bims-mepmim 2023-01-29 papers

bims-mepmim

Biomed News

on Metabolites in pathological microenvironments and immunometabolism

Issue of 2023‒01‒29
thirty papers selected by
Erika Mariana Palmieri
NIH/NCI Laboratory of Cancer ImmunoMetabolism

Mitochondrial SENP2 regulates the assembly of SDH complex under metabolic stress.
Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes.
Cx43 acts as a mitochondrial calcium regulator that promotes obesity by inducing the polarization of macrophages in adipose tissue.
Polyamine metabolism impacts T cell dysfunction in the oral mucosa of people living with HIV.
MicroRNA miR-1275 coordinately regulates AEA/LPA signals via targeting FAAH in lipid metabolism reprogramming of gastric cancer.
Cellular responses to 8-methyl nonanoic acid, a degradation by-product of dihydrocapsaicin, in 3T3-L1 adipocytes.
Mitochondrial NAD kinase in health and disease.
A concerted mechanism involving ACAT and SREBPs by which oxysterols deplete accessible cholesterol to restrict microbial infection.
Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation.
The mitochondrial inhibitor IF1 binds to the ATP synthase OSCP subunit and protects cancer cells from apoptosis.
The promise of targeting heme and mitochondrial respiration in normalizing tumor microenvironment and potentiating immunotherapy.
Tingible body macrophages arise from lymph node-resident precursors and uptake B cells by dendrites.
Lung macrophages utilize unique cathepsin K-dependent phagosomal machinery to degrade intracellular collagen.
Mass spectrometry imaging-based assays for aminotransferase activity reveal a broad substrate spectrum for a previously uncharacterized enzyme.
Interleukin 11 confers resistance to dextran sulfate sodium-induced colitis in mice.
Metabolic regulation of stress erythropoiesis, outstanding questions, and possible paradigms.
A metabolic readout of the urine metabolome of COVID-19 patients.
Estimation and implications of the genetic architecture of fasting and non-fasting blood glucose.
Inactivation of mitochondrial pyruvate carrier promotes NLRP3 inflammasome activation and gout development via metabolic reprogramming.
Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility.
Applications of spatially resolved omics in the field of endocrine tumors.
Mitochondria metabolism sets the species-specific tempo of neuronal development.
ACSS2-mediated NF-κB activation promotes alkaliptosis in human pancreatic cancer cells.
Amino acid slows nerve damage from diabetes, in mouse study.
Diet-induced gut dysbiosis and inflammation: Key drivers of obesity-driven NASH.
Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides.
Pericytes in the tumor microenvironment.
One-shot 13 C15 N-metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux.
The transcription factor ATF3 switches cell death from apoptosis to necroptosis in hepatic steatosis in male mice.
A phenome-wide comparative analysis of genetic discordance between obesity and type 2 diabetes.

Cell Rep. 2023 Jan 27. pii: S2211-1247(23)00052-9. [Epub ahead of print]42(2): 112041

Mitochondrial SENP2 regulates the assembly of SDH complex under metabolic stress.

Ying Liu, Kejia Liu, Rick F Thorne, Ronghua Shi, Qingyuan Zhang, Mian Wu, Lianxin Liu.

  Succinate dehydrogenase (SDH) is a heterotetrameric enzyme complex belonging to the mitochondrial respiratory chain and uniquely links the tricarboxylic acid (TCA) cycle with oxidative phosphorylation. Cancer-related SDH mutations promote succinate accumulation, which is regarded as an oncometabolite. Post-translational modifications of SDH complex components are known to regulate SDH activity, although the contribution of SUMOylation remains unclear. Here, we show that SDHA is SUMOylated by PIAS3 and deSUMOylated by SENP2, events dictating the assembly and activity of the SDH complex. Moreover, CBP acetylation of SENP2 negatively regulates its deSUMOylation activity. Under glutamine deprivation, CBP levels decrease, and the ensuing SENP2 activation and SDHA deSUMOylation serve to concurrently dampen the TCA cycle and electron transport chain (ETC) activity. Along with succinate accumulation, this mechanism avoids excessive reactive oxygen species (ROS) production to promote cancer cell survival. This study elucidates a major function of mitochondrial-localized SENP2 and expands our understanding of the role of SUMOylation in resolving metabolic stress.

Keywords:  CP: Cancer; CP: Metabolism; PTMs; SENP2; SUMOylation; TCA cycle; acetylation; metabolic stress; mitochondria; oxidative phosphorylation; succinate dehydrogenase

DOI:  https://doi.org/10.1016/j.celrep.2023.112041
Cell Rep. 2023 Jan 27. pii: S2211-1247(23)00057-8. [Epub ahead of print]42(2): 112046

Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes.

ImmGen Consortium

  The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one of the key physiological characteristics of the immune system. Here, we focus on understanding the metabolic variability of MNPs through metabolic network analysis applied to three large-scale transcriptional datasets: we introduce (1) an ImmGen MNP open-source dataset of 337 samples across 26 tissues; (2) a myeloid subset of ImmGen Phase I dataset (202 MNP samples); and (3) a myeloid mouse single-cell RNA sequencing (scRNA-seq) dataset (51,364 cells) assembled based on Tabula Muris Senis. To analyze such large-scale datasets, we develop a network-based computational approach, genes and metabolites (GAM) clustering, for unbiased identification of the key metabolic subnetworks based on transcriptional profiles. We define 9 metabolic subnetworks that encapsulate the metabolic differences within MNP from 38 different tissues. Obtained modules reveal that cholesterol synthesis appears particularly active within the migratory dendritic cells, while glutathione synthesis is essential for cysteinyl leukotriene production by peritoneal and lung macrophages.

Keywords:  CP: Immunology; CP: Metabolism; ImmGen; immunometabolism; mononuclear phagocytes; myeloid cells; network analysis; single-cell RNA-seq

DOI:  https://doi.org/10.1016/j.celrep.2023.112046
Cell Signal. 2023 Jan 18. pii: S0898-6568(23)00020-7. [Epub ahead of print] 110606

Cx43 acts as a mitochondrial calcium regulator that promotes obesity by inducing the polarization of macrophages in adipose tissue.

Qing Zhou, Yuyan Wang, Zongshi Lu, Chengkang He, Li Li, Mei You, Lijuan Wang, Tingbing Cao, Yu Zhao, Qiang Li, Aidi Mou, Wentao Shu, Hongbo He, Zhigang Zhao, Daoyan Liu, Zhiming Zhu, Peng Gao, Zhencheng Yan.

  Metabolic reprogramming of macrophages initiates the polarization of pro-inflammatory macrophages that exacerbates adipocyte dysfunction and obesity. The imbalance of mitochondrial Ca2+ homeostasis impairs mitochondrial function and promotes inflammation. Connexin 43 (Cx43), a ubiquitous gap junction protein, has been demonstrated to regulate intracellular Ca2+ homeostasis. Here we explored whether macrophage Cx43 affects the obesity process by regulating the polarization of macrophage. HFD treatment induced obesity and exacerbated macrophages infiltration with upregulation of macrophages Cx43. Macrophage-specific knockout of Cx43 reduced HFD-induced obesity by alleviating inflammation in adipose tissue, with less pro-inflammatory M1 macrophage infiltration. Consistently, inhibition or knockdown of Cx43 improved palmitic acid (PA) induced mitochondrial dysfunction, as indicated by improved oxidative phosphorylation (OXPHOS), reduced formation of mitochondria-associated membranes (MAM) and mitochondrial Ca2+ overload. Mechanistically, Cx43 interacted with the mitochondrial Ca2+ uniporter (MCU) and knockdown of Cx43 alleviated PA-induced succinate dehydrogenase (SDH) oxidation by lowering MCU-mediated mitochondrial Ca2+ uptake, which then, promoting the polarization of pro-inflammatory M1 macrophages. Thus, this study identified Cx43 as a mitochondrial Ca2+ regulator that aggravates obesity via promoting macrophages polarized to M1 pro-inflammatory phenotype and suggests that Cx43 might be a promising therapeutic target antagonizing obesity.

Keywords:  Cx43; Inflammation; Macrophage polarization; Mitochondrial Ca(2+) overload; Obesity

DOI:  https://doi.org/10.1016/j.cellsig.2023.110606
Nat Commun. 2023 Jan 25. 14(1): 399

Polyamine metabolism impacts T cell dysfunction in the oral mucosa of people living with HIV.

S S Mahalingam, S Jayaraman, N Bhaskaran, E Schneider, F Faddoul, A Paes da Silva, M M Lederman, R Asaad, K Adkins-Travis, L P Shriver, P Pandiyan.

Metabolic changes in immune cells contribute to both physiological and pathophysiological outcomes of immune reactions. Here, by comparing protein expression, transcriptome, and salivary metabolome profiles of uninfected and HIV+ individuals, we found perturbations of polyamine metabolism in the oral mucosa of HIV+ patients. Mechanistic studies using an in vitro human tonsil organoid infection model revealed that HIV infection of T cells also resulted in increased polyamine synthesis, which was dependent on the activities of caspase-1, IL-1β, and ornithine decarboxylase-1. HIV-1 also led to a heightened expression of polyamine synthesis intermediates including ornithine decarboxylase-1 as well as an elevated dysfunctional regulatory T cell (TregDys)/T helper 17 (Th17) cell ratios. Blockade of caspase-1 and polyamine synthesis intermediates reversed the TregDys phenotype showing the direct role of polyamine pathway in altering T cell functions during HIV-1 infection. Lastly, oral mucosal TregDys/Th17 ratios and CD4 hyperactivation positively correlated with salivary putrescine levels, which were found to be elevated in the saliva of HIV+ patients. Thus, by revealing the role of aberrantly increased polyamine synthesis during HIV infection, our study unveils a mechanism by which chronic viral infections could drive distinct T cell effector programs and Treg dysfunction.

DOI: https://doi.org/10.1038/s41467-023-36163-2
Cell Death Dis. 2023 Jan 26. 14(1): 62

MicroRNA miR-1275 coordinately regulates AEA/LPA signals via targeting FAAH in lipid metabolism reprogramming of gastric cancer.

Qian Yang, Shan Kong, Jiajia Yu, Yanhua Xu, Mei Tao, Shuo Ma, Chenxue Tang, Xianjuan Shen, Zhiyuan Tang, Shaoqing Ju.

Glycerophospholipid signal and fatty acid metabolism are closely related to the occurrence and progression of tumours, and metabolic reprogramming caused by hydrolytic enzymes plays an important role in gastric cancer (GC). Here, we performed whole transcriptome sequencing and combined qRT-PCR to screen out the significantly high expression of fatty acid amide hydrolase (FAAH) in GC tissues, which was further verified in both TCGA and Oncomine databases. Functional tests confirmed that FAAH played an oncogene role in GC, and silencing FAAH could delay tumour growth, inhibit tumour metastasis, and promote cell apoptosis both in vitro and in vivo. FAAH-mediated lipid metabolism reprogramming through coordinated regulation of arachidonoyl ethanolamide (AEA)/lysophosphatidic acid (LPA) signalling and activated the cyclooxygenase-2 (COX-2)/prostaglandin E2 (PGE2) axis to promote GC progression. Luciferase reporter assay and immunofluorescence-fluorescence in situ hybridization (IF-FISH) were applied to validate the interactions of miR-1275/FAAH. Overexpression and knockdown of miR-1275 in vitro could indirectly modulate the above lipid signalling by targeting FAAH, thereby affecting GC progression. Our study indicates that deregulated FAAH is a key lipid signal and the miR-1275/FAAH/AEA/LPA axis can serve as a diagnostic biomarker for GC or as a target for therapy development.

DOI: https://doi.org/10.1038/s41419-023-05584-8
BMC Complement Med Ther. 2023 Jan 21. 23(1): 18

Cellular responses to 8-methyl nonanoic acid, a degradation by-product of dihydrocapsaicin, in 3T3-L1 adipocytes.

Uthai Wichai, Ploychanok Keawsomnuk, Saowarose Thongin, Chaiyot Mukthung, Chatchai Boonthip, Pattama Pittayakhajonwut, Pimonrat Ketsawatsomkron, Nuntavan Bunyapraphatsara, Kenjiro Muta.

  BACKGROUND: Capsaicinoids, such as dihydrocapsaicin (DHC), exert the health-promoting effects of chili peppers on energy metabolism. The metabolic responses to capsaicinoids are primarily mediated through transient receptor potential cation channel subfamily V member 1 (TRPV1). However, the varying contributions of their metabolites to beneficial health outcomes remain unclear. 8-methyl nonanoic acid (8-MNA), a methyl-branched medium chain fatty acid (MCFA), is an in vivo degradation by-product of DHC. Since MCFAs have emerged as metabolic modulators in adipocytes, here we examined various cellular responses to 8-MNA in 3T3-L1 adipocytes.METHODS: The viability of 3T3-L1 adipocytes exposed to various concentrations of 8-MNA was assessed by the Calcein AM assay. Biochemical assays for lipid accumulation, AMP-activated protein kinase (AMPK) activity, lipolysis and glucose uptake were performed in 3T3-L1 adipocytes treated with 8-MNA during 48-h nutrient starvation or 5-day maturation.
RESULTS: 8-MNA caused no impact on cell viability. During nutrient starvation, 8-MNA decreased lipid amounts in association with AMPK activation, a molecular event that suppresses lipogenic processes. Moreover, 3T3-L1 adipocytes that were treated with 8-MNA during 5-day maturation exhibited a reduced lipolytic response to isoproterenol and an increased glucose uptake when stimulated with insulin.
CONCLUSIONS: These results suggest that 8-MNA derived from DHC modulates energy metabolism in adipocytes and also support the idea that the metabolic benefits of chili consumption are partly attributable to 8-MNA.

Keywords:  8-methyl nonanoic acid; Adipocytes; Capsaicinoids; Metabolic function

DOI:  https://doi.org/10.1186/s12906-023-03844-w
Redox Biol. 2023 Jan 18. pii: S2213-2317(23)00014-9. [Epub ahead of print]60 102613

Mitochondrial NAD kinase in health and disease.

Ren Zhang, Kezhong Zhang.

  Nicotinamide adenine dinucleotide phosphate (NADP), a co-enzyme and an electron carrier, plays crucial roles in numerous biological functions, including cellular metabolism and antioxidation. Because NADP is subcellular-membrane impermeable, eukaryotes compartmentalize NAD kinases (NADKs), the NADP biosynthetic enzymes. Mitochondria are fundamental organelles for energy production through oxidative phosphorylation. Ten years after the discovery of the mitochondrial NADK (known as MNADK or NADK2), a significant amount of knowledge has been obtained regarding its functions, mechanism of action, human biology, mouse models, crystal structures, and post-translation modifications. NADK2 phosphorylates NAD(H) to generate mitochondrial NADP(H). NADK2-deficient patients suffered from hyperlysinemia, elevated plasma C10:2-carnitine (due to the inactivity of relevant NADP-dependent enzymes), and neuronal development defects. Nadk2-deficient mice recapitulate key features of NADK2-deficient patients, including metabolic and neuronal abnormalities. Crystal structures of human NADK2 show a dimer, with the NADP+-binding site located at the dimer interface. NADK2 activity is highly regulated by post-translational modifications, including S188 phosphorylation, K76 and K304 acetylation, and C193 S-nitrosylation; mutations in each site affect NADK2 activity and function. In mice, hepatic Nadk2 functions as a major metabolic regulator upon increased energy demands by regulating sirtuin 3 activity and fatty acid oxidation. Hopefully, future research on NADK2 will not only elucidate its functional roles in health and disease but will also pave the way for novel therapeutics for both rare and common diseases, including NADK2 deficiency and metabolic syndrome.

Keywords:  Antioxidation; MNADK; Mitochondria; NAD; NADK; NADK2; NADP

DOI:  https://doi.org/10.1016/j.redox.2023.102613
Elife. 2023 Jan 25. pii: e83534. [Epub ahead of print]12

A concerted mechanism involving ACAT and SREBPs by which oxysterols deplete accessible cholesterol to restrict microbial infection.

David B Heisler, Kristen A Johnson, Duo H Ma, Maikke B Ohlson, Lishu Zhang, Michelle Tran, Chase D Corley, Michael E Abrams, Jeffrey G McDonald, John W Schoggins, Neal M Alto, Arun Radhakrishnan.

  Most of the cholesterol in the plasma membranes (PMs) of animal cells is sequestered through interactions with phospholipids and transmembrane domains of proteins. However, as cholesterol concentration rises above the PM's sequestration capacity, a new pool of cholesterol, called accessible cholesterol, emerges. The transport of accessible cholesterol between the PM and the endoplasmic reticulum (ER) is critical to maintain cholesterol homeostasis. This pathway has also been implicated in the suppression of both bacterial and viral pathogens by immunomodulatory oxysterols. Here, we describe a mechanism of depletion of accessible cholesterol from PMs by the oxysterol 25-hydroxycholesterol (25HC). We show that 25HC-mediated activation of acyl coenzyme A: cholesterol acyltransferase (ACAT) in the ER creates an imbalance in the equilibrium distribution of accessible cholesterol between the ER and PM. This imbalance triggers the rapid internalization of accessible cholesterol from the PM, which is sustained for long periods of time through 25HC-mediated suppression of SREBPs and continued activation of ACAT. In support of a physiological role for this mechanism, 25HC failed to suppress Zika virus and human coronavirus infection in ACAT-deficient cells, and Listeria monocytogenes infection in ACAT-deficient cells and mice. We propose that selective depletion of accessible PM cholesterol triggered by ACAT activation and sustained through SREBP suppression underpins the immunological activities of 25HC and a functionally related class of oxysterols.

Keywords:  cell biology; mouse; viruses

DOI:  https://doi.org/10.7554/eLife.83534
J Biol Chem. 2023 Jan 23. pii: S0021-9258(23)00073-X. [Epub ahead of print] 102941

Multiple oxidative post-translational modifications of human glutamine synthetase mediate peroxynitrite-dependent enzyme inactivation and aggregation.

Nicolás Campolo, Mauricio Mastrogiovanni, Michele Mariotti, Federico M Issoglio, Darío Estrin, Per Hägglund, Tilman Grune, Michael J Davies, Silvina Bartesaghi, Rafael Radi.

  Glutamine synthetase (GS), which catalyzes the ATP-dependent synthesis of L-glutamine from L-glutamate and ammonia, is a ubiquitous and conserved enzyme that plays a pivotal role in nitrogen metabolism across all life domains. In vertebrates, GS is highly expressed in astrocytes, where its activity sustains the glutamate-glutamine cycle at glutamatergic synapses and is thus essential for maintaining brain homeostasis. In fact, decreased GS levels or activity have been associated with neurodegenerative diseases, with these alterations attributed to oxidative post-translational modifications of the protein, in particular tyrosine nitration. In this study, we expressed and purified human GS (HsGS) and performed an in-depth analysis of its oxidative inactivation by peroxynitrite (ONOO-) in vitro. We found that ONOO- exposure led to a dose-dependent loss of HsGS activity, the oxidation of cysteine, methionine and tyrosine residues and also the nitration of tryptophan and tyrosine residues. Peptide mapping by LC-MS/MS through combined H216O/H218O trypsin digestion identified up to 10 tyrosine nitration sites and five types of dityrosine cross-links; these modifications were further scrutinized by structural analysis. Tyrosine residues 171, 185, 269, 283 and 336 were the main nitration targets; however, tyrosine-to-phenylalanine HsGS mutants revealed that their sole nitration was not responsible for enzyme inactivation. In addition, we observed that ONOO- induced HsGS aggregation and activity loss. Thiol oxidation was a key modification to elicit aggregation, as it was also induced by hydrogen peroxide treatment. Taken together, our results indicate that multiple oxidative events at various sites are responsible for the inactivation and aggregation of human GS.

Keywords:  aggregation; dityrosine; free radicals; glutamine synthetase; hydrogen peroxide; nitrotyrosine; oxidants; peroxynitrite; thiol oxidation

DOI:  https://doi.org/10.1016/j.jbc.2023.102941
Cell Death Dis. 2023 Jan 23. 14(1): 54

The mitochondrial inhibitor IF1 binds to the ATP synthase OSCP subunit and protects cancer cells from apoptosis.

Chiara Galber, Simone Fabbian, Cristina Gatto, Martina Grandi, Stefania Carissimi, Manuel Jesus Acosta, Gianluca Sgarbi, Natascia Tiso, Francesco Argenton, Giancarlo Solaini, Alessandra Baracca, Massimo Bellanda, Valentina Giorgio.

The mitochondrial protein IF1 binds to the catalytic domain of the ATP synthase and inhibits ATP hydrolysis in ischemic tissues. Moreover, IF1 is overexpressed in many tumors and has been shown to act as a pro-oncogenic protein, although its mechanism of action is still debated. Here, we show that ATP5IF1 gene disruption in HeLa cells decreases colony formation in soft agar and tumor mass development in xenografts, underlining the role of IF1 in cancer. Notably, the lack of IF1 does not affect proliferation or oligomycin-sensitive mitochondrial respiration, but it sensitizes the cells to the opening of the permeability transition pore (PTP). Immunoprecipitation and proximity ligation analysis show that IF1 binds to the ATP synthase OSCP subunit in HeLa cells under oxidative phosphorylation conditions. The IF1-OSCP interaction is confirmed by NMR spectroscopy analysis of the recombinant soluble proteins. Overall, our results suggest that the IF1-OSCP interaction protects cancer cells from PTP-dependent apoptosis under normoxic conditions.

DOI: https://doi.org/10.1038/s41419-023-05572-y
Front Oncol. 2022 ;12 1072739

The promise of targeting heme and mitochondrial respiration in normalizing tumor microenvironment and potentiating immunotherapy.

Zakia Akter, Narges Salamat, Md Yousuf Ali, Li Zhang.

  Cancer immunotherapy shows durable treatment responses and therapeutic benefits compared to other cancer treatment modalities, but many cancer patients display primary and acquired resistance to immunotherapeutics. Immunosuppressive tumor microenvironment (TME) is a major barrier to cancer immunotherapy. Notably, cancer cells depend on high mitochondrial bioenergetics accompanied with the supply of heme for their growth, proliferation, progression, and metastasis. This excessive mitochondrial respiration increases tumor cells oxygen consumption, which triggers hypoxia and irregular blood vessels formation in various regions of TME, resulting in an immunosuppressive TME, evasion of anti-tumor immunity, and resistance to immunotherapeutic agents. In this review, we discuss the role of heme, heme catabolism, and mitochondrial respiration on mediating immunosuppressive TME by promoting hypoxia, angiogenesis, and leaky tumor vasculature. Moreover, we discuss the therapeutic prospects of targeting heme and mitochondrial respiration in alleviating tumor hypoxia, normalizing tumor vasculature, and TME to restore anti-tumor immunity and resensitize cancer cells to immunotherapy.

Keywords:  angiogenesis; cancer immunotherapy; heme; hypoxia; mitochondrial respiration; tumor micoenvironment

DOI:  https://doi.org/10.3389/fonc.2022.1072739
J Exp Med. 2023 Apr 03. pii: e20222173. [Epub ahead of print]220(4):

Tingible body macrophages arise from lymph node-resident precursors and uptake B cells by dendrites.

Neta Gurwicz, Liat Stoler-Barak, Niklas Schwan, Arnab Bandyopadhyay, Michael Meyer-Hermann, Ziv Shulman.

Antibody affinity maturation depends on the formation of germinal centers (GCs) in lymph nodes. This process generates a massive number of apoptotic B cells, which are removed by a specialized subset of phagocytes, known as tingible body macrophages (TBMs). Although defects in these cells are associated with pathological conditions, the identity of their precursors and the dynamics of dying GC B cell disposal remained unknown. Here, we demonstrate that TBMs originate from pre-existing lymph node-resident precursors that enter the lymph node follicles in a GC-dependent manner. Intravital imaging shows that TBMs are stationary cells that selectively phagocytose GC B cells via highly dynamic protrusions and accommodate the final stages of B cell apoptosis. Cell-specific depletion and chimeric mouse models revealed that GC B cells drive TBM formation from bone marrow-derived precursors stationed within lymphoid organs prior to the immune challenge. Understanding TBM dynamics and function may explain the emergence of various antibody-mediated autoimmune conditions.

DOI: https://doi.org/10.1084/jem.20222173
Life Sci Alliance. 2023 Apr;pii: e202201535. [Epub ahead of print]6(4):

Lung macrophages utilize unique cathepsin K-dependent phagosomal machinery to degrade intracellular collagen.

Ivo Fabrik, Orsolya Bilkei-Gorzo, Maria Öberg, Daniela Fabrikova, Johannes Fuchs, Carina Sihlbom, Melker Göransson, Anetta Härtlova.

Resident tissue macrophages are organ-specialized phagocytes responsible for the maintenance and protection of tissue homeostasis. It is well established that tissue diversity is reflected by the heterogeneity of resident tissue macrophage origin and phenotype. However, much less is known about tissue-specific phagocytic and proteolytic macrophage functions. Here, using a quantitative proteomics approach, we identify cathepsins as key determinants of phagosome maturation in primary peritoneum-, lung-, and brain-resident macrophages. The data further uncover cathepsin K (CtsK) as a molecular marker for lung phagosomes required for intracellular protein and collagen degradation. Pharmacological blockade of CtsK activity diminished phagosomal proteolysis and collagenolysis in lung-resident macrophages. Furthermore, profibrotic TGF-β negatively regulated CtsK-mediated phagosomal collagen degradation independently from classical endocytic-proteolytic pathways. In humans, phagosomal CtsK activity was reduced in COPD lung macrophages and non-COPD lung macrophages exposed to cigarette smoke extract. Taken together, this study provides a comprehensive map of how peritoneal, lung, and brain tissue environment shapes phagosomal composition, revealing CtsK as a key molecular determinant of lung phagosomes contributing to phagocytic collagen clearance in lungs.

DOI: https://doi.org/10.26508/lsa.202201535
J Biol Chem. 2023 Jan 23. pii: S0021-9258(23)00071-6. [Epub ahead of print] 102939

Mass spectrometry imaging-based assays for aminotransferase activity reveal a broad substrate spectrum for a previously uncharacterized enzyme.

Markus de Raad, Kaan Koper, Kai Deng, Benjamin P Bowen, Hiroshi A Maeda, Trent R Northen.

  Aminotransferases (ATs) catalyze pyridoxal 5'-phosphate (PLP)-dependent transamination reactions between amino donor and keto acceptor substrates and play central roles in nitrogen metabolism of all organisms. ATs are involved in biosynthesis and degradation of both proteinogenic and non-proteinogenic amino acids, and also carry out a wide variety of functions in photorespiration, detoxification, and secondary metabolism. Despite the importance of ATs, their functionality is poorly understood as only a small fraction of putative ATs, predicted from DNA sequences, are associated with experimental data. Even for characterized ATs, the full spectrum of substrate specificity, among many potential substrates, has not been explored in most cases. This is largely due to the lack of suitable high-throughput assays that can screen for AT activity and specificity at scale. Here we present a new high-throughput platform for screening AT activity using bioconjugate chemistry and mass spectrometry imaging (MSI)-based analysis. Detection of AT reaction products is achieved by forming an oxime linkage between ketone groups of transaminated amino donors and a probe molecule that facilitates mass spectrometry-based analysis using nanostructure-initiator mass spectrometry (NIMS) or MALDI-MS. As a proof-of-principle, we applied the newly established method and found that a previously uncharacterized Arabidopsis thaliana tryptophan aminotransferase-related protein 1 (TAR1) is a highly promiscuous enzyme that can utilize 13 amino acid donors and 3 keto acid acceptors. These results demonstrate that this oxime-MSI AT assay enables high-throughput discovery and comprehensive characterization of AT enzymes leading to accurate understanding of the nitrogen metabolic network.

Keywords:  Aminotransferases; enzyme promiscuity; enzyme screening; high-throughput screening (HTS); mass spectrometry (MS); mass spectrometry imaging (MSI); nanostructure-initiator mass spectrometry (NIMS); pyridoxal-5'-phosphate (PLP)-dependent enzyme

DOI:  https://doi.org/10.1016/j.jbc.2023.102939
iScience. 2023 Feb 17. 26(2): 105934

Interleukin 11 confers resistance to dextran sulfate sodium-induced colitis in mice.

Takashi Nishina, Yutaka Deguchi, Mika Kawauchi, Chen Xiyu, Soh Yamazaki, Tetuo Mikami, Hiroyasu Nakano.

  Intestinal homeostasis is tightly regulated by epithelial cells, leukocytes, and stromal cells, and its dysregulation is associated with inflammatory bowel diseases. Interleukin (IL)-11, a member of the IL-6 family of cytokines, is produced by inflammatory fibroblasts during acute colitis. However, the role of IL-11 in the development of colitis is still unclear. Herein, we showed that IL-11 ameliorated DSS-induced acute colitis in mouse models. We found that deletion of Il11ra1 or Il11 rendered mice highly susceptible to DSS-induced colitis compared to the respective control mice. The number of apoptotic epithelial cells was increased in DSS-treated Il11ra1- or Il11-deficient mice. Moreover, we showed that IL-11 production was regulated by reactive oxygen species (ROS) produced by lysozyme M-positive myeloid cells. These findings indicate that fibroblast-produced IL-11 plays an important role in protecting the mucosal epithelium in acute colitis. Myeloid cell-derived ROS contribute to the attenuation of colitis through the production of IL-11.

Keywords:  Components of the immune system; Immunology; Molecular physiology

DOI:  https://doi.org/10.1016/j.isci.2023.105934
Front Physiol. 2022 ;13 1063294

Metabolic regulation of stress erythropoiesis, outstanding questions, and possible paradigms.

Baiye Ruan, Robert F Paulson.

  Steady state erythropoiesis produces new erythrocytes at a constant rate to replace the senescent cells that are removed by macrophages in the liver and spleen. However, infection and tissue damage disrupt the production of erythrocytes by steady state erythropoiesis. During these times, stress erythropoiesis is induced to compensate for the loss of erythroid output. The strategy of stress erythropoiesis is different than steady state erythropoiesis. Stress erythropoiesis generates a wave of new erythrocytes to maintain homeostasis until steady state conditions are resumed. Stress erythropoiesis relies on the rapid proliferation of immature progenitor cells that do not differentiate until the increase in serum Erythropoietin (Epo) promotes the transition to committed progenitors that enables their synchronous differentiation. Emerging evidence has revealed a central role for cell metabolism in regulating the proliferation and differentiation of stress erythroid progenitors. During the initial expansion stage, the immature progenitors are supported by extensive metabolic changes which are designed to direct the use of glucose and glutamine to increase the biosynthesis of macromolecules necessary for cell growth and division. At the same time, these metabolic changes act to suppress the expression of genes involved in erythroid differentiation. In the subsequent transition stage, changes in niche signals alter progenitor metabolism which in turn removes the inhibition of erythroid differentiation generating a bolus of new erythrocytes to alleviate anemia. This review summarizes what is known about the metabolic regulation of stress erythropoiesis and discusses potential mechanisms for metabolic regulation of proliferation and differentiation.

Keywords:  anabolic metabolism; epigenetic regulation; glycolysis; stress erythropoiesis; tissue regeneration

DOI:  https://doi.org/10.3389/fphys.2022.1063294
Metabolomics. 2023 Jan 24. 19(2): 7

A metabolic readout of the urine metabolome of COVID-19 patients.

F C Marhuenda-Egea, J Narro-Serrano, M J Shalabi-Benavent, J M Álamo-Marzo, C Amador-Prous, J T Algado-Rabasa, A M Garijo-Saiz, M Marco-Escoto.

  Analysis of urine samples from COVID-19 patients by 1H NMR reveals important metabolic alterations due to SAR-CoV-2 infection. Previous studies have identified biomarkers in urine that reflect metabolic alterations in COVID-19 patients. We have used 1H NMR to better define these metabolic alterations since this technique allows us to obtain a broad profile of the metabolites present in urine. This technique offers the advantage that sample preparation is very simple and gives us very complete information on the metabolites present. To detect these alterations, we have compared urine samples from COVID-19 patients (n = 35) with healthy people (n = 18). We used unsupervised (Robust PCA) and supervised (PLS-LDA) multivariate analysis methods to evaluate the differences between the two groups: COVID-19 and healthy controls. The differences focus on a group of metabolites related to energy metabolism (glucose, ketone bodies, glycine, creatinine, and citrate) and other processes related to bacterial flora (TMAO and formic acid) and detoxification (hippuric acid). The alterations in the urinary metabolome shown in this work indicate that SARS-CoV-2 causes a metabolic change from a normal situation of glucose consumption towards a gluconeogenic situation and possible insulin resistance.

Keywords:  COVID-19; Gut microbiota; Human metabolism; Metabolomics

DOI:  https://doi.org/10.1007/s11306-023-01971-6
Nat Commun. 2023 Jan 27. 14(1): 451

Estimation and implications of the genetic architecture of fasting and non-fasting blood glucose.

Lifelines Cohort Study

The genetic regulation of post-prandial glucose levels is poorly understood. Here, we characterise the genetic architecture of blood glucose variably measured within 0 and 24 h of fasting in 368,000 European ancestry participants of the UK Biobank. We found a near-linear increase in the heritability of non-fasting glucose levels over time, which plateaus to its fasting state value after 5 h post meal (h2 = 11%; standard error: 1%). The genetic correlation between different fasting times is > 0.77, suggesting that the genetic control of glucose is largely constant across fasting durations. Accounting for heritability differences between fasting times leads to a ~16% improvement in the discovery of genetic variants associated with glucose. Newly detected variants improve the prediction of fasting glucose and type 2 diabetes in independent samples. Finally, we meta-analysed summary statistics from genome-wide association studies of random and fasting glucose (N = 518,615) and identified 156 independent SNPs explaining 3% of fasting glucose variance. Altogether, our study demonstrates the utility of random glucose measures to improve the discovery of genetic variants associated with glucose homeostasis, even in fasting conditions.

DOI: https://doi.org/10.1038/s41467-023-36013-1
Immunology. 2023 Jan 28.

Inactivation of mitochondrial pyruvate carrier promotes NLRP3 inflammasome activation and gout development via metabolic reprogramming.

Lih-Chyang Chen, Yu-Jen Chen, Hsin-An Lin, Wu-Chien Chien, Kuen-Jou Tsai, Chi-Hsiang Chung, Jui-Yang Wang, Chien-Chou Chen, Nan-Shih Liao, Chieh-Tien Shih, Yi-Ying Lin, Chi-Ning Huang, David M Ojcius, Kuo-Yang Huang, Hsin-Chung Lin.

  The NLRP3 inflammasome plays a crucial role in innate immunity and is involved in the pathogenesis of autoinflammatory diseases. Glycolysis regulates NLRP3 inflammasome activation in macrophages. However, how lactic acid fermentation and pyruvate oxidation controlled by the mitochondrial pyruvate carrier (MPC) affect NLRP3 inflammasome activation and autoinflammatory disease remains elusive. We found that inactivation of MPC with genetic depletion or pharmacological inhibitors, MSDC-0160 or pioglitazone, increased NLRP3 inflammasome activation and IL-1β secretion in macrophages. Glycolytic reprogramming induced by MPC inhibition skewed mitochondrial ATP-associated oxygen consumption into cytosolic lactate production, which enhanced NLRP3 inflammasome activation in response to monosodium urate (MSU) crystals. As pioglitazone is an insulin sensitizer used for diabetes, its MPC inhibitory effect in diabetic individuals was investigated. The results showed that MPC inhibition exacerbated MSU-induced peritonitis in diabetic mice and increased the risk of gout in patients with diabetes. Altogether, we found that glycolysis controlled by MPC regulated NLRP3 inflammasome activation and gout development. Accordingly, prescriptions for medications targeting MPC should consider the increased risk of NLRP3-related autoinflammatory diseases. This article is protected by copyright. All rights reserved.

Keywords:  Gout; Mitochondrial pyruvate carrier; NLRP3 inflammasome; Pioglitazone

DOI:  https://doi.org/10.1111/imm.13628
Proc Natl Acad Sci U S A. 2023 Jan 31. 120(5): e2204427120

Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility.

Luke Olsen, Michaella Levy, J Kyle Medley, Huzaifa Hassan, Brandon Miller, Richard Alexander, Emma Wilcock, Kexi Yi, Laurence Florens, Kyle Weaver, Sean A McKinney, Robert Peuß, Jenna Persons, Alexander Kenzior, Ernesto Maldonado, Kym Delventhal, Andrew Gluesenkamp, Edward Mager, David Coughlin, Nicolas Rohner.

  Physical inactivity is a scourge to human health, promoting metabolic disease and muscle wasting. Interestingly, multiple ecological niches have relaxed investment into physical activity, providing an evolutionary perspective into the effect of adaptive physical inactivity on tissue homeostasis. One such example, the Mexican cavefish Astyanax mexicanus, has lost moderate-to-vigorous activity following cave colonization, reaching basal swim speeds ~3.7-fold slower than their river-dwelling counterpart. This change in behavior is accompanied by a marked shift in body composition, decreasing total muscle mass and increasing fat mass. This shift persisted at the single muscle fiber level via increased lipid and sugar accumulation at the expense of myofibrillar volume. Transcriptomic analysis of laboratory-reared and wild-caught cavefish indicated that this shift is driven by increased expression of pparγ-the master regulator of adipogenesis-with a simultaneous decrease in fast myosin heavy chain expression. Ex vivo and in vivo analysis confirmed that these investment strategies come with a functional trade-off, decreasing cavefish muscle fiber shortening velocity, time to maximal force, and ultimately maximal swimming speed. Despite this, cavefish displayed a striking degree of muscular endurance, reaching maximal swim speeds ~3.5-fold faster than their basal swim speeds. Multi-omic analysis suggested metabolic reprogramming, specifically phosphorylation of Pgm1-Threonine 19, as a key component enhancing cavefish glycogen metabolism and sustained muscle contraction. Collectively, we reveal broad skeletal muscle changes following cave colonization, displaying an adaptive skeletal muscle phenotype reminiscent to mammalian disuse and high-fat models while simultaneously maintaining a unique capacity for sustained muscle contraction via enhanced glycogen metabolism.

Keywords:  evolutionary physiology; physical activity; skeletal muscle metabolism

DOI:  https://doi.org/10.1073/pnas.2204427120
Front Endocrinol (Lausanne). 2022 ;13 993081

Applications of spatially resolved omics in the field of endocrine tumors.

Yinuo Hou, Yan Gao, Shudi Guo, Zhibin Zhang, Ruibing Chen, Xiangyang Zhang.

  Endocrine tumors derive from endocrine cells with high heterogeneity in function, structure and embryology, and are characteristic of a marked diversity and tissue heterogeneity. There are still challenges in analyzing the molecular alternations within the heterogeneous microenvironment for endocrine tumors. Recently, several proteomic, lipidomic and metabolomic platforms have been applied to the analysis of endocrine tumors to explore the cellular and molecular mechanisms of tumor genesis, progression and metastasis. In this review, we provide a comprehensive overview of spatially resolved proteomics, lipidomics and metabolomics guided by mass spectrometry imaging and spatially resolved microproteomics directed by microextraction and tandem mass spectrometry. In this regard, we will discuss different mass spectrometry imaging techniques, including secondary ion mass spectrometry, matrix-assisted laser desorption/ionization and desorption electrospray ionization. Additionally, we will highlight microextraction approaches such as laser capture microdissection and liquid microjunction extraction. With these methods, proteins can be extracted precisely from specific regions of the endocrine tumor. Finally, we compare applications of proteomic, lipidomic and metabolomic platforms in the field of endocrine tumors and outline their potentials in elucidating cellular and molecular processes involved in endocrine tumors.

Keywords:  endocrine tumors; liquid chromatography-mass spectrometry; mass spectrometry imaging; microextraction; multi-omics; spatially resolved microproteomics

DOI:  https://doi.org/10.3389/fendo.2022.993081
Science. 2023 Jan 27. eabn4705

Mitochondria metabolism sets the species-specific tempo of neuronal development.

Ryohei Iwata, Pierre Casimir, Emir Erkol, Leïla Boubakar, Mélanie Planque, Isabel M Gallego López, Martyna Ditkowska, Vaiva Gaspariunaite, Sofie Beckers, Daan Remans, Katlijn Vints, Anke Vandekeere, Suresh Poovathingal, Matthew Bird, Nikky Corthout, Pieter Vermeersch, Sébastien Carpentier, Kristofer Davie, Massimiliano Mazzone, Natalia V Gounko, Stein Aerts, Bart Ghesquière, Sarah-Maria Fendt, Pierre Vanderhaeghen.

Neuronal development in the human cerebral cortex is considerably prolonged compared to that of other mammals. We explored whether mitochondria influence the species-specific timing of cortical neuron maturation. By comparing human and mouse cortical neuronal maturation at high temporal and cell resolution, we found a slower mitochondria development in human cortical neurons compared with that in the mouse, together with lower mitochondria metabolic activity, particularly that of oxidative phosphorylation. Stimulation of mitochondria metabolism in human neurons resulted in accelerated development in vitro and in vivo, leading to maturation of cells weeks ahead of time, whereas its inhibition in mouse neurons led to decreased rates of maturation. Mitochondria are thus important regulators of the pace of neuronal development underlying human-specific brain neoteny.

DOI: https://doi.org/10.1126/science.abn4705
Sci Rep. 2023 Jan 27. 13(1): 1483

ACSS2-mediated NF-κB activation promotes alkaliptosis in human pancreatic cancer cells.

Dongwen Que, Feimei Kuang, Rui Kang, Daolin Tang, Jiao Liu.

Alkaliptosis is a recently discovered type of pH-dependent cell death used for tumor therapy. However, its underlying molecular mechanisms and regulatory networks are largely unknown. Here, we report that the acetate-activating enzyme acetyl-CoA short-chain synthase family member 2 (ACSS2) is a positive regulator of alkaliptosis in human pancreatic ductal adenocarcinoma (PDAC) cells. Using qPCR and western blot analysis, we found that the mRNA and protein expression of ACSS2 was upregulated in human PDAC cell lines (PANC1 and MiaPaCa2) in response to the classic alkaliptosis activator JTC801. Consequently, the knockdown of ACSS2 by shRNAs inhibited JTC801-induced cell death in PDAC cells, and was accompanied by an increase in cell clone formation and a decrease in intracellular pH. Mechanically, ACSS2-mediated acetyl-coenzyme A production and subsequent histone acetylation contributed to NF-κB-dependent CA9 downregulation, and this effect was enhanced by the histone deacetylase inhibitor trichostatin A. These findings may provide new insights for understanding the metabolic basis of alkaliptosis and establish a potential strategy for PDAC treatment.

DOI: https://doi.org/10.1038/s41598-023-28261-4
Nature. 2023 Jan 25.

Amino acid slows nerve damage from diabetes, in mouse study.

Nick Petrić Howe, Shamini Bundell.



Keywords:  Astronomical instrumentation; Metabolism; Publishing

DOI:  https://doi.org/10.1038/d41586-023-00213-y
iScience. 2023 Jan 20. 26(1): 105905

Diet-induced gut dysbiosis and inflammation: Key drivers of obesity-driven NASH.

Gideon G Kang, Natalie L Trevaskis, Andrew J Murphy, Mark A Febbraio.

  Sucrose, the primary circulating sugar in plants, contains equal amounts of fructose and glucose. The latter is the predominant circulating sugar in animals and thus the primary fuel source for various tissue and cell types in the body. Chronic excessive energy intake has, however, emerged as a major driver of obesity and associated pathologies including nonalcoholic fatty liver diseases (NAFLD) and the more severe nonalcoholic steatohepatitis (NASH). Consumption of a high-caloric, western-style diet induces gut dysbiosis and inflammation resulting in leaky gut. Translocation of gut-derived bacterial content promotes hepatic inflammation and ER stress, and when either or both of these are combined with steatosis, it can cause NASH. Here, we review the metabolic links between diet-induced changes in the gut and NASH. Furthermore, therapeutic interventions for the treatment of obesity and liver metabolic diseases are also discussed with a focus on restoring the gut-liver axis.

Keywords:  Biological sciences; Hepatology; Human metabolism; Immunology; Physiology

DOI:  https://doi.org/10.1016/j.isci.2022.105905
Science. 2023 Jan 27. 379(6630): 351-357

Structural basis of mammalian respiratory complex I inhibition by medicinal biguanides.

Hannah R Bridges, James N Blaza, Zhan Yin, Injae Chung, Michael N Pollak, Judy Hirst.

The molecular mode of action of biguanides, including the drug metformin, which is widely used in the treatment of diabetes, is incompletely characterized. Here, we define the inhibitory drug-target interaction(s) of a model biguanide with mammalian respiratory complex I by combining cryo-electron microscopy and enzyme kinetics. We interpret these data to explain the selectivity of biguanide binding to different enzyme states. The primary inhibitory site is in an amphipathic region of the quinone-binding channel, and an additional binding site is in a pocket on the intermembrane-space side of the enzyme. An independent local chaotropic interaction, not previously described for any drug, displaces a portion of a key helix in the membrane domain. Our data provide a structural basis for biguanide action and enable the rational design of medicinal biguanides.

DOI: https://doi.org/10.1126/science.ade3332
Cancer Lett. 2023 Jan 20. pii: S0304-3835(23)00025-3. [Epub ahead of print]556 216074

Pericytes in the tumor microenvironment.

Zhongyi Jiang, Jing Zhou, Luohong Li, Shan Liao, Junyu He, Shubo Zhou, Yanhong Zhou.

  Pericytes are a type of mural cell located between the endothelial cells of capillaries and the basement membrane, which function to regulate the capillary vasomotor and maintain normal microcirculation of local tissues and organs and have been identified as a significant component in the tumor microenvironment (TME). Pericytes have various interactions with different components of the TME, such as constituting the pre-metastatic niche, promoting the growth of cancer cells and drug resistance through paracrine activity, and inducing M2 macrophage polarization. While changes in the TME can affect the number, phenotype, and molecular markers of pericytes. For example, pericyte detachment from endothelial cells in the TME facilitates tumor cells in situ to invade the circulating blood and is beneficial to local capillary basement membrane enzymatic hydrolysis and endothelial cell proliferation and budding, which contribute to tumor angiogenesis and metastasis. In this review, we discuss the emerging role of pericytes in the TME, and tumor treatment related to pericytes. This review aimed to provide a more comprehensive understanding of the function of pericytes and the relationship between pericytes and tumors and to provide ideas for the treatment and prevention of malignant tumors.

Keywords:  Epithelial-mesenchymal transition; Pericytes; Tumor microenvironment; Tumor therapy; Tumor-associated macrophages

DOI:  https://doi.org/10.1016/j.canlet.2023.216074
Mol Syst Biol. 2023 Jan 27. e11099

One-shot 13 C15 N-metabolic flux analysis for simultaneous quantification of carbon and nitrogen flux.

Khushboo Borah Slater, Martin Beyß, Ye Xu, Jim Barber, Catia Costa, Jane Newcombe, Axel Theorell, Melanie J Bailey, Dany J V Beste, Johnjoe McFadden, Katharina Nöh.

  Metabolic flux is the final output of cellular regulation and has been extensively studied for carbon but much less is known about nitrogen, which is another important building block for living organisms. For the tuberculosis pathogen, this is particularly important in informing the development of effective drugs targeting the pathogen's metabolism. Here we performed 13 C15 N dual isotopic labeling of Mycobacterium bovis BCG steady state cultures, quantified intracellular carbon and nitrogen fluxes and inferred reaction bidirectionalities. This was achieved by model scope extension and refinement, implemented in a multi-atom transition model, within the statistical framework of Bayesian model averaging (BMA). Using BMA-based 13 C15 N-metabolic flux analysis, we jointly resolve carbon and nitrogen fluxes quantitatively. We provide the first nitrogen flux distributions for amino acid and nucleotide biosynthesis in mycobacteria and establish glutamate as the central node for nitrogen metabolism. We improved resolution of the notoriously elusive anaplerotic node in central carbon metabolism and revealed possible operation modes. Our study provides a powerful and statistically rigorous platform to simultaneously infer carbon and nitrogen metabolism in any biological system.

Keywords:  Bayesian metabolic flux analysis; Mycobacterium tuberculosis; carbon metabolism; isotope labeling; nitrogen metabolism

DOI:  https://doi.org/10.15252/msb.202211099
Nat Commun. 2023 Jan 23. 14(1): 167

The transcription factor ATF3 switches cell death from apoptosis to necroptosis in hepatic steatosis in male mice.

Yuka Inaba, Emi Hashiuchi, Hitoshi Watanabe, Kumi Kimura, Yu Oshima, Kohsuke Tsuchiya, Shin Murai, Chiaki Takahashi, Michihiro Matsumoto, Shigetaka Kitajima, Yasuhiko Yamamoto, Masao Honda, Shun-Ichiro Asahara, Kim Ravnskjaer, Shin-Ichi Horike, Shuichi Kaneko, Masato Kasuga, Hiroyasu Nakano, Kenichi Harada, Hiroshi Inoue.

Hepatocellular death increases with hepatic steatosis aggravation, although its regulation remains unclear. Here we show that hepatic steatosis aggravation shifts the hepatocellular death mode from apoptosis to necroptosis, causing increased hepatocellular death. Our results reveal that the transcription factor ATF3 acts as a master regulator in this shift by inducing expression of RIPK3, a regulator of necroptosis. In severe hepatic steatosis, after partial hepatectomy, hepatic ATF3-deficient or -overexpressing mice display decreased or increased RIPK3 expression and necroptosis, respectively. In cultured hepatocytes, ATF3 changes TNFα-dependent cell death mode from apoptosis to necroptosis, as revealed by live-cell imaging. In non-alcoholic steatohepatitis (NASH) mice, hepatic ATF3 deficiency suppresses RIPK3 expression and hepatocellular death. In human NASH, hepatocellular damage is correlated with the frequency of hepatocytes expressing ATF3 or RIPK3, which overlap frequently. ATF3-dependent RIPK3 induction, causing a modal shift of hepatocellular death, can be a therapeutic target for steatosis-induced liver damage, including NASH.

DOI: https://doi.org/10.1038/s41467-023-35804-w
Nat Metab. 2023 Jan 26.

A phenome-wide comparative analysis of genetic discordance between obesity and type 2 diabetes.

Daniel E Coral, Juan Fernandez-Tajes, Neli Tsereteli, Hugo Pomares-Millan, Hugo Fitipaldi, Pascal M Mutie, Naeimeh Atabaki-Pasdar, Sebastian Kalamajski, Alaitz Poveda, Tyne W Miller-Fleming, Xue Zhong, Giuseppe N Giordano, Ewan R Pearson, Nancy J Cox, Paul W Franks.

Obesity and type 2 diabetes are causally related, yet there is considerable heterogeneity in the consequences of both conditions and the mechanisms of action are poorly defined. Here we show a genetic-driven approach defining two obesity profiles that convey highly concordant and discordant diabetogenic effects. We annotate and then compare association signals for these profiles across clinical and molecular phenotypic layers. Key differences are identified in a wide range of traits, including cardiovascular mortality, fat distribution, liver metabolism, blood pressure, specific lipid fractions and blood levels of proteins involved in extracellular matrix remodelling. We find marginal differences in abundance of Bacteroidetes and Firmicutes bacteria in the gut. Instrumental analyses reveal prominent causal roles for waist-to-hip ratio, blood pressure and cholesterol content of high-density lipoprotein particles in the development of diabetes in obesity. We prioritize 17 genes from the discordant signature that convey protection against type 2 diabetes in obesity, which may represent logical targets for precision medicine approaches.

DOI: https://doi.org/10.1038/s42255-022-00731-5