Mitochondrial TCA cycle metabolites control physiology and disease

Consumption of sucrose-water rewires macronutrient uptake and utilization mechanisms in a tissue specific manner

Consumption of sugar-sweetened beverages (SSBs) have been linked to metabolic dysfunction, obesity, diabetes and enhanced risk of cardiovascular diseases across all age-groups globally. Decades of work that have provided insights into pathophysiological manifestations of sucrose overfeeding have employed paradigms that rarely mimic human consumption of SSBs. Thus, our understanding of multiorgan cross-talk and molecular and/or cellular mechanisms, which operate across scales and drive physiological derangement is still poor. By employing a paradigm of sucrose water feeding in mice that closely resembles chronic SSB consumption in humans (10% sucrose in water), we have unraveled hitherto unknown tissue-specific mechanistic underpinnings, which contribute towards perturbed physiology. Our findings illustrate that systemic impaired glucose homeostasis, mediated by hepatic gluconeogenesis and insulin resistance, does not involve altered gene expression programs in the liver. We have discovered the pivotal role of the small intestine, which in conjunction with liver and muscles, drives dyshomeostasis. Importantly, we have uncovered rewiring of molecular mechanisms in the proximal intestine that is either causal or consequential to systemic ill-effects of chronic sucrose water consumption including dysfunction of liver and muscle mitochondria. Tissue-specific molecular signatures, which we have unveiled as the primary outcome, clearly indicate that inefficient utilization of glucose is exacerbated by enhanced uptake by the gut. Besides providing systems-wide mechanistic insights, we propose that consumption of SSBs causes intestinal 'molecular addiction' for deregulated absorption of hexose-sugars, and drives diseases such as diabetes and obesity.

Metabolic profiling of abdominal subcutaneous adipose tissue reveals effects of apple polyphenols for reversing high-fat diet induced obesity in C57BL/6 J mice

Apple polyphenols (APP) can reduce obesity. However, the effects of APP on abdominal subcutaneous adipose tissue (aSAT) at metabolic level were unclear. In this study, 5-week APP intervenes were conducted on 10-week high-fat diet (HFD) feeding mice with doses of 200 and 500 mg/kg b.w./day, followed by ultra-high-performance liquid chromatography-mass spectrometry based untargeted metabolomics analysis. As expected, APP obviously reversed aSAT weight and index, as well as activities of myeloperoxidase, glutathione peroxidase, superoxide dismutase and catalase. Euclidean distance between HFD and normal chow diet (NCD) group was shortened. 64 and 127 differential metabolites were found in 200 and 500 mg/kg b.w./day group, with 12 and 13 changed pathways, respectively. Specifically, APP restored glycolysis, tricarboxylic acid cycle, amino acid metabolism, and lipid metabolism as dose-dependent manner. Finally, glucose-6-phosphate, xanthine and tyrosine were selected as critical junctures. Collectively, these findings underscore the potential of APP in reversing molecular alterations in aSAT.

Metabolism and therapeutic response in acute myeloid leukemia with IDH1/2 mutations

Pathogenic variants of isocitrate dehydrogenase 1 and 2 (IDH1/2) genes are present in approximately 20% of acute myeloid leukemia (AML) cases, resulting in the oncometabolite R-2-hydroxyglutarate (R-2-HG). The accumulation of R-2-HG in leukemic cells and in their niche induces epigenetic modifications, profound rewiring of the cellular metabolism, and microenvironmental remodeling. These changes promote cellular differentiation bias, enhancing the survival and proliferation of leukemic cells, and thus playing a pivotal role in leukemogenesis and resistance to standard AML therapy. This review focuses on the different perspectives offered by studying metabolism and resistance to standard treatments in AML with IDH1 or IDH2 pathogenic variants, for the development of new biomarkers and therapeutic solutions.

PHEMI-Phenylbutyrate in Patients With Lactic Acidosis: A Pilot, Single Arm, Phase I/II, Open-Label Trial

PURPOSE

The 6 months pilot, single arm, phase I/II, open-label clinical trial PHEMI investigated the safety and efficacy of daily administration of phenylbutyrate in reducing lactic acidosis by at least 20% in 3 children (ages 7-10 yrs) with pyruvate dehydrogenase deficiency and 6 adults with mitochondrial myopathy encephalopathy lactic acidosis and stroke-like episodes. As a side study, we investigated the response to phenylbutyrate treatment in skin fibroblasts and cybrids derived from PHEMI patients with the aim of unraveling a possible in vivo-in vitro correlation.

METHODS

Safety was assessed through the collection of vital signs, clinical evaluations, blood samples, and reported adverse events. Efficacy was evaluated on biochemical and clinical endpoints. In vitro analysis explored the effects of phenylbutyrate in patients' fibroblasts and cybrids.

FINDINGS

At the starting dosage regimen of 10 g/m2/day, phenylbutyrate was effective in reducing lactic acidosis (by a mean of 13%), but lead to the development of adverse events in all adults. The reduced dose of 5 g/m²/day was well tolerated but did not meet the study's primary outcome. In parallel, the in vitro analyses confirmed that phenylbutyrate led to a reduction in lactate measured in culture medium, an increase in cellular respiration, and a slight increase in the activity of the Respiratory Chain Complexes.

IMPLICATIONS

Our study fosters further research on phenylbutyrate in individuals with primary mitochondrial disease suffering from lactic acidosis. Future investigation should focus on a highly bioavailable, easier-to-administer drug formulation that allows the administration of a lower dosage regimen.

Metabolism in hematology: Technological advances open new perspectives on disease biology and treatment

The term metabolism refers to the multi-faceted biochemical reactions within a cell or an organism that occur to maintain energy homeostasis, cell growth, and oxidative balance. Cells possess a high metabolic plasticity, allowing them to adapt to the dynamic requirements of their functional state and environment. Deregulated cellular metabolism is a hallmark of many diseases, including benign and malignant hematological conditions. In the last decade, multiple technological innovations in the metabolism field have made in-depth metabolic analysis broadly applicable. Such studies are shedding new light on normal and malignant hematopoiesis and open avenues to a better understanding of the biology of hematological diseases. In this review, we will first give a brief overview of central metabolic processes. Furthermore, we discuss the most commonly used methods to study metabolism. We begin by elaborating on the use of next-generation sequencing to detect metabolism-related genomic mutations and study transcriptional signatures. Furthermore, we discuss methods for measuring protein expression, such as mass spectrometry (MS), flow cytometry, and cytometry time-of-flight. Next, we describe the use of nuclear magnetic resonance spectroscopy, MS, and flow cytometry for metabolite quantification. Finally, we highlight functional assays to probe metabolic pathways in real-time. We illustrate how these technologies and their combination have advanced our understanding of the role of metabolism. Our goal is to provide hematologists with a comprehensive guide to modern techniques in metabolism research, their benefits and disadvantages, and how they guide our understanding of disease and potentially future personalized therapy decisions.

[1H-13C]-NMR-Based Metabolic Kinetics Reveals Brain Neurochemical Alterations in Mice After Retinal Ischemia-Reperfusion Injury

Retinal ischemia-reperfusion injury (RIRI) is a pathological process that occurs in various blinding eye diseases and is often accompanied by anxiety and depression. However, the underlying metabolic mechanism of mood disorders remains unclear. This study aimed to investigate the metabolic dynamics of the brain after RIRI. C57BL/6 J mice were used to establish the RIRI model and assessed after 1 and 7 days. Mood-related behaviors were examined using open-field, elevated plus-maze, and forced swimming tests. Retinal injury histology was assessed using retinal hematoxylin and eosin staining. Retinal apoptosis was measured via the TdT-mediated dUTP nick-end labeling staining. The 13C-labeled metabolite information for six brain regions of interest was obtained using the [1H-13C]-NMR technique. Retinal tissue damage and cell apoptosis in the retina were observed 1 and 7 days after RIRI. One day after RIRI, mice displayed anxiety- and depression-like behaviors, and multiple metabolites involved in the glutamine (Gln)/glutamate (Glu)-γ-aminobutyric acid (GABA) and tricarboxylic acid (TCA) cycles exhibited reductions in all studied brain regions, with frontal cortex (FC) and temporal cortex (TC) being the most markedly altered. Metabolites and behavioral indicators nearly returned to normal after 7 days. Significant positive correlations between Gln/Glu-GABA and TCA cycle metabolites were observed in the RIRI brain. The results revealed that within a short period after RIRI, there was a reduction in brain metabolites and a disruption of the Gln/Glu-GABA and TCA cycles, which may contribute to mood disorders in mice.

Enhanced methanogenesis of wastewater anaerobic digestion by nanoscale zero-valent iron: Mechanism on intracellular energy conservation and amino acid metabolism

Nanoscale zero-valent iron (nZVI)-mediated anaerobic digestion commonly focuses on electron transfer between syntrophic bacteria, neglecting intracellular energy conservation strategies and amino acid metabolism. In this study, F420H2 dehydrogenase abundance increased by 5.1 %, 27.0 %, and 31.5 % at 10 mM, mM， 30 mM, and 50 mM nZVI dosing, respectively, enabling an efficient transmembrane proton-coupled electron transfer mode. Electron bifurcation (EB) enzymes involved in methanogenesis responded differently to nZVI, with HdrA2B2C2 initially increasing at 10 mM and decreasing at 30 mM and 50 mM, while MvhADG-HdrABC was completely down-regulated. Metabolomics further demonstrated that nZVI reduced riboflavin and flavin mononucleotide content, which is detrimental to the EB. Instead, an alternative measure to maintain electron flow and energy conservation under high nZVI exposure is high expression of ndh and F-type or V/A-type ATPase genes. Additionally, enhancing C1-unit carrier expression through amino acid metabolism regulation emerged as a key strategy. This study provides new perspectives on nZVI-mediated anaerobic digestion.

Structure of mitochondrial pyruvate carrier and its inhibition mechanism

The mitochondrial pyruvate carrier (MPC) governs the entry of pyruvate-a central metabolite that bridges cytosolic glycolysis with mitochondrial oxidative phosphorylation-into the mitochondrial matrix1-5. It thus serves as a pivotal metabolic gatekeeper and has fundamental roles in cellular metabolism. Moreover, MPC is a key target for drugs aimed at managing diabetes, non-alcoholic steatohepatitis and neurodegenerative diseases4-6. However, despite MPC's critical roles in both physiology and medicine, the molecular mechanisms underlying its transport function and how it is inhibited by drugs have remained largely unclear. Here our structural findings on human MPC define the architecture of this vital transporter, delineate its substrate-binding site and translocation pathway, and reveal its major conformational states. Furthermore, we explain the binding and inhibition mechanisms of MPC inhibitors. Our findings provide the molecular basis for understanding MPC's function and pave the way for the development of more-effective therapeutic reagents that target MPC.

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.

Microbiota, mitochondria, and epigenetics in health and disease: converging pathways to solve the puzzle

Dysbiosis, which refers to an imbalance in the composition of the gut microbiome, has been associated with a range of metabolic disorders, including type 2 diabetes, obesity, and metabolic syndrome. Although the exact mechanisms connecting gut dysbiosis to these conditions are not fully understood, various lines of evidence strongly suggest a substantial role for the interaction between the gut microbiome, mitochondria, and epigenetics. Current studies suggest that the gut microbiome has the potential to affect mitochondrial function and biogenesis through the production of metabolites. A well-balanced microbiota plays a pivotal role in supporting normal mitochondrial and cellular functions by providing metabolites that are essential for mitochondrial bioenergetics and signaling pathways. Conversely, in the context of illnesses, an unbalanced microbiota can impact mitochondrial function, leading to increased aerobic glycolysis, reduced oxidative phosphorylation and fatty acid oxidation, alterations in mitochondrial membrane permeability, and heightened resistance to cellular apoptosis. Mitochondrial activity can also influence the composition and function of the gut microbiota. Because of the intricate interplay between nuclear and mitochondrial communication, the nuclear epigenome can regulate mitochondrial function, and conversely, mitochondria can produce metabolic signals that initiate epigenetic changes within the nucleus. Given the epigenetic modifications triggered by metabolic signals from mitochondria in response to stress or damage, targeting an imbalanced microbiota through interventions could offer a promising strategy to alleviate the epigenetic alterations arising from disrupted mitochondrial signaling.

Mitochondrial NADPH fuels mitochondrial fatty acid synthesis and lipoylation to power oxidative metabolism

Nicotinamide adenine dinucleotide phosphate (NADPH) is a vital electron donor essential for macromolecular biosynthesis and protection against oxidative stress. Although NADPH is compartmentalized within the cytosol and mitochondria, the specific functions of mitochondrial NADPH remain largely unexplored. Here we demonstrate that NAD+ kinase 2 (NADK2), the principal enzyme responsible for mitochondrial NADPH production, is critical for maintaining protein lipoylation, a conserved lipid modification necessary for the optimal activity of multiple mitochondrial enzyme complexes, including the pyruvate dehydrogenase complex. The mitochondrial fatty acid synthesis (mtFAS) pathway utilizes NADPH for generating protein-bound acyl groups, including lipoic acid. By developing a mass-spectrometry-based method to assess mammalian mtFAS, we reveal that NADK2 is crucial for mtFAS activity. NADK2 deficiency impairs mtFAS-associated processes, leading to reduced cellular respiration and mitochondrial translation. Our findings support a model in which mitochondrial NADPH fuels the mtFAS pathway, thereby sustaining protein lipoylation and mitochondrial oxidative metabolism.

Biomarkers of GH deficiency identified in untreated and GH-treated Pit-1 mutant mice

Background

Growth Hormone Deficiency (GHD) is marked by insufficient growth hormone (GH) production, leading to disruptions in growth and metabolism. Its diagnosis is challenging due to the lack of sensitive, specific tests. To address this, we used a novel mouse model with a POU1F1 (Pit-1) gene mutation (K216E). This study aimed to identify metabolic biomarkers of GHD and assess their responsiveness to GH therapy, alongside pathway analysis to uncover disrupted metabolic pathways.

Methods

The Pit-1^K216E mouse model was validated for GHD through assessments of GH production, growth, and body composition. Metabolomic profiling was conducted to identify biomarkers, while pathway analysis examined disrupted metabolic pathways and their response to GH treatment. This approach aimed to improve understanding of GHD's metabolic impact and potential therapeutic strategies.

Results

The assessment of the Pit-1^K216E mouse confirmed GHD, as evidenced by reduced GH production and altered body composition. Metabolomic profiling identified three distinct biomarker groups associated with GHD: (1) GHD Biomarkers, found exclusively in GH-deficient mutant mice but absent in WT controls; (2) GH Treatment Responsive Biomarkers, which were altered in GH-deficient mutant mice (GHD) and further modulated following GH treatment, reflecting a response specific to the GHD condition and its treatment, but not observed in WT mice; and (3) GH Treatment-Specific Responsive Biomarkers, observed exclusively in the GHD condition after GH therapy. Pathway analysis revealed significant disruptions in purine metabolism, amino acid metabolism, and protein synthesis, with notable sex-specific differences. Male mice exhibited imbalances in taurine and hypotaurine metabolism, while female mice showed disruptions in tyrosine metabolism and mitochondrial function, highlighting sex-dependent metabolic responses to GHD and GH therapy.

Conclusion

The Pit-1^K216E mouse model offers a robust platform for exploring GHD's molecular mechanisms. The identification of distinct, sex-specific metabolic biomarkers provides insights into GHD-related metabolic disruptions and supports personalized management strategies. These findings establish a framework for leveraging metabolic biomarkers to enhance the diagnosis and monitoring of GHD, with promising applications for future human studies and therapeutic strategies.

Cytokines from parasites: manipulating host responses by molecular mimicry

Helminth parasites have evolved sophisticated methods for manipulating the host immune response to ensure long-term survival in their chosen niche, for example, by secreting products that interfere with the host cytokine network. Studies on the secretions of Heligmosomoides polygyrus have identified a family of transforming growth factor-β (TGF-β) mimics (TGMs), which bear no primary amino acid sequence similarity to mammalian TGF-β, but functionally replicate or antagonise TGF-β effects in restricted cell types. The prototypic member, TGM1, induces in vitro differentiation of Foxp3+ T regulatory cells and attenuates airway allergic and intestinal inflammation in animal models. TGM1 is one of a family of ten TGM proteins expressed by H. polygyrus. It is a five-domain modular protein in which domains 1-2 bind TGFBR1, and domain 3 binds TGFBR2; domains 4-5 increase its potency by binding a co-receptor, CD44, highly expressed on immune cells. Domains 4-5 are more diverse in other TGMs, which bind co-receptors on cells such as fibroblasts. One variant, TGM6, lacks domains 1-2 and hence cannot transduce a signal but binds TGFBR2 through domain 3 and a co-receptor expressed on fibroblasts through domains 4-5 and blocks TGF-β signalling in fibroblasts and epithelial cells; T cells do not express the co-receptor and are not inhibited by TGM6. Hence, different family members have evolved to act as agonists or antagonists on various cell types. TGMs, which function by molecularly mimicking binding of the host cytokine to the host TGF-β receptors, are examples of highly evolved immunomodulators from parasites, including those that block interleukin (IL)-13 and IL-33 signalling, modulate macrophage and dendritic cell responses and modify host cell metabolism. The emerging panoply and potency of helminth evasion molecules illustrates the range of strategies in play to maintain long-term infections in the mammalian host.

Mitochondrial metabolism is rapidly re-activated in mature neutrophils to support stimulation-induced response

Introduction

Neutrophils are highly abundant innate immune cells that are constantly produced from myeloid progenitors in the bone marrow. Differentiated neutrophils can perform an arsenal of effector functions critical for host defense. This study aims to quantitatively understand neutrophil mitochondrial metabolism throughout differentiation and activation, and to elucidate the impact of mitochondrial metabolism on neutrophil functions.

Methods

To study metabolic remodeling throughout neutrophil differentiation, murine ER-Hoxb8 myeloid progenitor-derived neutrophils and human induced pluripotent stem cell-derived neutrophils were assessed as models. To study the metabolic remodeling upon neutrophil activation, differentiated ER-Hoxb8 neutrophils and primary human neutrophils were activated with various stimuli, including ionomycin, monosodium urate crystals, and phorbol 12-myristate 13-acetate. Characterization of cellular metabolism by isotopic tracing, extracellular flux analysis, metabolomics, and fluorescence-lifetime imaging microscopy revealed dynamic changes in mitochondrial metabolism.

Results

As neutrophils mature, mitochondrial metabolism decreases drastically, energy production is offloaded from oxidative phosphorylation, and glucose oxidation through the TCA cycle is substantially reduced. Nonetheless, mature neutrophils retain the capacity for mitochondrial metabolism. Upon stimulation with certain stimuli, TCA cycle is rapidly activated. Mitochondrial pyruvate carrier inhibitors reduce this re-activation of the TCA cycle and inhibit the release of neutrophil extracellular traps. Treatment with these inhibitors also impacts neutrophil redox status, migration, and apoptosis without significantly changing overall bioenergetics.

Conclusions

Together, these results demonstrate that mitochondrial metabolism is dynamically remodeled and plays a significant role in neutrophils. Furthermore, these findings point to the therapeutic potential of mitochondrial pyruvate carrier inhibitors in a range of conditions where dysregulated neutrophil response drives inflammation and contributes to pathology.

Cell cycle arrest of cardiomyocytes in the context of cardiac regeneration

The limited capacity of adult mammalian cardiomyocytes to undergo cell division and proliferation is one of the key factors contributing to heart failure. In newborn mice, cardiac proliferation occurs during a brief window, but this proliferative capacity diminishes by 7 days after birth. Current studies on cardiac regeneration focused on elucidating changes in regulatory factors within the heart before and after this proliferative window, aiming to determine whether potential association between these factors and cell cycle arrest in cardiomyocytes. Facilitating the re-entry of cardiomyocytes into the cell cycle or reversing their exit from it represents a critical strategy for cardiac regeneration. This paper provides an overview of the role of cell cycle arrest in cardiac regeneration, briefly describes cardiomyocyte proliferation and cardiac regeneration, and systematically summarizes the regulation of the cell cycle arrest in cardiomyocytes, and the potential metabolic mechanisms underlying cardiomyocyte cycle arrest. Additionally, we highlight the development of cardiovascular disease drugs targeting cardiomyocyte cell cycle regulation and their status in clinical treatment. Our goal is to outline strategies for promoting cardiac regeneration and repair following cardiac injury, while also pointing toward future research directions that may offer new technologies and prospects for treating cardiovascular diseases, such as myocardial infarction, arrhythmia and heart failure.

Proteomic and metabolomic insights into oxidative stress response activation in mouse embryos generated by in vitro fertilization

STUDY QUESTION

How different is the global proteomic and metabolic profile of mouse blastocysts generated by IVF, cultured in optimal (5% O2) or stressful (20% O2) conditions, compared to in vivo generated blastocysts?

SUMMARY ANSWER

We found that in IVF-generated embryos: (i) the proteome was more sensitive to high oxygen levels than the global metabolomic profile; (ii) enzymes involved in splicing and the spliceosome are altered; (iii) numerous metabolic pathways, particularly amino acids metabolism, are altered (iv) there is activation of the integrated stress response (ISR) and downregulation of mTOR pathways.

WHAT IS KNOWN ALREADY

IVF culture conditions are known to affect the gene expression of embryos. However, comprehensive data on the global metabolic and proteomic changes that occur in IVF-generated embryos are unknown.

STUDY DESIGN SIZE DURATION

Mouse embryos were generated by natural mating (in vivo control or flushed blastocyst-FB-group) or by IVF using KSOM medium and two distinct oxygen concentrations: 5% O2 (optimal) and 20% O2 (stressful). Proteomic and metabolomic analyses were performed using state-of-the-art mass spectrometry techniques in triplicate (n = 100 blastocysts per replicate), allowing for detailed profiling of protein and metabolite alterations in each group.

PARTICIPANTS/MATERIALS SETTING METHODS

Mouse blastocysts were collected from CD-1 and B6D2F1 strains as specified above. High-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used for proteomics, while high-performance liquid chromatography coupled with mass spectrometry (HILIC-MS) was used for metabolomics. In addition, Immunofluorescence was used to assess the activation of stress response pathways, including the ISR.

MAIN RESULTS AND THE ROLE OF CHANCE

Proteomic analysis revealed significant changes in protein expression in embryos cultured under 20% O2 compared to 5% O2 and in vivo embryos. Compared to in vivo embryos, IVF embryos cultured under 20% O2 exhibited 599 differentially expressed proteins, with an increase in proteins involved in oxidative stress responses, aminoacyl-tRNA synthesis, and spliceosome pathways. In contrast, IVF embryos cultured under 5% O2 showed fewer changes, with 426 differentially expressed proteins, though still reflecting significant alterations compared to in vivo embryos. These results indicate that embryos in stressful conditions (20% O2) exhibit a stronger stress response and alterations in critical pathways for protein synthesis and DNA repair. Metabolomic analysis revealed that embryos cultured under 20% O2 showed changes in branch-chained amino acid levels, and decreased levels of key metabolites of the TCA cycle and pentose phosphate pathway. Embryos cultured under 5% O2 had increased pyruvate levels, suggesting altered glycolysis. Immunofluorescence confirmed that oxidative stress markers such as GCN2, EIF2α, and ATF4 were upregulated in IVF embryos, indicating ISR activation. Overall, IVF and embryo culture have a direct impact on embryo proteomes and metabolomes affecting amino acid metabolism and stress-related pathways.

LARGE SCALE DATA

N/A.

LIMITATIONS REASONS FOR CAUTION

Results in a murine model should be extrapolated with caution to human embryos.

WIDER IMPLICATIONS OF THE FINDINGS

These findings offer valuable insights into how different IVF culture conditions, specifically oxygen levels, impact the global metabolic and proteomic profiles of embryos. These findings provide critical insights into the profound impact of IVF culture conditions, particularly oxygen levels, on the global metabolic and proteomic landscapes of embryos. By identifying key metabolic pathways disrupted by oxidative stress, we highlight the potential clinical importance of proteomic and metabolomic analyses in understanding embryo quality, improving ART, and ultimately enhancing pregnancy outcomes. The integration of metabolomic and proteomic data offers a comprehensive understanding of how oxidative stress influences cellular function. These insights have direct clinical relevance, providing a foundation for optimizing ART protocols to mitigate oxidative stress.

STUDY FUNDING/COMPETING INTERESTS

This work was supported by grant R01 HD108166-01A1 from the National Institute of Child Health and Human Development (NICHD) to P.F.R. The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.

Resveratrol-Loaded Solid Lipid Nanoparticles Reinforced Hyaluronic Hydrogel: Multitarget Strategy for the Treatment of Diabetes-Related Periodontitis

Background/Objectives: Periodontitis and diabetes mellitus share a well-established bidirectional relationship, where hyperglycemia exacerbates periodontal inflammation, and periodontal disease further impairs glycemic control. Within the diabetic periodontal microenvironment, an imbalance between pro-inflammatory (M1) and anti-inflammatory (M2) macrophages promotes chronic inflammation, oxidative stress, delayed healing, and alveolar bone resorption. Resveratrol (RSV), a polyphenol with antioxidant, anti-inflammatory, and pro-osteogenic properties, holds potential to restore macrophage balance. However, its clinical application is limited by poor bioavailability and instability. This study aimed to develop and evaluate a novel RSV delivery system to overcome these limitations and promote periodontal tissue regeneration under diabetic conditions. Methods: A drug delivery system comprising RSV-loaded solid lipid nanoparticles embedded within a cross-linked hyaluronic acid hydrogel (RSV@CLgel) was formulated. The system was tested under hyperglycemic and inflammatory conditions for its effects on macrophage polarization, cytokine expression, oxidative stress, mitochondrial function, and osteoblast differentiation. Results: RSV@CLgel effectively suppressed pro-inflammatory cytokines (TNF-α, IL-1β, IL-6) while upregulating anti-inflammatory markers (IL-10, TGF-β). It significantly reduced oxidative stress by decreasing ROS and lipid peroxidation levels and improved mitochondrial function and antioxidant enzyme activity. Furthermore, RSV@CLgel enhanced osteoblast differentiation, as evidenced by increased ALP activity, calcium nodule formation, and upregulation of osteogenic genes (COL-I, RUNX2, OCN, OPN). It also inhibited RANKL-induced osteoclastogenesis, contributing to alveolar bone preservation. Conclusions: The RSV@CLgel delivery system presents a promising multifunctional strategy for the management of diabetic periodontitis. By modulating immune responses, reducing oxidative stress, and promoting periodontal tissue regeneration, RSV@CLgel addresses key pathological aspects of diabetes-associated periodontal disease.

Variations in Human Milk Metabolites After Gestational Diabetes: Associations with Infant Growth

BACKGROUND/OBJECTIVES

Gestational diabetes mellitus (GDM) is a condition characterized by hyperglycemia and is associated with increased risk of obesity and diabetes in exposed children. Differences in human milk composition between women with (GDM+) and without GDM (GDM-) suggest that GDM could impact milk production and composition, potentially influencing infant growth. However, this association remains poorly understood. The objective was to study the association between GDM and human milk composition and its influence on infant growth, focusing on metabolites and bioactive molecules involved in energy metabolism.

METHODS

Using a cross-sectional design, 24 metabolites were measured by GC-MS in human milk obtained at 2 months postpartum from 20 GDM+ women and 29 GDM- women. Anthropometric measures, as well as lipid and glycemic profiles, were collected. Infant weight and length data were obtained from health records.

RESULTS

Human milk metabolites significantly differ between GDM+ and GDM- mothers, with higher levels of myristic acid, glycerol, uracil, arachidonic acid, and cholesterol in GDM+ milk (p < 0.05). Specific human milk metabolites showed distinct correlations with maternal glycemic as well as infant growth, depending on GDM status. While maternal glycemia was associated with succinate and malate in all groups, maternal glycemia was specifically correlated with valine and glutamate in GDM+ mothers. Additionally, in GDM+ women, α-ketoglutarate and glycine were negatively correlated with infant growth.

CONCLUSIONS

The results of this study suggest that GDM can influence the mother's health beyond delivery, impacting the mammary gland biology with effects on the human milk composition. Further, correlations with infant growth suggest that GDM-dependent variations in milk composition potentially influence infant growth and metabolism.

SDH defective cancers: molecular mechanisms and treatment strategies

Succinate dehydrogenase (SDH), considered as the linkage between tricarboxylic acid cycle (TCA cycle) and electron transport chain, plays a vital role in adenosine triphosphate (ATP) production and cell physiology. SDH deficiency is a notable characteristic in many cancers. Recent studies have pinpointed the dysregulation of SDH can directly result its decreased catalytic activity and the accumulation of oncometabolite succinate, promoting tumor progression in different perspectives. This article expounds the various types of SDH deficiency in tumors and the corresponding pathological features. In addition, we discuss the mechanisms through which defective SDH fosters carcinogenesis, pioneering a categorization of these mechanisms as being either succinate-dependent or independent. Since SDH-deficient and cumulative succinate are regarded as the typical features of some cancers, like gastrointestinal stromal tumors, pheochromocytomas and paragangliomas, we summarize the presented medical management of SDH-deficient tumor patients in clinical and preclinical, identifying the potential strategies for future cancer therapeutics.

Metal-phenolic networks reverse the immunosuppressive tumor microenvironment via dual metabolism regulation and immunogenic cell death

Targeting cancer cell metabolism has emerged as a promising strategy to reverse the immunosuppressive tumor microenvironment (TME). Aerobic glycolysis, the dominant metabolic pathway in cancer cells, leads to glucose depletion and the accumulation of immunosuppressive metabolites such as lactate, ultimately limiting the efficacy of conventional immunotherapies. In this study, metal phenolic-networks (MPNs) are developed by coating zinc oxide (ZnO) nanoparticles with epigallocatechin gallate (EGCG) to modulate cancer metabolism for TME reprogramming and immune activation. Under acidic conditions, MPNs release Zn2+ ions and EGCG, inhibiting both glycolysis and mitochondrial metabolism, effectively regulating the metabolic ability of cancer cells. Furthermore, severe starvation stress induced by dual metabolic inhibition triggers immunogenic cell death (ICD) without the need for conventional ICD inducers. Consequently, MPN treatment reverses the immunosuppressive TME through dual metabolic regulation and ICD, which induces dendritic cell maturation, cytotoxic T cell activation, and regulatory T cell suppression. These findings highlight the potential of combining metabolic therapy with immunotherapy as a novel strategy to enhance antitumor immunity and overcome the limitations of current cancer treatments.

Complex Metabolomic Changes in a Combined Defect of Glycosylation and Oxidative Phosphorylation in a Patient with Pathogenic Variants in PGM1 and NDUFA13

Inherited metabolic disorders (IMDs) are genetic disorders that occur in as many as 1:2500 births worldwide. Nevertheless, they are quite rare individually and even more rare is the co-occurrence of two IMDs in one individual. To better understand the metabolic cross-talk between glycosylation changes and deficient energy metabolism, and its potential effect on outcomes, we evaluated patient fibroblasts with likely pathogenic variants in PGM1 and pathogenic variants in NDUFA13 derived from a patient who passed away at 16 years of age. The patient presented with characteristic of PGM1-CDG including bifid uvula, muscle involvement, abnormal glycosylation in blood, and elevated liver transaminases. In addition, hearing loss, seizures, elevated plasma and CSF lactate and a Leigh-like MRI brain pattern were present, which are commonly associated with Leigh syndrome. PGM1-CDG has been reported in about 70 individuals, while NDUFA13 deficiency has so far only been reported in 13 patients. As abundant energy is essential for glycosylation, and both PGM1 and NDUFA13 are linked to energy metabolism, we sought to better understand the underlying biochemical cause of the patient's clinical presentation. To do so, we performed extensive investigations including tracer metabolomics, lipidomics and enzymatic studies on the patient's fibroblasts. We found a profound depletion of UDP-hexoses, consistent with PGM1-CDG. Complex I enzyme activity and mitochondrial function were also impaired, corroborating complex I deficiency and Leigh syndrome. Further, lipidomics analysis showed similarities with both PGM1-CDG and OXPHOS-deficient patients. Based on our results, the patient was diagnosed with both PGM1-CDG and Leigh syndrome. In summary, we present the first case of combined CDG and Leigh syndrome, caused by (likely) pathogenic variants in PGM1 and NDUFA13, and underline the importance of considering the synergistic effects of multiple disease-causing variants in patients with complex clinical presentation, leading to the patient's early demise.

Establishment of an efficacy-oriented quality grading framework for herbal medicines: Phyllanthus emblica as an example

ETHNOPHARMACOLOGICAL RELEVANCE

Quality control is a powerful method for ensuring the effectiveness and safety of herbal medicines. Phyllanthus emblica L. fruit (PE) has been extensively used in both Ayurvedic and traditional Chinese medicine. However, the current Indian and Chinese pharmacopeias set a minimum concentration threshold of gallic acid to identify qualified PE samples, without providing a clear framework to distinguish superior-quality PE samples.

AIM OF THE STUDY

To establish an efficacy-oriented quality grading framework for herbal medicines, using PE, a medicinal plant known for its hepatoprotective activity, as an example.

METHODS

First, a mouse model of alcohol-induced liver injury was developed to evaluate the hepatoprotective effects of PE. Second, a combined strategy of serum pharmacochemistry, network pharmacology, metabolomics and experimental validation was employed to identify key quality markers (Q-markers) linked to the hepatoprotective effects of PE. Finally, PE samples from different sources were collected to assess their hepatoprotective activities and Q-marker concentrations. A discriminant analysis model was then developed to classify PE samples into different quality grades by using Q-marker concentration as the predictive factor and hepatoprotective activity as the evaluation criterion.

RESULTS

PE significantly alleviated liver damage, as evidenced by a reduction in pathological abnormalities and serum aminotransferase levels. Six hepatoprotective Q-markers in PE were identified and verified, including gallic acid, methyl gallate, corilagin, chebulagic acid, ellagic acid and quercitrin. Significant variability in Q-marker concentrations and hepatoprotective effects was observed among different sources of PF samples, and a discriminant analysis model accurately classified PE samples into distinct quality grades.

CONCLUSIONS

This study successfully established an efficacy-oriented quality grading framework for PE, providing a methodological approach for the quality classification of herbal medicines.

Active control of mitochondrial network morphology by metabolism-driven redox state

Mitochondria are dynamic organelles that constantly change morphology. What controls mitochondrial morphology however remains unresolved. Using actively respiring yeast cells growing in distinct carbon sources, we find that mitochondrial morphology and activity are unrelated. Cells can exhibit fragmented or networked mitochondrial morphology in different nutrient environments independent of mitochondrial activity. Instead, mitochondrial morphology is controlled by the intracellular redox state, which itself depends on the nature of electron entry into the electron transport chain (ETC)-through complex I/II or directly to coenzyme Q/cytochrome c. In metabolic conditions where direct electron entry is high, reactive oxygen species (ROS) increase, resulting in an oxidized cytosolic environment and rapid mitochondrial fragmentation. Decreasing direct electron entry into the ETC by genetic or chemical means, or reducing the cytosolic environment rapidly restores networked morphologies. Using controlled disruptions of electron flow to alter ROS and redox state, we demonstrate minute-scale, reversible control between networked and fragmented forms in an activity-independent manner. Mechanistically, the fission machinery through Dnm1 responds in minute-scale to redox state changes, preceding the change in mitochondrial form. Thus, the metabolic state of the cell and its consequent cellular redox state actively control mitochondrial form.

Fumarate Hydratase Restrains mtDNA Attenuates LPS-Induced Acute Lung Injury Through cGAS-STING Pathways

Background

The metabolic reprogramming of alveolar macrophages, particularly mitochondrial energy metabolism centered on the tricarboxylic acid (TCA) cycle, plays a pivotal role in acute lung injury (ALI). Fumarate hydratase (FH), a key enzyme catalyzing fumarate-to-malate conversion in the TCA cycle, is implicated in macrophage inflammatory responses, but its specific role in ALI remains unclear.

Methods

We employed FHIN1 to assess its regulatory effects in LPS-induced ALI models. Wildtype C57BL/6 mice were randomly divided into control group, FHIN1 group, LPS group and LPS+FHIN1 group. FHIN1 and RU.521 was used to explored the interaction of FH and cGAS-STING in THP-1 cells.

Results

LPS stimulation suppressed FH expression and induced fumarate accumulation in macrophages. Pharmacological FH inhibition exacerbated LPS-triggered inflammatory cytokine release, oxidative stress and aggravated lung injury in mice. Mechanistically, FH inhibition promoted mtDNA leakage, activating the cGAS-STING pathway to amplify inflammation. Blocking cGAS with RU.521 significantly attenuated FHIN1-driven inflammatory responses and mitigated lung injury exacerbation.

Conclusion

FH critically modulates ALI progression by restraining cGAS-STING-dependent inflammation. Targeting the FH-mtDNA-cGAS axis may offer therapeutic potential for ALI management.

Lactate metabolism and acute kidney injury

ABSTRACT

Acute kidney injury (AKI) is a common clinically critical syndrome in hospitalized patients with high morbidity and mortality. At present, the mechanism of AKI has not been fully elucidated, and no therapeutic drugs exist. As known, glycolytic product lactate is a key metabolite in physiological and pathological processes. The kidney is an important gluconeogenic organ, where lactate is the primary substrate of renal gluconeogenesis in physiological conditions. During AKI, altered glycolysis and gluconeogenesis in kidneys significantly disturb the lactate metabolic balance, which exert impacts on the severity and prognosis of AKI. Additionally, lactate-derived posttranslational modification, namely lactylation, is novel to AKI as it could regulate gene transcription of metabolic enzymes involved in glycolysis or Warburg effect. Protein lactylation widely exists in human tissues and may severely affect non-histone functions. Moreover, the strategies of intervening lactate metabolic pathways are expected to bring a new dawn for the treatment of AKI. This review focused on renal lactate metabolism, especially in proximal renal tubules after AKI, and updated recent advances of lactylation modification, which may help to explore potential therapeutic targets against AKI.

REDOX Imbalance and Oxidative Stress in the Intervertebral Disc: The Effect of Mechanical Stress and Cigarette Smoking on ER Stress and Mitochondrial Dysfunction

Low back pain is a widespread condition that significantly impacts quality of life, with intervertebral disc degeneration (IDD) being a major contributing factor. However, the underlying mechanisms of IDD remain poorly understood, necessitating further investigation. Environmental risk factors, such as mechanical stress and cigarette smoke, elevate reactive oxygen species levels from both endogenous and exogenous sources, leading to redox imbalance and oxidative stress. The endoplasmic reticulum (ER) and mitochondria, two key organelles responsible for protein folding and energy production, respectively, are particularly vulnerable to oxidative stress. Under oxidative stress conditions, ER stress and mitochondrial dysfunction occur, resulting in unfolded protein response activation, impaired biosynthetic processes, and disruptions in the tricarboxylic acid cycle and electron transport chain, ultimately compromising energy metabolism. Prolonged and excessive ER stress can further trigger apoptosis through ER-mitochondrial crosstalk. Given the unique microenvironment of the intervertebral disc (IVD)-characterized by hypoxia, glucose starvation, and region-specific cellular heterogeneity-the differential effects of environmental stressors on distinct IVD cell populations require further investigation. This review explores the potential mechanisms through which environmental risk factors alter IVD cell activities, contributing to IDD progression, and discusses future therapeutic strategies aimed at mitigating disc degeneration.

Mitochondrial Dysfunction and Reduced TCA Cycle Metabolite Levels in Inflammatory Bowel Disease Patients

Introduction

Inflammatory bowel disease (IBD) mainly includes ulcerative colitis (UC) and Crohn's disease (CD). These diseases are classified as chronic and recurrent inflammatory diseases affecting the digestive tract. An energy deficiency in intestinal cells is believed to be associated with IBD pathology.

Methods

Our study investigated the bioenergetic functionality of mitochondria using the plasma of patients with CD and UC by determining the concentration of intermediates of the tricarboxylic acid cycle (TCA), such as acetyl coenzyme A, succinate, fumarate, α-ketoglutarate, NADH2, IDH2, Cytochrome C Oxidase, Cytochrome C Reductase, and ATP.

Results

Our results show an imbalance in mitochondrial homeostasis and bioenergetics, demonstrated by reduced activity of respiratory complexes and reduced production of TCA intermediates in the plasma of patients with CD and UC. In the group of patients with CD, treatment with corticosteroids had a significant positive effect, as significantly higher IDH2 and succinate levels were found. Correlation analyses of mitochondrial functionality biomarkers with other blood markers revealed a significant relationship between CRP and ATP levels, with higher CRP significantly linked to lower ATP and a similar trend for succinate levels. Using the disease activity scale, we show that biomarkers such as IDH2, α-ketoglutarate, and succinate levels are significantly lower in patients with higher disease activity.

Conclusion

We conclude that reduced metabolites and respiratory complexes associated with the TCA indicate mitochondrial bioenergetic failure in IBD patients. Besides, Krebs cycle metabolites can be a good marker of predisposition to the disease and the course of IBD. They can be easily determined in a blood sample taken from the patient. Pharmacological protection of mitochondria in individuals predisposed to IBD development and compensation for the changed function of mitochondria in persons with the developed disease may become a new approach to personalized therapies focused on restoring the proper activity of mitochondrial enzymes.

Dietary succinate supplementation alleviates DSS-induced colitis via the IL-4Rα/Hif-1α Axis

Inflammatory bowel disease (IBD) remains a pressing global health challenge, necessitating novel therapeutic strategies. Succinate, a metabolite known for its role in type 2 immunity and tuft cell activation in the small intestine, presents its potential in IBD management. However, its impact on colonic inflammation has not been explored. Here, we demonstrate that succinate administration induces a type 2 immune response, significantly alleviating dextran sulfate sodium (DSS)-induced colonic inflammation. Succinate enhances antibacterial capacity, reduces intestinal permeability, and reshapes the colonic cytokine milieu. Mechanistically, succinate promotes myeloid cell expansion in peripheral blood, mesenteric lymph nodes, and the colonic lamina propria. The protective effects of succinate were abolished in Ccr2-/- mice, confirming the role of monocyte recruitment, but persisted in Rag1-/- mice, indicating independence from adaptive immunity. Adoptive transfer of monocytes from succinate-treated donors mitigated intestinal inflammation in recipient mice. Transcriptomic analysis revealed heightened expression of Il1b and Il6, and higher lactate production in monocytes upon lipopolysaccharide (LPS) stimulation, highlighting a reprogrammed pro-inflammatory trained immunity phenotype. Finally, we identify the IL-4Rα/Hif-1α axis is critical for succinate-mediated protection. These findings reveal the ability of succinate to reprogram monocytes into protective intestinal macrophages via induction of type 2 response, restoring homeostasis through enhanced barrier function and immune modulation. Our study positions thus uncover succinate as a promising therapeutic candidate for IBD.

Screening of patient-derived organoids identifies mitophagy as a cell-intrinsic vulnerability in colorectal cancer during statin treatment

Statins, commonly used to lower cholesterol, are associated with improved prognosis in colorectal cancer (CRC), though their effectiveness varies. This study investigates the anti-cancer effects of atorvastatin in CRC using patient-derived organoids (PDOs) and PDO-derived xenograft (PDOX) models. Our findings reveal that atorvastatin induces mitochondrial dysfunction, leading to apoptosis in cancer cells. In response, cancer cells induce mitophagy to clear damaged mitochondria, enhancing survival and reducing statin efficacy. Analysis of a clinical cohort confirms mitophagy's role in diminishing statin effectiveness. Importantly, inhibiting mitophagy significantly enhances the anti-cancer effects of atorvastatin in CRC PDOs, xenograft models, and azoxymethane (AOM)-dextran sulfate sodium (DSS) mouse models. These findings identify mitophagy as a critical pro-survival mechanism in CRC during statin treatment, providing insights into the variable responses observed in epidemiological studies. Targeting this vulnerability through combination therapy can elicit potent therapeutic responses.

Potential threat of environmental toxin palytoxin to cerebral nerves: A mechanism study in vitro and in vivo

Palytoxin (PTX), a toxin naturally synthesized by marine organisms like Palythoa, Ostreopsis and Trichodesmium spp. in tropical and temperate seas, bioaccumulates in fish and crustaceans, thereby exposing humans through the food chain. Although growing evidence highlights PTX's lethal hepatotoxicity, nephrotoxicity, and cardiotoxicity, its neurotoxic effects and the underlying mechanisms remain elusive. In this study, we assessed the cerebral neurotoxicity of PTX by using HT22 neuronal cells and a chronic mouse model, conducting a comprehensive analysis of phenotypic alterations and gene expression changes. Phenotypic analysis revealed significant damage to mitochondria, endoplasmic reticulum, and axons and disruptions in energy metabolism in PTX-treated neuronal cells and mouse brains. Transcriptome sequencing and real-time quantitative reverse transcription polymerase chain reaction indicated that key genes in the JNK/p38 MAPK signaling, mitochondrial stress, and endoplasmic reticulum stress pathways were significantly altered. Furthermore, pretreatment with JNK and p38 inhibitors significantly restored mitochondrial membrane potential, ATP content, and cell viability, while reducing the expression of pro-apoptotic genes in HT22 cells. These findings confirm that JNK/p38 MAPK signaling pathways activation, leading to mitochondrial stress, is a major contributor to PTX-induced neuronal cell death at the cellular level. Chronic exposure to PTX was shown to damage mammalian cerebral nerves, carrying a potential risk for neurodegenerative diseases. Our study provides insights into the environmental and health risks associated with PTX exposure and offers a foundation for risk assessment and intervention strategies.

Mitochondria in focus: From structure and function to their role in human diseases. A review

Mitochondria, double-membraned organelles within all eukaryotic cells, are essential for the proper functioning of the human organism. The frequently used phrase "powerhouses of the cell" fails to adequately capture their multifaceted roles. In addition to producing energy in the form of adenosine triphosphate through oxidative phosphorylation, mitochondria are also involved in apoptosis (programmed cell death), calcium regulation, and signaling through reactive oxygen species. Recent research suggests that they can communicate with one another and influence cellular processes. Impaired mitochondrial function on the one hand, can have widespread and profound effects on cellular and organismal health, contributing to various diseases and age-related conditions. Regular exercise on the other hand, promotes mitochondrial health by enhancing their volume, density, and functionality. Although research has made significant progress in the last few decades, mainly through the use of modern technologies, there is still a need to intensify research efforts in this field. Exploring new approaches to enhance mitochondrial health could potentially impact longevity. In this review, we focus on mitochondrial research and discoveries, examine the structure and diverse roles of mitochondria in the human body, explore their influence on energy metabolism and cellular signaling and emphasize their importance in maintaining overall health.

Bioenergetic biomarkers as predictive indicators and their relationship with cognitive function in newly diagnosed, drug-naïve patients with bipolar disorder

Mitochondrial dysfunction and disrupted bioenergetic processes are critical in the pathogenesis of bipolar disorder (BD), with cognitive impairment being a prominent symptom linked to mitochondrial anomalies. The tricarboxylic acid (TCA) cycle, integral to mitochondrial energy production, may be implicated in this cognitive dysfunction, yet its specific association with BD remains underexplored. In this cross-sectional study, 144 first-episode, drug-naive BD patients and 51 healthy controls were assessed. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), serum TCA cycle metabolites were quantified, and cognitive function was evaluated through the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and the Stroop color-word test. The study found that BD patients exhibited significantly elevated serum levels of several TCA metabolites compared to healthy controls, alongside lower cognitive function scores. Correlational analyses revealed that certain bioenergetic metabolites were significantly positively associated with anxiety and negatively correlated with cognitive performance in BD patients. Notably, succinic acid, α-Ketoglutaric acid (α-KG), and malic acid emerged as independent risk factors for BD, with their combined profile demonstrating diagnostic utility. These findings underscore the potential of serum bioenergetic metabolites as biomarkers for BD, providing insights into the mitochondrial dysfunction underlying cognitive impairment and offering a basis for early diagnosis and targeted therapeutic strategies.

Identification of a Novel Mitochondrial-Related Gene Signature for BMSCs in Osteoporosis Combining Single-Cell and Bulk Transcriptome Data

Osteoporosis (OS) is a prevalent skeletal disorder characterized by reduced bone mass and increased fracture risk, often linked to compromised functions of bone mesenchymal stem cells (BMSCs). Mitochondrial dysfunction and aberrant mitophagy are implicated in OS pathogenesis. This study aimed to identify a novel mitochondrial-related gene signature in BMSCs from OS patients by integrating single-cell and bulk transcriptome data. We analyzed single-cell RNA sequencing data from GSE147287 and bulk transcriptome data from GSE35956 to identify differentially expressed mitochondrial-related genes (MRGs) in BMSCs between healthy individuals and OS patients. Key genes were identified using LASSO logistic regression and random forest algorithms, and their differential expression was validated by RT-qPCR, Western blot, and immunofluorescence. Functional assays, including osteogenic differentiation and β-galactosidase staining, were conducted following siRNA-mediated knockdown of DUT. We identified 28 differentially expressed MRGs, with four key genes (DUT, UQCR10, DNAJC4, and MRPL33) further confirmed. Electron microscopy scanning showed damage to BMSCs mitochondria and decreased osteogenic differentiation ability in OS. Silencing DUT significantly impairs the mitochondrial function and osteogenic differentiation ability of BMSCs, indicating its potential role in OS development. This study identifies a mitochondrial gene signature in BMSCs linked to osteoporosis, with DUT emerging as a key regulator. DUT silencing impairs mitochondrial function and osteogenic differentiation, suggesting it as a potential therapeutic target for OS.

Identifying the metabolic profile of Hashimoto's thyroiditis from the METHAP clinical study

Hashimoto's thyroiditis (HT), one of the most common autoimmune diseases and the leading cause of hypothyroidism, is linked to metabolic and cellular dysfunctions that contribute to disease aetiopathogenesis. This case-control study aimed to identify potent metabolic biomarkers of HT employing machine learning techniques. 62 euthyroid patients with HT and 58 healthy individuals were included from the metabolic biomarkers in Hashimoto's thyroiditis and psoriasis (METHAP) clinical trial. Quantification of 73 metabolites was performed using gas-chromatography/mass spectrometry in plasma and urine samples of fasted participants. Changes in the tricarboxylic acid cycle, carbohydrate, neurotransmitter, microbiome and lipid metabolism were identified in the HT group. Ordinary least squares and beta regression modeling associated the presence of HT with methylmalonic acid, 4-hydroxyphenylpyruvic acid, palmitic acid, palmitoleic acid, myristoleic acid and total saturated fatty acids, adjusting for confounders. Artificial neural network analysis had good predictive accuracy with an AUC of 0.8, while debiased sparse partial correlation network analysis identified metabolite-metabolite interactions distinct for HT. These findings provide insights into novel biomarkers associated with HT, and we discuss their biological relevance and clinical significance. Hashimoto's thyroiditis is associated with mitochondrial dysfunction, micronutrient decreased bioavailability, microbiome imbalances, and carbohydrate and fatty acids dysfunctional metabolism.

Proteomic analysis of Toraya buffalo seminal plasma and sperm: uncovering insights to optimize reproductive success

The characterization of sperm and seminal plasma proteins is essential for understanding bull fertility and optimizing reproductive success in buffalo bulls. Despite its importance, the reproductive proteomic of Toraya buffalo, an indigenous breed in Indonesia, remains largely unexplored. This study aimed to examine the seminal plasma and sperm proteins of Toraya buffalo to uncover those critical for reproductive functions. Semen samples were collected from eight Toraya buffalo bulls aged 4 to 10 years. Protein profiling was performed using one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (1D-SDS-PAGE), followed by in-gel digestion and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Bioinformatics tools, including UniProt, PANTHER, DAVID, and STRING, were utilized to identify and annotate the detected proteins. This study successfully identified four key reproductive proteins: ADAM32 in seminal plasma and ZPBP, SPACA3, and CCDC136 in sperm. These proteins are essential for sperm motility, energy production, and acrosome formation, which are critical processes for fertilization. Additionally, many identified proteins were associated with metabolic pathways, particularly the tricarboxylic acid (TCA) cycle, which plays a fundamental role in energy supply for sperm function. In conclusion, this study offers the first comprehensive proteomic identification of seminal plasma and sperm proteins associated with reproductive functions in the Toraya buffalo. The findings highlight the presence of key proteins in sperm, including ZPBP, SPACA3, and CCDC136, as well as the identification of ADAM32 in seminal plasma, contributing to a deeper understanding of buffalo reproductive biology.

Cross-talks between Metabolic and Translational Controls during Beige Adipocyte Differentiation

Whether and how regulatory events at the translation stage shape the cellular and metabolic features of thermogenic adipocytes is hardly understood. In this study, we report two hitherto unidentified cross-talk pathways between metabolic and translational regulation in beige adipocytes. By analysing temporal profiles of translation activity and protein level changes during precursor-to-beige differentiation, we found selective translational down-regulation of OXPHOS component-coding mRNAs. The down-regulation restricted to Complexes I, III, IV, and V, is coordinated with enhanced translation of TCA cycle genes, engendering distinct stoichiometry of OXPHOS and TCA cycle components and altering the related metabolic activities in mitochondria of thermogenic adipocytes. Our high-resolution description of ribosome positioning unveiled potentiated ribosome pausing at glutamate codons. The increased stalling is attributable to remodelled glutamate metabolism that decreases glutamates for tRNA charging during pan-adipocyte differentiation. The ribosome pauses decrease protein synthesis and mRNA stability of glutamate codon-rich genes, such as actin cytoskeleton-associated genes.

Elevated Methylglyoxal: An Elusive Risk Factor Responsible for Early-Onset Cardiovascular Diseases in People Living with HIV-1 Infection

People living with HIV (PLWH) develop cardiovascular diseases (CVDs) about a decade earlier and at rates 2-3 times higher than the general population. At present, pharmacological strategies to delay the onset of CVDs in PLWH are unavailable, in part because of an incomplete understanding of its molecular causes. We and others recently uncovered elevated levels of the toxic glycolysis and inflammation-induced byproduct methylglyoxal (MG) in plasma from PLWH and from HIV-infected humanized mice (Hu-mice). We also found a reduction in expression of the primary MG-degrading enzyme glyoxalase I (Glo-I) in autopsied cardiac tissues from HIV-1-infected individuals and HIV-1-infected Hu-mice. Increasing the expression of Glo-I in HIV-1-infected Hu-mice not only attenuated heart failure but also reduced endothelial cell damage, increased the density of perfused microvessels, prevented microvascular leakage and micro-ischemia, and blunted the expression of the inflammation-induced protein vascular protein-1 (VAP-1), key mediators of CVDs. In this narrative review, we posit that elevated MG is a contributing cause for the early onset of CVDs in PLWH. Pharmacological strategies to prevent MG accumulation and delay the development of early-onset CVDs in PLWH are also discussed.

RNA aptamer-induced fluorescence enhancement for NADH monitoring in cellular environment

Cellular redox homeostasis is tightly regulated by the oxidation-reduction reactions of nicotinamide metabolites, including NAD(H) and NADP(H), which serve as essential cofactors in enzymatic processes related to energy metabolism. Monitoring intracellular NADH levels is therefore of significant interest. Most chemosensor designs to date rely on fluorescence turn-on mechanisms triggered by NADH oxidation, but these reaction-based sensors are inherently limited by NADH concentration and reaction kinetics. While NADH exhibits intrinsic fluorescence, its low quantum yield has led to the development of redox-sensitive substrates that emit fluorescence upon NADH oxidation. Here, we report an alternative fluorescence enhancement strategy based on an NADH-binding RNA aptamer. The interaction between NADH and a 49-base-pair RNA aptamer induces a 1.4-fold increase in fluorescence emission in vitro and an 1.8-fold increase in live-cell imaging. This fluorescence enhancement arises from aptamer-induced structural rigidity, analogous to the mechanism by which 4-(p-hydroxybenzylidene)-5-imidazolidinone (HBI) enhances fluorescence in green fluorescent protein. Using our aptamer-based assay, we established a live-cell fluorescence emission assay for real-time monitoring of cellular NADH dynamics.

Integrative analysis of mitochondrial-related gene profiling identifies prognostic clusters and drug resistance mechanisms in low-grade glioma

Mitochondrial dysfunction has emerged as a critical factor in the progression and prognosis of low-grade glioma (LGG). In this study, we explored the role of mitochondrial-related genes through consensus clustering analysis using multi-omics data from the TCGA, CGGA, and other independent datasets. Patients were categorized into three clusters (Cluster A, B, and C), with Cluster B consistently associated with poorer prognosis. Mutation landscape analysis revealed distinct genetic alterations and copy number variations among clusters, particularly in Cluster B, which exhibited unique genetic signatures. Immune infiltration analysis showed that Cluster B had higher expression levels of immune checkpoint genes, stronger immune evasion activity, and greater immune cell infiltration, suggesting an immunosuppressive tumor microenvironment. Furthermore, we identified mitochondrial-related prognostic markers and developed a MITscore based on gene expression patterns, which stratified patients into high- and low-risk groups. High MITscore groups displayed stronger stemness characteristics, poorer survival outcomes, and differential responses to chemotherapy and immunotherapy. Cross-validation with drug sensitivity and immunotherapy cohorts indicated that high MITscore patients were more sensitive to certain chemotherapeutic agents and responded better to immunotherapy. Finally, using the SRGA method, we identified novel biomarkers (KDR, LRRK2, SQSTM1) closely associated with mitochondrial function, which may serve as potential targets for therapeutic intervention. These findings highlight the critical role of mitochondrial dysfunction in LGG prognosis, tumor microenvironment regulation, and treatment response, providing new avenues for precision oncology.

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.

The Complexities of Interspecies Somatic Cell Nuclear Transfer: From Biological and Molecular Insights to Future Perspectives

For nearly three decades, interspecies somatic cell nuclear transfer (iSCNT) has been explored as a potential tool for cloning, regenerative medicine, and wildlife conservation. However, developmental inefficiencies remain a major challenge, largely due to persistent barriers in nucleocytoplasmic transport, mitonuclear communication, and epigenome crosstalk. This review synthesized peer-reviewed English articles from PubMed, Web of Science, and Scopus, spanning nearly three decades, using relevant keywords to explore the molecular mechanisms underlying iSCNT inefficiencies and potential improvement strategies. We highlight recent findings deepening the understanding of interspecies barriers in iSCNT, emphasizing their interconnected complexities, including the following: (1) nucleocytoplasmic incompatibility may disrupt nuclear pore complex (NPC) assembly and maturation, impairing the nuclear transport of essential transcription factors (TFs), embryonic genome activation (EGA), and nuclear reprogramming; (2) mitonuclear incompatibility could lead to nuclear and mitochondrial DNA (nDNA-mtDNA) mismatches, affecting electron transport chain (ETC) assembly, oxidative phosphorylation, and energy metabolism; (3) these interrelated incompatibilities can further influence epigenetic regulation, potentially leading to incomplete epigenetic reprogramming in iSCNT embryos. Addressing these challenges requires a multifaceted, species-specific approach that balances multiple incompatibilities rather than isolating a single factor. Gaining insight into the molecular interactions between the donor nucleus and recipient cytoplast, coupled with optimizing strategies tailored to specific pairings, could significantly enhance iSCNT efficiency, ultimately transforming experimental breakthroughs into real-world applications in reproductive biotechnology, regenerative medicine, and species conservation.

Bromine-Based Derivatization of Carboxyl-Containing Metabolites for Liquid Chromatography-Trapped Ion Mobility Spectrometry-Mass Spectrometry

The analysis of small carboxyl-containing metabolites (CCMs), such as tricarboxylic acid (TCA) cycle intermediates, provides highly useful information about the metabolic state of cells. However, their detection using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) methods can face sensitivity and specificity challenges given their low ionization efficiency and the presence of isomers. Ion mobility spectrometry (IMS), such as trapped ion mobility spectrometry (TIMS), provides additional specificity, but further signal loss can occur during the mobility separation process. We, therefore, developed a solution to boost CCM ionization and chromatographic separation as well as leverage specificity of IMS. Inspired by carbodiimide-mediated coupling of carboxylic acids with 4-bromo-N-methylbenzylamine (4-BNMA) for quantitative analysis, we newly report the benefits of this reagent for TIMS-based measurement. We observed a pronounced (orders of magnitude) increase in signal and enhanced isomer separations, particularly by LC. We found that utilization of a brominated reagent, such as 4-BNMA, offered unique benefits for untargeted CCM measurement. Derivatized CCMs displayed shifted mobility out of the metabolite and lipid region of the TIMS-MS space as well as characteristic isotope patterns, which were leveraged for data mining with Mass Spectrometry Query Language (MassQL) and indication of the number of carboxyl groups. The utility of our LC-ESI-TIMS-MS/MS method with 4-BMA derivatization was demonstrated via the characterization of alterations in CCM expression in bone marrow-derived macrophages upon activation with lipopolysaccharide. While metabolic reprogramming in activated macrophages has been characterized previously, especially with respect to TCA cycle intermediates, we report a novel finding that isomeric itaconic, mesaconic, and citraconic acid increase after 24 h, indicating possible roles in the inflammatory response.

High Glucose Contribution to the TCA Cycle Is a Feature of Aggressive Non-Small Cell Lung Cancer in Patients

SIGNIFICANCE

Intraoperative 13C-glucose infusions in patients with NSCLC show that tumors with high labeling of TCA cycle intermediates progress rapidly, resulting in metastasis and early death. Blocking this pathway suppresses metastasis of human NSCLC cells in mice.

Mitochondrial DNA copy number variation in asthma risk, severity, and exacerbations

BACKGROUND

Asthma pathophysiology is associated with mitochondrial dysfunction. Mitochondrial DNA copy number (mtDNA-CN) has been used as a proxy of mitochondrial function, with lower levels indicating mitochondrial dysfunction in population studies of cardiovascular diseases and cancers.

OBJECTIVES

We investigated whether lower levels of mtDNA-CN are associated with asthma diagnosis, severity, and exacerbations.

METHODS

mtDNA-CN is evaluated in blood from 2 cohorts: UK Biobank (UKB) (asthma, n = 39,147; no asthma, n = 302,302) and Severe Asthma Research Program (SARP) (asthma, n = 1283; nonsevere asthma, n = 703).

RESULTS

Individuals with asthma have lower mtDNA-CN compared to individuals without asthma in UKB (beta, -0.006 [95% confidence interval, -0.008 to -0.003], P = 6.23 × 10-6). Lower mtDNA-CN is associated with asthma prevalence, but not severity in UKB or SARP. mtDNA-CN declines with age but is lower in individuals with asthma than in individuals without asthma at all ages. In a 1-year longitudinal study in SARP, mtDNA-CN was associated with risk of exacerbation; those with highest mtDNA-CN had the lowest risk of exacerbation (odds ratio 0.333 [95% confidence interval, 0.173 to 0.542], P = .001). Biomarkers of inflammation and oxidative stress are higher in individuals with asthma than without asthma, but the lower mtDNA-CN in asthma is independent of general inflammation or oxidative stress. Mendelian randomization studies suggest a potential causal relationship between asthma-associated genetic variants and mtDNA-CN.

CONCLUSION

mtDNA-CN is lower in asthma than in no asthma and is associated with exacerbations. Low mtDNA-CN in asthma is not mediated through inflammation but is associated with a genetic predisposition to asthma.

Deciphering the interplay: circulating cell-free DNA, signaling pathways, and disease progression in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a lung disease with an unknown etiology and a short survival rate. There is no accurate method of early diagnosis, and it involves computed tomography (CT) or lung biopsy. Since diagnostic methods are not accurate due to their similarity to other lung pathologies, discovering new biomarkers is a key issue for diagnosticians. Currently, the use of ccf-DNA (circulating cell-free deoxyribonucleic acid) is an important focus due to its association with IPF-induced alterations in metabolic pathways, such as amino acid metabolism, energy metabolism, and lipid metabolism pathways. Other biomarkers associated with metabolic changes have been found, and they are related to changes in type II/type I alveolar epithelial cells (AECs I/II), changes in extracellular matrix (ECM), and inflammatory processes. Currently, IPF pathogenetic treatment remains unknown, and the mortality rates are increasing, and the patients are diagnosed at a late stage. Signaling pathways and metabolic dysfunction have a significant role in the disease occurrence, particularly the transforming growth factor-β (TGF-β) signaling pathway, which plays an essential role. TGF-β, Wnt, Hedgehog (Hh), and integrin signaling are the main drivers of fibrosis. These pathways activate the transformation of fibroblasts into myofibroblasts, extracellular matrix (ECM) deposition, and tissue remodeling fibrosis. Therapy targeting diverse signaling pathways to slow disease progression is crucial in the treatment of IPF. Two antifibrotic medications, including pirfenidone and nintedanib, are Food and Drug Administration (FDA)-approved for treatment. ccf-DNA could become a new biomarker for IPF diagnosis to detect the disease at the early stage, while FDA-approved therapies could help to prevent late conditions from forming and decrease mortality rates.

Increase in plasma succinate is associated with aerobic lactate production in a model of endotoxic shock

The Krebs or tricarboxylic acid (TCA) cycle plays a key role in the regulation of immune responses and adaptations to hypoxia that occur during sepsis. Although the concentrations of some of these intermediates have been reported to be increased in large cohorts of septic patients, a detailed analysis of their changes during sepsis is still lacking. Here, we investigated the plasma concentrations of several TCA intermediates in a swine model of endotoxic shock and the relationship between these TCA cycle intermediates and lactate production. Nine female swine were administered lipopolysaccharide to induce endotoxic shock, while four females served as controls. Plasma samples were collected at three time points: baseline, 3 and 6 h after lipopolysaccharide administration. Control samples were collected at parallel time points. Quantification of TCA intermediates, lactate and pyruvate was performed by high-performance liquid chromatography. Oxygen-derived variables were obtained by gas analysis of arterial and venous samples. The endotoxic shock group showed a significant increase in lactate, accompanied by stability of oxygen-derived variables and a low lactate:pyruvate ratio, indicative of aerobic conditions. Of all the TCA intermediates analysed, only citrate and succinate showed significant increases compared with controls. Furthermore, the changes in lactate were determined, in part, by the changes in succinate concentration. The increase in succinate concentrations was associated with the increase in lactate in global aerobic conditions. Our results suggest a potential role for succinate as a biomarker of aerobic lactate production.

The neglected PCK1/glucagon (inter)action in nutrient homeostasis beyond gluconeogenesis: Disease pathogenesis and treatment

BACKGROUND

Glucagon plays a central role in hepatic adaptation during fasting, with the upregulation of hepatic phosphoenolpyruvate carboxykinase 1 (PCK1) traditionally associated with increased gluconeogenesis. However, recent experimental models and clinical studies have challenged this view, suggesting a more complex interplay between PCK1 and glucagon, which extends beyond gluconeogenesis and has broader implications for metabolic regulation in health and disease.

SCOPE OF REVIEW

This review provides a comprehensive overview of the current evidence on the multifaceted roles of PCK1 in glucagon-dependent hepatic adaptation during fasting, which is crucial for maintaining systemic homeostasis not only of glucose, but also of lipids and amino acids. We explore the relationship between PCK1 deficiency and glucagon resistance in metabolic disorders, including inherited PCK1 deficiency and metabolic dysfunction-associated steatotic liver disease (MASLD), and compare findings from experimental animal models with whole-body or tissue-specific ablation of PCK1 or the glucagon receptor. We propose new research platforms to advance the therapeutic potential of targeting PCK1 in metabolic diseases.

MAJOR CONCLUSIONS

We propose that hepatic PCK1 deficiency might be an acquired metabolic disorder linking alterations in lipid metabolism with impaired glucagon signaling. Our findings highlight interesting links between glycerol, PCK1 deficiency, elevated plasma alanine levels and glucagon resistance. We conclude that the roles of PCK1 and glucagon in metabolic regulation are more complex than previously assumed. In this (un)expected scenario, hepatic PCK1 deficiency and glucagon resistance appear to exert limited control over glycemia, but have broader metabolic effects related to lipid and amino acid dysregulation. Given the shift in glucagon research from receptor inhibition to activation, we propose that a similar paradigm shift is needed in the study of hepatic PCK1. Understanding PCK1 expression and activity in the glucagon-dependent hepatic adaptation to fasting might provide new perspectives and therapeutic opportunities for metabolic diseases.

From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies

In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.