bims-lypmec Biomed News
on Lysosomal positioning and metabolism in cardiomyocytes
Issue of 2026–06–21
nine papers selected by
Satoru Kobayashi, New York Institute of Technology



  1. Circulation. 2026 Jun 17.
       BACKGROUND: Cardiac aging involves progressive mitochondrial dysfunction, contributing to heart failure. Cardiolipin (CL), essential for mitochondrial function, is increasingly depleted in aging cardiomyocytes, promoting mitochondrial decline. Lysosomal degradation relies on v-ATPase (vacuolar-type H+-ATPase)-mediated acidification, and although lysosomes regulate phospholipid metabolism, their roles in CL homeostasis during aging remains unclear. This study examines whether v-ATPase dysfunction drives age-related cardiac changes by disrupting CL metabolism and mitochondrial function.
    METHODS: To investigate underlying mechanisms and causality, we use RNA sequencing, targeted lipidomics, immunofluorescence microscopy, (co)immunoprecipitation, proximity ligation assays, subcellular fractionation, mitochondrial respiration analysis and echocardiography, a cardiolipin synthase-1 (Crsl1) knockout mouse model, and 2 v-ATPase knockout models. In addition, we assess whether a nutraceutical intervention targeting v-ATPase dysfunction can mitigate heart failure in aging mouse models and elderly people.
    RESULTS: Our present findings reveal a sequence of events driving age-related cardiomyopathy: declining cardiac nicotinamide adenine dinucleotide levels impair v-ATPase-mediated lysosomal acidification by weakening the interaction between nicotinamide adenine dinucleotide-dependent glycolytic enzyme aldolase and v-ATPase. This disruption increases lysosomal membrane permeability by reducing lysosomal acidification, allowing cathepsin B to leak into mitochondria. There, cathepsin B disrupts mitochondrial CRLS1 (cardiolipin synthase I), impairing CL synthesis and remodeling. The resulting CL deficiency causes mitochondrial oxidative stress and programmed cell death, leading to mitochondrial and cardiac dysfunction. Genetic or chemical inhibition of v-ATPase and of CRLS1 in mouse models reproduce these age-related defects, highlighting their central roles in cardiac aging. Restoring nicotinamide adenine dinucleotide levels rescues lysosomal acidification and CL metabolism, protecting against age-related cardiomyopathy in rodents and humans.
    CONCLUSIONS: Augmenting v-ATPase-mediated lysosomal acidification offers novel therapeutic strategies to combat age-related cardiomyopathy by rewiring CL homeostasis.
    Keywords:  aged heart; cardiolipin metabolism; cardiolipin synthase 1; lysosomal acidification; mitochondrial homeostasis; vacuolar H+-ATPase
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.125.078376
  2. Nat Commun. 2026 Jun 16.
      Correct trafficking of lysosomal transporters is essential for intracellular homeostasis. While most lysosomal membrane proteins are directed to the lysosome via sorting motifs, the cobalamin exporter ABCD4 is distinct, instead relying on LMBD1 as a dedicated chaperone for its trafficking. Dysfunction of either protein causes inherited cobalamin metabolism disorders. Despite its physiological significance, the molecular mechanism underlying this chaperone-dependent trafficking remains unclear. Here, we report the cryo-EM structures of ABCD4 complex with LMBD1 in the lumen-open, substrate-bound and cytosol-open states. LMBD1 contains nine transmembrane-helices (TMs) and a cytosolic domain, both of which engage ABCD4. Cell imaging shows that disruption of these interactions impairs the trafficking of ABCD4 to lysosomes. Structural and biochemical analyses provide insights into cobalamin recognition and reveal conformational states associated with the proposed cobalamin transport cycle. These findings provide molecular insights into cobalamin metabolism and illustrate a chaperone-assisted mechanism that supports proper trafficking of a lysosomal transporter.
    DOI:  https://doi.org/10.1038/s41467-026-74552-5
  3. Cell Rep. 2026 Jun 12. pii: S2211-1247(26)00622-4. [Epub ahead of print]45(6): 117544
      Cholesterol homeostasis depends on lysosomes liberating cholesterol from degraded lipids. We show that SARS-CoV-2 blocks lysosomal cholesterol egress through the viral protein ORF3a. ORF3a binds the HOPS subunit VPS39 via the W193 and Y184 residues. Disrupting this interface restores cholesterol trafficking. Mechanistically, the ORF3a-VPS39 interaction exerts dual effects. First, it traps the retromer complex on endolysosomes, preventing endosome-to-Golgi recycling and mislocalizing the cholesterol transporter NPC2. Retromer deletion reproduced these defects, whereas the ORF3a W193A mutant restored retromer trafficking. Second, ORF3a-VPS39 interaction reduces bis(monoacylglycerol)phosphates (BMPs), lysosomal lipids required for cholesterol egress, by disrupting the transfer of their precursor, phosphatidylglycerols, from mitochondria. Lipidomics revealed increased mitochondrial and decreased lysosomal phosphatidylglycerol metabolites. Disturbing autophagy or mitochondrion-derived vesicles did not alter BMP levels, whereas ORF3a reduced mitochondrion-lysosome membrane contacts. These findings identify dual functions of VPS39-regulating retromer trafficking and BMP biosynthesis-and also reveal how ORF3a blocks lysosomal cholesterol egress.
    Keywords:  BMPs; CP: cell biology; CP: microbiology; HOPS; bis(monoacylglycero)phosphates; cellular cholesterol transport; lysosome-mitochondrion interactions; retromer
    DOI:  https://doi.org/10.1016/j.celrep.2026.117544
  4. J Gen Physiol. 2026 Jul 06. pii: e202413745. [Epub ahead of print]158(4):
      Lysosomes are essential organelles in eukaryotic cells, required for autophagy, endocytosis, pathogen defense, cell signaling, and metabolic homeostasis. A model of lysosomal ion and water fluxes that captures the synchronized, interdependent operation of ion transporters and diffusion enables prediction of organellar responses to external perturbations and supports the design and interpretation of experiments. Particularly with the advent of organelle-targeted rhodopsin-based optogenetics, there is a pressing need to predict cellular outcomes following light-driven, specific ion transport in lysosomes and other organelles. Currently, no models of lysosomal ion balance fully align with existing experimental data or enable simulation of the organelle's response to stress. Here, we present an updated interactive model that recapitulates appropriate stress responses. We incorporated the functional activities of TPC1 and TMEM165, in addition to the previously included vATPase, ClC-7, TRPML1, and passive ion and water fluxes. The model remains robust during lysosomal maturation, membrane permeabilization, swelling, deacidification induced by vATPase inhibition or additional optogenetics-like proton efflux, and accumulation of weakly basic cationic amphiphilic drugs. Our simulations indicate that lysosomal Ca2+ depletion couples with organellar deacidification triggered by either increased proton leakage or vATPase inhibition, with potential involvement of TMEM165 weakening. Beyond predicting stress-response dynamics, the model enables investigation of highly selective perturbations that can be experimentally induced using optogenetics. Elucidating the mechanisms underlying stable, stress-resilient lysosomal function offers insights for developing anti-disease and antiaging interventions. Further model refinement critically depends on experimental characterization of the lysosomal NHE-like protein mediating sodium influx.
    DOI:  https://doi.org/10.1085/jgp.202413745
  5. Circ Res. 2026 Jun 16.
       BACKGROUND: Pathological cardiac remodeling and afterload-induced increases in energy demand together contribute to heart failure (HF). Lysosome-assisted processes, such as autophagy, coupled with alterations in mitochondrial oxidative capacity, play important roles in cardiac remodeling and HF. Furthermore, the lysosome is a hub for multiple signaling pathways governing hypertrophic growth. The TFEB (transcription factor EB) has emerged as a key regulator of lysosomal genes and mitochondrial function in multiple tissues, especially in response to external stress.
    METHODS: Leveraging a cardiomyocyte-specific TFEB knockout mouse (CTKO), pressure overload was induced by transverse aortic constriction (TAC) to elucidate the role of TFEB under hypertrophic stress conditions. Echocardiography was employed to assess cardiac function, and hearts were subsequently harvested for transcriptomic, proteomic, and metabolomic analyses. To glean further insight into the molecular mechanisms involved, we studied neonatal rat ventricular myocytes exposed to phenylephrine, an in vitro model of cardiomyocyte hypertrophy.
    RESULTS: We report that TFEB is rapidly activated and translocates to the nucleus in cardiomyocytes exposed to hypertrophic stress conditions, triggering a lysosomal gene program independent of autophagy gene changes. At baseline, contractile function measured by echocardiography appeared normal in these mice compared with their Cre-negative littermates. However, in pressure-overload stress induced by TAC, CTKO mice manifested an amplified hypertrophic response, leading rapidly to HF. Unlike WT hearts, CTKO hearts failed to increase lysosomal capacity after TAC. They manifested an increase in the steady-state levels of autophagosome-associated proteins, such as LC3II and p62, as well as accumulation of ubiquitinated proteins, suggesting a defect in protein turnover. Interestingly, CTKO mice harbored altered mitochondrial structure, reduced oxidative capacity, and reduced abundance of peroxisome PGC-1α-b (proliferator-activated receptor-1 alpha-b). Furthermore, CTKO hearts manifested reduced expression of key enzymes within metabolic pathways essential for normal myocardial metabolism, including fatty acid metabolism, carbon metabolism, and branched-chain amino acid metabolism. Surprisingly, AMPK (AMP-activated protein kinase) signaling, while normal at baseline, was significantly decreased in CTKO hearts after TAC. This reliance on TFEB for growth trigger-induced AMPK signaling was also observed in vitro in cells exposed to phenylephrine, as were the antihypertrophic effects of TFEB activation, supporting a direct role of TFEB in this process. Finally, we report that exogenous activation of AMPK in the absence of TFEB can completely rescue the exacerbated hypertrophic response both in vitro and in vivo, independent of lysosomal function. Notably, blunting of the hypertrophic response did not impact the decreased contractile function observed in TAC-treated CTKO mice, highlighting the importance of TFEB in regulating mitochondrial function in response to stress.
    CONCLUSIONS: Our findings demonstrate that TFEB antagonizes pathological hypertrophic cardiac remodeling through upregulation of lysosomal capacity, maintaining mitochondrial energetic function, and promoting AMPK signaling.
    Keywords:  autophagy; heart failure; hypertrophy; lysosomes; proteomics
    DOI:  https://doi.org/10.1161/CIRCRESAHA.125.328083
  6. Proc Natl Acad Sci U S A. 2026 Jun 23. 123(25): e2532309123
      Hypoxia is a common stress encountered by animal tissues during development, physiology, and disease. To cope with hypoxic stress, cells remodel metabolic and signaling networks to preserve viability and function. Lysosomes serve as central hubs for metabolic control and intracellular signaling, yet their role in hypoxic adaptation remains unclear. Here, we identify the lysosomal calcium transporter TMEM165 as a hypoxia-responsive regulator of cellular homeostasis. Under hypoxic conditions, TMEM165 expression increases, promoting calcium redistribution from the endoplasmic reticulum to lysosomes and expanding lysosomal calcium storage capacity. TMEM165 activation regulates autophagy and senescence through the AMPK-mTOR and ERK/p21 signaling pathways, respectively. In glioma, high TMEM165 expression correlates with poor prognosis, whereas its depletion suppresses glycolysis, proliferation, and tumor progression. These findings establish TMEM165 as a lysosomal hypoxia-responsive protein that integrates calcium signaling with metabolic and stress-response pathways, revealing a mechanistic link between oxygen availability, lysosomal function, and tumor adaptation.
    Keywords:  TMEM165; calcium signaling; cancer; hypoxia; lysosome
    DOI:  https://doi.org/10.1073/pnas.2532309123
  7. Cell Commun Signal. 2026 Jun 17.
      Lipid droplet (LD) accumulation and impaired lipid mobilization induce lipotoxic stress and contribute to metabolic, cardiovascular, cancer, and neurodegenerative diseases (NDDs). Although LD-selective autophagy (lipophagy) is being increasingly studied, the mechanisms that confer LD specificity and enable tissue- and stage-specific therapeutic modulation remain unclear. Effective lipophagic flux requires coordinated LD coat remodeling, nutrient and energy sensing, and organelle contact. Coat remodeling governs substrate access and droplet recognition. The AMPK-mTORC1-TFEB axis links autophagy induction to lysosome biogenesis and capacity. Endoplasmic reticulum (ER)-LD, mitochondria-LD, and LD-lysosome contact sites facilitate lipid transfer by coupling lysosomal hydrolysis to mitochondrial β-oxidation. Lipophagy is a highly stage- and cell-type-dependent process: it removes excess lipids to protect cells, but its dysregulation can promote inflammation and fibrogenesis or supply substrates to tumors. This review synthesizes mechanistic and translational evidence on lipophagy initiation, regulation, and disease relevance, and identifies the following priorities: robust biomarkers, distinction of cargo-recognition defects from lysosomal dysfunction, and precision interventions tailored to the tissue and disease stage.
    DOI:  https://doi.org/10.1186/s12964-026-03016-6
  8. Nat Cell Biol. 2026 Jun 19.
      Lysosomes are integral organelles that communicate cellular status to an entire tissue through mechanisms that are poorly defined. Here we developed an unbiased platform, integrating human plasma metabolomes and single-lysosome metabolomics, and show the byproducts of proteolysis are an unexpected class of signalling molecules. We show that dimethylarginine is a lysosomal-derived metabolite and a predictor of patient morbidity. Genetic depletion of a lysosomal exporter, cystinosin, accumulated dimethylarginine in lysosomes. Leveraging a lysosomal storage disease with cystinosin mutations, we show that the rapid plasticity of dimethylarginine compartmentalization ensures cell and tissue homeostasis. Strikingly, lysosomal entrapment of dimethylarginine in patients and disease models corresponds with lipid accumulation, lipid droplets and lipotoxicity. Exogenously restoring asymmetric dimethylarginine buffers oxidative stress, decreasing lipid peroxidation and cell death. These data show that dimethylarginine engages an interorganellar process-with peroxisomes, lysosomes and lipid droplets-that confers a crucial adaptive response mechanism.
    DOI:  https://doi.org/10.1038/s41556-026-01970-4
  9. Life Metab. 2026 Jun;5(3): loag007
    Life Metabolism Editorial Team
      
    DOI:  https://doi.org/10.1093/lifemeta/loag007