Balancing lysosome abundance in health and disease

Logic-Gated DNA Intelligent Nanorobots for Cellular Lysosome Interference and Enhanced Therapeutics

Environment-recognizing DNA nanodevices have proven promising for cellular manipulation and disease treatment, whereas how to sequentially respond to different cellular microenvironments remains a challenge. To this end, here we elaborate a logic-gated intelligent DNA nanorobot (Gi-DR) for the cascade response to inter- and intra-cellular microenvironments, thereby achieving lysosome-targeted cargo delivery for subcellular interference and tumor treatment with enhanced efficacy. Utilizing G-quadruplexes to respond to high-level K+ in cancer cell surrounding, this Gi-DR nanorobot can activate an aptamer-based transmembrane DNA machine that delivers molecular payloads to cellular lysosome. Accordingly, the nanoassembly of Gi-DR is promoted by the folding of heterodimeric i-motifs in the acidic microenvironment. Such a design allows the extra-/intra-cellular behaviors of the Gi-DR nanorobot to be programmed by an YES-AND logic circuit, with environmental K+ and H+ as two inputs. As a consequence, DNA nanostrips are controllably formed in living cells, interfering with lysosomal function and thereby preventing cellular proliferation. Further, a therapeutic agent (i.e. ligand-drug conjugate) is delivered into target cancer cells for synergistic tumor treatment in vivo, exhibiting the super-enhanced cancer cell lethality and anti-tumor efficacy. It well illustrates that our designed logic-gated DNA nanorobot has broad application prospects in modulating cellular function and precision disease treatment.

ESIPT Nano-Emitter to Probe Lysosome Biogenesis in Live Cells

Endosome-lysosome fusion and endo-lysosome fission-mediated lysosome biogenesis are crucial in regulating cellular health, and their dysregulation signifies disease. Tracking such intricate events with minimal disturbance remains elusive due to the scarcity of single-component synthetic probes capable of distinctly and simultaneously labeling both endosomes and lysosomes. Here, an amphiphilic π-conjugated imine probe is designed that forms micellar self-assemblies in water, called Nano-emitter, which distinctly and simultaneously labels endosomes and lysosomes upon monochromatic-wavelength excitation. ESIPT (Excited State Intramolecular Proton Transfer) active Nano-emitter shows red fluorescence at endosomal pH. Its hydrolysis to fluorescent amine, PEG-Naph at lysosomal pH illuminated lysosomes fluorescent green, with both imine and amine forms excitable using a 405 nm confocal laser. The two-color labeling of endosomes and lysosomes enabled tracking of their fusion and lysosome-biogenesis processes in living cells. Using multiplexed time-lapse imaging with Nano-emitter and anti-cancer drug doxorubicin, the role of these processes is investigated in lysosome-mediated doxorubicin sequestration in MCF-7 cells. The results show that endosomes as well as endo-lysosomes also sequestered doxorubicin apart from lysosomes. Interestingly, doxorubicin-sequestered endo-lysosomes underwent fission and generated more doxorubicin-sequestered lysosomes, preventing the drug's nuclear localization. Such versatile probes can enhance the understanding of drug sequestration and foster therapeutic strategies.

Early trigeminal and sensory impairment and lysosomal dysfunction in accurate models of Wolfram syndrome

Wolfram syndrome (WS) is a rare condition caused by homozygous or compound heterozygous mutations in the WFS1 gene primarily. It is diagnosed on the basis of early-onset diabetes mellitus and optic nerve atrophy. Patients complain of trigeminal-like migraines and show deficits in vibration sensation, but the underlying cause is unknown. Using accurate cell models and two separate, accurate rodent models of WS that show excellent face and construct validity, here we have examined trigeminus, sensation and sensory neuronal function in WS. Analysis of ex vivo and in vivo MRI sequences revealed profound trigeminal atrophy in each rodent model, a novel finding in WS. Optic nerve atrophy is a diagnostic sign in WS, and trigeminal atrophy occurred at the time of earliest loss of optic nerve volume. We also observed deficits in mechanical sensation in our mouse WS model, and pathological analysis revealed extensive inflammation in trigeminal sensory nucleus, both of which are novel findings in WS. Sensory neurons (dorsal root ganglia) showed impaired calcium handling upon depolarisation and reduced mitochondrial membrane potential. Finally, lysosomes were smaller, soma lysosome content was decreased and importantly, lysosome acidity was impaired in sensory neurons, all of which are novel findings in WS. We validated these findings using two separate publicly available datasets, both from WS patient fibroblast-derived neural stem cells. We observed a highly significant functional enrichment of GO cellular component lysosome-related terms among the differentially expressed proteins and genes, with the majority of lysosome-related proteins being downregulated. These data reveal extensive impairments in the trigeminal pathway and nociceptive neurons in WS that may contribute to trigeminal and sensory symptoms observed in patients. Moreover, we note that mutations in WFS1 are relatively common and, given the importance of WFS1 for sensory function, our data may also shed light on sensory impairments in general.

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST

Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multiomic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lysophosphatidylcholine species and multilamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.

Experimental tools and emerging principles of organellar mechanotransduction

Mechanotransduction is the process by which cells detect mechanical forces and convert them into biochemical or electrical signals. This process occurs across various cellular compartments, including the plasma membrane, cytoskeleton, and intracellular organelles. While research has focused mainly on force sensing at the plasma membrane, the mechanisms and significance of intracellular mechanotransduction are just beginning to be understood. This review summarizes current techniques for studying organellar mechanobiology, and highlights advances in our understanding of the mechanosensitive events occurring in organelles such as the endoplasmic reticulum (ER), Golgi apparatus, and endolysosomes. Additionally, some open questions and promising directions are identified for future research.

Painting lysosomes to study organelle heterogeneity

Like other organelles, the heterogeneity of lysosomes within a single cell has been challenging to capture and study in detail. In this issue, Chen and Gutierrez discuss new work that tackles this question using DNA-PAINT imaging, from Lakadamyali and colleagues (https://doi.org/10.1083/jcb.202403116).

Linking glycosphingolipid metabolism to disease-related changes in the plasma membrane proteome

Glycosphingolipids (GSLs) are vital components of the plasma membrane (PM), where they play crucial roles in cell function. GSLs form specialised membrane microdomains that organise lipids and proteins into functional platforms for cell adhesion and signalling. GSLs can also influence the function of membrane proteins and receptors, via direct protein-lipid interactions thereby affecting cell differentiation, proliferation, and apoptosis. Research into GSL-related diseases has primarily focussed on lysosomal storage disorders, where defective enzymes lead to the accumulation of GSLs within lysosomes, causing cellular dysfunction and disease. However, recent studies are uncovering the broader cellular impact of GSL imbalances including on a range of organelles and cellular compartments such as the mitochondria, endoplasmic reticulum and PM. In this review we describe the mechanisms by which GSL imbalances can influence the PM protein composition and explore examples of the changes that have been observed in the PM proteome upon GSL metabolic disruption. Identifying and understanding these changes to the PM protein composition will enable a more complete understanding of lysosomal storage diseases and provide new insights into the pathogenesis of other GSL-related diseases, including cancer and neurodegenerative disorders.

Precise Regulations at the Subcellular Level through Intracellular Polymerization, Assembly, and Transformation

A living cell is an intricate machine that creates subregions to operate cell functions effectively. Subcellular dysfunction has been identified as a potential druggable target for successful drug design and therapy. The treatments based on intracellular polymerization, self-assembly, or transformation offer various advantages, including enhanced blood circulation of monomers, long-term drug delivery pharmacokinetics, low drug resistance, and the ability to target deep tissues and organelles. In this review, we discuss the latest developments of intracellular synthesis applied to precisely control cellular functions. First, we discuss the design and applications of endogenous and exogenous stimuli-triggered intracellular polymerization, self-assembly, and dynamic morphology transformation of biomolecules at the subcellular level. Second, we highlight the benefits of these strategies applied in cancer diagnosis and treatment and modulating cellular states or cell metabolism of living systems. Finally, we conclude the recent progress in this field, discuss future perspectives, analyze the challenges of the intracellular functional reactions for regulation, and find future opportunities.

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST

Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multi-omic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1 -/- and NPC2 -/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lyso-phosphatidylcholine species and multi-lamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS-complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2 -/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.

A "lysosomal bomb" constructed based on amorphous calcium carbonate to induce tumor apoptosis by amplified sonodynamic therapy

The acidic nature of malignant tumors leads to increased drug sequestration and the evasion of apoptotic damage, which is further exacerbated by abnormal lysosomes in tumor cells. In this study, a "lysosomal bomb" will be constructed using a type of acid-neutralized amorphous calcium carbonate (ACC) to encapsulate the sonosensitizer protoporphyrin IX (PpIX), and then coated with homologous tumor cell membranes to increase water solubility and homologous targeting. The PpIX-ACC@CMs designed in this paper are popcorn-like structures, which can not only neutralize the tumor's acidic microenvironment to balance the pH value and release excess Ca2+, but also cause lysosomal dysfunction and achieve drug lysosomal escape to increase drug accumulation. Additionally, the CO2 gas nucleus produced by the acid reaction of ACC can increase the ultrasonic cavitation effect to amplify the sonodynamic therapy (SDT) effect. In vitro and in vivo experiments demonstrated that PpIX-ACC@CMs, serving as a "lysosomal bomb," successfully localized to lysosomes of tumor cells and exhibited lysosomal escape ability through its acid reaction ability, achieving excellent SDT efficacy under ultrasound stimulation. Furthermore, exogenous Ca2+ overload also increased the likelihood of tumor calcification, which could contribute to in vivo tumor inhibition and facilitate CT medical imaging to monitor treatment efficacy.

Lysosomal biogenesis and function in osteoclasts: a comprehensive review

Lysosomes serve as catabolic centers and signaling hubs in cells, regulating a multitude of cellular processes such as intracellular environment homeostasis, macromolecule degradation, intracellular vesicle trafficking and autophagy. Alterations in lysosomal level and function are crucial for cellular adaptation to external stimuli, with lysosome dysfunction being implicated in the pathogenesis of numerous diseases. Osteoclasts (OCs), as multinucleated cells responsible for bone resorption and maintaining bone homeostasis, have a complex relationship with lysosomes that is not fully understood. Dysregulated function of OCs can disrupt bone homeostasis leading to the development of various bone disorders. The regulation of OC differentiation and bone resorption for the treatment of bone disease have received considerable attention in recent years, yet the role and regulation of lysosomes in OCs, as well as the potential therapeutic implications of intervening in lysosomal biologic behavior for the treatment of bone diseases, remain relatively understudied. This review aims to elucidate the mechanisms involved in lysosomal biogenesis and to discuss the functions of lysosomes in OCs, specifically in relation to differentiation, bone resorption, and autophagy. Finally, we explore the potential therapeutic implication of targeting lysosomes in the treatment of bone metabolic disorders.

Transmembrane protein TMEM230, regulator of metalloproteins and motor proteins in gliomas and gliosis

Glial cells provide physical and chemical support and protection for neurons and for the extracellular compartments of neural tissue through secretion of soluble factors, insoluble scaffolds, and vesicles. Additionally, glial cells have regenerative capacity by remodeling their physical microenvironment and changing physiological properties of diverse cell types in their proximity. Various types of aberrant glial and macrophage cells are associated with human diseases, disorders, and malignancy. We previously demonstrated that transmembrane protein, TMEM230 has tissue revascularization and regenerating capacity by its ability to secrete pro-angiogenic factors and metalloproteinases, inducing endothelial cell sprouting and channel formation. In healthy normal neural tissue, TMEM230 is predominantly expressed in glial and marcophate cells, suggesting a prominent role in neural tissue homeostasis. TMEM230 regulation of the endomembrane system was supported by co-expression with RNASET2 (lysosome, mitochondria, and vesicles) and STEAP family members (Golgi complex). Intracellular trafficking and extracellular secretion of glial cellular components are associated with endocytosis, exocytosis and phagocytosis mediated by motor proteins. Trafficked components include metalloproteins, metalloproteinases, glycans, and glycoconjugate processing and digesting enzymes that function in phagosomes and vesicles to regulate normal neural tissue microenvironment, homeostasis, stress response, and repair following neural tissue injury or degeneration. Aberrantly high sustained levels TMEM230 promotes metalloprotein expression, trafficking and secretion which contribute to tumor associated infiltration and hypervascularization of high tumor grade gliomas. Following injury of the central nervous or peripheral systems, transcient regulated upregulation of TMEM230 promotes tissue wound healing, remodeling and revascularization by activating glial and macrophage generated microchannels/microtubules (referred to as vascular mimicry) and blood vessel sprouting and branching. Our results support that TMEM230 may act as a master regulator of motor protein mediated trafficking and compartmentalization of a large class of metalloproteins in gliomas and gliosis.

The nexus of nuclear envelope dynamics, circular economy and cancer cell pathophysiology

The nuclear envelope (NE) is a critical component in maintaining the function and structure of the eukaryotic nucleus. The NE and lamina are disassembled during each cell cycle to enable an open mitosis. Nuclear architecture construction and deconstruction is a prime example of a circular economy, as it fulfills a highly efficient recycling program bound to continuous assessment of the quality and functionality of the building blocks. Alterations in the nuclear dynamics and lamina structure have emerged as important contributors to both oncogenic transformation and cancer progression. However, the knowledge of the NE breakdown and reassembly is still limited to a fraction of participating proteins and complexes. As cancer cells contain highly diverse nuclei in terms of DNA content, but also in terms of nuclear number, size, and shape, it is of great interest to understand the intricate relationship between these nuclear features in cancer cell pathophysiology. In this review, we provide insights into how those NE dynamics are regulated, and how lamina destabilization processes may alter the NE circular economy. Moreover, we expand the knowledge of the lamina-associated domain region by using strategic algorithms, including Artificial Intelligence, to infer protein associations, assess their function and location, and predict cancer-type specificity with implications for the future of cancer diagnosis, prognosis and treatment. Using this approach we identified NUP98 and MECP2 as potential proteins that exhibit upregulation in Acute Myeloid Leukemia (LAML) patients with implications for early diagnosis.

Autophagic-lysosomal damage induced by swainsonine is protected by trehalose through activation of TFEB-regulated pathway in renal tubular epithelial cells

Swainsonine (SW) is the main toxic component of locoweed. Previous studies have shown that kidney damage is an early pathologic change in locoweed poisoning in animals. Trehalose induces autophagy and alleviates lysosomal damage, while its protective effect and mechanism against the toxic injury induced by SW is not clear. Based on the published literature, we hypothesize that transcription factor EB(TFEB) -regulated is targeted by SW and activating TFEB by trehalose would reverse the toxic effects. In this study, we investigate the mechanism of protective effects of trehalose using renal tubular epithelial cells. The results showed that SW induced an increase in the expression level of microtubule-associated protein light chain 3-II and p62 proteins and a decrease in the expression level of ATPase H+ transporting V1 Subunit A, Cathepsin B, Cathepsin D, lysosome-associated membrane protein 2 and TFEB proteins in renal tubular epithelial cells in a time and dose-dependent manner suggesting TFEB-regulated lysosomal pathway is adversely affected by SW. Conversely, treatment with trehalose, a known activator of TFEB promote TFEB nuclear translocation suggesting that TFEB plays an important role in protection against SW toxicity. We demonstrated in lysosome staining that SW reduced the number of lysosomes and increased the luminal pH, while trehalose could counteract these SW-induced effects. In summary, our results demonstrated for the first time that trehalose could alleviate the autophagy degradation disorder and lysosomal damage induced by SW. Our results provide an interesting method for reversion of SW-induced toxicity in farm animals and furthermore, activation of TFEB by trehalose suggesting novel mechanism of treating lysosomal storage diseases.

Swedish Alzheimer's disease variant perturbs activity of retrograde molecular motors and causes widespread derangement of axonal transport pathways

Experimental studies in flies, mice, and humans suggest a significant role of impaired axonal transport in the pathogenesis of Alzheimer's disease (AD). The mechanisms underlying these impairments in axonal transport, however, remain poorly understood. Here we report that the Swedish familial AD mutation causes a standstill of the amyloid precursor protein (APP) in the axons at the expense of its reduced anterograde transport. The standstill reflects the perturbed directionality of the axonal transport of APP, which spends significantly more time traveling in the retrograde direction. This ineffective movement is accompanied by an enhanced association of dynactin-1 with APP, which suggests that reduced anterograde transport of APP is the result of enhanced activation of the retrograde molecular motor dynein by dynactin-1. The impact of the Swedish mutation on axonal transport is not limited to the APP vesicles since it also reverses the directionality of a subset of early endosomes, which become enlarged and aberrantly accumulate in distal locations. In addition, it also reduces the trafficking of lysosomes due to their less effective retrograde movement. Altogether, our experiments suggest a pivotal involvement of retrograde molecular motors and transport in the mechanisms underlying impaired axonal transport in AD and reveal significantly more widespread derangement of axonal transport pathways in the pathogenesis of AD.

Berberine Alleviates Ischemic Brain Injury by Enhancing Autophagic Flux via Facilitation of TFEB Nuclear Translocation

Berberine has been demonstrated to alleviate cerebral ischemia/reperfusion injury, but its neuroprotective mechanism has yet to be understood. Studies have indicated that ischemic neuronal damage was frequently driven by autophagic/lysosomal dysfunction, which could be restored by boosting transcription factor EB (TFEB) nuclear translocation. Therefore, this study investigated the pharmacological effects of berberine on TFEB-regulated autophagic/lysosomal signaling in neurons after cerebral stroke. A rat model of ischemic stroke and a neuronal ischemia model in HT22 cells were prepared using middle cerebral artery occlusion (MCAO) and oxygen-glucose deprivation (OGD), respectively. Berberine was pre-administered at a dose of 100[Formula: see text]mg/kg/d for three days in rats and 90[Formula: see text][Formula: see text]M in HT22 neurons for 12[Formula: see text]h. 24[Formula: see text]h after MCAO and 2[Formula: see text]h after OGD, the penumbral tissues and OGD neurons were obtained to detect nuclear and cytoplasmic TFEB, and the key proteins in the autophagic/lysosomal pathway were examined using western blot and immunofluorescence, respectively. Meanwhile, neuron survival, infarct volume, and neurological deficits were assessed to evaluate the therapeutic efficacy. The results showed that berberine prominently facilitated TFEB nuclear translocation, as indicated by increased nuclear expression in penumbral neurons as well as in OGD HT22 cells. Consequently, both autophagic activity and lysosomal capacity were simultaneously augmented to alleviate the ischemic injury. However, berberine-conferred neuroprotection could be greatly counteracted by lysosomal inhibitor Bafilomycin A1 (Baf-A1). Meanwhile, autophagy inhibitor 3-Methyladenine (3-MA) also slightly neutralized the pharmacological effect of berberine on ameliorating autophagic/lysosomal dysfunction. Our study suggests that berberine-induced neuroprotection against ischemic stroke is elicited by enhancing autophagic flux via facilitation of TFEB nuclear translocation in neurons.

Nutrient signaling: Starvation flips a phosphoinositide switch on lysosomal catabolism

Lysosomes are highly dynamic organelles that rapidly respond to changes in cellular nutrient status. A new study identifies a phosphoinositide switch that dictates lysosome function during nutrient starvation.