ATP-citrate lyase links cellular metabolism to histone acetylation

Design, synthesis, and Biological evaluation of novel macrocyclic derivatives as potent ATP-citrate lyase inhibitors

ATP-citrate lyase (ACLY) is a key lipogenic enzyme involved in the synthesis of fatty acid and cholesterol, which converts cytosolic citrate to acetyl-CoA, a starting material for de novo lipogenesis. ACLY inhibitor is considered as potential therapeutic strategy for dyslipidemia and related diseases. In this study, we reported a series of novel macrocyclic derivatives as ACLY inhibitors, among them, compound 55 exhibited potent ACLY inhibitory activity (IC50 = 8.3 nM) and high binding affinity to ACLY. Notably, compound 55 demonstrated good pharmacokinetic profiles and potent in vivo hypolipidemic effect. Collectively, compound 55 deserved further development to provide potential candidate for treatment of hyperlipidemia and related diseases.

SSE-Net: A novel network based on sequence spatial equation for Camellia sinensis lysine acetylation identification

Lysine acetylation (Kace) is one of the most important post-translational modifications. It is key to identify Kace sites for understanding regulation mechanisms in Camellia sinensis. In this study, we defined a mathematical formula, named sequence spatial equation (SSE), which could give each amino acid coordinate in 3-D space by rotating and translating. Based on SSE, an optional network SSE-Net was constructed for representing spatial structure information. Centrality metrics of SSE-Net were used to design structure feature vectors for reflecting the importance of sites. The optimal features were fed into classifier to construct model SSE-ET. The results showed that SSE-ET outperformed the other classifiers. Meanwhile, all MCC results were higher than 0.7 for different machine learning, which indicated that SSE-Net was effective for representing Kace sites in Camellia sinensis. Moreover, we implemented the other models on our dataset. The results of comparison showed that SSE-ET was much more powerful than the others. Specifically, the result of SN was nearly 20 % higher than the other models. These results showed that the proposed SSE was a valuable mathematics concept for reflecting 3-D space Kace site information in Camellia sinensis, and SSE-Net may be an essential complementary for biology and bioinformatics research.

The Warburg effect: The hacked mitochondrial-nuclear communication in cancer

Mitochondrial-nuclear communication is vital for maintaining cellular homeostasis. This communication begins with mitochondria sensing environmental cues and transmitting signals to the nucleus through the retrograde cascade, involving metabolic signals such as substrates for epigenetic modifications, ATP and AMP levels, calcium flux, etc. These signals inform the nucleus about the cell's metabolic state, remodel epigenome and regulate gene expression, and modulate mitochondrial function and dynamics through the anterograde feedback cascade to control cell fate and physiology. Disruption of this communication can lead to cellular dysfunction and disease progression, particularly in cancer. The Warburg effect is the metabolic hallmark of cancer, characterized by disruption of mitochondrial respiration and increased lactate generation from glycolysis. This metabolic reprogramming rewires retrograde signaling, leading to epigenetic changes and dedifferentiation, further reprogramming mitochondrial function and promoting carcinogenesis. Understanding these processes and their link to tumorigenesis is crucial for uncovering tumorigenesis mechanisms. Therapeutic strategies targeting these disrupted pathways, including metabolic and epigenetic components, provide promising avenues for cancer treatment.

Mechanisms of metabolism-coupled protein modifications

Intricate coupling between metabolism and protein post-translational modifications (PTMs) has emerged as a fundamental aspect of cellular regulation. Recent studies demonstrate that protein modifications can originate from diverse metabolites, and that their regulation is closely tied to the cellular metabolic state. Here we explore recently uncovered PTMs, including the concept of 'modification of a modification', as well as associated feedback and feedforward regulatory mechanisms, in which modified proteins impact not only related metabolic pathways but also other signaling cascades affecting physiology and diseases. The recently uncovered role of nucleus-localized metabolic enzymes for histone modifications additionally highlights the importance of cell-compartment-specific metabolic states. We further comment on the utility of untargeted metabolomics and proteomics for previously unrecognized PTMs and associated metabolic patterns. Together, these advances have uncovered a dynamic interplay between metabolism and PTMs, offering new perspectives for understanding metabolic regulation and developing targeted therapeutic strategies.

Augmenting Macrophages Apoptosis Induced by Carnitine Palmitoyl Transferase 1A Inhibition via Acetyl-CoA-Associated Protein Acetylation

Macrophage apoptosis contributes to acute lung injury (ALI). However, the relationship between cell metabolism and the apoptosis of macrophages remains unclear. In our study, murine alveolar macrophages (MH-S) were stimulated by lipopolysaccharide (LPS) to induce an apoptosis model; cell viability, mitochondrial membrane potential (MMP) and apoptosis rate were determined. TCA metabolites and fatty acids were measured; qPCR and western blot were used to detect gene and protein expressions. The LPS-induced ALI mice model was established, and pathological changes, inflammatory cytokines, and protein acetylation were evaluated. The results showed that LPS exposure impaired cell viability and increased apoptosis of alveolar macrophages (AM) in a concentration-dependent manner. LPS also downregulated the expression of the FAO rate-limiting enzyme carnitine palmitoyl transferase 1A (CPT1A), which was accompanied by suppression of fatty acid oxidation (FAO) and alterations of the fatty acid profile. CPT1A inhibitor etomoxir also promoted cell apoptosis of AM and decreased MMP. Overexpression of CPT1A ameliorated cell apoptosis of AM induced by LPS. Etomoxir and LPS decreased acetyl-CoA levels, and supplementation of acetyl-CoA prevented LPS-induced cell apoptosis. In addition, LPS led to the alteration of acetylated protein profiles. In vivo study, excessive cell apoptosis, decreased expression of proteins related to FAO, and decreased acetyl-CoA levels were detected in ALI animal models. Acetyl-CoA could relieve the apoptosis and inflammation in the lung induced by LPS. These findings suggested the essential role of CPT1A and acetyl-CoA in cell apoptosis of AM induced by LPS.

ACLY Promotes Cardiac Fibrosis via the Regulation of DNL and Histone Acetylation

BACKGROUND

ATP citrate lyase (ACLY) is a key enzyme in de novo lipogenesis that generates acetyl-CoA from citrate. Although fatty acids are required for energy production and biomass synthesis in the heart, the regulatory mechanisms of ACLY-mediated de novo lipogenesis in pathological cardiac fibroblasts remain unknown. The aim of this study was to investigate the biological role of ACLY in cardiac remodeling.

METHODS

Adeno-associated virus serotype 9-mediated shRNA targeting Acly was intravenously injected into C57BL/6J male mice. The mice were subsequently continuously infused with a mixture of angiotensin II and phenylephrine. Cardiac phenotypes were evaluated via histological staining. Cell proliferation assays, stable isotope tracing with 13C-labeled glucose, and chromatin immunoprecipitation assays were performed using human cardiac fibroblasts.

RESULTS

ACLY expression was upregulated in the heart sections of mice treated with angiotensin II/phenylephrine, in particular in fibrotic areas. Masson trichrome staining revealed that Acly gene silencing significantly reduced cardiac fibrosis in these mice. Both siRNA-mediated ACLY knockdown and pharmacological ACLY inhibition suppressed the proliferation and expression of fibrous proteins in cultured human cardiac fibroblasts stimulated with transforming growth factor-β. Mechanistically, ACLY inhibition reduced de novo lipogenesis, limiting the fatty acid supply essential for cellular growth and proliferation. It also decreased H3K9 and H3K27 acetylation, in addition to the presence of acetylated H3K9 and H3K27 at the promoter regions of fibrotic genes.

CONCLUSIONS

Our findings demonstrate that ACLY plays an important role in maladaptive cardiac fibrosis. ACLY could be a novel therapeutic target to prevent the development of heart failure.

SIRT3 Represses Vascular Remodeling via Reducing Mitochondrial Ac-CoA Accumulation in Vascular Smooth Muscle Cells

BACKGROUND

Vascular remodeling characterized by vascular smooth muscle cell (VSMC) phenotypic switching is a key pathological process leading to numerous cardiovascular diseases, often accompanied by a decrease in mitochondrial oxidative phosphorylation. However, whether VSMC mitochondrial homeostasis plays a central role in vascular remodeling remains elusive. In this study, we investigated the role of SIRT3 (sirtuin 3), a deacetylase that maintains mitochondrial homeostasis, in vascular remodeling.

METHODS

We established a VSMC-specific SIRT3 knockout mouse and a VSMC-specific SIRT3 overexpression mouse. Mice were infused with Ang II (angiotensin II) to establish the conventional abdominal aortic aneurysm model and underwent carotid artery ligation to establish the neointima formation model to investigate the role of SIRT3 in vascular remodeling. In vitro, quiescent-state VSMCs were stimulated with PDGF-BB (platelet-derived growth factor type BB) to investigate the direct role of SIRT3 in VSMC phenotypic switching, and the detailed mechanisms were investigated.

RESULTS

The expression and activity of SIRT3 were decreased in the aortas from mice with Ang II-induced abdominal aortic aneurysm or ligation-induced neointima formation. VSMC-specific knockout of SIRT3 exacerbated vascular remodeling, whereas overexpression or activation of SIRT3 in VSMCs displayed therapeutic effect. Moreover, the reduction of SIRT3 was shown to increase the expression level of KLF4 (Kruppel-like factor 4), an important transcription factor that orchestrates VSMC phenotypic switching. Mechanistically, SIRT3 repression caused mitochondrial Ac-CoA (acetyl coenzyme A) accumulation that increased acetylated histone 3 lysine 27 levels in the KLF4 gene promoter region. Blockage of mitochondrial Ac-CoA transporting into the cytoplasm by inhibiting ACLY (ATP-citrate lyase) also inhibited VSMC phenotypic switching and thus attenuated vascular remodeling even when SIRT3 was knocked down.

CONCLUSIONS

This study provides evidence that mitochondrial dysfunction induced by SIRT3 inhibition is a major factor leading to VSMC phenotypic switching and vascular remodeling. Restoration of mitochondrial function and inhibition of mitochondrial Ac-CoA accumulation by activation of SIRT3 may help to treat remodeling-related cardiovascular damage.

Targeting the STAT3/ACLY axis attenuates pulmonary inflammation but delays Mycoplasma pneumoniae clearance via citrate metabolism

Airway epithelial cells play a pivotal role in the early host response to Mycoplasma pneumoniae colonization. Our previous study has revealed that M. pneumoniae infection induces metabolic reprogramming in bronchial epithelial cells. However, the mechanisms underlying these metabolic shifts and their contribution to the pathogenesis of pneumonia remain unclear. Herein, we demonstrate that M. pneumoniae infection activates signal transducer and activator of transcription 3 (STAT3), which drives citrate accumulation in airway epithelial cells. Citrate is metabolized by adenosine triphosphate-citrate lyase (ACLY) into acetyl coenzyme A, which is further converted to malonyl coenzyme A, promoting post-translational modifications such as histone acetylation and glyceraldehyde-3-phosphate dehydrogenase malonylation (GAPDH). In vivo, pharmacological inhibition of STAT3 or ACLY attenuated pulmonary inflammation and pro-inflammatory cytokine expression yet paradoxically delayed pathogen clearance, as evidenced by increased colonyforming units in bronchoalveolar lavage fluid and lung tissue. These findings demonstrate that targeting the STAT3/ACLY axis exerts antiinflammatory potential without direct antibacterial activity. Our work highlights the dual regulatory roles of citrate metabolism in inflammation and pathogen control and suggests that combined use of STAT3/ACLY inhibitors with conventional antibiotics may be necessary to achieve both immunomodulation and effective bacterial eradication.

Myeloid Fatty Acid Metabolism Activates Neighboring Hematopoietic Stem Cells to Promote Heart Failure With Preserved Ejection Fraction

BACKGROUND

Despite the high morbidity and mortality of heart failure with preserved ejection fraction (HFpEF), treatment options remain limited. The HFpEF syndrome is associated with a high comorbidity burden, including high prevalence of obesity and hypertension. Although inflammation is implicated to play a key role in HFpEF pathophysiology, underlying causal mechanisms remain unclear.

METHODS

Comparing patient samples and animal models, we defined the innate immune response during HFpEF in situ and through flow cytometry and single-cell RNA sequencing. After identifying transcriptional and cell signatures, we implemented a high-fat diet and hypertensive model of HFpEF and tested roles for myeloid and hematopoietic stem cells during HFpEF. Contributions of macrophage metabolism were also evaluated, including through mass spectrometry and carbon labeling. Primary macrophages were studied ex vivo to gain insight into complementary cell-intrinsic mechanisms.

RESULTS

Here we report evidence that patients with cardiometabolic HFpEF exhibit elevated peripheral blood hematopoietic stem cells. This phenotype was conserved across species in a murine mode of high-fat diet and hypertension. Hematopoietic stem cell proliferation was coupled to striking remodeling of the peripheral hematopoietic stem cell niche and expression of the macrophage adhesion molecule Vcam1. This could be partially inhibited by sodium-glucose cotransporter-2 inhibitors and explained by elevated fatty acid metabolism in macrophage mitochondria, which in turn remodeled the Vcam1 promoter to enhance its expression.

CONCLUSIONS

These findings identify a significant new stem cell signature of cardiometabolic HFpEF and support a role for myeloid maladaptive fatty acid metabolism in the promotion of systemic inflammation and cardiac diastolic dysfunction.

Dynamic metabolic regulation of histone modifications during the yeast metabolic cycle

Eukaryotes achieve a wide range of stable phenotypes by virtue of epigenetic modifications. However, what drives epigenetic diversification in the first place remains an open question. Here, we investigated the dynamic interplay between the production fluxes of epigenetic cosubstrates and histone post-translation modifications (PTMs) in Saccharomyces cerevisiae's Yeast Metabolic Cycle (YMC). We developed a novel approach integrating flux analysis with transcriptomic data to investigate the production fluxes of acetyl-CoA and SAM and their influence on histone marks H3K9Ac and H3K4me3. Our results show that acetyl-CoA and SAM flux dynamics are asynchronous during the YMC, suggesting distinct regulatory roles. Gene ontology analysis revealed that genes whose enrichment of H3K9Ac correlates with acetyl-CoA dynamics are associated with metabolic functions, while genes whose enrichment of H3K4me3 correlates with SAM dynamics are associated with translation processes. Finally, we found evidence that chromatin accessibility on genes promoter regions was a precondition for the metabolic fluxes influencing the enrichment of H3K4me3 and H3K9Ac. These findings support the concept that metabolism provides timely cosubstrates essential for histone PTMs.

The advances in acetylation modification in senescence and aging-related diseases

Aging is a process in which organisms or cells undergo a decline in their functions. Epigenetic modification changes have been recognized as a senescence hallmark in both natural aging and stimulation-induced senescence. An acetylation modification is a dynamic process, which plays a crucial role in the senescence process through DNA stability, metabolism, and signaling pathways. We summarized the role and regulatory pathways of acetylation modifications in senescence. Various cell fate-determining proteins regulate multiple cellular processes through acetylation modifications. These processes interact and coordinate with each other, forming an integrated regulatory network framework that collectively drives cellular senescence via multiple systemic mechanisms. Based on these findings, we proposed the "acetylation-network regulation-cellular senescence" model, to elaborate how acetylation contributes to senescence. We believe this insight could provide new directions and intervention strategies for senescence and aging-related diseases.

Chronic alcohol consumption reprograms hepatic metabolism through organelle-specific acetylation in mice

Post-translational acetylation of proteins by acetyl-CoA is a crucial regulator of proteostasis and substrate metabolism. Ethanol metabolism in the liver induces protein accumulation, acetylation and metabolic disruption. While acetylation impacts enzyme activity and stability, its role in ethanol-related protein accumulation and metabolic dysfunction remains unclear. Using stable isotope-based proteomics, acetylomics, and metabolic profiling in a mouse model of chronic ethanol-induced liver injury, we demonstrate that ethanol induces hepatic steatosis, inflammation, oxidative stress, and proteinopathy linked to altered protein turnover. Ethanol increased the cytosolic protein turnover related to oxidative stress and detoxification, while reducing turnover of mitochondrial metabolic enzymes. It also elevated the acetylation of mitochondrial enzymes and nuclear histones with minimal cytosolic changes, impairing mitochondrial protein degradation. These changes were associated with altered levels of acyl-CoAs and acyl-carnitines, amino acids, and tricarboxylic acid (TCA) cycle intermediates, reflecting impaired fatty acid oxidation, nitrogen disposal and TCA cycle activities. These results suggest that ethanol-induced acetylation contributes to liver injury and that targeting acetylation may offer treatment for alcohol-induced liver diseases.

Trained immunity-based Adjuvated vaccines (TIbAV) approach: β-glucans as example

The induction of trained immunity (TRIM) has emerged as an approach to fight against diseases. Several β-glucans and vaccines have been identified as trained immunity inductors, allowing heterologous protection for infectious diseases. Curiously, β-glucans from yeast, fungal, and plant species have been evaluated in clinical trials as vaccine adjuvants to combat infectious and non-communicable diseases. However, their adjuvant use for trained immunity-based vaccines (TIbV) remains scarcely studied. In this context, this review brings a scientific panorama of β-glucans and vaccines and offers perspectives on their combination to potentiate trained immunity induction and its benefits. In agreement with TRIM and TIbV concepts, we propose trained immunity-based adjuvanted vaccines (TIbAV) to refer to studies regarding this approach.

Unraveling the mystery of citrate transporters in Alzheimer's disease: An updated review

A key molecule in cellular metabolism, citrate is essential for lipid biosynthesis, energy production, and epigenetic control. The etiology of Alzheimer's disease (AD), a progressive neurodegenerative illness marked by memory loss and cognitive decline, may be linked to dysregulated citrate transport, according to recent research. Citrate transporters, which help citrate flow both inside and outside of cells, are becoming more and more recognized as possible participants in the molecular processes underlying AD. Citrate synthase (CS), a key enzyme in the tricarboxylic acid (TCA) cycle, supports mitochondrial function and neurotransmitter synthesis, particularly acetylcholine (ACh), essential for cognition. Changes in CS activity affect citrate availability, influencing energy metabolism and neurotransmitter production. Choline, a precursor for ACh, is crucial for neuronal function. Lipid metabolism, oxidative stress reactions, and mitochondrial function can all be affected by aberrant citrate transport, and these changes are linked to dementia. Furthermore, the two main pathogenic characteristics of AD, tau hyperphosphorylation and amyloid-beta (Aβ) aggregation, may be impacted by disturbances in citrate homeostasis. The goal of this review is to clarify the complex function of citrate transporters in AD and provide insight into how they contribute to the development and course of the illness. We aim to provide an in-depth idea of which particular transporters are dysregulated in AD and clarify the functional implications of these dysregulated transporters in brain cells. To reduce neurodegenerative processes and restore metabolic equilibrium, we have also discussed the therapeutic potential of regulating citrate transport. Gaining insight into the relationship between citrate transporters and the pathogenesis of AD may help identify new indicators for early detection and creative targets for treatment. This study offers hope for more potent ways to fight this debilitating illness and is a crucial step in understanding the metabolic foundations of AD.

The mitochondrial unfolded protein response inhibits pluripotency acquisition and mesenchymal-to-epithelial transition in somatic cell reprogramming

The mitochondrial unfolded protein response (UPRmt), a mitochondria-to-nucleus retrograde pathway that promotes the maintenance of mitochondrial function in response to stress, plays an important role in promoting lifespan extension in Caenorhabditis elegans1,2. However, its role in mammals, including its contributions to development or cell fate decisions, remains largely unexplored. Here, we show that transient UPRmt activation occurs during somatic reprogramming in mouse embryonic fibroblasts. We observe a c-Myc-dependent, transient decrease in mitochondrial proteolysis, accompanied by UPRmt activation at the early phase of pluripotency acquisition. UPRmt impedes the mesenchymal-to-epithelial transition (MET) through c-Jun, thereby inhibiting pluripotency acquisition. Mechanistically, c-Jun enhances the expression of acetyl-CoA metabolic enzymes and reduces acetyl-CoA levels, thereby affecting levels of H3K9Ac, linking mitochondrial signalling to the epigenetic state of the cell and cell fate decisions. c-Jun also decreases the occupancy of H3K9Ac at MET genes, further inhibiting MET. Our findings reveal the crucial role of mitochondrial UPR-modulated MET in pluripotent stem cell plasticity. Additionally, we demonstrate that the UPRmt promotes cancer cell migration and invasion by enhancing epithelial-to-mesenchymal transition (EMT). Given the crucial role of EMT in tumour metastasis3,4, our findings on the connection between the UPRmt and EMT have important pathological implications and reveal potential targets for tumour treatment.

Cholinergic T cells revitalize the tumor immune microenvironment: TIME to ChAT

Crosstalk between the nervous system and the immune system shapes the tumor microenvironment. Cholinergic T cells, a unique population of T cell antigen receptor-induced acetylcholine-producing T cells, have emerged as an integrative interface between these two fundamental body systems. Here we review the distinct characteristics and functions of cholinergic T cells in cancer settings. We first outline the expression of choline acetyltransferase and the cholinergic machinery in T cells. We then describe the dysfunctional state of choline acetyltransferase-expressing T cells in cancer and delve into their modulatory effects on T cells, cancer cells and the tumor microenvironment, including its populations of immune cells, its vasculature and its nerves. We also discuss the clinical implications of harnessing the potential of cholinergic T cells and future directions for increasing our understanding of their importance and possible exploitation.

Mitonuclear Communication in Stem Cell Function

Mitochondria perform multiple functions within the cell, including the production of ATP and a great deal of metabolic intermediates, while also contributing to the cellular stress response. The majority of mitochondrial proteins are encoded by nuclear genomes, highlighting the importance of mitonuclear communication for sustaining mitochondrial homeostasis and functional. As a crucial part of the intracellular signalling network, mitochondria can impact stem cell fate determinations. Considering the essential function of stem cells in tissue maintenance, regeneration and aging, it is important to understand how mitochondria influence stem cell fate. This review explores the significant roles of mitonuclear communication and mitochondrial proteostasis, highlighting their influence on stem cells. We also examine how mitonuclear interactions contribute to cellular homeostasis, stem cell therapies, and the potential for extending lifespan.

Oncogene-induced senescence mitochondrial metabolism and bioenergetics drive the secretory phenotype: further characterization and comparison with other senescence-inducing stimuli

Cellular senescence is characterized by proliferation arrest and a senescence-associated secretory phenotype (SASP), that plays a role in aging and the progression of various age-related diseases. Although various metabolic alterations have been reported, no consensus exists regarding mitochondrial bioenergetics. Here we compared mitochondrial metabolism of human fibroblasts after inducing senescence with different stimuli: the oxidant hydrogen peroxide (H2O2), the genotoxic doxorubicin, serial passage, or expression of the H-RASG12V oncogene (RAS). In senescence induced by H2O2, doxorubicin or serial passage a decrease in respiratory control ratio (RCR) and coupling efficiency was noted, in relation to control cells. On the contrary, oncogene-induced senescent cells had an overall increase in respiration rates, RCR, spare respiratory capacity and coupling efficiency. In oncogene-induced senescence (OIS) the increase in respiration rates was accompanied by an increase in fatty acid catabolism, AMPK activation, and a persistent DNA damage response (DDR), that were not present in senescent cells induced by either H2O2 or doxorubicin. Inhibition of AMPK reduced mitochondrial oxygen consumption and secretion of proinflammatory cytokines in OIS. Assessment of enzymes involved in acetyl-CoA metabolism in OIS showed a 3- to 7.5-fold increase in pyruvate dehydrogenase complex (PDH), a 40% inhibition of mitochondrial aconitase, increased phosphorylation and activation of ATP-citrate lyase (ACLY), and inhibition of acetyl-CoA carboxylase (ACC). There was also a significant increase in expression and nuclear levels of the deacetylase sirtuin 6 (SIRT6). These changes can influence the sub-cellular distribution of acetyl-CoA and modulate protein acetylation reactions in the cytoplasm and nuclei. In fact, ACLY inhibition reduced histone 3 acetylation (H3K9Ac) in OIS and secretion of SASP components. In summary, our data show marked heterogeneity in mitochondrial energy metabolism of senescent cells, depending on the inducing stimulus, reveal new metabolic features of oncogene-induced senescent cells and identify AMPK and ACLY as potential targets for SASP modulation.

Mitochondria - the CEO of the cell

As we have learned more about mitochondria over the past decades, including about their essential cellular roles and how altered mitochondrial biology results in disease, it has become apparent that they are not just powerplants pumping out ATP at the whim of the cell. Rather, mitochondria are dynamic information and energy processors that play crucial roles in directing dozens of cellular processes and behaviors. They provide instructions to enact programs that regulate various cellular operations, such as complex metabolic networks, signaling and innate immunity, and even control cell fate, dictating when cells should divide, differentiate or die. To help current and future generations of cell biologists incorporate the dynamic, multifaceted nature of mitochondria and assimilate modern discoveries into their scientific framework, mitochondria need a 21st century 'rebranding'. In this Opinion article, we argue that mitochondria should be considered as the 'Chief Executive Organelle' - the CEO - of the cell.

Plant-made trained immunity-based vaccines: Beyond one approach

Plant-made vaccines and trained immunity-based vaccines (TIbV or TRAIMbV) represent two strategies for enhancing immunity against diseases. Plants provide an effective and cost-efficient vaccine production platform, while TIbV induces innate immune memory that can protect against both homologous and heterologous diseases. Both strategies are generally compatible; however, they have not been explored in a transdisciplinary manner. Despite their strengths in vaccinology, each faces limitations that hinder widespread adoption and health benefits. This review revisits both strategies, discussing their fundamental knowledge alongside practical and experimental examples, ultimately highlighting their limitations and perspectives to pave the way for a unified approach to combat diseases. Future scenarios are envisioned and presented if research on plant-made trained immunity-based vaccines is adopted.

PKA plays a conserved role in regulating gene expression and metabolic adaptation by phosphorylating Rpd3/HDAC1

Cells need to reprogram their metabolism to adapt to extracellular nutrient changes. The yeast histone acetyltransferase SAGA (Spt-Ada-Gcn5-acetyltransferase) has been reported to acetylate its subunit Ada3 and form homo-dimers to enhance its ability to acetylate nucleosomes and facilitate metabolic gene transcription. How cells transduce extracellular nutrient changes to SAGA structure and function changes remains unclear. Here, we found that SAGA is deacetylated by Rpd3L complex and uncover how its deacetylase activity is repressed by nutrient sensor protein kinase A (PKA). When sucrose is used as the sole carbon source, PKA catalytic subunit Tpk2 is activated, which phosphorylates Rpd3L catalytic subunit Rpd3 to inhibit its ability to deacetylate Ada3. Moreover, Tpk2 phosphorylates Rpd3L subunit Ash1, which specifically reduces the interaction between Rpd3L and SAGA. By phosphorylating both Rpd3 and Ash1, Tpk2 inhibits Rpd3L-mediated Ada3 deacetylation, which promotes SAGA dimerization, nucleosome acetylation and transcription of genes involved in sucrose utilization and tricarboxylate (TCA) cycle, resulting in metabolic shift from glycolysis to TCA cycle. Most importantly, PKA phosphorylates HDAC1, the Rpd3 homolog in mammals to repress its deacetylase activity, promote TCA cycle gene transcription and facilitate cell growth. Our work hence reveals a conserved role of PKA in regulating Rpd3/HDAC1 and metabolic adaptation.

The Evolving Role of Macrophage Metabolic Reprogramming in Obesity

Recent research has extensively explored the critical role of energy metabolism in shaping the inflammatory response and polarization of macrophages in obesity. This rapidly growing field emphasizes the need to understand the connection between metabolic processes that support macrophage polarization in obesity. Although most published research in this area has focused on glucose and fatty acids, how the flux through other metabolic pathways (such as ketone and amino acid oxidation) in macrophages is altered in obesity is not well defined. This review summarizes the main alterations in uptake, storage, and oxidation of oxidative substrates (glucose, fatty acids, ketone bodies, and amino acids) in macrophages and how these alterations are linked to macrophage polarization and contribution to augmented inflammatory markers in obesity. The review also discusses how oxidative substrates could modulate macrophage energy metabolism and inflammatory responses via feeding into other nonoxidative pathways (such as the pentose phosphate pathway, triacylglycerol synthesis/accumulation), via acting as signalling molecules, or via mediating post-translational modifications (such as O-GlcNAcylation or β-hydroxybutyrylation). The review also identifies several critical unanswered questions regarding the characteristics (functional and metabolic) of macrophages from different origins (adipose tissue, skeletal muscle, bone marrow) in obesity and how these characteristics contribute to early vs late phases of obesity. We also identified a number of new therapeutic targets that could be evaluated in future investigations. Targeting macrophage metabolism in obesity is an exciting and active area of research with significant potential to help identify new treatments to limit the detrimental effects of inflammation in obesity.

Unraveling the nexus: Genomic instability and metabolism in cancer

The DNA-damage response (DDR) is a signaling network that enables cells to detect and repair genomic damage. Over the past three decades, inhibiting DDR has proven to be an effective cancer therapeutic strategy. Although cancer drugs targeting DDR have received approval for treating various cancers, tumor cells often develop resistance to these therapies, owing to their ability to undergo energetic metabolic reprogramming. Metabolic intermediates also influence tumor cells' ability to sense oxidative stress, leading to impaired redox metabolism, thus creating redox vulnerabilities. In this review, we summarize recent advances in understanding the crosstalk between DDR and metabolism. We discuss combination therapies that target DDR, metabolism, and redox vulnerabilities in cancer. We also outline potential obstacles in targeting metabolism and propose strategies to overcome these challenges.

Alpha-synuclein mutations mislocalize cytoplasmic p300 compromising autophagy, which is rescued by ACLY inhibition

Triplications and certain point mutations in the SNCA gene, encoding alpha-synuclein (α-Syn), cause Parkinson's disease (PD). Here, we demonstrate that the PD-causing A53T α-Syn mutation and elevated α-Syn expression perturb acetyl-coenzyme A (CoA) and p300 biology in human neurons and in the CNS of zebrafish and mice. This dysregulation is mediated by activation of ATP-citrate lyase (ACLY), a key enzyme that generates acetyl-CoA in the cytoplasm, via two mechanisms. First, ACLY activity increases acetyl-CoA levels, which activate p300. Second, ACLY activation increases LKB1 acetylation, which inhibits AMPK, leading to increased cytoplasmic and decreased nuclear p300. This lowers histone acetylation and increases acetylation of cytoplasmic p300 substrates, like raptor, which causes mechanistic target of rapamycin complex 1 (mTORC1) hyperactivation, thereby impairing autophagy. ACLY inhibitors rescue pathological phenotypes in PD neurons, organoids, zebrafish, and mouse models, suggesting that this pathway is a core feature of α-Syn toxicity and that ACLY may be a suitable therapeutic target.

ATP citrate lyase is an essential player in the metabolic rewiring induced by PTEN loss during T-ALL development

ABSTRACT

Alterations inactivating the tumor suppressor gene PTEN drive the development of solid and hematologic cancers, such as T-cell acute lymphoblastic leukemia (T-ALL), in which phosphatase and tensin homolog (PTEN) loss defines poor-prognosis patients. We investigated the metabolic rewiring induced by PTEN loss in T-ALL, aiming to identify novel metabolic vulnerabilities. We showed that the enzyme adenosine triphosphate (ATP) citrate lyase (ACLY) is strictly required for the transformation of thymic immature progenitors and the growth of human T-ALL, which remain dependent on ACLY activity even upon transformation. Although Pten-mutant mice all died within 17 weeks, the concomitant Acly deletion prevented disease initiation in 70% of the animals. In these animals, ACLY promoted B-cell lymphoma (BCL-2) epigenetic upregulation and prevented the apoptosis of premalignant double-positive thymocytes. Transcriptomic and metabolic analysis of primary T-ALL cells next translated our findings to the human pathology, showing that PTEN-altered T-ALL cells activate ACLY and are sensitive to its genetic targeting. ACLY activation thus represents a metabolic vulnerability with therapeutic potential for high-risk patients with T-ALL.

HIF-1 regulates mitochondrial function in bone marrow-derived macrophages but not in tissue-resident alveolar macrophages

HIF-1α plays a critical role in shaping macrophage phenotype and effector function. We have previously shown that tissue-resident alveolar macrophages (TR-AMs) have extremely low glycolytic capacity at steady-state but can shift toward glycolysis under hypoxic conditions. Here, we generated mice with tamoxifen-inducible myeloid lineage cell specific deletion of Hif1a (Hif1afl/fl:LysM-CreERT2+/-) and from these mice, we isolated TR-AMs and bone marrow-derived macrophages (BMDMs) in which Hif1a is deleted. We show that TR-AM HIF-1α is required for the glycolytic shift under prolyl hydroxylase inhibition but is dispensable at steady-state for inflammatory effector function. In contrast, HIF-1α deletion in BMDMs led to diminished glycolytic capacity at steady-state and reduced inflammatory capacity, but higher mitochondrial function. Gene set enrichment analysis revealed enhanced c-Myc transcriptional activity in Hif1a-/- BMDMs, and upregulation of gene pathways related to ribosomal biogenesis and cellular proliferation. We conclude that HIF-1α regulates mitochondrial function in BMDMs but not in TR-AMs. The findings highlight the heterogeneity of HIF-1α function in distinct macrophage populations and provide new insight into how HIF-1α regulates gene expression, inflammation, and metabolism in different types of macrophages.

PI3Kβ functions as a protein kinase to promote cellular protein O-GlcNAcylation and acetyl-CoA production for tumor growth

Phosphatidylinositol 3-kinase (PI3K) phosphorylates PI(4,5)P2 to produce PI(3,4,5)P3, thereby activating AKT and other effector proteins. However, whether PI3K has non-PI(3,4,5)P3-related functions critical for tumor development remains unclear. Here, we demonstrate that high glucose induces PI3Kβ binding to O-linked β-D-N-acetylglucosamine (O-GlcNAc) transferase (OGT) in glioblastoma cells, dependent on hexokinase 1 (HK1)-mediated OGT Y889 phosphorylation and subsequent p85α recruitment. Importantly, PI3Kβ functions as a protein kinase, phosphorylating OGT at T985 and enhancing OGT activity and total cellular protein O-GlcNAcylation. Activated OGT O-GlcNAcylates ATP-citrate synthase (ACLY) at T639 and S667, leading to ACLY activation-dependent acetyl-coenzyme A (CoA) production to increase fatty acid levels and histone H3 acetylation for gene transcription. Intervention in PI3Kβ-mediated OGT phosphorylation and ACLY O-GlcNAcylation inhibits glioblastoma cell proliferation and tumor growth in xenografts. These findings underscore the critical role of PI3Kβ in governing protein O-GlcNAcylation, fatty acid metabolism, and chromatin modification through its protein kinase activity and provide instrumental insight into the roles of PI3K in tumor progression.

ACC1 is a dual metabolic-epigenetic regulator of Treg stability and immune tolerance

OBJECTIVE

Regulatory T cells (Tregs) are essential in maintaining immune tolerance and controlling inflammation. Treg stability relies on transcriptional and post-translational mechanisms, including histone acetylation at the Foxp3 locus and FoxP3 protein acetylation. Additionally, Tregs depend on specific metabolic programs for differentiation, yet the underlying molecular mechanisms remain elusive. We aimed to investigate the role of acetyl-CoA carboxylase 1 (ACC1) in the differentiation, stability, and function of regulatory T cells (Tregs).

METHODS

We used either T cell-specific ACC1 knockout mice or ACC1 inhibition via a pharmacological agent to examine the effects on Treg differentiation and stability. The impact of ACC1 inhibition on Treg function was assessed in vivo through adoptive transfer models of Th1/Th17-driven inflammatory diseases.

RESULTS

Inhibition or genetic deletion of ACC1 led to an increase in acetyl-CoA availability, promoting enhanced histone and protein acetylation, and sustained FoxP3 transcription even under inflammatory conditions. Mice with T cell-specific ACC1 deletion exhibited an enrichment of double positive RORγt+FoxP3+ cells. Moreover, Tregs treated with an ACC1 inhibitor demonstrated superior long-term stability and an enhanced capacity to suppress Th1/Th17-driven inflammatory diseases in adoptive transfer models.

CONCLUSIONS

We identified ACC1 as a metabolic checkpoint in Treg biology. Our data demonstrate that ACC1 inhibition promotes Treg differentiation and long-term stability in vitro and in vivo. Thus, ACC1 serves as a dual metabolic and epigenetic hub, regulating immune tolerance and inflammation by balancing de novo lipid synthesis and protein acetylation.

Metabolic reprogramming and interventions in angiogenesis

BACKGROUND

Endothelial cell (EC) metabolism plays a crucial role in the process of angiogenesis. Intrinsic metabolic events such as glycolysis, fatty acid oxidation, and glutamine metabolism, support secure vascular migration and proliferation, energy and biomass production, as well as redox homeostasis maintenance during vessel formation. Nevertheless, perturbation of EC metabolism instigates vascular dysregulation-associated diseases, especially cancer.

AIM OF REVIEW

In this review, we aim to discuss the metabolic regulation of angiogenesis by EC metabolites and metabolic enzymes, as well as prospect the possible therapeutic opportunities and strategies targeting EC metabolism.

KEY SCIENTIFIC CONCEPTS OF REVIEW

In this work, we discuss various aspects of EC metabolism considering normal and diseased vasculature. Of relevance, we highlight that the implications of EC metabolism-targeted intervention (chiefly by metabolic enzymes or metabolites) could be harnessed in orchestrating a spectrum of pathological angiogenesis-associated diseases.

Trained immunity-based mucosal immunotherapies for the prevention of respiratory infections

The devastating impact of respiratory infections demonstrates the critical need for novel prophylactic vaccines. In this opinion article, we advocate for bacterial immunotherapies as a complementary tool in our fight against respiratory infections. These immunotherapies can activate a wide spectrum of immunological mechanisms, with trained immunity (TI) being particularly significant. This phenomenon has led to the concept of trained immunity-based vaccines (TIbVs), which represent a novel approach in vaccinology. We discuss examples of TIbVs, including the tuberculosis vaccine Bacille Calmette-Guérin (BCG) and the polybacterial immunotherapy MV130. From our viewpoint, illustrating the mode of action and clinical evidence supports the proposal that TIbVs should be considered as next-generation vaccines to confer protection against a wide range of respiratory infections.

Crosstalk between metabolism and epigenetics during macrophage polarization

Macrophage polarization is a dynamic process driven by a complex interplay of cytokine signaling, metabolism, and epigenetic modifications mediated by pathogens. Upon encountering specific environmental cues, monocytes differentiate into macrophages, adopting either a pro-inflammatory (M1) or anti-inflammatory (M2) phenotype, depending on the cytokines present. M1 macrophages are induced by interferon-gamma (IFN-γ) and are characterized by their reliance on glycolysis and their role in host defense. In contrast, M2 macrophages, stimulated by interleukin-4 (IL-4) and interleukin-13 (IL-13), favor oxidative phosphorylation and participate in tissue repair and anti-inflammatory responses. Metabolism is tightly linked to epigenetic regulation, because key metabolic intermediates such as acetyl-coenzyme A (CoA), α-ketoglutarate (α-KG), S-adenosylmethionine (SAM), and nicotinamide adenine dinucleotide (NAD+) serve as cofactors for chromatin-modifying enzymes, which in turn, directly influences histone acetylation, methylation, RNA/DNA methylation, and protein arginine methylation. These epigenetic modifications control gene expression by regulating chromatin accessibility, thereby modulating macrophage function and polarization. Histone acetylation generally promotes a more open chromatin structure conducive to gene activation, while histone methylation can either activate or repress gene expression depending on the specific residue and its methylation state. Crosstalk between histone modifications, such as acetylation and methylation, further fine-tunes macrophage phenotypes by regulating transcriptional networks in response to metabolic cues. While arginine methylation primarily functions in epigenetics by regulating gene expression through protein modifications, the degradation of methylated proteins releases arginine derivatives like asymmetric dimethylarginine (ADMA), which contribute directly to arginine metabolism-a key factor in macrophage polarization. This review explores the intricate relationships between metabolism and epigenetic regulation during macrophage polarization. A better understanding of this crosstalk will likely generate novel therapeutic insights for manipulating macrophage phenotypes during infections like tuberculosis and inflammatory diseases such as diabetes.

Mitochondrial reactive oxygen species regulate acetyl-CoA flux between cytokine production and fatty acid synthesis in effector T cells

Genetic and environmental factors shape an individual's susceptibility to autoimmunity. To identify genetic variations regulating effector T cell functions, we used a forward genetics screen of inbred mouse strains and uncovered genomic loci linked to cytokine expression. Among the candidate genes, we characterized a mitochondrial inner membrane protein, TMEM11, as an important determinant of Th1 responses. Loss of TMEM11 selectively impairs Th1 cell functions, reducing autoimmune symptoms in mice. Mechanistically, Tmem11-/- Th1 cells exhibit altered cristae architecture, impaired respiration, and increased mitochondrial reactive oxygen species (mtROS) production. Elevated mtROS hindered histone acetylation while promoting neutral lipid accumulation. Further experiments using genetic, biochemical, and pharmacological tools revealed that mtROS regulate acetyl-CoA flux between histone acetylation and fatty acid synthesis. Our findings highlight the role of mitochondrial cristae integrity in directing metabolic pathways that influence chromatin modifications and lipid biosynthesis in Th1 cells, providing new insights into immune cell metabolism.

Pyruvate Regulates the Expression of DLAT to Promote Follicular Growth

Increasing evidence has suggested that dihydrolipoamide S-acetyltransferase (DLAT), a subunit of the pyruvate dehydrogenase complex, is crucial for pyruvate metabolism and the regulation of cell death. The excessive death of granulosa cells (GCs) hinders the progression of follicular growth. However, the relationship between DLAT and follicular growth is poorly understood. Here, we found that pyruvate significantly shortened the age of pubertal initiation in mice and promoted follicular growth by promoting the proliferation of GCs. In addition, pyruvate up-regulated the expression of DLAT and the high level of DLAT was observed in large follicles, which were associated with follicular growth. Mechanistically, DLAT increased the mRNA and protein levels of proliferation pathways such as PCNA and MCL1 to promote GC proliferation. Additionally, DLAT bound to CASP3 and CASP9 proteins to inhibit the apoptosis of GCs. Taken together, these results reveal a mechanism that pyruvate regulated DLAT to promote follicular growth, and DLAT represents a promising target that supports new strategies for improving the growth of follicles.

Nanomedicines Targeting Metabolic Pathways in the Tumor Microenvironment: Future Perspectives and the Role of AI

Background: Tumor cells engage in continuous self-replication by utilizing a large number of resources and capabilities, typically within an aberrant metabolic regulatory network to meet their own demands. This metabolic dysregulation leads to the formation of the tumor microenvironment (TME) in most solid tumors. Nanomedicines, due to their unique physicochemical properties, can achieve passive targeting in certain solid tumors through the enhanced permeability and retention (EPR) effect, or active targeting through deliberate design optimization, resulting in accumulation within the TME. The use of nanomedicines to target critical metabolic pathways in tumors holds significant promise. However, the design of nanomedicines requires the careful selection of relevant drugs and materials, taking into account multiple factors. The traditional trial-and-error process is relatively inefficient. Artificial intelligence (AI) can integrate big data to evaluate the accumulation and delivery efficiency of nanomedicines, thereby assisting in the design of nanodrugs. Methods: We have conducted a detailed review of key papers from databases, such as ScienceDirect, Scopus, Wiley, Web of Science, and PubMed, focusing on tumor metabolic reprogramming, the mechanisms of action of nanomedicines, the development of nanomedicines targeting tumor metabolism, and the application of AI in empowering nanomedicines. We have integrated the relevant content to present the current status of research on nanomedicines targeting tumor metabolism and potential future directions in this field. Results: Nanomedicines possess excellent TME targeting properties, which can be utilized to disrupt key metabolic pathways in tumor cells, including glycolysis, lipid metabolism, amino acid metabolism, and nucleotide metabolism. This disruption leads to the selective killing of tumor cells and disturbance of the TME. Extensive research has demonstrated that AI-driven methodologies have revolutionized nanomedicine development, while concurrently enabling the precise identification of critical molecular regulators involved in oncogenic metabolic reprogramming pathways, thereby catalyzing transformative innovations in targeted cancer therapeutics. Conclusions: The development of nanomedicines targeting tumor metabolic pathways holds great promise. Additionally, AI will accelerate the discovery of metabolism-related targets, empower the design and optimization of nanomedicines, and help minimize their toxicity, thereby providing a new paradigm for future nanomedicine development.

Metabolic expression profiling analysis reveals pyruvate-mediated EPHB2 upregulation promotes lymphatic metastasis in head and neck squamous cell carcinomas

Lymphatic metastasis is a well-known factor for initiating distant metastasis of head and neck squamous cell carcinoma (HNSCC), which caused major death in most patients with cancer. Meanwhile, metabolic reprogramming to support metastasis is regarded as a prominent hallmark of cancers. However, how metabolic disorders drive in HNSCC remains unclear. We firstly established a new classification of HNSCC patients based on metabolism gene expression profiles from the TCGA and GEO database, and identified an enriched carbohydrate metabolism subgroup which was significantly associated with lymphatic metastasis and worse clinical outcome. Moreover, we found that highly activated pyruvate metabolism endowed tumors with EPHB2 upregulation and promoted tumor lymphangiogenesis independently of VEGF-C/VEGFR3 signaling pathway. Mechanically, high nuclear acetyl-CoA production from pyruvate metabolism promoted histone acetylation, which in turn transcriptionally upregulated EPHB2 expression and secretion in tumor cells. EPHB2 bound with EFNB1 in lymphatic endothelial cells promoted YAP/TAZ cytoplasmic retention, which alleviated YAP/TAZ-mediated prospero homeobox protein 1 (PROX1) transcriptional repression, and then triggered tumor lymphangiogenesis. Importantly, combined treatment with EFNB1-Fc and VEGFR3 inhibitor synergistic abrogated lymphangiogenesis in vitro and in vivo, suggesting that targeting EPHB2 might be a potential strategy to patients with no or slight response to VEGFR3 inhibitor. These findings uncover the mechanism by which pyruvate metabolism is linked to lymphatic metastasis of tumor and provides a promising therapeutic strategy for the prevention of HNSCC metastasis.

Research on the mechanism of resistance exercise in promoting glucose metabolic shift to regulate muscle satellite cell proliferation in type 2 diabetic rats

Skeletal muscle atrophy is a common complication in patients with type 2 diabetes (T2D) and is associated with dysfunction of muscle satellite cells. The activation and proliferation of muscle satellite cells involve a switch in glucose metabolism, which is regulated by driving the acetylation of histones to control the expression of related genes. Studies have confirmed that resistance exercise can improve insulin resistance and activate muscle satellite cells, but the specific molecular mechanisms are not yet clear. This study aims to investigate whether resistance exercise can promote the proliferation of muscle satellite cells and improve muscle atrophy in type 2 diabetic rats by enhancing glucose metabolism in skeletal muscles. A T2D rat model was induced by combining a high-fat diet with streptozotocin injection. After 8 weeks of resistance exercise, the activity of key enzymes (Pyruvate Kinase, Phosphofructokinase, Pyruvate Dehydrogenase) in glucose metabolism in the skeletal muscles of T2D rats significantly increased, the expression of Sirtuin 1 (Sirt1) and Nicotin -amide Phosphoribosyltransferase (Nampt) in the skeletal muscles of the rats decreased, and the expression of acetylation of lysine 16 on histone H4 (H4K16ac) significantly increased, indicating an elevated level of the H4K16ac. The expression of paired box 7 (Pax7) and myogenic differentiation (MyoD) was significantly upregulated, indicating that exercise promoted the proliferation of muscle satellite cells. These results suggest that resistance exercise may promote glucose metabolism in skeletal muscles of T2D rats by regulating the activity of key enzymes in sugar metabolism, further regulating Sirt1-mediated histone H4K16ac, thereby promoting the proliferation of muscle satellite cells and improving muscle atrophy.

Regulation of gene expression through protein-metabolite interactions

Organisms have to adapt to changes in their environment. Cellular adaptation requires sensing, signalling and ultimately the activation of cellular programs. Metabolites are environmental signals that are sensed by proteins, such as metabolic enzymes, protein kinases and nuclear receptors. Recent studies have discovered novel metabolite sensors that function as gene regulatory proteins such as chromatin associated factors or RNA binding proteins. Due to their function in regulating gene expression, metabolite-induced allosteric control of these proteins facilitates a crosstalk between metabolism and gene expression. Here we discuss the direct control of gene regulatory processes by metabolites and recent progresses that expand our abilities to systematically characterize metabolite-protein interaction networks. Obtaining a profound map of such networks is of great interest for aiding metabolic disease treatment and drug target identification.

Histone acetylation and BRD4 binding are associated with induction of TNF mRNA expression by temporal high-glucose exposure and subsequent low-glucose culture in juvenile macrophage-like THP-1 cells

BACKGROUND

Postprandial hyperglycemia induces expression of inflammatory cytokines including tumor necrosis factor (TNF), which promotes the onset of type 2 diabetes and cardiovascular diseases. In this study, we investigated whether a transient high-glucose culture enhanced sustained expression of TNF, or whether the induction is associated with histone acetylation, and bromodomain protein containing protein 4 (BRD4), which binds acetylated histone, in human juvenile macrophage-like THP-1 cells.

METHODS

THP-1 cells were cultured in medium with high-glucose in the presence or absence of (+)-JQ1, an inhibitor of bromodomain and extra-terminal domain family, for 24 h (day 0). Thereafter, the cells were returned to a low-glucose medium without (+)-JQ1 and cultured for 2 or 4 days and samples were collected. mRNA expression of inflammation genes, and histone H3 K9/14 acetylation and binding of BRD4 and RNA polymerase II around the TNF gene were measured by RT-qPCR and chromatin immunoprecipitation, respectively.

RESULTS

TNF mRNA levels, histone H3 K9/14 acetylation, and bindings of BRD4 and RNA polymerase II to the TNF gene were higher in cells exposed to high-glucose culture for 24 h and subsequently cultured in low-glucose medium for 2-4 days, compared with cells cultured in a low-glucose medium. The addition of (+)-JQ1 to the high-glucose medium for 24 h reduced histone H3 K9/14 acetylation, and BRD4 and RNA polymerase II bindings around TNF gene, and the mRNA levels.

CONCLUSIONS

Histone H3 K9/14 acetylation and BRD4 binding are associated with the sustained expression of TNF mRNA induced by temporal high-glucose exposure in juvenile macrophage-like THP-1 cells.

Impact of fish oil on epigenetic regulation in perirenal adipose tissue of obese mice

It has been demonstrated that fish oil (FO), a source of omega-3 polyunsaturated fatty acids (n-3 PUFA), offers partial protection to mice from the adverse effects of a high-fat diet (HFD) by altering the expression of genes involved in adipogenesis and adipocyte metabolism. Histone 3 lysine 27 (H3K27) modifiers, namely Ezh2, Kdm6a, Kdm6b, Crebbp and Ep300, are vital for the appropriate differentiation and metabolism of adipocytes, as they can either silence or activate transcription. The expansion of perirenal adipose tissue (AT) in obesity is associated with a number of complications, including hypertension and kidney disease. The aim of this study was to assess the expression of H3K27 modifiers and genes involved in adipogenesis and adipocyte metabolism in perirenal AT of HFD-fed and FO-treated (5DHA:1EPA) mice using real-time PCR. This study demonstrates, for the first time, that a high-fat diet (HFD) increases the expression of Kdm6b (H3K27 demethylase) in perirenal AT, and that treatment with FO can completely reverse this effect. Conversely, the expression of the Acly gene, which encodes an enzyme that provides a substrate for histone acetylases, was found to be reduced in HFD-fed mice and this was not reversed by FO treatment. Additionally, transcription factor genes, such as Tbx1, exhibited diminished expression in perirenal AT of mice fed an HFD. These observations suggest that a HFD affects the expression of chromatin modifiers, transcription factors, and metabolic genes in perirenal AT, and that FO can reverse some of these effects, offering a promising avenue for the treatment of obesity.

Cytometry at the Intersection of Metabolism and Epigenetics in Lymphocyte Dynamics

Landmark studies at the turn of the century revealed metabolic reprogramming as a driving force for lymphocyte differentiation and function. In addition to metabolic changes, differentiating lymphocytes must remodel their epigenetic landscape to properly rewire their gene expression. Recent discoveries have shown that metabolic shifts can shape the fate of lymphocytes by altering their epigenetic state, bringing together these two areas of inquiry. The ongoing evolution of high-dimensional cytometry has enabled increasingly comprehensive analyses of metabolic and epigenetic landscapes in lymphocytes that transcend the technical limitations of the past. Here, we review recent insights into the interplay between metabolism and epigenetics in lymphocytes and how its dysregulation can lead to immunological dysfunction and disease. We also discuss the latest technical advances in cytometry that have enabled these discoveries and that we anticipate will advance future work in this area.

Long-chain acylcarnitine deficiency promotes hepatocarcinogenesis

Despite therapy with potent antiviral agents, chronic hepatitis B (CHB) patients remain at high risk of hepatocellular carcinoma (HCC). While metabolites have been rediscovered as active drivers of biological processes including carcinogenesis, the specific metabolites modulating HCC risk in CHB patients are largely unknown. Here, we demonstrate that baseline plasma from CHB patients who later developed HCC during follow-up exhibits growth-promoting properties in a case-control design nested within a large-scale, prospective cohort. Metabolomics analysis reveals a reduction in long-chain acylcarnitines (LCACs) in the baseline plasma of patients with HCC development. LCACs preferentially inhibit the proliferation of HCC cells in vitro at a physiological concentration and prevent the occurrence of HCC in vivo without hepatorenal toxicity. Uptake and metabolism of circulating LCACs increase the intracellular level of acetyl coenzyme A, which upregulates histone H3 Lys14 acetylation at the promoter region of KLF6 gene and thereby activates KLF6/p21 pathway. Indeed, blocking LCAC metabolism attenuates the difference in KLF6/p21 expression induced by baseline plasma of HCC/non-HCC patients. The deficiency of circulating LCACs represents a driver of HCC in CHB patients with viral control. These insights provide a promising direction for developing therapeutic strategies to reduce HCC risk further in the antiviral era.

Macrophage metabolic reprogramming: A trigger for cardiac damage in autoimmune diseases

Macrophage metabolic reprogramming has a central role in the progression of autoimmune and auto-inflammatory diseases. The heart is a major target organ in many autoimmune conditions and can sustain functional and structural impairments, potentially leading to irreversible cardiac damage. There is mounting clinical evidence pointing to a link between autoimmune disease and cardiac damage. However, this association remains poorly understood, and numerous patients do not receive appropriate preventive measures, which poses serious cardiovascular risks and significantly impacts their quality of life. This review discusses the relationship between macrophage metabolic reprogramming and cardiac damage in patients with autoimmune diseases and the role of adaptive immunity in macrophage reprogramming. It also provides an overview of the immunosuppressive therapies used at present. Exploiting the properties of macrophage reprogramming could lead to development of novel treatments for patients with autoimmune-related cardiac damage.

ACSS2 and metabolic diseases: from lipid metabolism to therapeutic target

Elevated incidence of metabolic disorders has been reported worldwide in the recent decade, highlighting the need for developing efficient therapies. These diseases result from a complex interplay of various factors that contribute to disease progression, complications, and resistance to current treatment options. Acetyl-CoA Synthetase Short Chain Family Member 2 (ACSS2) is a nucleo-cytosolic enzyme with both lipogenic and metabolic regulatory roles. Studies on ACSS2 have shown that it is involved in pathways commonly dysregulated in metabolic disorders, leading to fat deposition and disrupted cellular signaling. Although multiple studies have suggested a role of ACSS2 in the metabolic rewiring during tumorigenesis, few studies have examined its involvement in the pathophysiology of metabolic diseases. Recent evidence indicates that ACSS2 may contribute to the pathogenesis of various metabolic disorders making its examination of great interest and potentially aiding in the development of new therapeutic strategies. The objective of this review is to summarize the current understanding of ACSS2's role in metabolic disorders and its potential as a therapeutic target.

A genetically encoded fluorescent biosensor for visualization of acetyl-CoA in live cells

Acetyl-coenzyme A is a central metabolite that participates in many cellular pathways. Evidence suggests that acetyl-CoA metabolism is highly compartmentalized in mammalian cells. Yet methods to measure acetyl-CoA in living cells are lacking. Herein, we engineered an acetyl-CoA biosensor from the bacterial protein PanZ and circularly permuted green fluorescent protein (cpGFP). The sensor, "PancACe," has a maximum change of ∼2-fold and a response range of ∼10 μM-2 mM acetyl-CoA. We demonstrated that the sensor has a greater than 7-fold selectivity over coenzyme A, butyryl-CoA, malonyl-CoA, and succinyl-CoA, and a 2.3-fold selectivity over propionyl-CoA. We expressed the sensor in E. coli and showed that it enables detection of rapid changes in acetyl-CoA levels. By localizing the sensor to either the cytoplasm, nucleus, or mitochondria in human cells, we showed that it enables subcellular detection of changes in acetyl-CoA levels, the magnitudes of which agreed with an orthogonal PicoProbe assay.

Lactylation in cancer: metabolic mechanism and therapeutic strategies

Recent progress in cancer metabolism research has identified lactylation as a critical post-translational modification influencing tumor development and progression. The process relies on lactate accumulation and the activation of lactate-sensitive acyltransferases. Beyond its role in epigenetic regulation, lactylation has emerged as a significant factor in tumor metabolism and evolution, offering fresh opportunities for developing targeted therapies that transcend traditional approaches. This review explores the growing importance of lactylation in cancer biology and highlights its potential for advancing diagnostic tools and therapeutic strategies.

ATP-CITRATE LYASEB1 supplies materials for sporopollenin biosynthesis and microspore development in Arabidopsis

Acetyl-CoA is the main substrate of lipid metabolism and functions as an energy source for plant development. In the cytoplasm, acetyl-CoA is mainly produced by ATP-citrate lyase (ACL), which is composed of ACLA and ACLB subunits. In this study, we isolated the restorer-4 (res4) of the thermo-sensitive genic male sterile mutant reversible male sterile-2 (rvms-2) in Arabidopsis (Arabidopsis thaliana). RES4 encodes ACLB1, and res4 harbors a point mutation (Gly584 to Arg) in the citryl-CoA lyase domain. Both the ACLA and ACLB subunits are expressed in the tapetal layer of anthers. RES4 is regulated by MS188, and the res4 point mutation leads to pollen with a defective exine structure. In res4, lipid accumulation was significantly reduced within the tapetum and locules. These results indicate that acetyl-CoA synthesized by ACL is used for sporopollenin biosynthesis in the tapetum. Microspore diameter was significantly smaller in res4 than in wild type, indicating that acetyl-CoA from the tapetum supplies microspore development. Previous studies have shown that delayed degradation of the tetrad wall in res2 and res3 provides additional protection for rvms-2 microspores. The reduced volume of res4 microspores may lessen the requirement for cell wall protection to restore rvms-2 fertility. This study reveals the function of ACL in anther development and the mechanisms of fertility restoration in photoperiod- and thermo-sensitive genic male sterile lines.

Metabolization of microbial postbiotic pentanoate drives anti-cancer CAR T cells

The microbiome is a complex host factor and key determinant of the outcome of antibody-based and cellular immunotherapy. Its postbiotics are a blend of soluble commensal byproducts that are released into the host environment and have been associated with the regulation of immune homeostasis, particularly through impacts on epigenetics and cell signaling. In this study, we show that the postbiotic pentanoate is metabolized to citrate within the TCA cycle via both the acetyl- and succinyl-CoA entry points, a feature uniquely enabled by the chemical structure of the C5 aliphatic chain. We identified ATP-citrate lyase as the crucial factor that redirects pentanoate-derived citrate from the succinyl-CoA route to the nucleus, thereby linking metabolic output and histone acetylation. This epigenetic-metabolic crosstalk mitigated T cell exhaustion and promoted naive-like differentiation in pentanoate-programmed chimeric antigen receptor (CAR) T cells. The predictive and therapeutic potential of pentanoate was corroborated in two independent patient cohorts and three syngeneic models of CAR T adoptive therapy. Our data demonstrate that postbiotics are integrated into mitochondrial metabolism and subsequently incorporated as epigenetic imprints. This bridge between microbial and mammalian interspecies communication can ultimately impact T cell differentiation and efficacy.

CitGATA7 interact with histone acetyltransferase CitHAG28 to promote citric acid degradation by regulating the glutamine synthetase pathway in citrus

Organic acid is a crucial indicator of fruit quality traits. Citric acid, the predominant organic acid in citrus fruit, directly influences its edible quality and economic value. While the transcriptional regulatory mechanisms of citric acid metabolism have been extensively studied, the understanding about the transcriptional and epigenetic co-regulation mechanisms is limited. This study characterized a transcription factor, CitGATA7, which directly binds to and activates the expression of genes associated with the glutamine synthetase pathway regulating citric acid degradation. These genes include the aconitase encoding gene CitACO3, the isocitrate dehydrogenase encoding gene CitIDH1, and the glutamine synthetase encoding gene CitGS1. Furthermore, CitGATA7 physically interacts with the histone acetyltransferase CitHAG28 to enhance histone 3 acetylation levels near the transcription start site of CitACO3, CitIDH1, and CitGS1, thereby increasing their transcription and promoting citric acid degradation. The findings demonstrate that the CitGATA7-CitHAG28 protein complex transcriptionally regulate the expression of the GS pathway genes, i.e., CitACO3, CitIDH1, and CitGS1, via histone acetylation, thus promoting citric acid catabolism. This study establishes a direct link between transcriptional regulation and histone acetylation regarding citric acid metabolism, providing insights for strategies to manipulate organic acid accumulation in fruit.

Mitochondrial CLPB is a pro-survival factor at the onset of granulocytic differentiation of mouse myeloblastic cells

Loss-of-function mutations in the CLPB gene lead to congenital neutropenia due to impaired neutrophil differentiation. CLPB, a member of the AAA+ family of proteins, resides in the intermembrane space of mitochondria. The mechanism by which a loss of CLPB elicits defects in the differentiation program of neutrophil precursor cells is not understood. Here, we used 32D clone 3 (32Dcl3) cells, an interleukin-3 (IL-3)-dependent mouse myeloblastic cell line model, to investigate the effects of CLPB knockout on myeloblast-to-neutrophil differentiation in vitro. We found that CLPB-deficient 32Dcl3 cells showed a decreased mitochondrial membrane potential and increased levels of insoluble HAX1 aggregates in mitochondria, as compared to control cells. Despite those abnormalities, CLPB loss did not affect cell proliferation rates in the presence of IL-3 but it increased apoptosis after IL-3 withdrawal and simultaneous induction of cell differentiation with granulocytic colony stimulating factor (G-CSF). CLPB-deficient cells that survived the stress associated with IL-3 withdrawal/G-CSF treatment expressed the same levels of differentiation markers as control cells. Moreover, we found that increased apoptosis of CLPB-deficient cells is linked to production of reactive oxygen species (ROS). N-acetylcysteine, exogenous free fatty acids, or exogenous citrate protected CLPB-deficient 32Dcl3 cells from apoptosis at the onset of differentiation. The protective effect of citrate was abolished by inhibition of ATP-citrate lyase (ACLY), an enzyme that converts cytosolic citrate into acetyl-CoA, a substrate for protein acetylation. We propose that citrate supplementation may help mitigate the effects of CLPB loss by facilitating ACLY-dependent ROS detoxification in granulocytic precursor cells.

IL-7 promotes integrated glucose and amino acid sensing during homeostatic CD4+ T cell proliferation

Interleukin (IL)-7 promotes T cell expansion during lymphopenia. We studied the metabolic basis in CD4+ T cells, observing increased glucose usage for nucleotide synthesis and oxidation in the tricarboxylic acid (TCA) cycle. Unlike other TCA metabolites, glucose-derived citrate does not accumulate upon IL-7 exposure, indicating diversion into other processes. In agreement, IL-7 promotes glucose-dependent histone acetylation and chromatin accessibility, notable at the loci of the amino acid-sensing Ragulator complex. Consistently, the expression of its subunit late endosomal/lysosomal adaptor, MAPK and mTOR activator 5 (LAMTOR5) is promoted by IL-7 in a glucose-dependent manner, and glucose availability determines amino acid-dependent mechanistic target of rapamycin (mTOR) activation, confirming integrated nutrient sensing. LAMTOR5 deletion impairs IL-7-mediated T cell expansion, establishing that glycolysis in the absence of Ragulator activation is insufficient to support this. Clinically, CD4+ T cells from stem cell transplant recipients demonstrate coordinated upregulation of glycolytic and TCA cycle enzymes, amino acid-sensing machinery, and mTOR targets, highlighting the potential to therapeutically target this pathway to fine-tune lymphopenia-induced T cell proliferation.