bims-celmim Biomed News
on Cellular and mitochondrial metabolism
Issue of 2024–12–22
25 papers selected by
Marc Segarra Mondejar



  1. PLoS Biol. 2024 Dec;22(12): e3002941
      Phospholipids are critical building blocks of mitochondria, and proper mitochondrial function and architecture rely on phospholipids that are primarily transported from the endoplasmic reticulum (ER). Here, we show that mitochondrial form and function rely on synthesis of phosphatidylserine (PS) in the ER through phosphatidylserine synthase (PSS), trafficking of PS from ER to mitochondria (and within mitochondria), and the conversion of PS to phosphatidylethanolamine (PE) by phosphatidylserine decarboxylase (PISD) in the inner mitochondrial membrane (IMM). Using a forward genetic screen in Drosophila, we found that Slowmo (SLMO) specifically transfers PS from the outer mitochondrial membrane (OMM) to the IMM within the inner boundary membrane (IBM) domain. Thus, SLMO is required for shaping mitochondrial morphology, but its putative conserved binding partner, dTRIAP, is not. Importantly, SLMO's role in maintaining mitochondrial morphology is conserved in humans via the SLMO2 protein and is independent of mitochondrial dynamics. Our results highlight the importance of a conserved PSS-SLMO-PISD pathway in maintaining the structure and function of mitochondria.
    DOI:  https://doi.org/10.1371/journal.pbio.3002941
  2. Methods Mol Biol. 2025 ;2888 167-191
      Membrane biogenesis requires an extensive traffic of lipids between different cell compartments. Two main pathways, the vesicular and non-vesicular pathways, are involved in such a process. Whereas the mechanisms involved in vesicular trafficking are well understood, less is known about non-vesicular lipid trafficking, particularly in plants. This pathway involves the direct exchange of lipids at membrane contact sites (MCSs) between organelles. In plants, extensive traffic of the chloroplast-synthesized digalactosyldiacylglycerol (DGDG) to mitochondria is specifically promoted during phosphate starvation. This lipid exchange likely occurs by non-vesicular trafficking pathways at MCSs between mitochondria and plastids. By a biochemical approach, a mitochondrial lipoproteic super-complex called MTL (mitochondrial transmembrane lipoprotein complex) involved in mitochondrial lipid trafficking has been identified in Arabidopsis thaliana. This protocol describes the method used to separate the MTL complex and to study the implication of a component of this complex (AtMic60) in mitochondrial lipid transport.
    Keywords:  CN-PAGE; Lipid transfer; MTL complex; Mass spectrometry; Mitochondria
    DOI:  https://doi.org/10.1007/978-1-0716-4318-1_12
  3. BMC Cancer. 2024 Dec 18. 24(1): 1515
       BACKGROUND: Serine/glycine are critical for the growth and survival of cancer cells. Some cancer cells are more dependent on exogenous serine/glycine than endogenously synthesized serine/glycine. However, the function and underlying mechanisms of exogenous serine/glycine in renal cell carcinoma (RCC) remain unclear.
    METHODS: We conducted a comprehensive assessment of RCC progression under conditions of exogenous serine/glycine deprivation and explored the underlying mechanism via immunofluorescence, autophagic flux analysis, extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) measurements.
    RESULTS: The expression of the serine synthesis pathway enzymes was decreased in RCC specimens, the de novo serine synthesis pathway (SSP) was reduced in RCC. And the levels of endogenously synthesized serine/glycine were little. Yet, the exogenous serine/glycine deprivation significantly inhibited the growth of RCC cells both in vitro and in vivo, indicating that exogenous serine/glycine were important for RCC progression. Mechanistically, the deprivation of exogenous serine/glycine disrupted one-carbon metabolism and increased the ratio of NAD(P)+/NAD(P)H, resulting in the accumulation of reactive oxygen species (ROS) and oxidative stress, which induced autophagic flux and enhanced lysosome membrane permeabilization (LMP), leading to the release of lysosomal cathepsins into the cytoplasm, which ultimately triggered lysosomal dependent cell death (LDCD) and inhibited the progression of RCC.
    CONCLUSIONS: Our results indicate that exogenous serine/glycine are critical for RCC progression by maintaining one-carbon metabolism-dependent redox homeostasis, which provides new insights for the development of dietary serine/glycine starvation-based therapeutic approaches for RCC.
    Keywords:  Lysosomal dependent cell death; Lysosome membrane permeabilization; ROS; Renal cell carcinoma; Serine/glycine
    DOI:  https://doi.org/10.1186/s12885-024-13304-4
  4. Methods Mol Biol. 2025 ;2888 1-11
      Phosphatidylcholine (PC) is a major phospholipid that forms biological membranes in eukaryotes. PC is mainly synthesized in the endoplasmic reticulum (ER) and Golgi apparatus and then transported to other organelle membranes via multiple mechanisms. Such interorganelle lipid transport is thought to play an important role in the maintenance of cell morphology, organelle functions, and homeostasis, though the details of this process have not yet been well investigated. This chapter describes a technology for the selective labeling and fluorescence imaging of PC in target organelles. This approach involves the metabolic incorporation of azidocholine, followed by a spatially restricted bioorthogonal click reaction that enables the visualization and quantitative analysis of interorganelle PC transport in live cells using confocal microscopy.
    Keywords:  Endoplasmic reticulum; Interorganelle lipid transport; Live-cell imaging; Mitochondria; Organelle-selective click reaction; Phosphatidylcholine
    DOI:  https://doi.org/10.1007/978-1-0716-4318-1_1
  5. Elife. 2024 Dec 20. pii: e105191. [Epub ahead of print]13
      Measuring mitochondrial respiration in frozen tissue samples provides the first comprehensive atlas of how aging affects mitochondrial function in mice.
    Keywords:  aging; cellular respiration; computational biology; mitochondria; mouse; respiration atlas; sex; systems biology
    DOI:  https://doi.org/10.7554/eLife.105191
  6. Biochim Biophys Acta Rev Cancer. 2024 Dec 17. pii: S0304-419X(24)00180-X. [Epub ahead of print] 189249
      Mitochondrial DNA (mtDNA), a circular double-stranded DNA located within mitochondria, plays a pivotal role in mitochondrial-induced innate immunity, particularly via the cyclic GMP-AMP synthase (cGAS)-STING pathway, which recognizes double-stranded DNA and is crucial for pathogen resistance. Recent studies elucidate the interplay among mtDNA, the cGAS-STING pathway, and neutrophil extracellular traps (NETs) in the context of cancer. mtDNA uptake by recipient cells activates the cGAS-STING pathway, while mtDNA leakage reciprocally regulates NET release, amplifying inflammation and promoting NETosis, a mechanism of tumor cell death. Autophagy modulates these processes by clearing damaged mitochondria and degrading cGAS, thus preventing mtDNA recognition. Tumor microenvironmental factors, such as metabolic reprogramming and lipid accumulation, induce mitochondrial stress, ROS production, and further mtDNA leakage. This review explores strategies in cancer drug development that leverage mtDNA leakage to activate the cGAS-STING pathway, potentially converting 'cold tumors' into 'hot tumors,' while discussing advancements in targeted therapies and proposing new research methodologies.
    Keywords:  Cancer; Innate immune; Mitochondria DNA; cGAS-STING
    DOI:  https://doi.org/10.1016/j.bbcan.2024.189249
  7. J Biomed Opt. 2024 Dec;29(12): 126501
       Significance: Cellular metabolic dynamics can occur within milliseconds, yet there are no optimal tools to spatially and temporally capture these events. Autofluorescence imaging can provide metabolic information on the cellular level due to the intrinsic fluorescence of reduced nicotinamide adenine dinucleotide (phosphate) [NAD(P)H] and flavin adenine dinucleotide (FAD).
    Aim: Our goal is to build and evaluate a widefield microscope optimized for rapid autofluorescence imaging of metabolic changes in cells.
    Approach: A widefield, fluorescence microscope was assembled from an inverted microscope base, an light-emitting diode (LED) for excitation, and an image splitter for simultaneous but separate imaging of two bandwidths of emission (451/106 and 560/94 nm) on a single scientific complementary metal-oxide-semiconductor (sCMOS) camera. MCF-7 cells and primary murine hippocampal neurons were metabolically perturbed using cyanide and imaged to optimize illumination and camera exposure. To capture a rapid change in metabolism, MCF-7 cells were starved for 1 h and imaged while reintroduced to glucose.
    Results: Significant differences in the optical redox ratio (ORR) and intensity of NAD(P)H divided by the summed intensities of NAD(P)H and FAD were quantified for cyanide-treated neurons and MCF-7 cells at illumination powers above 0.30 mW and camera exposures as low as 5 ms; however, low illumination and camera exposures hindered the ability to identify subcellular features. Minimal photobleaching was quantified for 30 s of continuous imaging for illuminations at 4.14 mW and below. Using the optimized illumination power of 4.14 mW and an exposure of 10 ms, continuous autofluorescence imaging of starved MCF-7 cells demonstrated a rapid, yet heterogeneous, increase in the ORR of cells upon exposure to glucose.
    Conclusions: Ultimately, this widefield autofluorescence imaging system allowed for dynamic imaging and quantification of cellular metabolism at 99.6 Hz.
    Keywords:  autofluorescence; cellular metabolism; flavin adenine dinucleotide; fluorescence microscopy; live cell imaging; nicotinamide adenine dinucleotide (phosphate)
    DOI:  https://doi.org/10.1117/1.JBO.29.12.126501
  8. bioRxiv. 2024 Dec 02. pii: 2024.11.26.625487. [Epub ahead of print]
      Understanding the physiological processes underlying age-related cardiovascular disease (CVD) requires examination of endothelial cell (EC) mitochondrial networks, because mitochondrial function and adenosine triphosphate production are crucial in EC metabolism, and consequently influence CVD progression. Although current biochemical assays and immunofluorescence microscopy can reveal how mitochondrial function influences cellular metabolism, they cannot achieve live observation and tracking changes in mitochondrial networks through fusion and fission events. Holotomographic microscopy (HTM) has emerged as a promising technique for real-time, label-free visualization of ECs and their organelles, such as mitochondria. This non-destructive, non-interfering live cell imaging method offers unprecedented opportunities to observe mitochondrial network dynamics. However, because existing image processing tools based on immunofluorescence microscopy techniques are incompatible with HTM images, a machine-learning model is required. Here, we developed a model using a U-net learner with a Resnet18 encoder to identify four classes within HTM images: mitochondrial networks, cell borders, ECs, and background. This method accurately identifies mitochondrial structures and positions. With high accuracy and similarity metrics, the output image successfully provides visualization of mitochondrial networks within HTM images of ECs. This approach enables the study of mitochondrial networks and their effects, and holds promise in advancing understanding of CVD mechanisms.
    DOI:  https://doi.org/10.1101/2024.11.26.625487
  9. Cancer Metab. 2024 Dec 18. 12(1): 37
       BACKGROUND: The efficacy of tyrosine kinase inhibitors (TKIs) targeting the EGFR is limited due to the persistence of drug-tolerant cell populations, leading to therapy resistance. Non-genetic mechanisms, such as metabolic rewiring, play a significant role in driving lung cancer cells into the drug-tolerant state, allowing them to persist under continuous drug treatment.
    METHODS: Our study employed a comprehensive approach to examine the impact of the glycolytic regulator 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB3) on the adaptivity of lung cancer cells to EGFR TKI therapies. We conducted metabolomics to trace glucose rerouting in response to PFKFB3 inhibition during TKI treatment. Live cell imaging and DCFDA oxidation were used to quantify levels of oxidation stress. Immunocytochemistry and Neutral Comet assay were employed to evaluate DNA integrity in response to therapy-driven oxidative stress.
    RESULTS: Our metabolic profiling revealed that PFKFB3 inhibition significantly alters the metabolic profile of TKI-treated cells. It limited glucose utilization in the polyol pathway, glycolysis, and TCA cycle, leading to a depletion of ATP levels. Furthermore, pharmacological inhibition of PFKFB3 overcome TKI-driven redox capacity by diminishing the expression of glutathione peroxidase 4 (GPX4), thereby exacerbating oxidative stress. Our study also unveiled a novel role of PFKFB3 in DNA oxidation and damage by controlling the expression of DNA-glycosylases involved in base excision repair. Consequently, PFKFB3 inhibition improved the cytotoxicity of EGFR-TKIs by facilitating ROS-dependent cell death.
    CONCLUSIONS: Our results suggest that PFKFB3 inhibition reduces glucose utilization and DNA damage repair, limiting the adaptivity of the cells to therapy-driven oxidative stress and DNA integrity insults. Inhibiting PFKFB3 can be an effective strategy to eradicate cancer cells surviving under EGFR TKI therapy before they enter the drug-resistant state. These findings may have potential implications in the development of new therapies for drug-resistant cancer treatment.
    Keywords:  Base excision DNA repair; EGFR; GPX4; Non-small cell lung carcinoma; Oxidative stress; PFKFB3; ROS-dependent cell death
    DOI:  https://doi.org/10.1186/s40170-024-00366-y
  10. Metabolomics. 2024 Dec 15. 21(1): 9
       INTRODUCTION: Outside of case-control settings, ethnicity specific changes in the human metabolome are understudied especially in community dwelling, ageing men. Characterising serum for age and ethnicity specific features can enable tailored therapeutics research and improve our understanding of the interplay between age, ethnicity, and metabolism in global populations.
    OBJECTIVE: A metabolomics approach was adopted to profile serum metabolomes in middle-aged and elderly men of different ethnicities from the Northwest of England, UK.
    METHODS: Serum samples from 572 men of White European (WE), South Asian (SA), and African-Caribbean (AC) ethnicities, ranging between 40 and 86 years were analysed. A combination of liquid chromatography (LC) and gas chromatography (GC) coupled to high-resolution mass spectrometry (MS) was used to generate the metabolomic profiles. Partial Least Squares Discriminant Analysis (PLS-DA) based classification models were built and validated using resampling via bootstrap analysis and permutation testing. Features were putatively annotated using public Human Metabolome Database (HMDB) and Golm Metabolite Database (GMD). Variable Importance in Projection (VIP) scores were used to determine features of interest, after which pathway enrichment analysis was performed.
    RESULTS: Using profiles from our analysis we classify subjects by their ethnicity with an average correct classification rate (CCR) of 90.53% (LC-MS data) and 85.58% (GC-MS data). Similar classification by age (< 60 vs. ≥ 60 years) returned CCRs of 90.20% (LC-MS) and 71.13% (GC-MS). VIP scores driven feature selection revealed important compounds from putatively annotated lipids (subclasses including fatty acids and carboxylic acids, glycerophospholipids, steroids), organic acids, amino acid derivatives as key contributors to the classifications. Pathway enrichment analysis using these features revealed statistically significant perturbations in energy metabolism (TCA cycle), N-Glycan and unsaturated fatty acid biosynthesis linked pathways amongst others.
    CONCLUSION: We report metabolic differences measured in serum that can be attributed to ethnicity and age in healthy population. These results strongly emphasise the need to consider confounding effects of inherent metabolic variations driven by ethnicity of participants in population-based metabolic profiling studies. Interpretation of energy metabolism, N-Glycan and fatty acid biosynthesis should be carefully decoupled from the underlying differences in ethnicity of participants.
    Keywords:  Ethnicity; Healthy ageing; Mass spectrometry; Metabolomics; Serum
    DOI:  https://doi.org/10.1007/s11306-024-02199-8
  11. Methods Mol Biol. 2025 ;2888 35-52
      Cholesterol is a fundamental component of cellular membranes, and its organization, distribution, and recycling are tightly regulated. Cholesterol can form, together with other lipids and proteins, membrane nanodomains, which play important roles in membrane trafficking, the spatiotemporal organization of signal transduction, or the modulation of plasma membrane transporters, among others. Not surprisingly then, the misregulation of cholesterol biosynthetic and transport pathways has been related to numerous diseases, including neurodegenerative and metabolic disorders. Here, we focus on the cholesterol-binding domain 4 (D4) of perfringolysin O (PFO, theta toxin) and its use as a probe to define the dynamics and subcellular localization of yeast sterols using time-lapse live-cell fluorescence microscopy. In combination with drugs that acutely interfere with sterol synthesis, such as terbinafine, the probe can also be used to monitor in real-time the extraction of sterols from specialized endoplasmic reticulum subdomains named ERSES (endoplasmic reticulum sterol exit sites) by the OSBP-related protein Osh2.
    Keywords:  D4H; Ergosterol; Membrane trafficking; Perfringolysin O; Yeast
    DOI:  https://doi.org/10.1007/978-1-0716-4318-1_4
  12. Cell Death Dis. 2024 Dec 18. 15(12): 891
      Acute kidney injury (AKI) is a significant global health issue, which is often caused by cisplatin therapy and characterized by mitochondrial dysfunction. Restoring mitochondrial homeostasis in tubular cells could exert therapeutic effects. Here, we investigated Slc25a21, a mitochondrial carrier, as a potential target for AKI intervention. Renal Slc25a21 expression is negatively associated with kidney function in both AKI patients and cisplatin-induced murine models. Sustaining renal expression of Slc25a21 slowed down AKI progression by reducing cellular apoptosis, necroptosis, and the inflammatory response, likely through its regulation of 2-oxoadipate conversion. Slc25a21 is highly expressed in proximal tubular epithelial cells, and its down-regulation contributes to compromised mitochondrial biogenesis and integrity, as well as impaired oxidative phosphorylation. Mechanistically, reduced Slc25a21 in AKI disrupts mitochondrial 2-oxoadipate transport, affecting related metabolites influx and the tricarboxylic acid cycle. These findings demonstrate a previously unappreciated metabolic function of Slc25a21 in tubular cells, and suggest that targeting mitochondrial metabolic homeostasis by sustaining Slc25a21 expression could be a potential novel therapeutic strategy for AKI.
    DOI:  https://doi.org/10.1038/s41419-024-07231-2
  13. NMR Biomed. 2025 Jan;38(1): e5309
      Alterations in tricarboxylic acid (TCA) cycle metabolism are associated with hepatic metabolic disorders. Elevated hepatic acetate concentrations, often attributed to high caloric intake, are recognized as a pivotal factor in the etiology of obesity and metabolic syndrome. Therefore, the assessment of acetate breakdown and TCA cycle activity plays a central role in understanding the impact of diet-induced alterations on liver metabolism. Magnetic resonance-based deuterium metabolic imaging (DMI) could help to unravel the underlying mechanisms involved in disease development and progression, however, the application of conventional deuterated glucose does not lead to substantial enrichment in hepatic glutamine and glutamate. This study aimed to demonstrate the feasibility of DMI for tracking deuterated acetate breakdown via the TCA cycle in lean and diet-induced fatty liver (FL) rats using 3D DMI after an intraperitoneal infusion of sodium acetate-d3 at 9.4T. Localized and nonlocalized liver spectra acquired at 10 time points post-injection over a 130-min study revealed similar intrahepatic acetate uptake in both animal groups (AUCFL = 717.9 ± 131.1 mM▯min-1, AUClean = 605.1 ± 119.9 mM▯min-1, p = 0.62). Metabolic breakdown could be observed in both groups with an emerging glutamine/glutamate (Glx) peak as a downstream metabolic product (AUCFL = 113.6 ± 23.8 mM▯min-1, AUClean = 136.7 ± 41.7 mM▯min-1, p = 0.68). This study showed the viability of DMI for tracking substrate flux through the TCA cycle, underscoring its methodological potential for imaging metabolic processes in the body.
    Keywords:  MASLD; TCA cycle; acetate; deuterium metabolic imaging; fatty liver disease; metabolism
    DOI:  https://doi.org/10.1002/nbm.5309
  14. PLoS One. 2024 ;19(12): e0312397
      Estrogen (E2) deficiency is a risk factor for cardiovascular disease (CVD), however, the exact mechanism for the E2 protective effect on CVD remains unclear. This study aimed to investigate the estrogen receptor (ER) and non-receptor mediated effects of E2 treatment on the cardiac expression of adenosine monophosphate-dependent protein kinase (AMPK), autophagic, mitophagy and mitochondrial homeostasis-regulating genes in ovariectomized (OVX) rats. Female rats were divided into two main groups; sham and bilaterally OVX rats, then each group was subdivided into four subgroups according to treatment; untreated, subcutaneously treated with E2 (30 μg/kg), or Fulvestrant (F) (5 mg/Kg), or a combination of both drugs for 28 days. The OVX rats or F-treated sham rats showed dyslipidemia, and marked disturbances in parameters of AMPK signaling, autophagy, mitophagy, mitochondrial fission, fusion and biogenesis. E2 administration to OVX or F-treated sham rats has corrected the disturbed lipid and cardiac profiles, increased AMPK, and restored the balance of cardiac autophagy, mitophagy, and mitochondrial dynamics and homeostasis. Most of these effects in OVX rats were blocked by the ER antagonist (F). Estrogen treatment has cardioprotective effects in OVX females through modulating cardiac mitochondrial homeostasis, mitophagy and autophagy and restoring the AMPK signaling pathway. As witnessed by Fulvestrant, these effects suggest the main role of ER-mediated signaling in regulating mitophagy and plasma and cardiac lipids along with the existence of a post-translational control mechanism or the involvement of estrogenic non-receptor pathway controlling the postmenopausal cardiac mitochondrial energy production machinery that needs further investigation.
    DOI:  https://doi.org/10.1371/journal.pone.0312397
  15. Plant Direct. 2024 Dec;8(12): e70030
      In plants, the nonproteinogenic amino acid β-alanine plays a role in response to hypoxia, flooding, drought, heat, and heavy metal stress conditions. It is also a key intermediate in the synthesis of essential molecules including vitamin B5 and coenzyme A (CoA) through the condensation reaction with pantoate. While the syntheses of pantoate, vitamin B5, and CoA appear to be conserved across plants and bacteria, the synthesis of β-alanine is not. Bacteria and fungi use aspartate, whereas plants can use uracil, spermidine, or propionate to synthesize β-alanine. Given that these three precursors can be formed from the metabolism of glutamine, arginine, isoleucine, and valine, the synthesis of β-alanine could be linked to numerous pathways. Studies of valine catabolism in Arabidopsis suggested that some branched-chain amino acids could in fact serve as precursors for the synthesis of β-alanine. Using GC-MS and isotopically labeled isoleucine and propionate, we linked their metabolism to the synthesis of β-alanine via a proposed transamination of malonate semialdehyde. We then identified three aminotransferases that each catalyzed this final reversible transamination reaction. These results affirm our hypothesis that isoleucine metabolism is also linked to the synthesis of β-alanine via the transamination of metabolic intermediates.
    Keywords:  aminotransferase; arabidopsis; propionate (or propionyl‐CoA); β‐Alanine
    DOI:  https://doi.org/10.1002/pld3.70030
  16. Nat Commun. 2024 Dec 17. 15(1): 10670
      Lysosome/vacuole-mediated intracellular degradation pathways, collectively known as autophagy, play crucial roles in the maintenance and regulation of various cellular functions. However, little is known about the relationship between different modes of autophagy. In the budding yeast Saccharomyces cerevisiae, nitrogen starvation triggers both macronucleophagy and micronucleophagy, in which nuclear components are degraded via macroautophagy and microautophagy, respectively. We previously revealed that Atg39-mediated macronucleophagy is important for cell survival under nitrogen starvation; however, the underlying mechanism remains unknown. Here, we reveal that defective Atg39-mediated macronucleophagy leads to the hyperactivation of micronucleophagy, resulting in the excessive transport of various nuclear components into the vacuole. Micronucleophagy occurs at the nucleus-vacuole junction (NVJ). We show that nuclear membrane proteins localized to the NVJ, including Nvj1, which is responsible for micronucleophagy, are degraded via macronucleophagy. Therefore, defective Atg39-mediated macronucleophagy results in the accumulation of Nvj1, which contributes to micronucleophagy enhancement. Blocking micronucleophagy almost completely suppresses cell death caused by the absence of Atg39, whereas enhanced micronucleophagy correlates with death in Atg39-mutant cells under nitrogen starvation. These results suggest that macronucleophagy modulates micronucleophagy in order to prevent the excess removal of nuclear components, thereby maintaining nuclear and cellular homeostasis during nitrogen starvation.
    DOI:  https://doi.org/10.1038/s41467-024-55045-9
  17. Nat Commun. 2024 Dec 19. 15(1): 10704
      The NADPH/NADP+ redox couple is central to metabolism and redox signalling. NADP redox state is differentially regulated by distinct enzymatic machineries at the subcellular compartment level. Nonetheless, a detailed understanding of subcellular NADP redox dynamics is limited by the availability of appropriate tools. Here, we introduce NAPstars, a family of genetically encoded, fluorescent protein-based NADP redox state biosensors. NAPstars offer real-time, specific measurements, across a broad-range of NADP redox states, with subcellular resolution. NAPstar measurements in yeast, plants, and mammalian cell models, reveal a conserved robustness of cytosolic NADP redox homoeostasis. NAPstars uncover cell cycle-linked NADP redox oscillations in yeast and illumination- and hypoxia-dependent NADP redox changes in plant leaves. By applying NAPstars in combination with selective impairment of the glutathione and thioredoxin antioxidative pathways under acute oxidative challenge, we find an unexpected and conserved role for the glutathione system as the primary mediator of antioxidative electron flux.
    DOI:  https://doi.org/10.1038/s41467-024-55302-x
  18. Cell Death Dis. 2024 Dec 18. 15(12): 899
      The Triple-Negative Breast Cancer (TNBC) subtype constitutes 15-20% of breast cancer cases and is associated with the poorest clinical outcomes. Distant metastasis, particularly to the lungs, is a major contributor to the high mortality rates in breast cancer patients. Despite this, there has been a lack of comprehensive insights into the heterogeneity of metastatic tumors and their surrounding ecosystem in the lungs. In this study, we utilized spatial RNA sequencing technology to investigate the heterogeneity of lung metastatic tumors and their microenvironment in two spontaneous lung metastatic mouse models. Our findings revealed an increase in metabolic-related genes within the cancer cells, with the hub gene Dlat (Dihydrolipoamide S-Acetyltransferase) showing a significant association with the development of lung metastatic tumors. Upregulation of Dlat led to the reprogramming of fatty acid utilization, markedly enhancing the bioenergetic capacity of cancer cells. This finding was corroborated by the increased dependence on fatty acid utilization in lung metastatic cancer cells, and inhibition of Dlat in breast cancer cells exhibited a reduced oxygen consumption rate. Consequently, inhibition of Dlat resulted in decreased survival capacity of breast cancer by reducing cancer stem cell properties and cell adhesion in the lung in vivo. The three cell components within the lung metastatic niche, including CD163+ macrophages, neutrophils, and endothelial cells, expressed elevated levels of ApoE, leading to the secretion of various protumorigenic molecules that promote cancer cell growth in the lung. These molecules include galectin-1, S100A10, S100A4, and S100A6. Collectively, our findings highlight the lipid metabolism reprogramming of cancer and components of the tumor microenvironment that support lung metastasis of TNBC breast cancer.
    DOI:  https://doi.org/10.1038/s41419-024-07205-4
  19. Methods Mol Biol. 2025 ;2894 35-42
      Experimental models of cardiac ischemia/reperfusion injury have served as useful tools in isolating the sequence of events and mechanisms involved following an infarct. The in vitro coverslip ischemia model in neonatal myocytes is key in observing acute cellular and organelle changes during ischemia and in reperfusion. Here we use neonatal mouse ventricular myocytes, and describe two experimental readouts of lactate dehydrogenase assay, for cell damage/injury and measurement of mitochondrial membrane potential.
    Keywords:  Acute ischemia/reperfusion; Cell culture; Mitochondria potential; Neonatal mouse ventricular myocytes
    DOI:  https://doi.org/10.1007/978-1-0716-4342-6_4
  20. Trends Microbiol. 2024 Dec 18. pii: S0966-842X(24)00312-3. [Epub ahead of print]
      The traditional view of metabolism as merely supplying energy and biosynthetic precursors is undergoing a paradigm shift. Metabolic dynamics not only regulates gene expression but also orchestrates cellular processes with remarkable precision. Most bacterial pathogens exhibit exceptional metabolic plasticity, enabling them to adapt to diverse environments, including hostile conditions within a host. While the role of intracellular bacterial metabolism in pathogen-host interactions has been extensively studied, the contributions of the extracellularly released or secreted bacterial metabolites (referred to here as the bacterial 'exometabolome') to metabolic adaptations and disease pathogenesis remain largely unexplored. In this review, we highlight the significant and intriguing roles of bacterial exometabolomes in drug tolerance, immune suppression, and disease pathogenesis, opening a new frontier in our understanding of bacterial-host interactions.
    Keywords:  and pathogenesis; bacterial pathogens; exometabolome; metabolic footprinting; metabolism; virulence
    DOI:  https://doi.org/10.1016/j.tim.2024.11.009
  21. Methods Mol Biol. 2025 ;2888 193-200
      This chapter describes two imaging-based approaches for examining the localization of bridge-like lipid transfer proteins at membrane contact sites during native biological processes. These approaches use multi-color fluorescence imaging, enabling high spatial and temporal resolution and overcoming the limitations of biochemical methods. The first approach involves immunofluorescence in fixed cells, while the second utilizes time-lapse imaging in live cells. These methods are showcased through the example of ATG2, an essential autophagy-related protein, and demonstrate the ability to overcome technical difficulties such as large protein size, lack of high-quality antibodies, and imaging highly dynamic subcellular structures. These described methods provide a powerful tool for understanding protein function and biological processes and can be widely applied to various research questions in cell biology.
    Keywords:  ATG2; Autophagy; Fluorescence microscopy; Lipid transport; Membrane contact site
    DOI:  https://doi.org/10.1007/978-1-0716-4318-1_13
  22. Nat Metab. 2024 Dec;6(12): 2319-2337
      The coenzyme NAD+ is consumed by signalling enzymes, including poly-ADP-ribosyltransferases (PARPs) and sirtuins. Ageing is associated with a decrease in cellular NAD+ levels, but how cells cope with persistently decreased NAD+ concentrations is unclear. Here, we show that subcellular NAD+ pools are interconnected, with mitochondria acting as a rheostat to maintain NAD+ levels upon excessive consumption. To evoke chronic, compartment-specific overconsumption of NAD+, we engineered cell lines stably expressing PARP activity in mitochondria, the cytosol, endoplasmic reticulum or peroxisomes, resulting in a decline of cellular NAD+ concentrations by up to 50%. Isotope-tracer flux measurements and mathematical modelling show that the lowered NAD+ concentration kinetically restricts NAD+ consumption to maintain a balance with the NAD+ biosynthesis rate, which remains unchanged. Chronic NAD+ deficiency is well tolerated unless mitochondria are directly targeted. Mitochondria maintain NAD+ by import through SLC25A51 and reversibly cleave NAD+ to nicotinamide mononucleotide and ATP when NMNAT3 is present. Thus, these organelles can maintain an additional, virtual NAD+ pool. Our results are consistent with a well-tolerated ageing-related NAD+ decline as long as the vulnerable mitochondrial pool is not directly affected.
    DOI:  https://doi.org/10.1038/s42255-024-01174-w
  23. Methods Mol Biol. 2025 ;2888 23-34
      Phosphatidylinositol (PI) is an inositol-containing phospholipid synthesized in the endoplasmic reticulum (ER). PI is a precursor lipid for PI 4,5-bisphosphate (PI(4,5)P2) in the plasma membrane (PM) important for Ca2+ signaling in response to extracellular stimuli. Thus, ER-to-PM PI transfer becomes essential for cells to maintain PI(4,5)P2 homeostasis during receptor stimulation. In this chapter, we discuss two live-cell imaging protocols to analyze ER-to-PM PI transfer at ER-PM contact sites, where the two membrane compartments make close appositions accommodating PI transfer. First, we describe how to monitor PI(4,5)P2 replenishment following receptor stimulation as a readout of PI transfer using a PI(4,5)P2 biosensor and total internal reflection microscopy. The second protocol directly visualizes PI transfer proteins that accumulate at ER-PM contact sites and mediate PI(4,5)P2 replenishment with PI in the ER in stimulated cells. These methods provide spatial and temporal analysis of ER-to-PM PI transfer during receptor stimulation and can be adapted to other research questions related to this topic.
    Keywords:  ER-PM contact sites; PI; PI transfer protein; PI(4,5)P2 biosensor; PI(4,5)P2 replenishment
    DOI:  https://doi.org/10.1007/978-1-0716-4318-1_3
  24. Elife. 2024 Dec 16. pii: RP99914. [Epub ahead of print]13
      TIMM50, an essential TIM23 complex subunit, is suggested to facilitate the import of ~60% of the mitochondrial proteome. In this study, we characterized a TIMM50 disease-causing mutation in human fibroblasts and noted significant decreases in TIM23 core protein levels (TIMM50, TIMM17A/B, and TIMM23). Strikingly, TIMM50 deficiency had no impact on the steady-state levels of most of its putative substrates, suggesting that even low levels of a functional TIM23 complex are sufficient to maintain the majority of TIM23 complex-dependent mitochondrial proteome. As TIMM50 mutations have been linked to severe neurological phenotypes, we aimed to characterize TIMM50 defects in manipulated mammalian neurons. TIMM50 knockdown in mouse neurons had a minor effect on the steady state level of most of the mitochondrial proteome, supporting the results observed in patient fibroblasts. Amongst the few affected TIM23 substrates, a decrease in the steady state level of components of the intricate oxidative phosphorylation and mitochondrial ribosome complexes was evident. This led to declined respiration rates in fibroblasts and neurons, reduced cellular ATP levels, and defective mitochondrial trafficking in neuronal processes, possibly contributing to the developmental defects observed in patients with TIMM50 disease. Finally, increased electrical activity was observed in TIMM50 deficient mice neuronal cells, which correlated with reduced levels of KCNJ10 and KCNA2 plasma membrane potassium channels, likely underlying the patients' epileptic phenotype.
    Keywords:  Action potential; TIM23; TIMM50; TIMM50 disease; biochemistry; chemical biology; human; import disease; mitochondria; mitochondrial protein import; mouse; neuroscience
    DOI:  https://doi.org/10.7554/eLife.99914
  25. Small. 2024 Dec 15. e2406942
      Cuproptosis, a newly defined cell death process, represents a novel modality with significant therapeutic potential in cancer treatment. Nevertheless, the modest concentration and transient half-life of copper ions in the bloodstream constrain their efficient delivery into tumor cells. In this study, a copper-based prussian blue nanostructure loaded with serine metabolic inhibitor (NCT-503@Cu-HMPB) is constructed for selectively inducing cuproptosis combined with disrupting serine metabolism. Released within the tumor cells, NCT-503 is found to inhibit cellular serine metabolism and GSH production, ultimately causing metabolic dysfunction, redox imbalance, and increased the formation of Cu+ that disrupts mitochondrial respiration chain, inducing lipoylated protein dihydrolipoamide S-acetyltransferase (DLAT) aggregation and consequential iron-sulfur cluster protein loss, which leads to proteotoxic stress and ultimately results in cell death. The findings provide a novel paradigm for tumor therapy based on cuproptosis and metabolic reprogramming, offering prospects for the development of innovative nanotherapeutic platforms in the future.
    Keywords:  cuproptosis; nanomedicine; prussian blue; serine metabolism; tumor therapy
    DOI:  https://doi.org/10.1002/smll.202406942