bims-imseme 2022-11-27 papers

bims-imseme

Biomed News

on Immunosenescence and T cell metabolism

Issue of 2022‒11‒27
eleven papers selected by
Pierpaolo Ginefra
Ludwig Institute for Cancer Research

Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T cells.
Mitochondria as disease-relevant organelles in rheumatoid arthritis.
The influence of three-dimensional structure on naïve T cell homeostasis and aging.
Mitochondrial connections with immune system in Zebrafish.
Systematic single-cell pathway analysis to characterize early T cell activation.
Dopaminergic Signalling Enhances IL-2 Production and Strengthens Anti-Tumour Response Exerted by Cytotoxic T Lymphocytes in a Melanoma Mouse Model.
Autophagy promotes cell survival by maintaining NAD levels.
Inosine, Gut Microbiota, and Cancer Immunometabolism.
Survivin promotes a glycolytic switch in CD4+ T cells by suppressing the transcription of PFKFB3 in rheumatoid arthritis.
A central role for STAT5 in the transcriptional programing of T helper cell metabolism.
Targeting the CD47/thrombospondin-1 signaling axis regulates immune cell bioenergetics in the tumor microenvironment to potentiate antitumor immune response.

Sci Adv. 2022 Nov 25. 8(47): eadc9346

Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T cells.

Jinwoo Nah, Rho H Seong.

Exhausted CD8 T cells during chronic inflammatory responses against viral infections and cancer are phenotypically and functionally heterogeneous. In particular, CD8 T cells with cytolytic effector function have been recently identified among the exhausted CD8 T cell subsets. However, the regulation of their differentiation and function remains largely unknown. Here, we report that Krüppel-like factor 4 (KLF4) is a critical regulator of the exhaustion process, promoting the cytolytic effector function of exhausted CD8 T cells. KLF4-expressing CD8 T cells in exhaustion contexts showed the features of transitory effector CD8 T cells. Enforced KLF4 expression increased CD8 T cell differentiation into transitory effector subsets and enhanced their antitumor immunity. We further demonstrated that KLF4 also showed a capacity of reinvigorating exhausted CD8 T cells. Last, high KLF4 expression was positively correlated with a favorable prognosis in human patients with cancer. Our study highlights the potential impacts of KLF4 on CD8 T cell exhaustion and antitumor immune therapy.

DOI: https://doi.org/10.1126/sciadv.adc9346
Clin Exp Immunol. 2022 Nov 24. pii: uxac107. [Epub ahead of print]

Mitochondria as disease-relevant organelles in rheumatoid arthritis.

Cornelia M Weyand, Bowen Wu, Tao Huang, Zhaolan Hu, Jörg J Goronzy.

  Mitochondria are the controllers of cell metabolism and are recognized as decision makers in cell death pathways, organizers of cytoplasmic signaling networks, managers of cellular stress responses and regulators of nuclear gene expression. Cells of the immune system are particularly dependent on mitochondrial resources, as they must swiftly respond to danger signals with activation, trafficking, migration, and generation of daughter cells. Analogously, faulty immune responses that lead to autoimmunity and tissue inflammation rely on mitochondria to supply energy, cell building blocks and metabolic intermediates. Emerging data endorse the concept that mitochondrial fitness, and the lack of it, is of particular relevance in the autoimmune disease rheumatoid arthritis (RA) where deviations of bioenergetic and biosynthetic flux affect T cells during early and late stages of disease. During early stages of RA, mitochondrial deficiency allows naïve RA T cells to lose self-tolerance, biasing fundamental choices of the immune system towards immune-mediated tissue damage and away from host protection. During late stages of RA, mitochondrial abnormalities shape the response patterns of RA effector T cells engaged in the inflammatory lesions, enabling chronicity of tissue damage and tissue remodeling. In the inflamed joint, autoreactive T cells partner with metabolically reprogrammed tissue macrophages that specialize in antigen-presentation and survive by adapting to the glucose-deplete tissue microenvironment. Here, we summarize recent data on dysfunctional mitochondria and mitochondria-derived signals relevant in the RA disease process that offer novel opportunities to deter autoimmune tissue inflammation by metabolic interference.

Keywords:  T cells; autoimmunity; macrophages; mitochondria; rheumatoid arthritis; tumor necrosis factor

DOI:  https://doi.org/10.1093/cei/uxac107
Front Aging. 2022 ;3 1045648

The influence of three-dimensional structure on naïve T cell homeostasis and aging.

Simon Lambert, Wenqiang Cao, Huimin Zhang, Alex Colville, Jie-Yu Liu, Cornelia M Weyand, Jorg J Goronzy, Claire E Gustafson.

  A breakdown in cellular homeostasis is thought to drive naïve T cell aging, however the link between naïve T cell homeostasis and aging in humans is poorly understood. To better address this, we developed a lymphoid organoid system that maintains resting naïve T cells for more than 2 weeks, in conjunction with high CD45RA expression. Deep phenotypic characterization of naïve T cells across age identified reduced CD45RA density as a hallmark of aging. A conversion from CD45RAhigh naive cells to a CD45RAlow phenotype was reproduced within our organoid system by structural breakdown, but not by stromal cell aging or reduced lymphocyte density, and mediated by alternative CD45 splicing. Together, these data suggest that external influences within the lymph node microenvironment may cause phenotypic conversion of naïve T cells in older adults.

Keywords:  alternative splicing; homeostasis; immune age; naïve T cells; organoids; secondary lymphoid tissues

DOI:  https://doi.org/10.3389/fragi.2022.1045648
Fish Shellfish Immunol Rep. 2021 Dec;2 100019

Mitochondrial connections with immune system in Zebrafish.

Mariana Abrantes do Amaral, Lais Cavalieri Paredes, Barbara Nunes Padovani, Juliana Moreira Mendonça-Gomes, Luan Fávero Montes, Niels Olsen Saraiva Câmara, Camila Morales Fénero.

  Mitochondria are organelles commonly associated with adenosine triphosphate (ATP) formation through the oxidative phosphorylation (OXPHOS) process. However, mitochondria are also responsible for functions such as calcium homeostasis, apoptosis, autophagy, and production of reactive oxygen species (ROS) that, in conjunction, can lead to different cell fate decisions. Mitochondrial morphology changes rely on nutrients' availability and the bioenergetics demands of the cells, in a process known as mitochondrial dynamics, which includes both fusion and fission. This organelle senses the microenvironment and can modify the cells to either a pro or anti-inflammatory profile. The zebrafish has been increasingly used to research mitochondrial dynamics and its connection with the immune system since the pathways and molecules involved in these processes are conserved on this fish. Several genetic tools and technologies are currently available to analyze the behavior of mitochondria in zebrafish. However, even though zebrafish presents several similar processes known in mammals, the effect of the mitochondria in the immune system has not been so broadly studied in this model. In this review, we summarize the current knowledge in zebrafish studies regarding mitochondrial function and immuno metabolism.

Keywords:  Fish; Immuno metabolism; Immunology; Metabolism; Mitochondria; Mitochondrial functions

DOI:  https://doi.org/10.1016/j.fsirep.2021.100019
Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01571-6. [Epub ahead of print]41(8): 111697

Systematic single-cell pathway analysis to characterize early T cell activation.

Jack A Bibby, Divyansh Agarwal, Tilo Freiwald, Natalia Kunz, Nicolas S Merle, Erin E West, Parul Singh, Andre Larochelle, Fariba Chinian, Somabha Mukherjee, Behdad Afzali, Claudia Kemper, Nancy R Zhang.

  Pathway analysis is a key analytical stage in the interpretation of omics data, providing a powerful method for detecting alterations in cellular processes. We recently developed a sensitive and distribution-free statistical framework for multisample distribution testing, which we implement here in the open-source R package single-cell pathway analysis (SCPA). We demonstrate the effectiveness of SCPA over commonly used methods, generate a scRNA-seq T cell dataset, and characterize pathway activity over early cellular activation. This reveals regulatory pathways in T cells, including an intrinsic type I interferon system regulating T cell survival and a reliance on arachidonic acid metabolism throughout T cell activation. A systems-level characterization of pathway activity in T cells across multiple tissues also identifies alpha-defensin expression as a hallmark of bone-marrow-derived T cells. Overall, this work provides a widely applicable tool for single-cell pathway analysis and highlights regulatory mechanisms of T cells.

Keywords:  CP: Immunology; SCPA; T cell; arachidonic acid; cytokines; gene set; metabolism; pathway analysis; single-cell RNA-seq; single-cell pathway analysis; type I interferon

DOI:  https://doi.org/10.1016/j.celrep.2022.111697
Cells. 2022 Nov 09. pii: 3536. [Epub ahead of print]11(22):

Dopaminergic Signalling Enhances IL-2 Production and Strengthens Anti-Tumour Response Exerted by Cytotoxic T Lymphocytes in a Melanoma Mouse Model.

Ornella Chovar-Vera, Ernesto López, Felipe Gálvez-Cancino, Carolina Prado, Dafne Franz, Diego A Figueroa, Alexandra Espinoza, Claudio Figueroa, Alvaro Lladser, Rodrigo Pacheco.

  Dopamine has emerged as an important regulator of immunity. Recent evidence has shown that signalling through low-affinity dopamine receptors exerts anti-inflammatory effects, whilst stimulation of high-affinity dopamine receptors potentiates immunity in different models. However, the dopaminergic regulation of CD8+ T-cells in anti-tumour immunity remains poorly explored. Here, we studied the role of dopamine receptor D3 (DRD3), which displays the highest affinity for dopamine, in the function of CD8+ T-cells and its consequences in the anti-tumour immune response. We observed that the deficiency of Drd3 (the gene encoding DRD3) in CD8+ T-cells limits their in vivo expansion, leading to an impaired anti-tumour response in a mouse melanoma model. Mechanistic analyses suggest that DRD3 stimulation favours the production of interleukin 2 (IL-2) and the surface expression of CD25, the α-chain IL-2 receptor, which are required for expansion and effector differentiation of CD8+ T-cells. Thus, our results provide genetic and pharmacologic evidence indicating that DRD3 favours the production of IL-2 by CD8+ T-cells, which is associated with higher expansion and acquisition of effector function of these cells, promoting a more potent anti-tumour response in a melanoma mouse model. These findings contribute to understanding how dopaminergic signalling affects the cellular immune response and represent an opportunity to improve melanoma therapy.

Keywords:  CD8+ T-cells; dopamine; tumour

DOI:  https://doi.org/10.3390/cells11223536
Dev Cell. 2022 Nov 21. pii: S1534-5807(22)00760-2. [Epub ahead of print]57(22): 2584-2598.e11

Autophagy promotes cell survival by maintaining NAD levels.

Tetsushi Kataura, Lucia Sedlackova, Elsje G Otten, Ruchika Kumari, David Shapira, Filippo Scialo, Rhoda Stefanatos, Kei-Ichi Ishikawa, George Kelly, Elena Seranova, Congxin Sun, Dorothea Maetzel, Niall Kenneth, Sergey Trushin, Tong Zhang, Eugenia Trushina, Charles C Bascom, Ryan Tasseff, Robert J Isfort, John E Oblong, Satomi Miwa, Michael Lazarou, Rudolf Jaenisch, Masaya Imoto, Shinji Saiki, Manolis Papamichos-Chronakis, Ravi Manjithaya, Oliver D K Maddocks, Alberto Sanz, Sovan Sarkar, Viktor I Korolchuk.

  Autophagy is an essential catabolic process that promotes the clearance of surplus or damaged intracellular components. Loss of autophagy in age-related human pathologies contributes to tissue degeneration through a poorly understood mechanism. Here, we identify an evolutionarily conserved role of autophagy from yeast to humans in the preservation of nicotinamide adenine dinucleotide (NAD) levels, which are critical for cell survival. In respiring mouse fibroblasts with autophagy deficiency, loss of mitochondrial quality control was found to trigger hyperactivation of stress responses mediated by NADases of PARP and Sirtuin families. Uncontrolled depletion of the NAD(H) pool by these enzymes ultimately contributed to mitochondrial membrane depolarization and cell death. Pharmacological and genetic interventions targeting several key elements of this cascade improved the survival of autophagy-deficient yeast, mouse fibroblasts, and human neurons. Our study provides a mechanistic link between autophagy and NAD metabolism and identifies targets for interventions in human diseases associated with autophagic, lysosomal, and mitochondrial dysfunction.

Keywords:  DNA damage; NAD; PARP; Sirtuins; ageing; autophagy; metabolism; mitochondria; mitophagy

DOI:  https://doi.org/10.1016/j.devcel.2022.10.008
Am J Physiol Endocrinol Metab. 2022 Nov 23.

Inosine, Gut Microbiota, and Cancer Immunometabolism.

Elham Samami, Elahe Aleebrahim-Dehkordi, Mehdi Mohebalizadeh, Shakila Yaribash, Amene Saghazadeh, Nima Rezaei.

  This article briefly reviews cancer immunity and the role of gut microbiota in carcinogenesis, followed by an understanding of mechanisms by which inosine is involved in cancer immunometabolism. Constitutional cells of immune systems play a paradoxical role in cancer treatment. Anti-tumor immunity depends on the T-cell priming against tumor antigens, while the pro-tumor signaling is triggered by inflammatory mediators present in the tumor microenvironment. Studies link the microbiome with metabolism and immunity-two main factors implicated in carcinogenesis. Gut microbiota has been shown to affect both anti-tumor immunity and pro-tumor immune signaling. Additionally, there is mounting evidence that the human microbiome can play a role in the immunotherapeutic effects, both response and resistance. Inosine-5'-monophosphate dehydrogenase (IMPDH) is a highly conservative enzyme widely expressed in mammals. Cell signaling pathways utilize molecular inosine, which is a crucial secondary metabolite in purine metabolism and a molecular messenger in the process. Recent research has identified inosine as a critical regulator of immune checkpoint inhibition (ICB) therapeutic response in various tumor types. Three bacterial species, Bifidobacterium pseudopodium, Lactobacillus, and Olsenella, were found to produce inosine or its metabolite hypoxanthine and induce Th1 differentiation and effector functions via the inosine-A2AR-cAMP-PKA pathway upon ICB initiation, after being injected into the systemic circulation. Moreover, inosine acts as a substitute carbon source for T cell metabolism in glucose-restricted environments, i.e., the tumor microenvironment, assisting T cell proliferation and differentiation while enhancing sensitivity to ICB, reinforcing the notion that inosine metabolism may contribute to anti-tumor immunity. Also, inosine is a strong agonist of the adenosine receptor, A2AR, and A2AR signaling can affect T cell responses and anti-tumor immunity, making the inosine-A2AR pathway blockage a candidate for cancer treatment. Further research is required to investigate inosine as a cancer immunometabolism therapy.

Keywords:  Cancer; Immunity; Immunometabolism; Immunotherapy; Inosine

DOI:  https://doi.org/10.1152/ajpendo.00207.2022
iScience. 2022 Dec 22. 25(12): 105526

Survivin promotes a glycolytic switch in CD4+ T cells by suppressing the transcription of PFKFB3 in rheumatoid arthritis.

Malin C Erlandsson, Karin M E Andersson, Nina Y Oparina, Venkataragavan Chandrasekaran, Tibor Saghy, Anastasios Damdimopoulos, Maria-Jose Garcia-Bonete, Zakaria Einbeigi, Sofia T Silfverswärd, Marcela Pekna, Gergely Katona, Maria I Bokarewa.

  In this study, we explore the role of nuclear survivin in maintaining the effector phenotype of IFNγ-producing T cells acting through the transcriptional control of glucose utilization. High expression of survivin in CD4+T cells was associated with IFNγ-dependent phenotype and anaerobic glycolysis. Transcriptome of CD4+ cells and sequencing of survivin-bound chromatin showed that nuclear survivin had a genome-wide and motif-specific binding to regulatory regions of the genes controlling cell metabolism. Survivin coprecipitates with transcription factors IRF1 and SMAD3, which repressed the transcription of the metabolic check-point enzyme phosphofructokinase 2 gene PFKFB3 and promoted anaerobic glycolysis. Combining transcriptome analyses of CD4+ cells and functional studies in glucose metabolism, we demonstrated that the inhibition of survivin reverted PFKFB3 production, inhibited glucose uptake, and reduces interferon effects in CD4+ cells. These results present a survivin-dependent mechanism in coordinating the metabolic adaptation of CD4+T cells and propose an attractive strategy to counteract IFNγ-dependent inflammation in autoimmunity.

Keywords:  Biological sciences; Immunology; Transcriptomics

DOI:  https://doi.org/10.1016/j.isci.2022.105526
Sci Immunol. 2022 Nov 25. 7(77): eabl9467

A central role for STAT5 in the transcriptional programing of T helper cell metabolism.

Alejandro V Villarino, Arian Dj Laurence, Fred P Davis, Luis Nivelo, Stephen R Brooks, Hong-Wei Sun, Kan Jiang, Behdad Afzali, Daniela Frasca, Lothar Hennighausen, Yuka Kanno, John J O'Shea.

Activated lymphocytes adapt their metabolism to meet the energetic and biosynthetic demands imposed by rapid growth and proliferation. Common gamma chain (cγ) family cytokines are central to these processes, but the role of downstream signal transducer and activator of transcription 5 (STAT5) signaling, which is engaged by all cγ members, is poorly understood. Using genome-, transcriptome-, and metabolome-wide analyses, we demonstrate that STAT5 is a master regulator of energy and amino acid metabolism in CD4+ T helper cells. Mechanistically, STAT5 localizes to an array of enhancers and promoters for genes encoding essential enzymes and transporters, where it facilitates p300 recruitment and epigenetic remodeling. We also find that STAT5 licenses the activity of two other key metabolic regulators, the mTOR signaling pathway and the MYC transcription factor. Building on the latter, we present evidence for transcriptome-wide cooperation between STAT5 and MYC in both normal and transformed T cells. Together, our data provide a molecular framework for transcriptional programing of T cell metabolism downstream of cγ cytokines and highlight the JAK-STAT pathway in mediating cellular growth and proliferation.

DOI: https://doi.org/10.1126/sciimmunol.abl9467
J Immunother Cancer. 2022 Nov;pii: e004712. [Epub ahead of print]10(11):

Targeting the CD47/thrombospondin-1 signaling axis regulates immune cell bioenergetics in the tumor microenvironment to potentiate antitumor immune response.

Elizabeth R Stirling, Masaki Terabe, Adam S Wilson, Mitra Kooshki, Liliya M Yamaleyeva, Martha A Alexander-Miller, Wei Zhang, Lance D Miller, Pierre L Triozzi, David R Soto-Pantoja.

  BACKGROUND: CD47 is an integral membrane protein that alters adaptive immunosurveillance when bound to the matricellular glycoprotein thrombospondin-1 (TSP1). We examined the impact of the CD47/TSP1 signaling axis on melanoma patient response to anti-PD-1 therapy due to alterations in T cell activation, proliferation, effector function, and bioenergetics.METHODS: A syngeneic B16 mouse melanoma model was performed to determine if targeting CD47 as monotherapy or in combination with anti-PD-1 impacted tumor burden. Cytotoxic (CD8+) T cells from Pmel-1 transgenic mice were used for T cell activation, cytotoxic T lymphocyte, and cellular bioenergetic assays. Single-cell RNA-sequencing, ELISA, and flow cytometry was performed on peripheral blood mononuclear cells and plasma of melanoma patients receiving anti-PD-1 therapy to examine CD47/TSP1 expression.
RESULTS: Human malignant melanoma tissue had increased CD47 and TSP1 expression within the tumor microenvironment compared with benign tissue. Due to the negative implications CD47/TSP1 can have on antitumor immune responses, we targeted CD47 in a melanoma model and observed a decrease in tumor burden due to increased tumor oxygen saturation and granzyme B secreting CD8+ T cells compared with wild-type tumors. Additionally, Pmel-1 CD8+ T cells exposed to TSP1 had reduced activation, proliferation, and effector function against B16 melanoma cells. Targeting CD47 allowed CD8+ T cells to overcome this TSP1 interaction to sustain these functions. TSP1 exposed CD8+ T cells have a decreased rate of glycolysis; however, targeting CD47 restored glycolysis when CD8+ T cells were exposed to TSP1, suggesting CD47 mediated metabolic reprogramming of T cells. Additionally, non-responding patients to anti-PD-1 therapy had increased T cells expressing CD47 and circulating levels of TSP1 compared with responding patients. Since CD47/TSP1 signaling axis negatively impacts CD8+ T cells and non-responding patients to anti-PD-1 therapy have increased CD47/TSP1 expression, we targeted CD47 in combination with anti-PD-1 in a melanoma model. Targeting CD47 in combination with anti-PD-1 treatment further decreased tumor burden compared with monotherapy and control.
CONCLUSION: CD47/TSP1 expression could serve as a marker to predict patient response to immune checkpoint blockade treatment, and targeting this pathway may preserve T cell activation, proliferation, effector function, and bioenergetics to reduce tumor burden as a monotherapy or in combination with anti-PD-1.

Keywords:  adaptive immunity; immunotherapy; melanoma; metabolic networks and pathways

DOI:  https://doi.org/10.1136/jitc-2022-004712