bims-imseme Biomed News
on Immunosenescence and T cell metabolism
Issue of 2021‒05‒02
fourteen papers selected by
Pierpaolo Ginefra
Ludwig Institute for Cancer Research
  1. Evolving concepts in NAD+ metabolism.
  2. Identification and Validation of Nutrient State-Dependent Serum Protein Mediators of Human CD4+ T Cell Responsiveness.
  3. Tinkering under the Hood: Metabolic Optimisation of CAR-T Cell Therapy.
  4. Mitochondria Turnover and Lysosomal Function in Hematopoietic Stem Cell Metabolism.
  5. Control of T Cell Metabolism by Cytokines and Hormones.
  6. Metabolic barriers to cancer immunotherapy.
  7. Tim-3 adaptor protein Bat3 is a molecular checkpoint of T cell terminal differentiation and exhaustion.
  8. Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity.
  9. Metabolomics, Lipidomics, and Immunometabolism.
  10. Time-domain single photon-excited autofluorescence lifetime for label-free detection of T cell activation.
  11. RNA Flow Cytometry for the Study of T Cell Metabolism.
  12. Role of TCF-1 in differentiation, exhaustion, and memory of CD8+ T cells: A review.
  13. Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance.
  14. Inhibition of mitochondrial translation suppresses glioblastoma stem cell growth.
  1. Cell Metab. 2021 Apr 22. pii: S1550-4131(21)00169-8. [Epub ahead of print]
    Evolving concepts in NAD+ metabolism.
    Claudia C S Chini, Julianna D Zeidler, Sonu Kashyap, Gina Warner, Eduardo Nunes Chini.
      NAD(H) and NADP(H) have traditionally been viewed as co-factors (or co-enzymes) involved in a myriad of oxidation-reduction reactions including the electron transport in the mitochondria. However, NAD pathway metabolites have many other important functions, including roles in signaling pathways, post-translational modifications, epigenetic changes, and regulation of RNA stability and function via NAD-capping of RNA. Non-oxidative reactions ultimately lead to the net catabolism of these nucleotides, indicating that NAD metabolism is an extremely dynamic process. In fact, recent studies have clearly demonstrated that NAD has a half-life in the order of minutes in some tissues. Several evolving concepts on the metabolism, transport, and roles of these NAD pathway metabolites in disease states such as cancer, neurodegeneration, and aging have emerged in just the last few years. In this perspective, we discuss key recent discoveries and changing concepts in NAD metabolism and biology that are reshaping the field. In addition, we will pose some open questions in NAD biology, including why NAD metabolism is so fast and dynamic in some tissues, how NAD and its precursors are transported to cells and organelles, and how NAD metabolism is integrated with inflammation and senescence. Resolving these questions will lead to significant advancements in the field.
    Keywords:  NAD pathway metabolites; NAD(+); aging; disease; humans; mitochondria; transport; vitamin B3
    DOI:  https://doi.org/10.1016/j.cmet.2021.04.003
  2. Nutrients. 2021 Apr 28. pii: 1492. [Epub ahead of print]13(5):
    Identification and Validation of Nutrient State-Dependent Serum Protein Mediators of Human CD4+ T Cell Responsiveness.
    Kim Han, Komudi Singh, Matthew J Rodman, Shahin Hassanzadeh, Yvonne Baumer, Rebecca D Huffstutler, Jinguo Chen, Julián Candia, Foo Cheung, Katherine E R Stagliano, Mehdi Pirooznia, Tiffany M Powell-Wiley, Michael N Sack.
      Intermittent fasting and fasting mimetic diets ameliorate inflammation. Similarly, serum extracted from fasted healthy and asthmatic subjects' blunt inflammation in vitro, implicating serum components in this immunomodulation. To identify the proteins orchestrating these effects, SOMAScan technology was employed to evaluate serum protein levels in healthy subjects following an overnight, 24-h fast and 3 h after refeeding. Partial least square discriminant analysis identified several serum proteins as potential candidates to confer feeding status immunomodulation. The characterization of recombinant IGFBP1 (elevated following 24 h of fasting) and PYY (elevated following refeeding) in primary human CD4+ T cells found that they blunted and induced immune activation, respectively. Furthermore, integrated univariate serum protein analysis compared to RNA-seq analysis from peripheral blood mononuclear cells identified the induction of IL1RL1 and MFGE8 levels in refeeding compared to the 24-h fasting in the same study. Subsequent quantitation of these candidate proteins in lean versus obese individuals identified an inverse regulation of serum levels in the fasted subjects compared to the obese subjects. In parallel, IL1RL1 and MFGE8 supplementation promoted increased CD4+ T responsiveness to T cell receptor activation. Together, these data show that caloric load-linked conditions evoke serological protein changes, which in turn confer biological effects on circulating CD4+ T cell immune responsiveness.
    Keywords:  CD4+ T cell activation; IGFBP1; IL1RL1; MFGE8; PYY; SOMAscan; fasting; integrative bioinformatics; refeeding
    DOI:  https://doi.org/10.3390/nu13051492
  3. Antibodies (Basel). 2021 Apr 26. pii: 17. [Epub ahead of print]10(2):
    Tinkering under the Hood: Metabolic Optimisation of CAR-T Cell Therapy.
    Yasmin Jenkins, Joanna Zabkiewicz, Oliver Ottmann, Nicholas Jones.
      Chimeric antigen receptor (CAR)-T cells are one of the most exciting areas of immunotherapy to date. Clinically available CAR-T cells are used to treat advanced haematological B-cell malignancies with complete remission achieved at around 30-40%. Unfortunately, CAR-T cell success rates are even less impressive when considering a solid tumour. Reasons for this include the paucity of tumour specific targets and greater degree of co-expression on normal tissues. However, there is accumulating evidence that considerable competition for nutrients such as carbohydrates and amino acids within the tumour microenvironment (TME) coupled with immunosuppression result in mitochondrial dysfunction, exhaustion, and subsequent CAR-T cell depletion. In this review, we will examine research avenues being pursued to dissect the various mechanisms contributing to the immunosuppressive TME and outline in vitro strategies currently under investigation that focus on boosting the metabolic program of CAR-T cells as a mechanism to overcome the immunosuppressive TME. Various in vitro and in vivo techniques boost oxidative phosphorylation and mitochondrial fitness in CAR-T cells, resulting in an enhanced central memory T cell compartment and increased anti-tumoural immunity. These include intracellular metabolic enhancers and extracellular in vitro culture optimisation pre-infusion. It is likely that the next generation of CAR-T products will incorporate these elements of metabolic manipulation in CAR-T cell design and manufacture. Given the importance of immunometabolism and T cell function, it is critical that we identify ways to metabolically armour CAR-T cells to overcome the hostile TME and increase clinical efficacy.
    Keywords:  CAR-T cells; immunometabolism; metabolism; oncometabolism; tumour microenvironment
    DOI:  https://doi.org/10.3390/antib10020017
  4. Int J Mol Sci. 2021 Apr 28. pii: 4627. [Epub ahead of print]22(9):
    Mitochondria Turnover and Lysosomal Function in Hematopoietic Stem Cell Metabolism.
    Makiko Mochizuki-Kashio, Hiroko Shiozaki, Toshio Suda, Ayako Nakamura-Ishizu.
      Hematopoietic stem cells (HSCs) reside in a hypoxic microenvironment that enables glycolysis-fueled metabolism and reduces oxidative stress. Nonetheless, metabolic regulation in organelles such as the mitochondria and lysosomes as well as autophagic processes have been implicated as essential for the determination of HSC cell fate. This review encompasses the current understanding of anaerobic metabolism in HSCs as well as the emerging roles of mitochondrial metabolism and lysosomal regulation for hematopoietic homeostasis.
    Keywords:  ROS; autophagy; folliculin; hematopoietic stem cells; lysosome; mitochondria
    DOI:  https://doi.org/10.3390/ijms22094627
  5. Front Immunol. 2021 ;12 653605
    Control of T Cell Metabolism by Cytokines and Hormones.
    Emma L Bishop, Nancy Gudgeon, Sarah Dimeloe.
      Dynamic, coordinated changes in metabolic pathway activity underpin the protective and inflammatory activity of T cells, through provision of energy and biosynthetic precursors for effector functions, as well as direct effects of metabolic enzymes, intermediates and end-products on signaling pathways and transcriptional mechanisms. Consequently, it has become increasingly clear that the metabolic status of the tissue microenvironment directly influences T cell activity, with changes in nutrient and/or metabolite abundance leading to dysfunctional T cell metabolism and interlinked immune function. Emerging evidence now indicates that additional signals are integrated by T cells to determine their overall metabolic phenotype, including those arising from interaction with cytokines and hormones in their environment. The impact of these on T cell metabolism, the mechanisms involved and the pathological implications are discussed in this review article.
    Keywords:  T cell; cytokine; glycolysis; hormone; metabolism; mitochdonrion
    DOI:  https://doi.org/10.3389/fimmu.2021.653605
  6. Nat Rev Immunol. 2021 Apr 29.
    Metabolic barriers to cancer immunotherapy.
    Kristin DePeaux, Greg M Delgoffe.
      Several non-redundant features of the tumour microenvironment facilitate immunosuppression and limit anticancer immune responses. These include physical barriers to immune infiltration, the recruitment of suppressive immune cells and the upregulation of ligands on tumour cells that bind to inhibitory receptors on immune cells. Recent insights into the importance of the metabolic restrictions imposed by the tumour microenvironment on antitumour T cells have begun to inform immunotherapeutic anticancer strategies. Therapeutics that target metabolic restrictions, such as low glucose levels, a low pH, hypoxia and the generation of suppressive metabolites, have shown promise as combination therapies for different types of cancer. In this Review, we discuss the metabolic aspects of the antitumour T cell response in the context of immune checkpoint blockade, adoptive cell therapy and treatment with oncolytic viruses, and discuss emerging combination strategies.
    DOI:  https://doi.org/10.1038/s41577-021-00541-y
  7. Sci Adv. 2021 Apr;pii: eabd2710. [Epub ahead of print]7(18):
    Tim-3 adaptor protein Bat3 is a molecular checkpoint of T cell terminal differentiation and exhaustion.
    Chen Zhu, Karen O Dixon, Kathleen Newcomer, Guangxiang Gu, Sheng Xiao, Sarah Zaghouani, Markus A Schramm, Chao Wang, Huiyuan Zhang, Kouichiro Goto, Elena Christian, Manu Rangachari, Orit Rosenblatt-Rosen, Hitoshi Okada, Tak Mak, Meromit Singer, Aviv Regev, Vijay Kuchroo.
      T cell exhaustion has been associated with poor prognosis in persistent viral infection and cancer. Conversely, in the context of autoimmunity, T cell exhaustion has been favorably correlated with long-term clinical outcome. Understanding the development of exhaustion in autoimmune settings may provide underlying principles that can be exploited to quell autoreactive T cells. Here, we demonstrate that the adaptor molecule Bat3 acts as a molecular checkpoint of T cell exhaustion, with deficiency of Bat3 promoting a profound exhaustion phenotype, suppressing autoreactive T cell-mediated neuroinflammation. Mechanistically, Bat3 acts as a critical mTORC2 inhibitor to suppress Akt function. As a result, Bat3 deficiency leads to increased Akt activity and FoxO1 phosphorylation, indirectly promoting Prdm1 expression. Transcriptional analysis of Bat3 -/- T cells revealed up-regulation of dysfunction-associated genes, concomitant with down-regulation of genes associated with T cell effector function, suggesting that absence of Bat3 can trigger T cell dysfunction even under highly proinflammatory autoimmune conditions.
    DOI:  https://doi.org/10.1126/sciadv.abd2710
  8. Nat Metab. 2021 Apr 26.
    Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity.
    Hans-Georg Sprenger, Thomas MacVicar, Amir Bahat, Kai Uwe Fiedler, Steffen Hermans, Denise Ehrentraut, Katharina Ried, Dusanka Milenkovic, Nina Bonekamp, Nils-Göran Larsson, Hendrik Nolte, Patrick Giavalisco, Thomas Langer.
      Cytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. Here, we show that mtDNA-dependent immune signalling via the cyclic GMP-AMP synthase‒stimulator of interferon genes‒TANK-binding kinase 1 (cGAS-STING-TBK1) pathway is under metabolic control and is induced by cellular pyrimidine deficiency. The mitochondrial protease YME1L preserves pyrimidine pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC25A33. Deficiency of YME1L causes inflammation in mouse retinas and in cultured cells. It drives the release of mtDNA and a cGAS-STING-TBK1-dependent inflammatory response, which requires SLC25A33 and is suppressed upon replenishment of cellular pyrimidine pools. Overexpression of SLC25A33 is sufficient to induce immune signalling by mtDNA. Similarly, depletion of cytosolic nucleotides upon inhibition of de novo pyrimidine synthesis triggers mtDNA-dependent immune responses in wild-type cells. Our results thus identify mtDNA release and innate immune signalling as a metabolic response to cellular pyrimidine deficiencies.
    DOI:  https://doi.org/10.1038/s42255-021-00385-9
  9. Methods Mol Biol. 2021 ;2285 319-328
    Metabolomics, Lipidomics, and Immunometabolism.
    Fortunata Carbone, Sara Bruzzaniti, Clorinda Fusco, Alessandra Colamatteo, Teresa Micillo, Paola De Candia, Fabrizia Bonacina, Giuseppe Danilo Norata, Giuseppe Matarese.
      Metabolomics, lipidomics, and the study of cellular metabolism are gaining increasing interest particularly in the field of immunology, since the activation and effector functions of immune cells are profoundly controlled by changes in cellular metabolic asset. Among the different techniques that can be used for the evaluation of cellular metabolism, the Seahorse Extracellular Flux Analyzer allows the real time measurement of both glycolytic and mitochondrial respiration pathways in cells of interest, through the assessment of extracellular acidification and oxygen consumption rate. Metabolomics, on the other hand, is the high-throughput analysis of metabolites, i.e., the substrates, intermediates, and products of cellular metabolism, starting from biofluids, cells or tissues. The metabolome does not include lipids as their properties are different from water-soluble metabolites and are classified under the lipidome. Lipidomics analysis allows the identification and quantification of lipid species. Metabolomics and lipidomics are currently performed with mass-spectrometry coupled with liquid or gas chromatography (LC-MS or GC-MS) and/or nuclear-magnetic resonance (NMR). Here we describe the protocol for the evaluation of metabolic rate, metabolomics, and lipidomics in T cells, examining the detailed experimental approaches.
    Keywords:  Bioenergetics; Glycolysis; Lipidomics; Metabolism; Metabolomics; Mitochondrial respiration; T cells
    DOI:  https://doi.org/10.1007/978-1-0716-1311-5_24
  10. Opt Lett. 2021 May 01. 46(9): 2168-2171
    Time-domain single photon-excited autofluorescence lifetime for label-free detection of T cell activation.
    Kayvan Samimi, Emmanuel Contreras Guzman, Steven M Trier, Dan L Pham, Tongcheng Qian, Melissa C Skala.
      Fluorescence lifetime imaging microscopy (FLIM) is a powerful technique, capable of label-free assessment of the metabolic state and function within single cells. The FLIM measurements of autofluorescence were recently shown to be sensitive to the functional state and subtype of T cells. Therefore, autofluorescence FLIM could improve cell manufacturing technologies for adoptive immunotherapy, which currently require a time-intensive process of cell labeling with fluorescent antibodies. However, current autofluorescence FLIM implementations are typically too slow, bulky, and prohibitively expensive for use in cell manufacturing pipelines. Here we report a single photon-excited confocal whole-cell autofluorescence system that uses fast field-programmable gate array-based time tagging electronics to achieve time-correlated single photon counting (TCSPC) of single-cell autofluorescence. The system includes simultaneous near-infrared bright-field imaging and is sensitive to variations in the fluorescence decay profile of the metabolic coenzyme NAD(P)H in human T cells due to the activation state. The classification of activated and quiescent T cells achieved high accuracy and precision (area under the receiver operating characteristic curve, AUC = 0.92). The lower-cost, higher acquisition speed, and resistance to pile-up effects at high photon flux compared to traditional multiphoton-excited FLIM and TCSPC implementations with similar SNR make this system attractive for integration into flow cytometry, sorting, and quality control in cell manufacturing.
    DOI:  https://doi.org/10.1364/OL.422445
  11. Int J Mol Sci. 2021 Apr 09. pii: 3906. [Epub ahead of print]22(8):
    RNA Flow Cytometry for the Study of T Cell Metabolism.
    Alessandra Rossi, Ilenia Pacella, Silvia Piconese.
      T cells undergo activation and differentiation programs along a continuum of states that can be tracked through flow cytometry using a combination of surface and intracellular markers. Such dynamic behavior is the result of transcriptional and post-transcriptional events, initiated and sustained by the activation of specific transcription factors and by epigenetic remodeling. These signaling pathways are tightly integrated with metabolic routes in a bidirectional manner: on the one hand, T cell receptors and costimulatory molecules activate metabolic reprogramming; on the other hand, metabolites modify T cell transcriptional programs and functions. Flow cytometry represents an invaluable tool to analyze the integration of phenotypical, functional, metabolic and transcriptional features, at the single cell level in heterogeneous T cell populations, and from complex microenvironments, with potential clinical application in monitoring the efficacy of cancer immunotherapy. Here, we review the most recent advances in flow cytometry-based analysis of gene expression, in combination with indicators of mitochondrial activity, with the aim of revealing and characterizing major metabolic pathways in T cells.
    Keywords:  RNA; T cells; flow cytometry; metabolism; mitochondria
    DOI:  https://doi.org/10.3390/ijms22083906
  12. FASEB J. 2021 May;35(5): e21549
    Role of TCF-1 in differentiation, exhaustion, and memory of CD8+ T cells: A review.
    Jiaxue Zhang, Tong Lyu, Yaming Cao, Hui Feng.
      T cell factor-1 (TCF-1) (encoded by the TCF7 gene) is a transcription factor that plays important role during the T cell development and differentiation for T cell to exercise its functions including producing memory T cells. Not only TCF-1 can modulate the T cell development but also exerts various effects on the differentiation and function of mature CD8+ T cells. In addition, it drives the production and maintenance of the immune response of CD8+ T cells after PD-1 checkpoint blockade therapy. TCF-1 can serve as a potential target of immunotherapy and may provide promising novel treatment strategies for patients with cancer and infections. Moreover, TCF-1 is a potential biomarker of CD8+ T cell functionality to predict the efficacy of immunotherapy in fighting against cancer and infections. Herein, we summarize the role of TCF-1 in T cell development and its applications in the treatment of cancer and infectious diseases.
    Keywords:  CD8+ T cells; TCF-1; cancer; exhaustion; immune memory; viral Infection
    DOI:  https://doi.org/10.1096/fj.202002566R
  13. Cell Metab. 2021 Apr 21. pii: S1550-4131(21)00167-4. [Epub ahead of print]
    Tumors exploit FTO-mediated regulation of glycolytic metabolism to evade immune surveillance.
    Yi Liu, Guanghao Liang, Hongjiao Xu, Wenxin Dong, Ze Dong, Zhiwei Qiu, Zihao Zhang, Fangle Li, Yue Huang, Yilin Li, Jun Wu, Shenyi Yin, Yawei Zhang, Peijin Guo, Jun Liu, Jianzhong Jeff Xi, Peng Jiang, Dali Han, Cai-Guang Yang, Meng Michelle Xu.
      The ever-increasing understanding of the complexity of factors and regulatory layers that contribute to immune evasion facilitates the development of immunotherapies. However, the diversity of malignant tumors limits many known mechanisms in specific genetic and epigenetic contexts, manifesting the need to discover general driver genes. Here, we have identified the m6A demethylase FTO as an essential epitranscriptomic regulator utilized by tumors to escape immune surveillance through regulation of glycolytic metabolism. We show that FTO-mediated m6A demethylation in tumor cells elevates the transcription factors c-Jun, JunB, and C/EBPβ, which allows the rewiring of glycolytic metabolism. Fto knockdown impairs the glycolytic activity of tumor cells, which restores the function of CD8+ T cells, thereby inhibiting tumor growth. Furthermore, we developed a small-molecule compound, Dac51, that can inhibit the activity of FTO, block FTO-mediated immune evasion, and synergize with checkpoint blockade for better tumor control, suggesting reprogramming RNA epitranscriptome as a potential strategy for immunotherapy.
    Keywords:  RNA m6A modification; demethylase FTO; epitranscriptome; glycolytic metabolism; immune surveillance and immunotherapy
    DOI:  https://doi.org/10.1016/j.cmet.2021.04.001
  14. Cell Rep. 2021 Apr 27. pii: S2211-1247(21)00338-7. [Epub ahead of print]35(4): 109024
    Inhibition of mitochondrial translation suppresses glioblastoma stem cell growth.
    Denise Sighel, Michela Notarangelo, Shintaro Aibara, Angela Re, Gianluca Ricci, Marianna Guida, Alessia Soldano, Valentina Adami, Chiara Ambrosini, Francesca Broso, Emanuele Filiberto Rosatti, Sara Longhi, Mariachiara Buccarelli, Quintino G D'Alessandris, Stefano Giannetti, Simone Pacioni, Lucia Ricci-Vitiani, Joanna Rorbach, Roberto Pallini, Sandrine Roulland, Alexey Amunts, Ines Mancini, Angelika Modelska, Alessandro Quattrone.
      Glioblastoma stem cells (GSCs) resist current glioblastoma (GBM) therapies. GSCs rely highly on oxidative phosphorylation (OXPHOS), whose function requires mitochondrial translation. Here we explore the therapeutic potential of targeting mitochondrial translation and report the results of high-content screening with putative blockers of mitochondrial ribosomes. We identify the bacterial antibiotic quinupristin/dalfopristin (Q/D) as an effective suppressor of GSC growth. Q/D also decreases the clonogenicity of GSCs in vitro, consequently dysregulating the cell cycle and inducing apoptosis. Cryoelectron microscopy (cryo-EM) reveals that Q/D binds to the large mitoribosomal subunit, inhibiting mitochondrial protein synthesis and functionally dysregulating OXPHOS complexes. These data suggest that targeting mitochondrial translation could be explored to therapeutically suppress GSC growth in GBM and that Q/D could potentially be repurposed for cancer treatment.
    Keywords:  OXPHOS; cryo-EM; dalfopristin; drug repurposing; glioblastoma; glioblastoma stem cells; high-content screening; mitochondrial translation; mitoribosome; quinupristin
    DOI:  https://doi.org/10.1016/j.celrep.2021.109024
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