bims-mepmim 2023-06-04 papers

bims-mepmim

Biomed News

on Metabolites in pathological microenvironments and immunometabolism

Issue of 2023–06–04
34 papers selected by
Erika Mariana Palmieri, NIH/NCI Laboratory of Cancer ImmunoMetabolism

Pyruvate metabolism controls chromatin remodeling during CD4+ T cell activation.
Mitochondrial pyruvate metabolism and glutaminolysis toggle steady-state and emergency myelopoiesis.
Pancreatic tumors exhibit myeloid-driven amino acid stress and upregulate arginine biosynthesis.
Uptake of tumor-derived microparticles induces metabolic reprogramming of macrophages in the early metastatic lung.
Limiting mitochondrial plasticity by targeting DRP1 induces metabolic reprogramming and reduces breast cancer brain metastases.
Reprogramming of iron metabolism confers ferroptosis resistance in ECM-detached cells.
Targeted Lipidomics Reveals a Novel Role for Glucosylceramides in Glucose Response.
Aspartate-glutamate carrier 2 (citrin): a role in glucose and amino acid metabolism in the liver.
ALDH1L2 regulation of formate, formyl-methionine, and ROS controls cancer cell migration and metastasis.
Inflammatory and alternatively activated macrophages independently induce metaplasia but cooperatively drive pancreatic precancerous lesion growth.
Structural basis of purine nucleotide inhibition of human uncoupling protein 1.
ULK1-mediated metabolic reprogramming regulates Vps34 lipid kinase activity by its lactylation.
Lipid droplets are a metabolic vulnerability in melanoma.
NLRP12-PANoptosome activates PANoptosis and pathology in response to heme and PAMPs.
Lipid droplet-associated lncRNA LIPTER preserves cardiac lipid metabolism.
Nicotinamide N-methyltransferase sustains a core epigenetic program that promotes metastatic colonization in breast cancer.
Cellular redox homeostasis maintained by malic enzyme 2 is essential for MYC-driven T cell lymphomagenesis.
Hepatic stellate cells maintain liver homeostasis through paracrine neurotrophin-3 signaling that induces hepatocyte proliferation.
In situ tumour arrays reveal early environmental control of cancer immunity.
Tuft cells mediate commensal remodeling of the small intestinal antimicrobial landscape.
GPR116 promotes ferroptosis in sepsis-induced liver injury by suppressing system Xc-/GSH/GPX4.
Mechanism of action for small-molecule inhibitors of triacylglycerol synthesis.
Biallelic NFATC1 mutations cause an inborn error of immunity with impaired CD8+ T-cell function and perturbed glycolysis.
Integrative processing of untargeted metabolomic and lipidomic data using MultiABLER.
An unexpected pathway to polyamines in pancreatic cancer.
Liver and muscle circadian clocks cooperate to support glucose tolerance in mice.
A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes.
The G protein preference of orexin receptors is currently an unresolved issue.
Emerging field: O-GlcNAcylation in ferroptosis.
Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours.
TGFβ blockade in pancreatic cancer enhances sensitivity to combination chemotherapy.
Reporting on FH-deficient renal cell carcinoma using circulating succinylated metabolites.
Sensory ataxia and cardiac hypertrophy caused by neurovascular oxidative stress in chemogenetic transgenic mouse lines.
Multi-omic approach characterises the neuroprotective role of retromer in regulating lysosomal health.

Cell Rep. 2023 Jun 01. pii: S2211-1247(23)00594-6. [Epub ahead of print]42(6): 112583

Pyruvate metabolism controls chromatin remodeling during CD4+ T cell activation.

Enric Mocholi, Laura Russo, Keshav Gopal, Andrew G Ramstead, Sophia M Hochrein, Harmjan R Vos, Geert Geeven, Adeolu O Adegoke, Anna Hoekstra, Robert M van Es, Jose Ramos Pittol, Sebastian Vastert, Jared Rutter, Timothy Radstake, Jorg van Loosdregt, Celia Berkers, Michal Mokry, Colin C Anderson, Ryan M O'Connell, Martin Vaeth, John Ussher, Boudewijn M T Burgering, Paul J Coffer.

  Upon antigen-specific T cell receptor (TCR) engagement, human CD4+ T cells proliferate and differentiate, a process associated with rapid transcriptional changes and metabolic reprogramming. Here, we show that the generation of extramitochondrial pyruvate is an important step for acetyl-CoA production and subsequent H3K27ac-mediated remodeling of histone acetylation. Histone modification, transcriptomic, and carbon tracing analyses of pyruvate dehydrogenase (PDH)-deficient T cells show PDH-dependent acetyl-CoA generation as a rate-limiting step during T activation. Furthermore, T cell activation results in the nuclear translocation of PDH and its association with both the p300 acetyltransferase and histone H3K27ac. These data support the tight integration of metabolic and histone-modifying enzymes, allowing metabolic reprogramming to fuel CD4+ T cell activation. Targeting this pathway may provide a therapeutic approach to specifically regulate antigen-driven T cell activation.

Keywords:  CP: Metabolism; T cell; citrate; epigenetics; epigenome remodeling; glucose metabolism; glycolysis; histone acetylation; nuclear metabolism; pyruvate; pyruvate dehydrogenase

DOI:  https://doi.org/10.1016/j.celrep.2023.112583
J Exp Med. 2023 Sep 04. pii: e20221373. [Epub ahead of print]220(9):

Mitochondrial pyruvate metabolism and glutaminolysis toggle steady-state and emergency myelopoiesis.

Hannah A Pizzato, Yahui Wang, Michael J Wolfgang, Brian N Finck, Gary J Patti, Deepta Bhattacharya.

To define the metabolic requirements of hematopoiesis, we examined blood lineages in mice conditionally deficient in genes required for long-chain fatty acid oxidation (Cpt2), glutaminolysis (Gls), or mitochondrial pyruvate import (Mpc2). Genetic ablation of Cpt2 or Gls minimally impacted most blood lineages. In contrast, deletion of Mpc2 led to a sharp decline in mature myeloid cells and a slower reduction in T cells, whereas other hematopoietic lineages were unaffected. Yet MPC2-deficient monocytes and neutrophils rapidly recovered due to a transient and specific increase in myeloid progenitor proliferation. Competitive bone marrow chimera and stable isotope tracing experiments demonstrated that this proliferative burst was progenitor intrinsic and accompanied by a metabolic switch to glutaminolysis. Myeloid recovery after loss of MPC2 or cyclophosphamide treatment was delayed in the absence of GLS. Reciprocally, MPC2 was not required for myeloid recovery after cyclophosphamide treatment. Thus, mitochondrial pyruvate metabolism maintains myelopoiesis under steady-state conditions, while glutaminolysis in progenitors promotes emergency myelopoiesis.

DOI: https://doi.org/10.1084/jem.20221373
Elife. 2023 May 31. pii: e81289. [Epub ahead of print]12

Pancreatic tumors exhibit myeloid-driven amino acid stress and upregulate arginine biosynthesis.

Juan J Apiz Saab, Lindsey N Dzierozynski, Patrick B Jonker, Roya AminiTabrizi, Hardik Shah, Rosa Elena Menjivar, Andrew J Scott, Zeribe C Nwosu, Zhou Zhu, Riona N Chen, Moses Oh, Colin Sheehan, Daniel R Wahl, Marina Pasca di Magliano, Costas A Lyssiotis, Kay F Macleod, Christopher R Weber, Alexander Muir.

  Nutrient stress in the tumor microenvironment requires cancer cells to adopt adaptive metabolic programs for survival and proliferation. Therefore, knowledge of microenvironmental nutrient levels and how cancer cells cope with such nutrition is critical to understand the metabolism underpinning cancer cell biology. Previously, we performed quantitative metabolomics of the interstitial fluid (the local perfusate) of murine pancreatic ductal adenocarcinoma (PDAC) tumors to comprehensively characterize nutrient availability in the microenvironment of these tumors (M. R. Sullivan, Danai, et al., 2019). Here, we develop Tumor Interstitial Fluid Medium (TIFM), a cell culture medium that contains nutrient levels representative of the PDAC microenvironment, enabling us to study PDAC metabolism ex vivo under physiological nutrient conditions. We show that PDAC cells cultured in TIFM adopt a cellular state closer to that of PDAC cells present in tumors compared to standard culture models. Further, using the TIFM model, we found arginine biosynthesis is active in PDAC and allows PDAC cells to maintain levels of this amino acid despite microenvironmental arginine depletion. We also show that myeloid derived arginase activity is largely responsible for the low levels of arginine in PDAC tumors. Altogether, these data indicate that nutrient availability in tumors is an important determinant of cancer cell metabolism and behavior, and cell culture models that incorporate physiological nutrient availability have improved fidelity to in vivo systems and enable the discovery of novel cancer metabolic phenotypes.

Keywords:  biochemistry; cancer biology; chemical biology; human; mouse

DOI:  https://doi.org/10.7554/eLife.81289
Cell Rep. 2023 May 30. pii: S2211-1247(23)00593-4. [Epub ahead of print]42(6): 112582

Uptake of tumor-derived microparticles induces metabolic reprogramming of macrophages in the early metastatic lung.

Kelly Kersten, Ran You, Sophia Liang, Kevin M Tharp, Joshua Pollack, Valerie M Weaver, Matthew F Krummel, Mark B Headley.

  Pre-metastatic niche formation is a critical step during the metastatic spread of cancer. One way by which primary tumors prime host cells at future metastatic sites is through the shedding of tumor-derived microparticles as a consequence of vascular sheer flow. However, it remains unclear how the uptake of such particles by resident immune cells affects their phenotype and function. Here, we show that ingestion of tumor-derived microparticles by macrophages induces a rapid metabolic and phenotypic switch that is characterized by enhanced mitochondrial mass and function, increased oxidative phosphorylation, and upregulation of adhesion molecules, resulting in reduced motility in the early metastatic lung. This reprogramming event is dependent on signaling through the mTORC1, but not the mTORC2, pathway and is induced by uptake of tumor-derived microparticles. Together, these data support a mechanism by which uptake of tumor-derived microparticles induces reprogramming of macrophages to shape their fate and function in the early metastatic lung.

Keywords:  CP: Cancer; CP: Metabolism; infinity flow; lung; macrophages; metastasis

DOI:  https://doi.org/10.1016/j.celrep.2023.112582
Nat Cancer. 2023 May 29.

Limiting mitochondrial plasticity by targeting DRP1 induces metabolic reprogramming and reduces breast cancer brain metastases.

Pravat Kumar Parida, Mauricio Marquez-Palencia, Suvranil Ghosh, Nitin Khandelwal, Kangsan Kim, Vidhya Nair, Xiao-Zheng Liu, Hieu S Vu, Lauren G Zacharias, Paula I Gonzalez-Ericsson, Melinda E Sanders, Bret C Mobley, Jeffrey G McDonald, Andrew Lemoff, Yan Peng, Cheryl Lewis, Gonçalo Vale, Nils Halberg, Carlos L Arteaga, Ariella B Hanker, Ralph J DeBerardinis, Srinivas Malladi.

Disseminated tumor cells with metabolic flexibility to utilize available nutrients in distal organs persist, but the precise mechanisms that facilitate metabolic adaptations remain unclear. Here we show fragmented mitochondrial puncta in latent brain metastatic (Lat) cells enable fatty acid oxidation (FAO) to sustain cellular bioenergetics and maintain redox homeostasis. Depleting the enriched dynamin-related protein 1 (DRP1) and limiting mitochondrial plasticity in Lat cells results in increased lipid droplet accumulation, impaired FAO and attenuated metastasis. Likewise, pharmacological inhibition of DRP1 using a small-molecule brain-permeable inhibitor attenuated metastatic burden in preclinical models. In agreement with these findings, increased phospho-DRP1 expression was observed in metachronous brain metastasis compared with patient-matched primary tumors. Overall, our findings reveal the pivotal role of mitochondrial plasticity in supporting the survival of Lat cells and highlight the therapeutic potential of targeting cellular plasticity programs in combination with tumor-specific alterations to prevent metastatic recurrences.

DOI: https://doi.org/10.1038/s43018-023-00563-6
iScience. 2023 Jun 16. 26(6): 106827

Reprogramming of iron metabolism confers ferroptosis resistance in ECM-detached cells.

Jianping He, Abigail M Abikoye, Brett P McLaughlin, Ryan S Middleton, Ryan Sheldon, Russell G Jones, Zachary T Schafer.

  Cancer cells often acquire resistance to cell death programs induced by loss of integrin-mediated attachment to extracellular matrix (ECM). Given that adaptation to ECM-detached conditions can facilitate tumor progression and metastasis, there is significant interest in effective elimination of ECM-detached cancer cells. Here, we find that ECM-detached cells are remarkably resistant to the induction of ferroptosis. Although alterations in membrane lipid content are observed during ECM detachment, it is instead fundamental changes in iron metabolism that underlie resistance of ECM-detached cells to ferroptosis. More specifically, our data demonstrate that levels of free iron are low during ECM detachment because of changes in both iron uptake and iron storage. In addition, we establish that lowering the levels of ferritin sensitizes ECM-detached cells to death by ferroptosis. Taken together, our data suggest that therapeutics designed to kill cancer cells by ferroptosis may be hindered by lack of efficacy toward ECM-detached cells.

Keywords:  Cancer; Cell biology

DOI:  https://doi.org/10.1016/j.isci.2023.106827
J Lipid Res. 2023 May 26. pii: S0022-2275(23)00067-6. [Epub ahead of print] 100394

Targeted Lipidomics Reveals a Novel Role for Glucosylceramides in Glucose Response.

Mark A Xatse, Andre F C Vieira, Chloe Byrne, Carissa Perez Olsen.

  The addition of excess glucose to the diet drives a coordinated response of lipid metabolism pathways to tune the membrane composition to the altered diet. Here, we have employed targeted lipidomic approaches to quantify the specific changes in the phospholipid and sphingolipid populations that occur in elevated glucose conditions. The lipids within wildtype Caenorhabditis elegans are strikingly stable with no significant changes identified in our global mass spectrometry-based analysis. Previous work has identified ELO-5, an elongase that is critical for the synthesis of monomethyl-branched chain fatty acids (mmBCFAs), as essential for surviving elevated glucose conditions. Therefore, we performed targeted lipidomics on elo-5 RNAi-fed animals and identified several significant changes in these animals in lipid species that contain mmBCFAs as well as in species that do not contain mmBCFAs. Of particular note, we identified a specific glucosylceramide (GlcCer 17:1;O2/22:0;O) that is also significantly upregulated with glucose in wildtype animals. Furthermore, compromising the production of the glucosylceramide pool with elo-3 or cgt-3 RNAi leads to premature death in glucose-fed animals. Taken together, our lipid analysis has expanded the mechanistic understanding of metabolic rewiring with glucose feeding and has identified a new role for the GlcCer 17:1;O2/22:0;O.

Keywords:  Caenorhabditis elegans.; RNAi; elevated glucose conditions; elongase; lipid metabolism pathways; mass spectrometry; membrane composition; monomethyl-branched chain fatty acids; phospholipids; sphingolipids

DOI:  https://doi.org/10.1016/j.jlr.2023.100394
BMB Rep. 2023 May 31. pii: 5907. [Epub ahead of print]

Aspartate-glutamate carrier 2 (citrin): a role in glucose and amino acid metabolism in the liver.

Milan Holeček.

Aspartate-glutamate carrier 2 (AGC2, citrin) is a mitochondrial carrier expressed in the liver that transports aspartate from mitochondria into cytosol in exchange with glutamate. The AGC2 is the main component of malate-aspartate shuttle (MAS) that ensures indirect transport of NADH produced in cytosol during glycolysis, lactate oxidation to pyruvate, and ethanol oxidation to acetaldehyde into mitochondria. Through MAS, AGC2 is necessary for maintaining intracellular redox balance, mitochondrial respiration, and ATP synthesis. Through elevated cytosolic Ca2+ level, the AGC2 is stimulated by catecholamines and glucagon during starvation, exercise, and muscle wasting disorders. In these conditions, AGC2 increases aspartate input to the urea cycle, where aspartate is a source of one of two nitrogen atoms in the urea molecule (the next is ammonia) and a substrate for synthesis of fumarate that is gradually converted to oxaloacetate, the starting substrate for gluconeogenesis. Furthermore, aspartate is a substrate for synthesis of asparagine, nucleotides, and proteins. It is concluded that AGC2 has a fundamental role in compartmentalization of aspartate and glutamate metabolism and linking the reactions of MAS, glycolysis, gluconeogenesis, amino acid catabolism, urea cycle, protein synthesis, and cell proliferation. Targeting of AGC genes may represent a new therapeutic strategy to fight cancer.
Cell Rep. 2023 May 26. pii: S2211-1247(23)00573-9. [Epub ahead of print]42(6): 112562

ALDH1L2 regulation of formate, formyl-methionine, and ROS controls cancer cell migration and metastasis.

Marc Hennequart, Steven E Pilley, Christiaan F Labuschagne, Jack Coomes, Loic Mervant, Paul C Driscoll, Nathalie M Legrave, Younghwan Lee, Peter Kreuzaler, Benedict Macintyre, Yulia Panina, Julianna Blagih, David Stevenson, Douglas Strathdee, Deborah Schneider-Luftman, Eva Grönroos, Eric C Cheung, Mariia Yuneva, Charles Swanton, Karen H Vousden.

  Mitochondrial 10-formyltetrahydrofolate (10-formyl-THF) is utilized by three mitochondrial enzymes to produce formate for nucleotide synthesis, NADPH for antioxidant defense, and formyl-methionine (fMet) to initiate mitochondrial mRNA translation. One of these enzymes-aldehyde dehydrogenase 1 family member 2 (ALDH1L2)-produces NADPH by catabolizing 10-formyl-THF into CO2 and THF. Using breast cancer cell lines, we show that reduction of ALDH1L2 expression increases ROS levels and the production of both formate and fMet. Both depletion of ALDH1L2 and direct exposure to formate result in enhanced cancer cell migration that is dependent on the expression of the formyl-peptide receptor (FPR). In various tumor models, increased ALDH1L2 expression lowers formate and fMet accumulation and limits metastatic capacity, while human breast cancer samples show a consistent reduction of ALDH1L2 expression in metastases. Together, our data suggest that loss of ALDH1L2 can support metastatic progression by promoting formate and fMet production, resulting in enhanced FPR-dependent signaling.

Keywords:  ALDH1L2; CP: Cancer; CP: Metabolism; ROS; breast cancer; formate; formyl-methionine; metastasis; one-carbon metabolism; serine

DOI:  https://doi.org/10.1016/j.celrep.2023.112562
iScience. 2023 Jun 16. 26(6): 106820

Inflammatory and alternatively activated macrophages independently induce metaplasia but cooperatively drive pancreatic precancerous lesion growth.

Geou-Yarh Liou, Alicia K Fleming Martinez, Heike R Döppler, Ligia I Bastea, Peter Storz.

  The innate immune system has a key role in pancreatic cancer initiation, but the specific contribution of different macrophage populations is still ill-defined. While inflammatory (M1) macrophages have been shown to drive acinar-to-ductal metaplasia (ADM), a cancer initiating event, alternatively activated (M2) macrophages have been attributed to lesion growth and fibrosis. Here, we determined cytokines and chemokines secreted by both macrophage subtypes. Then, we analyzed their role in ADM initiation and lesion growth, finding that while M1 secrete TNF, CCL5, and IL-6 to drive ADM, M2 induce this dedifferentiation process via CCL2, but the effects are not additive. This is because CCL2 induces ADM by generating ROS and upregulating EGFR signaling, thus using the same mechanism as cytokines from inflammatory macrophages. Therefore, while effects on ADM are not additive between macrophage polarization types, both act synergistically on the growth of low-grade lesions by activating different MAPK pathways.

Keywords:  Cancer; Cell biology; Immunology; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2023.106820
Sci Adv. 2023 Jun 02. 9(22): eadh4251

Structural basis of purine nucleotide inhibition of human uncoupling protein 1.

Scott A Jones, Prerana Gogoi, Jonathan J Ruprecht, Martin S King, Yang Lee, Thomas Zögg, Els Pardon, Deepak Chand, Stefan Steimle, Danielle M Copeman, Camila A Cotrim, Jan Steyaert, Paul G Crichton, Vera Moiseenkova-Bell, Edmund R S Kunji.

Mitochondrial uncoupling protein 1 (UCP1) gives brown adipose tissue of mammals its specialized ability to burn calories as heat for thermoregulation. When activated by fatty acids, UCP1 catalyzes the leak of protons across the mitochondrial inner membrane, short-circuiting the mitochondrion to generate heat, bypassing ATP synthesis. In contrast, purine nucleotides bind and inhibit UCP1, regulating proton leak by a molecular mechanism that is unclear. We present the cryo-electron microscopy structure of the GTP-inhibited state of UCP1, which is consistent with its nonconducting state. The purine nucleotide cross-links the transmembrane helices of UCP1 with an extensive interaction network. Our results provide a structural basis for understanding the specificity and pH dependency of the regulatory mechanism. UCP1 has retained all of the key functional and structural features required for a mitochondrial carrier-like transport mechanism. The analysis shows that inhibitor binding prevents the conformational changes that UCP1 uses to facilitate proton leak.

DOI: https://doi.org/10.1126/sciadv.adh4251
Sci Adv. 2023 Jun 02. 9(22): eadg4993

ULK1-mediated metabolic reprogramming regulates Vps34 lipid kinase activity by its lactylation.

Mengshu Jia, Xiao Yue, Weixia Sun, Qianjun Zhou, Cheng Chang, Weihua Gong, Jian Feng, Xie Li, Ruonan Zhan, Kemin Mo, Lijuan Zhang, Yajie Qian, Yuying Sun, Aoxue Wang, Yejun Zou, Weicai Chen, Yan Li, Li Huang, Yi Yang, Yuzheng Zhao, Xiawei Cheng.

Autophagy and glycolysis are highly conserved biological processes involved in both physiological and pathological cellular programs, but the interplay between these processes is poorly understood. Here, we show that the glycolytic enzyme lactate dehydrogenase A (LDHA) is activated upon UNC-51-like kinase 1 (ULK1) activation under nutrient deprivation. Specifically, ULK1 directly interacts with LDHA, phosphorylates serine-196 when nutrients are scarce and promotes lactate production. Lactate connects autophagy and glycolysis through Vps34 lactylation (at lysine-356 and lysine-781), which is mediated by the acyltransferase KAT5/TIP60. Vps34 lactylation enhances the association of Vps34 with Beclin1, Atg14L, and UVRAG, and then increases Vps34 lipid kinase activity. Vps34 lactylation promotes autophagic flux and endolysosomal trafficking. Vps34 lactylation in skeletal muscle during intense exercise maintains muscle cell homeostasis and correlates with cancer progress by inducing cell autophagy. Together, our findings describe autophagy regulation mechanism and then integrate cell autophagy and glycolysis.

DOI: https://doi.org/10.1126/sciadv.adg4993
Nat Commun. 2023 Jun 02. 14(1): 3192

Lipid droplets are a metabolic vulnerability in melanoma.

Dianne Lumaquin-Yin, Emily Montal, Eleanor Johns, Arianna Baggiolini, Ting-Hsiang Huang, Yilun Ma, Charlotte LaPlante, Shruthy Suresh, Lorenz Studer, Richard M White.

Melanoma exhibits numerous transcriptional cell states including neural crest-like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here, we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets, the specialized organelle responsible for lipid storage. Single-cell RNA-sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake, an increased number of lipid droplets, and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients, these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle.

DOI: https://doi.org/10.1038/s41467-023-38831-9
Cell. 2023 May 29. pii: S0092-8674(23)00524-X. [Epub ahead of print]

NLRP12-PANoptosome activates PANoptosis and pathology in response to heme and PAMPs.

Balamurugan Sundaram, Nagakannan Pandian, Raghvendra Mall, Yaqiu Wang, Roman Sarkar, Hee Jin Kim, R K Subbarao Malireddi, Rajendra Karki, Laura J Janke, Peter Vogel, Thirumala-Devi Kanneganti.

  Cytosolic innate immune sensors are critical for host defense and form complexes, such as inflammasomes and PANoptosomes, that induce inflammatory cell death. The sensor NLRP12 is associated with infectious and inflammatory diseases, but its activating triggers and roles in cell death and inflammation remain unclear. Here, we discovered that NLRP12 drives inflammasome and PANoptosome activation, cell death, and inflammation in response to heme plus PAMPs or TNF. TLR2/4-mediated signaling through IRF1 induced Nlrp12 expression, which led to inflammasome formation to induce maturation of IL-1β and IL-18. The inflammasome also served as an integral component of a larger NLRP12-PANoptosome that drove inflammatory cell death through caspase-8/RIPK3. Deletion of Nlrp12 protected mice from acute kidney injury and lethality in a hemolytic model. Overall, we identified NLRP12 as an essential cytosolic sensor for heme plus PAMPs-mediated PANoptosis, inflammation, and pathology, suggesting that NLRP12 and molecules in this pathway are potential drug targets for hemolytic and inflammatory diseases.

Keywords:  DAMP; IRF1; NLRP12; PAMP; RIPK3; TLR2; TLR4; apoptosis; caspase; caspase-1; caspase-8; gasdermin; heme; hemolysis; inflammasome; inflammatory cell death; necroptosis; pyroptosis

DOI:  https://doi.org/10.1016/j.cell.2023.05.005
Nat Cell Biol. 2023 Jun 01.

Lipid droplet-associated lncRNA LIPTER preserves cardiac lipid metabolism.

Lei Han, Dayang Huang, Shiyong Wu, Sheng Liu, Cheng Wang, Yi Sheng, Xiongbin Lu, Hal E Broxmeyer, Jun Wan, Lei Yang.

Lipid droplets (LDs) are cellular organelles critical for lipid homeostasis, with intramyocyte LD accumulation implicated in metabolic disorder-associated heart diseases. Here we identify a human long non-coding RNA, Lipid-Droplet Transporter (LIPTER), essential for LD transport in human cardiomyocytes. LIPTER binds phosphatidic acid and phosphatidylinositol 4-phosphate on LD surface membranes and the MYH10 protein, connecting LDs to the MYH10-ACTIN cytoskeleton and facilitating LD transport. LIPTER and MYH10 deficiencies impair LD trafficking, mitochondrial function and survival of human induced pluripotent stem cell-derived cardiomyocytes. Conditional Myh10 deletion in mouse cardiomyocytes leads to LD accumulation, reduced fatty acid oxidation and compromised cardiac function. We identify NKX2.5 as the primary regulator of cardiomyocyte-specific LIPTER transcription. Notably, LIPTER transgenic expression mitigates cardiac lipotoxicity, preserves cardiac function and alleviates cardiomyopathies in high-fat-diet-fed and Leprdb/db mice. Our findings unveil a molecular connector role of LIPTER in intramyocyte LD transport, crucial for lipid metabolism of the human heart, and hold significant clinical implications for treating metabolic syndrome-associated heart diseases.

DOI: https://doi.org/10.1038/s41556-023-01162-4
EMBO J. 2023 Jun 01. e112559

Nicotinamide N-methyltransferase sustains a core epigenetic program that promotes metastatic colonization in breast cancer.

Joana Pinto Couto, Milica Vulin, Charly Jehanno, Marie-May Coissieux, Baptiste Hamelin, Alexander Schmidt, Robert Ivanek, Atul Sethi, Konstantin Bräutigam, Anja L Frei, Carolina Hager, Madhuri Manivannan, Jorge Gómez-Miragaya, Milan Ms Obradović, Zsuzsanna Varga, Viktor H Koelzer, Kirsten D Mertz, Mohamed Bentires-Alj.

  Metastatic colonization of distant organs accounts for over 90% of deaths related to solid cancers, yet the molecular determinants of metastasis remain poorly understood. Here, we unveil a mechanism of colonization in the aggressive basal-like subtype of breast cancer that is driven by the NAD+ metabolic enzyme nicotinamide N-methyltransferase (NNMT). We demonstrate that NNMT imprints a basal genetic program into cancer cells, enhancing their plasticity. In line, NNMT expression is associated with poor clinical outcomes in patients with breast cancer. Accordingly, ablation of NNMT dramatically suppresses metastasis formation in pre-clinical mouse models. Mechanistically, NNMT depletion results in a methyl overflow that increases histone H3K9 trimethylation (H3K9me3) and DNA methylation at the promoters of PR/SET Domain-5 (PRDM5) and extracellular matrix-related genes. PRDM5 emerged in this study as a pro-metastatic gene acting via induction of cancer-cell intrinsic transcription of collagens. Depletion of PRDM5 in tumor cells decreases COL1A1 deposition and impairs metastatic colonization of the lungs. These findings reveal a critical activity of the NNMT-PRDM5-COL1A1 axis for cancer cell plasticity and metastasis in basal-like breast cancer.

Keywords:  NNMT; breast cancer; collagen; colonization; metastasis

DOI:  https://doi.org/10.15252/embj.2022112559
Proc Natl Acad Sci U S A. 2023 Jun 06. 120(23): e2217869120

Cellular redox homeostasis maintained by malic enzyme 2 is essential for MYC-driven T cell lymphomagenesis.

Wei Li, Junjie Kou, Zhenxi Zhang, Haoyue Li, Li Li, Wenjing Du.

  T cell lymphomas (TCLs) are a group of rare and heterogeneous tumors. Although proto-oncogene MYC has an important role in driving T cell lymphomagenesis, whether MYC carries out this function remains poorly understood. Here, we show that malic enzyme 2 (ME2), one of the NADPH-producing enzymes associated with glutamine metabolism, is essential for MYC-driven T cell lymphomagenesis. We establish a CD4-Cre; Myc flox/+transgenic mouse mode, and approximately 90% of these mice develop TCL. Interestingly, knockout of Me2 in Myc transgenic mice almost completely suppresses T cell lymphomagenesis. Mechanistically, by transcriptionally up-regulating ME2, MYC maintains redox homeostasis, thereby increasing its tumorigenicity. Reciprocally, ME2 promotes MYC translation by stimulating mTORC1 activity through adjusting glutamine metabolism. Treatment with rapamycin, an inhibitor of mTORC1, blocks the development of TCL both in vitro and in vivo. Therefore, our findings identify an important role for ME2 in MYC-driven T cell lymphomagenesis and reveal that MYC-ME2 circuit may be an effective target for TCL therapy.

Keywords:  MYC; T cell lymphomas; glutamine metabolism; malic enzyme 2; redox homeostasis

DOI:  https://doi.org/10.1073/pnas.2217869120
Sci Signal. 2023 May 30. 16(787): eadf6696

Hepatic stellate cells maintain liver homeostasis through paracrine neurotrophin-3 signaling that induces hepatocyte proliferation.

Vincent Quoc-Huy Trinh, Ting-Fang Lee, Sara Lemoinne, Kevin C Ray, Maria D Ybanez, Takuma Tsuchida, James K Carter, Judith Agudo, Brian D Brown, Kemal M Akat, Scott L Friedman, Youngmin A Lee.

Organ size is maintained by the controlled proliferation of distinct cell populations. In the mouse liver, hepatocytes in the midlobular zone that are positive for cyclin D1 (CCND1) repopulate the parenchyma at a constant rate to preserve liver mass. Here, we investigated how hepatocyte proliferation is supported by hepatic stellate cells (HSCs), pericytes that are in close proximity to hepatocytes. We used T cells to ablate nearly all HSCs in the murine liver, enabling the unbiased characterization of HSC functions. In the normal liver, complete loss of HSCs persisted for up to 10 weeks and caused a gradual reduction in liver mass and in the number of CCND1+ hepatocytes. We identified neurotrophin-3 (Ntf-3) as an HSC-produced factor that induced the proliferation of midlobular hepatocytes through the activation of tropomyosin receptor kinase B (TrkB). Treating HSC-depleted mice with Ntf-3 restored CCND1+ hepatocytes in the midlobular region and increased liver mass. These findings establish that HSCs form the mitogenic niche for midlobular hepatocytes and identify Ntf-3 as a hepatocyte growth factor.

DOI: https://doi.org/10.1126/scisignal.adf6696
Nature. 2023 May 31.

In situ tumour arrays reveal early environmental control of cancer immunity.

Guadalupe Ortiz-Muñoz, Markus Brown, Catherine B Carbone, Ximo Pechuan-Jorge, Vincent Rouilly, Henrik Lindberg, Alex T Ritter, Gautham Raghupathi, Qianbo Sun, Tess Nicotra, Shreya R Mantri, Angela Yang, Jonas Doerr, Deepti Nagarkar, Spyros Darmanis, Benjamin Haley, Sanjeev Mariathasan, Yulei Wang, Carlos Gomez-Roca, Carlos Eduardo de Andrea, David Spigel, Thomas Wu, Lelia Delamarre, Johannes Schöneberg, Zora Modrusan, Richard Price, Shannon J Turley, Ira Mellman, Christine Moussion.

The immune phenotype of a tumour is a key predictor of its response to immunotherapy1-4. Patients who respond to checkpoint blockade generally present with immune-inflamed5-7 tumours that are highly infiltrated by T cells. However, not all inflamed tumours respond to therapy, and even lower response rates occur among tumours that lack T cells (immune desert) or that spatially exclude T cells to the periphery of the tumour lesion (immune excluded)8. Despite the importance of these tumour immune phenotypes in patients, little is known about their development, heterogeneity or dynamics owing to the technical difficulty of tracking these features in situ. Here we introduce skin tumour array by microporation (STAMP)-a preclinical approach that combines high-throughput time-lapse imaging with next-generation sequencing of tumour arrays. Using STAMP, we followed the development of thousands of arrayed tumours in vivo to show that tumour immune phenotypes and outcomes vary between adjacent tumours and are controlled by local factors within the tumour microenvironment. Particularly, the recruitment of T cells by fibroblasts and monocytes into the tumour core was supportive of T cell cytotoxic activity and tumour rejection. Tumour immune phenotypes were dynamic over time and an early conversion to an immune-inflamed phenotype was predictive of spontaneous or therapy-induced tumour rejection. Thus, STAMP captures the dynamic relationships of the spatial, cellular and molecular components of tumour rejection and has the potential to translate therapeutic concepts into successful clinical strategies.

DOI: https://doi.org/10.1038/s41586-023-06132-2
Proc Natl Acad Sci U S A. 2023 Jun 06. 120(23): e2216908120

Tuft cells mediate commensal remodeling of the small intestinal antimicrobial landscape.

Connie Fung, Lisa M Fraser, Gabriel M Barrón, Matthew B Gologorsky, Samantha N Atkinson, Elias R Gerrick, Michael Hayward, Jennifer Ziegelbauer, Jessica A Li, Katherine F Nico, Miles D W Tyner, Leila B DeSchepper, Amy Pan, Nita H Salzman, Michael R Howitt.

  Succinate produced by the commensal protist Tritrichomonas musculis (T. mu) stimulates chemosensory tuft cells, resulting in intestinal type 2 immunity. Tuft cells express the succinate receptor SUCNR1, yet this receptor does not mediate antihelminth immunity nor alter protist colonization. Here, we report that microbial-derived succinate increases Paneth cell numbers and profoundly alters the antimicrobial peptide (AMP) landscape in the small intestine. Succinate was sufficient to drive this epithelial remodeling, but not in mice lacking tuft cell chemosensory components required to detect this metabolite. Tuft cells respond to succinate by stimulating type 2 immunity, leading to interleukin-13-mediated epithelial and AMP expression changes. Moreover, type 2 immunity decreases the total number of mucosa-associated bacteria and alters the small intestinal microbiota composition. Finally, tuft cells can detect short-term bacterial dysbiosis that leads to a spike in luminal succinate levels and modulate AMP production in response. These findings demonstrate that a single metabolite produced by commensals can markedly shift the intestinal AMP profile and suggest that tuft cells utilize SUCNR1 and succinate sensing to modulate bacterial homeostasis.

Keywords:  Paneth cell; antimicrobial peptides; succinate; tuft cell; type 2 immunity

DOI:  https://doi.org/10.1073/pnas.2216908120
Cell Biol Toxicol. 2023 Jun 02.

GPR116 promotes ferroptosis in sepsis-induced liver injury by suppressing system Xc-/GSH/GPX4.

Ying Wang, Ting Wang, Qian Xiang, Na Li, Jun Wang, Jiahao Liu, Yan Zhang, Tao Yang, Jinjun Bian.

  The disease sepsis is caused by an infection that damages organs. Liver injury, with ferroptosis playing a key role, is an early sign of sepsis. G protein-coupled receptor 116 (GPR116) is essential in the maintenance of functional homeostasis in various systems of the body and has been proven to play a protective role in septic lung injury. However, it's role in septic liver injury remains unclear. In this study, we found that hepatic ferroptosis during sepsis was accompanied by GPR116 upregulation. Hepatocyte-specific GPR116 gene deletion can prevent hepatic ferroptosis, thereby alleviating sepsis-induced liver dysfunction and improving mouse survival, which was verified in vivo. Mechanistically, GPR116 aggravated mitochondrial damage and lipid peroxidation in hepatocytes by inhibiting system Xc-/GSH/GPX4 in overexpression experiments. In conclusion, we have identified GPR116 as a vital mediator of ferroptosis in sepsis-induced liver injury. It is thus an attractive therapeutic target in sepsis.

Keywords:  Ferroptosis; GPR116; Lipid peroxidation; Liver dysfunction; Sepsis

DOI:  https://doi.org/10.1007/s10565-023-09815-8
Nat Commun. 2023 May 29. 14(1): 3100

Mechanism of action for small-molecule inhibitors of triacylglycerol synthesis.

Xuewu Sui, Kun Wang, Kangkang Song, Chen Xu, Jiunn Song, Chia-Wei Lee, Maofu Liao, Robert V Farese, Tobias C Walther.

Inhibitors of triacylglycerol (TG) synthesis have been developed to treat metabolism-related diseases, but we know little about their mechanisms of action. Here, we report cryo-EM structures of the TG-synthesis enzyme acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1), a membrane bound O-acyltransferase (MBOAT), in complex with two different inhibitors, T863 and DGAT1IN1. Each inhibitor binds DGAT1's fatty acyl-CoA substrate binding tunnel that opens to the cytoplasmic side of the ER. T863 blocks access to the tunnel entrance, whereas DGAT1IN1 extends further into the enzyme, with an amide group interacting with more deeply buried catalytic residues. A survey of DGAT1 inhibitors revealed that this amide group may serve as a common pharmacophore for inhibition of MBOATs. The inhibitors were minimally active against the related MBOAT acyl-CoA:cholesterol acyltransferase 1 (ACAT1), yet a single-residue mutation sensitized ACAT1 for inhibition. Collectively, our studies provide a structural foundation for developing DGAT1 and other MBOAT inhibitors.

DOI: https://doi.org/10.1038/s41467-023-38934-3
Blood. 2023 May 30. pii: blood.2022018303. [Epub ahead of print]

Biallelic NFATC1 mutations cause an inborn error of immunity with impaired CD8+ T-cell function and perturbed glycolysis.

Sevgi Kostel Bal, Sarah Giuliani, Jana Block, Peter Repiscak, Christoph Hafemeister, Tala Shahin, Nurhan Kasap, Bernhard Ransmayr, Yirun Miao, Cheryl van de Wetering, Alexandra Frohne, Raul Jimenez-Heredia, Michael K Schuster, Samaneh Zoghi, Vanessa Hertlein, Marini Thian, Aleksandr Bykov, Royala Babayeva, Sevgi Bilgic Eltan, Elif Karakoc-Aydiner, Lisa E Shaw, Iftekhar Chowdury, Markku Varjosalo, Rafael Jose Argüello, Matthias Farlik, Ahmet Ozen, Edgar Albert Ernst Serfling, Loïc Dupré, Christoph Bock, Florian Halbritter, J Thomas Hannich, Irinka Castanon, Michael J Kraakman, Safa Baris, Kaan Boztug.

The NFAT family of transcription factors plays central roles in adaptive immunity in murine models, however, their contribution to human immune homeostasis remains poorly defined. In a multigenerational pedigree, we identified three patients carrying germline biallelic missense variants in NFATC1, presenting with recurrent infections, hypogammaglobulinemia and decreased antibody responses. The compound heterozygous NFATC1 variants identified in the patients caused decreased stability and reduced binding of DNA and interacting proteins. We observed defects in early activation and proliferation of T and B cells from these patients, amenable to reconstitution upon genetic rescue. Following stimulation, T-cell activation and proliferation were impaired, reaching that of healthy controls with delay indicative of an adaptive capacity of the cells. Assessment of the metabolic capacity of patient T cells, revealed that NFATc1-dysfunction rendered T cells unable to engage in glycolysis following stimulation, although oxidative metabolic processes were intact. We hypothesized that NFATc1-mutant T cells could compensate for the energy deficit due to defective glycolysis by enhanced lipid metabolism as an adaptation, leading to a delayed, but not lost activation responses. Indeed, we observed increased 13C-labelled palmitate incorporation into citrate indicating higher fatty acid oxidation and we demonstrated that metformin and rosiglitazone improved patient T-cell effector functions. Collectively, enabled by our molecular dissection of NFATC1 mutations and extending the role of NFATc1 in human immunity beyond receptor signaling, and reveal evidence of metabolic plasticity in the context of impaired glycolysis observed in patient T cells to remedy delayed effector responses.

DOI: https://doi.org/10.1182/blood.2022018303
iScience. 2023 Jun 16. 26(6): 106881

Integrative processing of untargeted metabolomic and lipidomic data using MultiABLER.

Ian C H Lee, Sergey Tumanov, Jason W H Wong, Roland Stocker, Joshua W K Ho.

  Mass spectrometry (MS)-based untargeted metabolomic and lipidomic approaches are being used increasingly in biomedical research. The adoption and integration of these data are critical to the overall multi-omic toolkit. Recently, a sample extraction method called Multi-ABLE has been developed, which enables concurrent generation of proteomic and untargeted metabolomic and lipidomic data from a small amount of tissue. The proteomics field has a well-established set of software for processing of acquired data; however, there is a lack of a unified, off-the-shelf, ready-to-use bioinformatics pipeline that can take advantage of and prepare concurrently generated metabolomic and lipidomic data for joint downstream analyses. Here we present an R pipeline called MultiABLER as a unified and simple upstream processing and analysis pipeline for both metabolomics and lipidomics datasets acquired using liquid chromatography-tandem mass spectrometry. The code is available via an open-source license at https://github.com/holab-hku/MultiABLER.

Keywords:  Biological sciences research methodologies; Biological sciences tools; Lipidomics; Metabolomics

DOI:  https://doi.org/10.1016/j.isci.2023.106881
Mol Cell. 2023 Jun 01. pii: S1097-2765(23)00368-4. [Epub ahead of print]83(11): 1765-1766

An unexpected pathway to polyamines in pancreatic cancer.

Dominik Awad, Costas A Lyssiotis.

In most adult tissues, arginine is the precursor to polyamines, poly-cationic metabolites that interact with negatively charged biomolecules like DNA. Lee et al.1 discovered that pancreatic cancers synthesize polyamines from glutamine, illuminating a new pathway and underscoring their metabolic flexibility.

DOI: https://doi.org/10.1016/j.molcel.2023.05.014
Cell Rep. 2023 Jun 01. pii: S2211-1247(23)00599-5. [Epub ahead of print]42(6): 112588

Liver and muscle circadian clocks cooperate to support glucose tolerance in mice.

Jacob G Smith, Kevin B Koronowski, Thomas Mortimer, Tomoki Sato, Carolina M Greco, Paul Petrus, Amandine Verlande, Siwei Chen, Muntaha Samad, Ekaterina Deyneka, Lavina Mathur, Ronnie Blazev, Jeffrey Molendijk, Arun Kumar, Oleg Deryagin, Mireia Vaca-Dempere, Valentina Sica, Peng Liu, Valerio Orlando, Benjamin L Parker, Pierre Baldi, Patrick-Simon Welz, Cholsoon Jang, Selma Masri, Salvador Aznar Benitah, Pura Muñoz-Cánoves, Paolo Sassone-Corsi.

  Physiology is regulated by interconnected cell and tissue circadian clocks. Disruption of the rhythms generated by the concerted activity of these clocks is associated with metabolic disease. Here we tested the interactions between clocks in two critical components of organismal metabolism, liver and skeletal muscle, by rescuing clock function either in each organ separately or in both organs simultaneously in otherwise clock-less mice. Experiments showed that individual clocks are partially sufficient for tissue glucose metabolism, yet the connections between both tissue clocks coupled to daily feeding rhythms support systemic glucose tolerance. This synergy relies in part on local transcriptional control of the glucose machinery, feeding-responsive signals such as insulin, and metabolic cycles that connect the muscle and liver. We posit that spatiotemporal mechanisms of muscle and liver play an essential role in the maintenance of systemic glucose homeostasis and that disrupting this diurnal coordination can contribute to metabolic disease.

Keywords:  Bmal1; CP: Metabolism; autonomy; circadian rhythms; endocrinology; glucose; inter-organ crosstalk; liver; metabolism; muscle; systems biology

DOI:  https://doi.org/10.1016/j.celrep.2023.112588
Nat Metab. 2023 May;5(5): 861-879

A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes.

Viktoria Glunk, Samantha Laber, Nasa Sinnott-Armstrong, Debora R Sobreira, Sophie M Strobel, Thiago M Batista, Phil Kubitz, Bahareh Nemati Moud, Hannah Ebert, Yi Huang, Beate Brandl, Garrett Garbo, Julius Honecker, David R Stirling, Nezar Abdennur, Virtu Calabuig-Navarro, Thomas Skurk, Soeren Ocvirk, Kerstin Stemmer, Beth A Cimini, Anne E Carpenter, Simon N Dankel, Cecilia M Lindgren, Hans Hauner, Marcelo A Nobrega, Melina Claussnitzer.

Recent large-scale genomic association studies found evidence for a genetic link between increased risk of type 2 diabetes and decreased risk for adiposity-related traits, reminiscent of metabolically obese normal weight (MONW) association signatures. However, the target genes and cellular mechanisms driving such MONW associations remain to be identified. Here, we systematically identify the cellular programmes of one of the top-scoring MONW risk loci, the 2q24.3 risk locus, in subcutaneous adipocytes. We identify a causal genetic variant, rs6712203, an intronic single-nucleotide polymorphism in the COBLL1 gene, which changes the conserved transcription factor motif of POU domain, class 2, transcription factor 2, and leads to differential COBLL1 gene expression by altering the enhancer activity at the locus in subcutaneous adipocytes. We then establish the cellular programme under the genetic control of the 2q24.3 MONW risk locus and the effector gene COBLL1, which is characterized by impaired actin cytoskeleton remodelling in differentiating subcutaneous adipocytes and subsequent failure of these cells to accumulate lipids and develop into metabolically active and insulin-sensitive adipocytes. Finally, we show that perturbations of the effector gene Cobll1 in a mouse model result in organismal phenotypes matching the MONW association signature, including decreased subcutaneous body fat mass and body weight along with impaired glucose tolerance. Taken together, our results provide a mechanistic link between the genetic risk for insulin resistance and low adiposity, providing a potential therapeutic hypothesis and a framework for future identification of causal relationships between genome associations and cellular programmes in other disorders.

DOI: https://doi.org/10.1038/s42255-023-00807-w
Nat Commun. 2023 Jun 01. 14(1): 3162

The G protein preference of orexin receptors is currently an unresolved issue.

Jyrki P Kukkonen.

DOI: https://doi.org/10.1038/s41467-023-38764-3
Front Mol Biosci. 2023 ;10 1203269

Emerging field: O-GlcNAcylation in ferroptosis.

Hongshuo Zhang, Juan Zhang, Haojie Dong, Ying Kong, Youfei Guan.

  In 2012, researchers proposed a non-apoptotic, iron-dependent form of cell death caused by lipid peroxidation called ferroptosis. During the past decade, a comprehensive understanding of ferroptosis has emerged. Ferroptosis is closely associated with the tumor microenvironment, cancer, immunity, aging, and tissue damage. Its mechanism is precisely regulated at the epigenetic, transcriptional, and post-translational levels. O-GlcNAc modification (O-GlcNAcylation) is one of the post-translational modifications of proteins. Cells can modulate cell survival in response to stress stimuli, including apoptosis, necrosis, and autophagy, through adaptive regulation by O-GlcNAcylation. However, the function and mechanism of these modifications in regulating ferroptosis are only beginning to be understood. Here, we review the relevant literature within the last 5 years and present the current understanding of the regulatory function of O-GlcNAcylation in ferroptosis and the potential mechanisms that may be involved, including antioxidant defense system-controlled reactive oxygen species biology, iron metabolism, and membrane lipid peroxidation metabolism. In addition to these three areas of ferroptosis research, we examine how changes in the morphology and function of subcellular organelles (e.g., mitochondria and endoplasmic reticulum) involved in O-GlcNAcylation may trigger and amplify ferroptosis. We have dissected the role of O-GlcNAcylation in regulating ferroptosis and hope that our introduction will provide a general framework for those interested in this field.

Keywords:  O-GlcNAcylation; ROS biology; ferroptosis; iron metabolism; lipid peroxidation; subcellular organelle

DOI:  https://doi.org/10.3389/fmolb.2023.1203269
Nature. 2023 May 31.

Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours.

Avishai Gavish, Michael Tyler, Alissa C Greenwald, Rouven Hoefflin, Dor Simkin, Roi Tschernichovsky, Noam Galili Darnell, Einav Somech, Chaya Barbolin, Tomer Antman, Daniel Kovarsky, Thomas Barrett, L Nicolas Gonzalez Castro, Debdatta Halder, Rony Chanoch-Myers, Julie Laffy, Michael Mints, Adi Wider, Rotem Tal, Avishay Spitzer, Toshiro Hara, Maria Raitses-Gurevich, Chani Stossel, Talia Golan, Amit Tirosh, Mario L Suvà, Sidharth V Puram, Itay Tirosh.

Each tumour contains diverse cellular states that underlie intratumour heterogeneity (ITH), a central challenge of cancer therapeutics1. Dozens of recent studies have begun to describe ITH by single-cell RNA sequencing, but each study typically profiled only a small number of tumours and provided a narrow view of transcriptional ITH2. Here we curate, annotate and integrate the data from 77 different studies to reveal the patterns of transcriptional ITH across 1,163 tumour samples covering 24 tumour types. Among the malignant cells, we identify 41 consensus meta-programs, each consisting of dozens of genes that are coordinately upregulated in subpopulations of cells within many tumours. The meta-programs cover diverse cellular processes including both generic (for example, cell cycle and stress) and lineage-specific patterns that we map into 11 hallmarks of transcriptional ITH. Most meta-programs of carcinoma cells are similar to those identified in non-malignant epithelial cells, suggesting that a large fraction of malignant ITH programs are variable even before oncogenesis, reflecting the biology of their cell of origin. We further extended the meta-program analysis to six common non-malignant cell types and utilize these to map cell-cell interactions within the tumour microenvironment. In summary, we have assembled a comprehensive pan-cancer single-cell RNA-sequencing dataset, which is available through the Curated Cancer Cell Atlas website, and leveraged this dataset to carry out a systematic characterization of transcriptional ITH.

DOI: https://doi.org/10.1038/s41586-023-06130-4
Gastroenterology. 2023 May 30. pii: S0016-5085(23)00809-0. [Epub ahead of print]

TGFβ blockade in pancreatic cancer enhances sensitivity to combination chemotherapy.

Li Qiang, Megan T Hoffman, Lestat R Ali, Jaime I Castillo, Lauren Kageler, Ayantu Temesgen, Patrick Lenehan, S Jennifer Wang, Elisa Bello, Victoire Cardot-Ruffino, Giselle A Uribe, Annan Yang, Michael Dougan, Andrew J Aguirre, Srivatsan Raghavan, Marc Pelletier, Viviana Cremasco, Stephanie K Dougan.

   BACKGROUND AND AIMS: TGFβ plays pleiotropic roles in pancreatic cancer including promoting metastasis, attenuating CD8 T cell activation, and enhancing myofibroblast differentiation and deposition of extracellular matrix. However, single-agent TGFβ inhibition has shown limited efficacy against pancreatic cancer in mice or humans.
METHODS: We evaluated the TGFβ blocking antibody NIS793 in combination with either gemcitabine/n(ab)-paclitaxel or FOLFIRINOX chemotherapy in orthotopic pancreatic cancer models. Single-cell RNA-seq and immunofluorescence were used to evaluate changes in tumor cell state and the tumor microenvironment.
RESULTS: Blockade of TGFβ with chemotherapy reduced tumor burden in poorly immunogenic pancreatic cancer, without affecting the metastatic rate of cancer cells. Efficacy of combination therapy was not dependent on CD8 T cells, as response to TGFβ blockade was preserved in CD8-depleted or RAG2-/- mice. TGFβ blockade decreased total αSMA+ fibroblasts but had minimal effect on fibroblast heterogeneity. Bulk RNA-seq on tumor cells sorted ex vivo revealed that tumor cells treated with TGFβ blockade adopted a classical lineage consistent with enhanced chemosensitivity, and immunofluorescence for cleaved caspase 3 confirmed that TGFβ blockade increased chemotherapy-induced cell death in vivo.
CONCLUSIONS: TGFβ regulates pancreatic cancer cell plasticity between classical and basal cell states. TGFβ blockade in orthotropic models of pancreatic cancer enhances sensitivity to chemotherapy by promoting a classical malignant cell state. This study provides scientific rationale for evaluation of NIS793 with either FOLFIRINOX or gemcitabine/n(ab)paclitaxel chemotherapy backbone in the clinical setting and supports the concept of manipulating cancer cell plasticity to increase the efficacy of combination therapy regimens.

Keywords:  TGFβ; chemotherapy; immunotherapy; pancreatic cancer; tumor microenvironment

DOI:  https://doi.org/10.1053/j.gastro.2023.05.038
J Clin Invest. 2023 Jun 01. pii: e170195. [Epub ahead of print]133(11):

Reporting on FH-deficient renal cell carcinoma using circulating succinylated metabolites.

Divya Bezwada, James Brugarolas.

Fumarate hydratase-deficient (FH-deficient) renal cell carcinoma (RCC) represents a particularly aggressive form of kidney cancer. FH-deficient RCC arises in the setting of germline, or solely somatic, mutations in the FH gene, a two-hit tumor suppressor gene. Early detection can be curative, but there are no biomarkers, and in the sporadic setting, establishing a diagnosis of FH-deficient RCC is challenging. In this issue of the JCI, Zheng, Zhu, and co-authors report untargeted plasma metabolomic analyses to identify putative biomarkers. They discovered two plasma metabolites directly linked to fumarate overproduction by tumor cells, succinyl-adenosine and succinic-cysteine, which correlate with tumor burden. The identification of circulating biomarkers of FH-deficient RCC may aid in the diagnosis of FH-deficient RCC and provide a means for longitudinal follow-up.

DOI: https://doi.org/10.1172/JCI170195
Nat Commun. 2023 May 29. 14(1): 3094

Sensory ataxia and cardiac hypertrophy caused by neurovascular oxidative stress in chemogenetic transgenic mouse lines.

Shambhu Yadav, Markus Waldeck-Weiermair, Fotios Spyropoulos, Roderick Bronson, Arvind K Pandey, Apabrita Ayan Das, Alexander C Sisti, Taylor A Covington, Venkata Thulabandu, Shari Caplan, William Chutkow, Benjamin Steinhorn, Thomas Michel.

Oxidative stress is associated with cardiovascular and neurodegenerative diseases. Here we report studies of neurovascular oxidative stress in chemogenetic transgenic mouse lines expressing yeast D-amino acid oxidase (DAAO) in neurons and vascular endothelium. When these transgenic mice are fed D-amino acids, DAAO generates hydrogen peroxide in target tissues. DAAO-TGCdh5 transgenic mice express DAAO under control of the putatively endothelial-specific Cdh5 promoter. When we provide these mice with D-alanine, they rapidly develop sensory ataxia caused by oxidative stress and mitochondrial dysfunction in neurons within dorsal root ganglia and nodose ganglia innervating the heart. DAAO-TGCdh5 mice also develop cardiac hypertrophy after chronic chemogenetic oxidative stress. This combination of ataxia, mitochondrial dysfunction, and cardiac hypertrophy is similar to findings in patients with Friedreich's ataxia. Our observations indicate that neurovascular oxidative stress is sufficient to cause sensory ataxia and cardiac hypertrophy. Studies of DAAO-TGCdh5 mice could provide mechanistic insights into Friedreich's ataxia.

DOI: https://doi.org/10.1038/s41467-023-38961-0
Nat Commun. 2023 May 29. 14(1): 3086

Multi-omic approach characterises the neuroprotective role of retromer in regulating lysosomal health.

James L Daly, Chris M Danson, Philip A Lewis, Lu Zhao, Sara Riccardo, Lucio Di Filippo, Davide Cacchiarelli, Daehoon Lee, Stephen J Cross, Kate J Heesom, Wen-Cheng Xiong, Andrea Ballabio, James R Edgar, Peter J Cullen.

Retromer controls cellular homeostasis through regulating integral membrane protein sorting and transport and by controlling maturation of the endo-lysosomal network. Retromer dysfunction, which is linked to neurodegenerative disorders including Parkinson's and Alzheimer's diseases, manifests in complex cellular phenotypes, though the precise nature of this dysfunction, and its relation to neurodegeneration, remain unclear. Here, we perform an integrated multi-omics approach to provide precise insight into the impact of Retromer dysfunction on endo-lysosomal health and homeostasis within a human neuroglioma cell model. We quantify widespread changes to the lysosomal proteome, indicative of broad lysosomal dysfunction and inefficient autophagic lysosome reformation, coupled with a reconfigured cell surface proteome and secretome reflective of increased lysosomal exocytosis. Through this global proteomic approach and parallel transcriptomic analysis, we provide a holistic view of Retromer function in regulating lysosomal homeostasis and emphasise its role in neuroprotection.

DOI: https://doi.org/10.1038/s41467-023-38719-8