pressure regulation, and myocardial infarction. However, the possible role of PANX1 in cardiomyocytes in the progression of heart failure has not yet been investigated.
    METHOD: We generated a novel mouse line with constitutive deletion of PANX1 in cardiomyocytes (Panx1MyHC6).
    RESULTS: PANX1 deletion in cardiomyocytes had no effect on unstressed heart function but increased the glycolytic metabolism and resulting glycolytic ATP production, with a concurrent decrease in oxidative phosphorylation, both in vivo and in vitro. In vitro, treatment of H9c2 cardiomyocytes with isoproterenol led to PANX1-dependent release of ATP and Yo-Pro-1 uptake, as assessed by pharmacological blockade with spironolactone and siRNA-mediated knockdown of PANX1. To investigate nonischemic heart failure and the preceding cardiac hypertrophy, we administered isoproterenol, and we demonstrated that Panx1MyHC6 mice were protected from systolic and diastolic left ventricle volume increases as a result of cardiomyocyte hypertrophy. Moreover, we found that Panx1MyHC6 mice showed decreased isoproterenol-induced recruitment of immune cells (CD45+), particularly neutrophils (CD11b+, Ly6g+), to the myocardium.
    CONCLUSIONS: Together, these data demonstrate that PANX1 deficiency in cardiomyocytes increases glycolytic metabolism and protects against cardiac hypertrophy in nonischemic heart failure at least in part by reducing immune cell recruitment. Our study implies PANX1 channel inhibition as a therapeutic approach to ameliorate cardiac dysfunction in patients with heart failure.
    Keywords:  heart failure; macrophages; neutrophils; prevalence; stroke volume
    DOI:  https://doi.org/10.1161/CIRCRESAHA.124.324650
  18. Sci Rep. 2024 Jul 05. 14(1): 15557
    IRF5 suppresses metastasis through the regulation of tumor-derived extracellular vesicles and pre-metastatic niche formation.
    Bailey K Roberts, Dan Iris Li, Carter Somerville, Bharati Matta, Vaishali Jha, Adison Steinke, Zarina Brune, Lionel Blanc, Samuel Z Soffer, Betsy J Barnes.
      Metastasis is driven by extensive cooperation between a tumor and its microenvironment, resulting in the adaptation of molecular mechanisms that evade the immune system and enable pre-metastatic niche (PMN) formation. Little is known of the tumor-intrinsic factors that regulate these mechanisms. Here we show that expression of the transcription factor interferon regulatory factor 5 (IRF5) in osteosarcoma (OS) and breast carcinoma (BC) clinically correlates with prolonged survival and decreased secretion of tumor-derived extracellular vesicles (t-dEVs). Conversely, loss of intra-tumoral IRF5 establishes a PMN that supports metastasis. Mechanistically, IRF5-positive tumor cells retain IRF5 transcripts within t-dEVs that contribute to altered composition, secretion, and trafficking of t-dEVs to sites of metastasis. Upon whole-body pre-conditioning with t-dEVs from IRF5-high or -low OS and BC cells, we found increased lung metastatic colonization that replicated findings from orthotopically implanted cancer cells. Collectively, our findings uncover a new role for IRF5 in cancer metastasis through its regulation of t-dEV programming of the PMN.
    DOI:  https://doi.org/10.1038/s41598-024-66168-w
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