Metabolic analysis of mouse bone-marrow-derived dendritic cells using an extracellular flux analyzer

Tolerogenic dendritic cell-mediated regulatory T cell differentiation by Chinese herbal formulation attenuates colitis progression

INTRODUCTION

Ulcerative colitis (UC) is a chronic inflammatory disease characterized by loss of immune tolerance to luminal antigens and progressive intestinal tissue injury. Thus, the re-establishment of immune tolerance is crucial for suppressing aberrant immune responses and UC progression.

OBJECTIVES

This study aimed to investigate the mechanisms underlying the action of CDD-2103 and its bioactive compounds in mediating immune regulation in mouse models of colitis.

METHODS

Two experimental colitis models, chronic 2,4,6-trinitrobenzene sulfonic acid (TNBS)- and T-cell transfer-induced Rag1-/- mice, were used to determine the effects of CDD-2103 on colitis progression. Single-cell transcriptome analysis was used to profile the immune landscape and its interactions after CDD-2103 treatment. Liquid chromatography-mass spectrometry (LC-MS) was used to analyze the major components interacting with lymphoid cells. A primary cell co-culture system was used to confirm the effects of bioactive component.

RESULTS

CDD-2103 dose-dependently suppresses the progression of colitis induced by chemicals or T cell transplantation in Rag1-/- mice. The effect of CDD-2103 is primarily attributable to an increase in the de novo generation of regulatory T cells (Tregs) in the lamina propria (LP). Single-cell transcriptomic analysis revealed that CDD-2103 treatment increased the number of tolerogenic dendritic cells (DCs). Mechanistically, CDD-2103 promoted tolerogenic DCs accumulation and function by upregulating several genes in the electron transport chain related to oxidative phosphorylation, leading to increased differentiation of Tregs. Further LC-MS analysis identified several compounds in CDD-2103, particularly those distributed within the mesenteric lymph nodes of mice. Subsequent studies revealed that palmatine and berberine promoted tolerogenic bone marrow-derived dendritic cells (BMDC)-mediated Treg differentiation.

CONCLUSION

Overall, our study demonstrated that the clinically beneficial effect of CDD-2103 in the treatment of UC is based on the induction of immune tolerance. In addition, this study supports berberine and palmatine as potential chemical entities in CDD-2103 that modulate immune tolerance.

Analyzing mitochondrial respiration of human induced pluripotent stem cell-derived myeloid progenitors using Seahorse technology

Mitochondrial metabolism is critical in hematopoietic stem cell maintenance and differentiation. Here, we present a step-by-step protocol to efficiently differentiate human induced pluripotent stem cells into myeloid progenitors by a robust feeder- and serum-free system. Furthermore, we provide a protocol to subsequently assess mitochondrial function in iPSC-derived myeloid progenitors. We comprehensively describe a protocol to analyze and to quantify key parameters of mitochondrial respiration of iPSC-derived myeloid progenitors by the Seahorse XFe96 Analyzer. Additionally, our protocol includes extensive troubleshooting suggestions. For complete details on the use and execution of this protocol, please refer to Fan et al. (2022).1.

Putrescine accelerates the differentiation of bone marrow derived dendritic cells via inhibiting phosphorylation of STAT3 at Tyr705

Dendritic cells (DCs) play pivotal roles in immune responses. The differentiation and function of DCs are regulated by environmental metabolites. Putrescine is ubiquitous in various metabolic microenvironments and its immunoregulation has been of increasing interest. However, the mechanisms associated with its DC-induced immunoregulation remain unclear. In this study, we found putrescine promoted induction of immature bone marrow derived DCs (BMDCs), along with the increased phagocytosis and migration, and altered cytokine secretion in immature BMDCs. Transcriptomic profiles indicated significantly impaired inflammatory-related pathways, elevated oxidative phosphorylation, and decreased p-STAT3 (Tyr705) expression. Additionally, putrescine performed minor influence on the lipopolysaccharide (LPS)-induced maturation of BMDCs but significantly impaired LPS-induced DC-elicited allogeneic T-cell proliferation as well as the cytokine secretion. Furthermore, molecular docking and dynamics on the conjugation between putrescine and STAT3 revealed that putrescine could be stably bound to the hydrophilic cavity in STAT3 and performed significant influence on the Tyr705 phosphorylation. CUT&Tag analysis uncovered altered motifs, downregulated IFN-γ response, and upregulated p53 pathway in Putrescine group compared with Control group. In summary, our results demonstrated for the first time that putrescine might accelerate the differentiation of BMDCs by inhibiting the phosphorylation of STAT3 at Tyr705. Given that both DCs and putrescine have ubiquitous and distinct roles in various immune responses and pathogeneses, our findings may provide more insights into polyamine immunoregulation on DCs, as well as distinct strategies in the clinical utilization of DCs by targeting polyamines.

Live-cell metabolic analysis of oligodendroglia isolated from postnatal mouse brain and spinal cord

This protocol describes isolation and live-cell metabolic analysis of O4+ oligodendroglia from brain and spinal cord of postnatal mice. We have optimized existing protocols for O4+ isolation from neonatal brain and expanded the protocol to include isolation of highly viable oligodendroglia from spinal cords of postnatal mice up to 18 days of age. Isolated oligodendroglia can be used in multiple downstream analyses, and here we describe an optimized real-time metabolic assay using Agilent Seahorse Analyzer to measure mitochondrial respiration. For complete details on the use and execution of this protocol, please refer to Khandker et al. (2022).

Isolation of human and mouse myeloid-derived suppressor cells for metabolic analysis

Metabolic reprogramming is associated with myeloid-derived suppressor cell (MDSC) immunosuppressive function. Here, we outline the process for acquiring MDSCs from human and murine sources for subsequent analysis of fatty acid oxidation, oxidative phosphorylation, and glycolysis using the Seahorse XFe 96 Analyzer. Murine MDSCs can be isolated directly from tumor-bearing mice or derived through IL-6 and GM-CSF culture of bone marrow cells from non-tumor-bearing mice. To generate human MDSCs, peripheral blood mononuclear cells (PBMCs) can be cultured with IL-6 and GM-CSF. For complete details on the use and execution of this protocol, please refer to Mohammadpour et al. (2021).

Protocol for the assessment of human T cell activation by real-time metabolic flux analysis

The elevation of glycolysis in autoreactive T cells is a key target for the prevention and treatment of T cell-related autoimmune diseases, such as type 1 diabetes (T1D). Here, we describe a simple and efficient protocol for isolating human peripheral blood mononuclear cells (PBMCs) and T cells, and the subsequent assessment of T cell glycolysis using Seahorse analyzer. This protocol is useful to analyze different subsets of T cells and applicable to different autoimmune disease models (i.e., T1D, multiple sclerosis). For complete details on the use and execution of this profile, please refer to Kong et al. (2021).

Attenuating Effect of Chlorella Extract on NLRP3 Inflammasome Activation by Mitochondrial Reactive Oxygen Species

The NOD-like receptor family, pyrin domain-containing protein 3 (NLRP3) inflammasome has been linked to the pathogenesis of a wide variety of human diseases. Although many drugs and inhibitors have been developed to treat NLRP3-associated diseases, only limited clinical data support their efficacy and safety. Chlorella, a unicellular green alga that is widely and safely used as a food supplement, contains various antioxidants. In this study, we obtained a fat-soluble extract from Chlorella (CE) and demonstrated that it reduced NLRP3 inflammasome activation by inhibiting mitochondrial reactive oxygen species and caspase-1 activation. In addition, CE supplementation attenuated lipopolysaccharide-induced interleukin 1β transcription through activation of hypoxia-inducible factor 1α in vitro and in vivo. As Chlorella is a safe and useful food supplement, it may be a practical pharmacological approach for treating NLRP3-driven diseases.

Measuring CPT-1-mediated respiration in permeabilized cells and isolated mitochondria

Carnitine palmitoyltransferase-1 (CPT-1) is a rate-controlling enzyme for long-chain fatty acid oxidation. This manuscript provides protocols for measuring CPT-1-mediated respiration in permeabilized, adherent cell monolayers and mitochondria freshly isolated from tissue, along with examples to assess the potency and specificity of interventions targeting CPT-1. Strengths of the approach include ease, speed, and breadth of analysis, whereas drawbacks include loss of physiological regulation in reductionist systems and indirect assessment of CPT-1 enzymatic activity.

For complete details on the use and execution of this protocol, please refer to Divakaruni et al. (2018).

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Protocol for pathway-specific respiration using Seahorse XF Analyzer

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Detailed steps for both isolated mitochondria and plasma membrane-permeabilized cells

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Examples given for specific inhibition of long-chain fatty acid oxidation

Mitochondrial Reactive Oxygen Species Are Essential for the Development of Psoriatic Inflammation

Psoriasis is a common immune-mediated, chronic, inflammatory skin disease that affects approximately 2-3% of the population worldwide. Although there is increasing evidence regarding the essential roles of the interleukin (IL)-23/IL-17 axis and dendritic cell (DC)-T cell crosstalk in the development of skin inflammation, the contributions of mitochondrial function to psoriasis are unclear. In a mouse model of imiquimod (IMQ)-induced psoriasiform skin inflammation, we found that hematopoietic cell-specific genetic deletion of p32/C1qbp, a regulator of mitochondrial protein synthesis and metabolism, protects mice from IMQ-induced psoriatic inflammation. Additionally, we demonstrate that p32/C1qbp is an important regulator of IMQ-induced DC activation, both in vivo and in vitro. We also found that p32/C1qbp-deficient DCs exhibited impaired production of IL-1β, IL-23, and mitochondrial reactive oxygen species (mtROS) after IMQ stimulation. Because the inhibition of mtROS suppressed IMQ-induced DC activation and psoriatic inflammation, we presume that p32/C1qbp and mtROS can serve as therapeutic targets in psoriasis.