bims-imseme Biomed News
on Immunosenescence and T cell metabolism
Issue of 2021–05–09
seventeen papers selected by
Pierpaolo Ginefra, Ludwig Institute for Cancer Research
  1. Aging-dependent mitochondrial dysfunction mediated by ceramide signaling inhibits antitumor T cell response.
  2. Immunotherapy breaches low-sugar dieting of tumor Treg cells.
  3. A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer.
  4. The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors.
  5. The Key Role of NAD+ in Anti-Tumor Immune Response: An Update.
  6. Inhibition of CDK4/6 promotes CD8 T-cell memory formation.
  7. LIMIT is an immunogenic lncRNA in cancer immunity and immunotherapy.
  8. Too much of a good thing: Excess exercise can harm mitochondria.
  9. Mitochondria ensure immune surveillance by retro-communication with the nucleus.
  10. Hypoxia-sensing CAR T cells provide safety and efficacy in treating solid tumors.
  11. Adenosine-related small molecules show utility of recall antigen assay to screen compounds for off-target effects on memory T cells.
  12. A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness.
  13. A subset of cytotoxic effector memory T cells enhances CAR T cell efficacy in a model of pancreatic ductal adenocarcinoma.
  14. A T-rojan horse strategy for cancer immunotherapy.
  15. Pharmacological modulation of T cell immunity results in long-term remission of autoimmune arthritis.
  16. Neutrophils fuel effective immune responses through gluconeogenesis and glycogenesis.
  17. The serine's call: Suppressing interferon responses.
  1. Cell Rep. 2021 May 04. pii: S2211-1247(21)00407-1. [Epub ahead of print]35(5): 109076
    Aging-dependent mitochondrial dysfunction mediated by ceramide signaling inhibits antitumor T cell response.
    Silvia Vaena, Paramita Chakraborty, Han Gyul Lee, Alhaji H Janneh, Mohamed Faisal Kassir, Gyda Beeson, Zachariah Hedley, Ahmet Yalcinkaya, M Hanief Sofi, Hong Li, Monica L Husby, Robert V Stahelin, Xue-Zhong Yu, Shikhar Mehrotra, Besim Ogretmen.
      We lack a mechanistic understanding of aging-mediated changes in mitochondrial bioenergetics and lipid metabolism that affect T cell function. The bioactive sphingolipid ceramide, induced by aging stress, mediates mitophagy and cell death; however, the aging-related roles of ceramide metabolism in regulating T cell function remain unknown. Here, we show that activated T cells isolated from aging mice have elevated C14/C16 ceramide accumulation in mitochondria, generated by ceramide synthase 6, leading to mitophagy/mitochondrial dysfunction. Mechanistically, aging-dependent mitochondrial ceramide inhibits protein kinase A, leading to mitophagy in activated T cells. This aging/ceramide-dependent mitophagy attenuates the antitumor functions of T cells in vitro and in vivo. Also, inhibition of ceramide metabolism or PKA activation by genetic and pharmacologic means prevents mitophagy and restores the central memory phenotype in aging T cells. Thus, these studies help explain the mechanisms behind aging-related dysregulation of T cells' antitumor activity, which can be restored by inhibiting ceramide-dependent mitophagy.
    Keywords:  CerS6; PKA; SS SphK2; T cell; aging; immunotherapy; lipid signaling; melanoma; mitophagy; sphingolipids and ceramide
    DOI:  https://doi.org/10.1016/j.celrep.2021.109076
  2. Cell Metab. 2021 May 04. pii: S1550-4131(21)00176-5. [Epub ahead of print]33(5): 851-852
    Immunotherapy breaches low-sugar dieting of tumor Treg cells.
    Clarissa Campbell, Alexander Y Rudensky.
      Glycolysis supports effector T cell function but is detrimental to the immunosuppressive activity of regulatory T cells. In a recent issue of Nature, two papers address a role for glucose and lactate availability within the tumor microenvironment for the balance of pro- and anti-tumoral effects of T cells and the efficacy of neoadjuvant cancer immunotherapy.
    DOI:  https://doi.org/10.1016/j.cmet.2021.04.010
  3. Nat Med. 2021 May 06.
    A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer.
    Ayse Bassez, Hanne Vos, Laurien Van Dyck, Giuseppe Floris, Ingrid Arijs, Christine Desmedt, Bram Boeckx, Marlies Vanden Bempt, Ines Nevelsteen, Kathleen Lambein, Kevin Punie, Patrick Neven, Abhishek D Garg, Hans Wildiers, Junbin Qian, Ann Smeets, Diether Lambrechts.
      Immune-checkpoint blockade (ICB) combined with neoadjuvant chemotherapy improves pathological complete response in breast cancer. To understand why only a subset of tumors respond to ICB, patients with hormone receptor-positive or triple-negative breast cancer were treated with anti-PD1 before surgery. Paired pre- versus on-treatment biopsies from treatment-naive patients receiving anti-PD1 (n = 29) or patients receiving neoadjuvant chemotherapy before anti-PD1 (n = 11) were subjected to single-cell transcriptome, T cell receptor and proteome profiling. One-third of tumors contained PD1-expressing T cells, which clonally expanded upon anti-PD1 treatment, irrespective of tumor subtype. Expansion mainly involved CD8+ T cells with pronounced expression of cytotoxic-activity (PRF1, GZMB), immune-cell homing (CXCL13) and exhaustion markers (HAVCR2, LAG3), and CD4+ T cells characterized by expression of T-helper-1 (IFNG) and follicular-helper (BCL6, CXCR5) markers. In pre-treatment biopsies, the relative frequency of immunoregulatory dendritic cells (PD-L1+), specific macrophage phenotypes (CCR2+ or MMP9+) and cancer cells exhibiting major histocompatibility complex class I/II expression correlated positively with T cell expansion. Conversely, undifferentiated pre-effector/memory T cells (TCF7+, GZMK+) or inhibitory macrophages (CX3CR1+, C3+) were inversely correlated with T cell expansion. Collectively, our data identify various immunophenotypes and associated gene sets that are positively or negatively correlated with T cell expansion following anti-PD1 treatment. We shed light on the heterogeneity in treatment response to anti-PD1 in breast cancer.
    DOI:  https://doi.org/10.1038/s41591-021-01323-8
  4. Cells. 2021 Apr 30. pii: 1074. [Epub ahead of print]10(5):
    The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors.
    Veronica Della Chiara, Lucia Daxinger, Frank J T Staal.
      Hematopoietic multipotent progenitors seed the thymus and then follow consecutive developmental stages until the formation of mature T cells. During this process, phenotypic changes of T cells entail stage-specific transcriptional programs that underlie the dynamic progression towards mature lymphocytes. Lineage-specific transcription factors are key drivers of T cell specification and act in conjunction with epigenetic regulators that have also been elucidated as crucial players in the establishment of regulatory networks necessary for proper T cell development. In this review, we summarize the activity of transcription factors and epigenetic regulators that together orchestrate the intricacies of early T cell development with a focus on regulation of T cell lineage commitment.
    Keywords:  Bcl11b; Dnmt3; Polycomb genes; T cell commitment; T cell development; Tcf1; chromatin modifiers; epigenetic regulators; transcription factors
    DOI:  https://doi.org/10.3390/cells10051074
  5. Front Immunol. 2021 ;12 658263
    The Key Role of NAD+ in Anti-Tumor Immune Response: An Update.
    Fabio Morandi, Alberto Leonardo Horenstein, Fabio Malavasi.
      Nicotinamide adenine dinucleotide (NAD+) is an important molecule that functions as a co-enzyme in numerous metabolic processes. Generated both through de novo synthesis and via salvage pathways, NAD+ is the substrate for a variety of NAD+-consuming enzymes. Among them is CD38, a cell surface ecto-enzyme widely expressed on different types of cells and endowed with the function of cADP-ribose synthases/NAD+ glycohydrolase. Surface CD38 expression is increased in different hematological and solid tumors, where it cooperates with other ecto-enzymes to produce the immunosuppressive molecule adenosine (ADO). Few studies have explored the correlation of NAD+ levels with T-cell mediated anti-tumor response in preclinical models. We therefore discuss these novel findings, examining the possible contribution of NAD+ depletion, along with ADO production, in the immunosuppressive activities of CD38 in the context of human tumors. Lastly, we discuss the use of pharmacological inhibitors of CD38 and supplementation of different NAD+ precursors to increase NAD+ levels and to boost T cell responses. Such molecules may be employed as adjuvant therapies, in combination with standard treatments, for cancer patients.
    Keywords:  CD38; NAD+; T cells; human tumors; immune response
    DOI:  https://doi.org/10.3389/fimmu.2021.658263
  6. Cancer Discov. 2021 May 03. pii: candisc.1540.2020. [Epub ahead of print]
    Inhibition of CDK4/6 promotes CD8 T-cell memory formation.
    Max Heckler, Lestat R Ali, Eleanor Clancy-Thompson, Li Qiang, Katherine S Ventre, Patrick Lenehan, Kevin Roehle, Adrienne Luoma, Kelly Boelaars, Vera Peters, Julia McCreary, Tamara Boschert, Eric S Wang, Shengbao Suo, Francesco Marangoni, Thorsten R Mempel, Henry W Long, Kai W Wucherpfennig, Michael Dougan, Nathanael S Gray, Guo-Cheng Yuan, Shom Goel, Sara M Tolaney, Stephanie K Dougan.
      CDK4/6 inhibitors are approved to treat breast cancer and are in trials for other malignancies. We examined CDK4/6 inhibition in mouse and human CD8 T cells during early stages of activation. Mice receiving tumor-specific CD8 T cells treated with CDK4/6 inhibitors displayed increased T cell persistence and immunologic memory. CDK4/6 inhibition upregulated Mxd4, a negative regulator of Myc, in both mouse and human CD8 T cells. Silencing of Mxd4 or Myc in mouse CD8 T cells demonstrated the importance of this axis for memory formation. We used single cell transcriptional profiling and TCR clonotype tracking to evaluate recently activated human CD8 T cells in breast cancer patients before and during treatment with either palbociclib or abemaciclib. CDK4/6 inhibitor therapy in humans increases the frequency of CD8 memory precursors and downregulates their expression of MYC target genes, suggesting that CDK4/6 inhibitors in cancer patients may augment long-term protective immunity.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1540
  7. Nat Cell Biol. 2021 May 06.
    LIMIT is an immunogenic lncRNA in cancer immunity and immunotherapy.
    Gaopeng Li, Ilona Kryczek, Jutaek Nam, Xiong Li, Shasha Li, Jing Li, Shuang Wei, Sara Grove, Linda Vatan, Jiajia Zhou, Wan Du, Heng Lin, Ton Wang, Chitra Subramanian, James J Moon, Marcin Cieslik, Mark Cohen, Weiping Zou.
      Major histocompatibility complex-I (MHC-I) presents tumour antigens to CD8+ T cells and triggers anti-tumour immunity. Humans may have 30,000-60,000 long noncoding RNAs (lncRNAs). However, it remains poorly understood whether lncRNAs affect tumour immunity. Here, we identify a lncRNA, lncRNA inducing MHC-I and immunogenicity of tumour (LIMIT), in humans and mice. We found that IFNγ stimulated LIMIT, LIMIT cis-activated the guanylate-binding protein (GBP) gene cluster and GBPs disrupted the association between HSP90 and heat shock factor-1 (HSF1), thereby resulting in HSF1 activation and transcription of MHC-I machinery, but not PD-L1. RNA-guided CRISPR activation of LIMIT boosted GBPs and MHC-I, and potentiated tumour immunogenicity and checkpoint therapy. Silencing LIMIT, GBPs and/or HSF1 diminished MHC-I, impaired antitumour immunity and blunted immunotherapy efficacy. Clinically, LIMIT, GBP- and HSF1-signalling transcripts and proteins correlated with MHC-I, tumour-infiltrating T cells and checkpoint blockade response in patients with cancer. Together, we demonstrate that LIMIT is a cancer immunogenic lncRNA and the LIMIT-GBP-HSF1 axis may be targetable for cancer immunotherapy.
    DOI:  https://doi.org/10.1038/s41556-021-00672-3
  8. Cell Metab. 2021 May 04. pii: S1550-4131(21)00174-1. [Epub ahead of print]33(5): 847-848
    Too much of a good thing: Excess exercise can harm mitochondria.
    Mark W Pataky, K Sreekumaran Nair.
      Health benefits of aerobic exercise are indisputable and are closely related to the maintenance of mitochondrial energy homeostasis and insulin sensitivity. Flockhart et al. (2021) demonstrate, however, that a high volume of high-intensity aerobic exercise adversely affects mitochondrial function and may cause impaired glucose tolerance.
    DOI:  https://doi.org/10.1016/j.cmet.2021.04.008
  9. Cell Metab. 2021 May 04. pii: S1550-4131(21)00179-0. [Epub ahead of print]33(5): 853-855
    Mitochondria ensure immune surveillance by retro-communication with the nucleus.
    Manuel Rigon, Amelia R Townley, Michelangelo Campanella.
      Mitochondria cover several functions within the cell, including an influence on the transcription of nuclear genes. Recent work by Tigano et al. (2021) in Nature has identified a pathway of mitochondrial retrograde communication in which the nucleus senses aberrations in the mtDNA to drive the innate immune response.
    DOI:  https://doi.org/10.1016/j.cmet.2021.04.013
  10. Cell Rep Med. 2021 Apr 20. 2(4): 100227
    Hypoxia-sensing CAR T cells provide safety and efficacy in treating solid tumors.
    Paris Kosti, James W Opzoomer, Karen I Larios-Martinez, Rhonda Henley-Smith, Cheryl L Scudamore, Mary Okesola, Mustafa Y M Taher, David M Davies, Tamara Muliaditan, Daniel Larcombe-Young, Natalie Woodman, Cheryl E Gillett, Selvam Thavaraj, John Maher, James N Arnold.
      Utilizing T cells expressing chimeric antigen receptors (CARs) to identify and attack solid tumors has proven challenging, in large part because of the lack of tumor-specific targets to direct CAR binding. Tumor selectivity is crucial because on-target, off-tumor activation of CAR T cells can result in potentially lethal toxicities. This study presents a stringent hypoxia-sensing CAR T cell system that achieves selective expression of a pan-ErbB-targeted CAR within a solid tumor, a microenvironment characterized by inadequate oxygen supply. Using murine xenograft models, we demonstrate that, despite widespread expression of ErbB receptors in healthy organs, the approach provides anti-tumor efficacy without off-tumor toxicity. This dynamic on/off oxygen-sensing safety switch has the potential to facilitate unlimited expansion of the CAR T cell target repertoire for treating solid malignancies.
    Keywords:  CAR T cells; HIF1α; HypoxiCAR; T cell; cancer; chimeric antigen receptor; cytokine release syndrome; hypoxia; immunotherapy; toxicity
    DOI:  https://doi.org/10.1016/j.xcrm.2021.100227
  11. Sci Rep. 2021 May 05. 11(1): 9561
    Adenosine-related small molecules show utility of recall antigen assay to screen compounds for off-target effects on memory T cells.
    Eden Kleiman, Gloria Sierra, Binchen Mao, Dennie Magcase, Marybeth V George, Pirouz M Daftarian.
      Extracellular adenosine suppresses T cell immunity in the tumor microenvironment and in vitro treatment of memory T cells with adenosine can suppress antigen-mediated memory T cell expansion. We describe utilizing the recall antigen assay platform to screen small molecule drug off-target effects on memory T cell expansion/function using a dosing regimen based on adenosine treatment. As a proof of principle, we show low dose GS-5734, a monophosphoramidate prodrug of an adenosine analog, does not alter memory T cell recall at lower doses whereas toxicity observed at high dose favors antigen-specific memory T cell survival/proliferation over non-specific CD8+ T cells. Conversely, parent nucleoside GS-441524 at high dosage does not result in cellular toxicity and reduces antigen-specific T cell recall in most donors. Despite similar chemical structure, these drugs displayed opposing effects on memory T cell expansion and viability highlighting the sensitivity of this assay setup in screening compounds for off-target effects.
    DOI:  https://doi.org/10.1038/s41598-021-88965-3
  12. Nat Immunol. 2021 May 06.
    A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness.
    Kerstin B Kaufmann, Andy G X Zeng, Etienne Coyaud, Laura Garcia-Prat, Efthymia Papalexi, Alex Murison, Estelle M N Laurent, Michelle Chan-Seng-Yue, Olga I Gan, Kristele Pan, Jessica McLeod, Héléna Boutzen, Sasan Zandi, Shin-Ichiro Takayanagi, Rahul Satija, Brian Raught, Stephanie Z Xie, John E Dick.
      Continuous supply of immune cells throughout life relies on the delicate balance in the hematopoietic stem cell (HSC) pool between long-term maintenance and meeting the demands of both normal blood production and unexpected stress conditions. Here we identified distinct subsets of human long-term (LT)-HSCs that responded differently to regeneration-mediated stress: an immune checkpoint ligand CD112lo subset that exhibited a transient engraftment restraint (termed latency) before contributing to hematopoietic reconstitution and a primed CD112hi subset that responded rapidly. This functional heterogeneity and CD112 expression are regulated by INKA1 through direct interaction with PAK4 and SIRT1, inducing epigenetic changes and defining an alternative state of LT-HSC quiescence that serves to preserve self-renewal and regenerative capacity upon regeneration-mediated stress. Collectively, our data uncovered the molecular intricacies underlying HSC heterogeneity and self-renewal regulation and point to latency as an orchestrated physiological response that balances blood cell demands with preserving a stem cell reservoir.
    DOI:  https://doi.org/10.1038/s41590-021-00925-1
  13. Sci Transl Med. 2021 May 05. pii: eabc3196. [Epub ahead of print]13(592):
    A subset of cytotoxic effector memory T cells enhances CAR T cell efficacy in a model of pancreatic ductal adenocarcinoma.
    Vanaja Konduri, Sujith K Joseph, Tiara T Byrd, Zeid Nawas, Jonathan Vazquez-Perez, Colby J Hofferek, Matthew M Halpert, Dongliang Liu, Zhengdong Liang, Yunyu Baig, Vita S Salsman, Damilola Oyewole-Said, Anna Tsimelzon, Briana A Burns, Changyi Chen, Jonathan M Levitt, Qizhi Yao, Nabil M Ahmed, Meenakshi Hegde, William K Decker.
      In humans, the natural killer (NK) cell marker CD161 identifies several subsets of T cells, including a polyclonal CD8 αβ T cell receptor-expressing subset with characteristic specificity for tissue-localized viruses. This subset also displays enhanced cytotoxic and memory phenotypes. Here, we characterized this unique T cell subset and determined its potential suitability for use in chimeric antigen receptor (CAR) T cell therapy. In mice, gene expression profiling among the CD161-equivalent CD8+ T cell populations (CD8+NK1.1+) revealed substantial up-regulation of granzymes, perforin, killer lectin-like receptors, and innate signaling molecules in comparison to CD8+NK1.1- T cells. Adoptive transfer of CD8+NK1.1+ cells from previously exposed animals offered substantially enhanced protection and improved survival against melanoma tumors and influenza infection compared to CD8+NK1.1- cells. Freshly isolated human CD8+CD61+ T cells exhibited heightened allogeneic killing activity in comparison to CD8+CD61- T cells or total peripheral blood mononuclear cells (PBMCs). To determine whether this subset might improve the antitumor efficacy of CAR T cell therapy against solid tumors, we compared bulk PBMCs, CD8+CD161-, and CD8+CD161+ T cells transduced with a human epidermal growth factor receptor-2 (HER2)-specific CAR construct. In vitro, CD8+CD161+ CAR-transduced T cells killed HER2+ targets faster and with greater efficiency. Similarly, these cells mediated enhanced in vivo antitumor efficacy in xenograft models of HER2+ pancreatic ductal adenocarcinoma, exhibiting elevated expression of granzymes and reduced expression of exhaustion markers. These data suggest that this T cell subset presents an opportunity to improve CAR T cell therapy for the treatment of solid tumors.
    DOI:  https://doi.org/10.1126/scitranslmed.abc3196
  14. Sci Immunol. 2021 May 07. pii: eabj3098. [Epub ahead of print]6(59):
    A T-rojan horse strategy for cancer immunotherapy.
    Christine Rafie, Asha Pillai.
      CDK4/6 inhibitor-treated breast cancer cells recruit T cells via metabolic stress-induced chemokines.
    DOI:  https://doi.org/10.1126/sciimmunol.abj3098
  15. Proc Natl Acad Sci U S A. 2021 May 11. pii: e2100939118. [Epub ahead of print]118(19):
    Pharmacological modulation of T cell immunity results in long-term remission of autoimmune arthritis.
    Yi-Shu Huang, Wen-Yi Tseng, Felix I L Clanchy, Louise M Topping, Joy Ogbechi, Kay McNamee, Dany Perocheau, Nien-Yi Chiang, Peter Ericsson, Anette Sundstedt, Zhong-Tian Xue, Leif G Salford, Hans-Olov Sjögren, Trevor W Stone, Hsi-Hsien Lin, Shue-Fen Luo, Richard O Williams.
      Chronic inflammatory diseases like rheumatoid arthritis are characterized by a deficit in fully functional regulatory T cells. DNA-methylation inhibitors have previously been shown to promote regulatory T cell responses and, in the present study, we evaluated their potential to ameliorate chronic and acute animal models of rheumatoid arthritis. Of the drugs tested, decitabine was the most effective, producing a sustained therapeutic effect that was dependent on indoleamine 2,3-dioxygenase (IDO) and was associated with expansion of induced regulatory T cells, particularly at the site of disease activity. Treatment with decitabine also caused apoptosis of Th1 and Th17 cells in active arthritis in a highly selective manner. The molecular basis for this selectivity was shown to be ENT1, a nucleoside transporter, which facilitates intracellular entry of the drug and is up-regulated on effector T cells during active arthritis. It was further shown that short-term treatment with decitabine resulted in the generation of a population of regulatory T cells that were able to suppress arthritis upon adoptive transfer. In summary, a therapeutic approach using an approved drug is described that treats active inflammatory disease effectively and generates robust regulatory T cells with the IDO-dependent capacity to maintain remission.
    Keywords:  DNA-methylation inhibitor; autoimmunity; indoleamine 2,3-dioxygenase; rheumatoid arthritis
    DOI:  https://doi.org/10.1073/pnas.2100939118
  16. Cell Metab. 2021 May 04. pii: S1550-4131(21)00125-X. [Epub ahead of print]33(5): 1062-1064
    Neutrophils fuel effective immune responses through gluconeogenesis and glycogenesis.
    Pranvera Sadiku, Joseph A Willson, Eilise M Ryan, David Sammut, Patricia Coelho, Emily R Watts, Robert Grecian, Jason M Young, Martin Bewley, Simone Arienti, Ananda S Mirchandani, Manuel A Sanchez Garcia, Tyler Morrison, Ailing Zhang, Leila Reyes, Tobias Griessler, Privjyot Jheeta, Gordon G Paterson, Christopher J Graham, John P Thomson, Kenneth Baillie, A A Roger Thompson, Jessie-May Morgan, Abel Acosta-Sanchez, Veronica M Dardé, Jordi Duran, Joan J Guinovart, Gio Rodriguez-Blanco, Alex Von Kriegsheim, Richard R Meehan, Massimiliano Mazzone, David H Dockrell, Bart Ghesquiere, Peter Carmeliet, Moira K B Whyte, Sarah R Walmsley.
      
    DOI:  https://doi.org/10.1016/j.cmet.2021.03.018
  17. Cell Metab. 2021 May 04. pii: S1550-4131(21)00178-9. [Epub ahead of print]33(5): 849-850
    The serine's call: Suppressing interferon responses.
    Benedikt Agerer, Alexander Lercher, Andreas Bergthaler.
      Cellular metabolism and immune function are closely linked. In this issue of Cell Metabolism, Shen et al. (2021) identify serine metabolism as a central integration hub of cellular metabolism, antiviral immunity, and epigenetic regulation.
    DOI:  https://doi.org/10.1016/j.cmet.2021.04.012
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