Sepsis-associated lung injury arises from a dysregulated response to infection and frequently involves acute respiratory distress syndrome, or ARDS. A meta-analysis cited in the review estimated that ARDS develops in 34.0% of patients with sepsis, with a 95% confidence interval of 29.0% to 39.3%. Lysosomes and related endolysosomal compartments sit directly at the host–pathogen interface: acidic phagolysosomes support microbial killing in macrophages, lamellar bodies participate in surfactant biology in type II alveolar epithelial cells, and lysosomal degradation and trafficking contribute to endothelial repair and fibroblast matrix turnover. Infection-related stress could therefore compromise both pathogen control and the cellular processes needed to preserve the lung’s gas-exchange barrier. The proposed link between these defects and lysosomal pH remains incompletely mapped, however, particularly in human disease.

Central to the hypothesis is the V-ATPase complex, which hydrolyzes ATP to pump protons into lysosomal compartments and create the acidic conditions required by many lysosomal hydrolases. V-ATPase is also a signaling platform influenced by nutrient sensing, trafficking, complex assembly and stress. In macrophages, the ATP6V0D2 subunit has been associated with autophagosome–lysosome fusion and restrained inflammasome activation during bacterial challenge, illustrating that its role cannot be reduced to setting basal acidity. The mTORC1–TFEB pathway provides another connection between nutrient status, lysosomal biogenesis, autophagy and stress adaptation, but the review cautions that TFEB does not uniformly increase every acidification-related transporter across cell types or conditions. Similarly, PI3K–AKT signaling may influence lysosomal resilience indirectly through metabolism, mitochondrial function and membrane stability; a direct AKT-driven alkalinization mechanism has not been established in septic lung cells.

Acidification also depends on the movement of counterions. ClC-7 is a late-endosomal and lysosomal chloride–proton exchanger that requires the accessory protein OSTM1 for stability. Recent work indicates that ClC-7 promotes chloride accumulation in mature phagosomes, hydrolase activity and phagosome resolution. Its influence on bulk lysosomal acidity is more complicated, with genetic studies reporting altered chloride distribution and storage phenotypes without consistent loss of acidification. The authors therefore describe ClC-7 primarily as a regulator of luminal chloride with context-dependent effects on pH. TMEM175, an endolysosomal potassium channel implicated in membrane potential and pH stability, presents another unresolved question. Models disagree over whether it conducts protons or predominantly potassium, and the evidence comes largely from heterologous systems or non-septic neurodegeneration-related models. Its role in pulmonary sepsis has not been directly tested.

A further complication is that lysosomal pH is not equivalent to every other sign of lysosomal dysfunction. The review distinguishes increased luminal pH from membrane permeabilization, reduced hydrolase activity, impaired autophagic flux and changes in lysosomal mass or biogenesis. Markers such as LC3-II, p62, cathepsin abundance and LysoTracker intensity can each be altered by organelle number, trafficking, cargo load, membrane damage or probe behavior. LC3-II accumulation, for example, may reflect either increased autophagy or failure of lysosomal degradation. Direct acidity evidence ideally comes from compartment-targeted ratiometric probes calibrated in situ with ionophores and defined-pH buffers. Single-wavelength acidotropic dyes are useful for locating lysosomes but cannot, by themselves, provide stand-alone pH values. This distinction is especially important in sepsis, where cell death, systemic acid–base disturbances and changes in organelle abundance can confound commonly used readouts.

Microbial and host signals could disturb lysosomal homeostasis in several ways. Lipopolysaccharide activates TLR4–MyD88/TRIF and NF-κB inflammatory signaling in pulmonary immune and structural cells, but available evidence does not show universal repression of acidification machinery. Instead, changes in trafficking, cytokines, nitroxidative stress, metabolism and autophagic flux may indirectly alter lysosomal function. Tumor necrosis factor alpha, interleukin-1 beta and interleukin-6 can promote reactive oxygen species, mitochondrial injury, metabolic reprogramming and dysregulated autophagy–lysosome flux. Persistent stress may reduce ATP-dependent proton pumping, disturb membrane stability or overload degradative capacity. Lysosomal membrane permeabilization can then release cathepsins and other contents into the cytosol. Cathepsin B has been linked to NLRP3 inflammasome activation and pyroptosis-related signaling in experimental sepsis-associated lung injury, but its contribution depends on the cell and stimulus. Reduced lysosomal acidity is thus best considered a possible permissive amplifier working with mitochondrial reactive oxygen species, potassium efflux, danger signals and defective autophagic clearance, not as the sole trigger of inflammation.

The consequences may differ sharply among the cells that form and defend the alveolar–capillary barrier. In macrophages and dendritic cells, impaired lysosomal or phagolysosomal function may reduce microbial killing, cargo degradation and antigen processing, which is why indiscriminate suppression of lysosomal activity could be counterproductive. In epithelial and endothelial cells, lysosomal injury may contribute to protease release, junctional disruption, vascular leakage and defective repair through convergent mechanisms, but direct pH-to-junction causality has not been established. Type II epithelial lamellar bodies have specialized functions in calcium handling and surfactant secretion that should not be equated automatically with canonical lysosomes. During persistent or non-resolving injury, impaired lysosomal degradation may also hinder removal of damaged mitochondria, oxidized lipids and mitochondrial DNA, potentially sustaining TLR9, cGAS–STING and NLRP3 pathways. Evidence linking lysosomal pH to fibrotic matrix remodeling comes mainly from pulmonary fibrosis research, and direct human evidence in post-sepsis lung injury remains limited.

Mitophagy and inter-organelle proton transfer add another possible dimension. Mitochondria and lysosomes communicate through mitophagy, reactive oxygen species, lipid transfer and direct membrane contact sites. Mitochondrial injury can restrict the ATP and redox conditions needed for V-ATPase activity, while defective lysosomal trafficking can reduce mitochondrial clearance and allow dysfunctional mitochondria to accumulate. Studies in yeast and human cells have now shown proton transfer from mitochondria to lysosomes at contact sites, with experimental organelle tethering improving acidification, cargo degradation and autophagic flux. These observations are mechanistically relevant but were not conducted in septic lung models, and no cited sepsis study simultaneously quantified mitochondria–lysosome contacts and lysosomal pH. The relative contributions of V-ATPase and counterion dysfunction, membrane damage and contact-mediated proton transfer therefore remain unresolved in this disease context.

Because the model is not yet ready for clinical application, the authors propose measured rather than diagnostic biomarker panels. A bronchoalveolar lavage fluid strategy could combine calibrated lysosomal pH in recovered alveolar macrophages, intralysosomal cathepsin B and D activity, cytosolic cathepsin redistribution, and extracellular cathepsin or LAMP1/2. A high-pH, low-hydrolase phenotype with limited extracellular release would be consistent with impaired acidification, whereas cathepsin redistribution and extracellular release would favor membrane injury. A less invasive blood panel could assess calibrated pH in circulating monocytes, cathepsin localization and autophagic flux, although neither LC3-II nor p62 alone would establish alkalinization. These are proposed test strategies rather than validated signatures and would require longitudinal cohorts, comparison with established measures such as oxygenation, lactate, procalcitonin and inflammatory markers, and analysis of whether blood and lung samples identify the same phenotypes.

Therapeutic development would likewise need to distinguish disease phase and molecular phenotype. An alkalinization-dominant state with impaired phagocyte degradation could justify testing controlled restoration of acidification or lysosomal biogenesis. One compound, ZLN005, increased lysosomal acidity and biogenesis in phagocytes and improved bacterial killing and survival in experimental polymicrobial sepsis, but its effects also involved PGC-1α, PI3K and TFEB, preventing attribution of benefit solely to pH correction. Selectively applicable clinical V-ATPase activators are not established. Conversely, a membrane-injury phenotype without clear alkalinization would support testing membrane stabilization or carefully titrated protease modulation, since broad cathepsin inhibition could interfere with microbial killing and tissue remodeling. Future experiments should combine spatial or single-cell identification of lysosomal stress with calibrated pH measurement, hydrolase assays, membrane-permeabilization tests and flux analysis in infection models, co-cultures, organoids and precision-cut lung slices. The defensible conclusion is that lysosomal pH homeostasis deserves testing as a mechanistic and stratification axis for sepsis-associated lung injury, not that it has already been established as a precision-medicine target.

Subject of Research: Lysosomal pH dysregulation as a candidate amplifier of sepsis-associated lung injury

Article Title: Lysosomal pH dysregulation as a candidate signal-amplifying hub in sepsis-associated lung injury

Article References: Tu, G., Deng, Z., Li, Y., Tian, P., Shen, Y., Deng, Y., Zhang, Z., Liu, Y., Zhong, S., Wu, J., Zhu, H., Ma, J., & Li, J. (2026). Lysosomal pH dysregulation as a candidate signal-amplifying hub in sepsis-associated lung injury. Frontiers in Cellular and Infection Microbiology, 16, Article 1953667. https://doi.org/10.3389/fcimb.2026.1953667

Image Credits: AI Generated

DOI: 10.3389/fcimb.2026.1953667

Keywords: lysosomal pH, sepsis, lung injury, ARDS, V-ATPase, inflammation, autophagy, mitochondria–lysosome crosstalk, host–pathogen interaction, Lysosomal, dysregulation, candidate

The review, led by Shruthi Bandyadka and Kimberly McCall of Boston University together with Hila Toledano of the University of Haifa, focuses on germline cysts. In most animals, germ cells do not develop as isolated units. Germline stem cells give rise to daughters that divide with incomplete cytokinesis, producing clusters of cells joined by intercellular bridges. In the testis, every cell of such a cyst differentiates into a spermatocyte. In the ovary, typically one cell becomes the oocyte while the others serve as nurse cells that pump their cytoplasmic contents into the developing egg. These cysts are ancient, found in the male germline of most if not all animals, and they present a logistical puzzle: how do you eliminate part of an interconnected collective without damaging the tissue around it?

The answer, the authors argue, is phagoptosis, a form of regulated cell death in which the phagocytic machinery of one cell is turned against another cell that would otherwise remain alive. Phagocytes classically clear corpses, engulfing cells that have already died by apoptosis and displaying eat-me signals such as phosphatidylserine. In phagoptosis, the phagocyte is the executioner. The phenomenon was first characterised in the brain, where microglia engulf viable but stressed neurons, and it has since been documented in multiple tissues. What the new review highlights is that the germline, of all places, has emerged as a premier model for this cellular assassination.

The most thoroughly analysed system is the Drosophila ovary. Each egg chamber contains the oocyte, its nurse cells and a monolayer of somatic follicle cells. Two distinct death paradigms operate here. Under starvation or stress, a checkpoint roughly halfway through oogenesis, between stages 7 and 9, triggers degeneration of the entire egg chamber; this midstage death is apoptotic and autophagic, and follicle cells expressing the phagocytic receptor Draper engulf the dying germ cells. But the developmental death of nurse cells at the end of a healthy oogenesis, from stages 12 to 14, is something else entirely. It proceeds despite disruption of caspases and autophagy genes in the germline, ruling out both apoptosis and autophagy as essential mechanisms.

Genetic ablation experiments revealed that a specialised subset of follicle cells, the stretch follicle cells that extend between the nurse cells, are required for nurse cell death. These epithelial cells act as non-professional phagocytes. They require the phagocytosis genes draper, ced-12 and the JNK signalling pathway, and loss of any of these blocks the DNA fragmentation and nuclear lamina breakdown that characterise nurse cell death. Remarkably, four to five stretch follicle cells collaborate around each nurse cell, and complete coverage by this phagocytic collective is required for clearance. This is not the single phagocytic cup of textbook engulfment; it is a coordinated, multi-cell strangling operation.

The final blow is delivered by acidification. Vacuolar ATPases, proton pumps normally confined to lysosomal membranes, become enriched on the plasma membrane of the stretch follicle cells, secreting protons into the extracellular space around the nurse cell remnants. Chloride channels localise similarly, presumably balancing the ion gradient. The low pH activates cathepsin proteases such as CP1 released by the follicle cells, and together with DNaseII these enzymes degrade the nurse cell lamins and chromatin. The transcription factor Mitf, a master regulator of V-ATPase genes, is required, and Draper is needed for acidification itself, suggesting the receptor influences proton pump deployment. In effect, the lysosomal acidification machinery is repurposed for extracellular killing: the nurse cells are digested from outside rather than inside a phagolysosome.

Strikingly similar logic operates in the Drosophila testis. Spermatogonial cysts, clutches of 2, 4, 8 or 16 interconnected germ cells wrapped by somatic cyst cells, die spontaneously under homeostatic conditions; imaging of fixed testes suggests 20 to 30 percent of mitotic cysts are engaged in death at any time, and the process takes more than 24 hours from initiation to completion. This death is non-apoptotic: loss of the effector caspases Drice and Dcp-1 does not reduce it, autophagy mutants do not affect it, and the caspase-9 homologue Dronc acts atypically, independently of its catalytic activity. Dying cysts co-stain with LysoTracker and TUNEL, and mutants in lysosomal genes including cathepsin D, deep-orange, carnation and DNaseII significantly decrease the number of dying cysts, squarely implicating lysosomes.

Live imaging then established that the somatic cyst cells are the killers. Lamp1-positive phagosomes of cyst cell origin aggregate between cyst cells and germ cells before acidification begins, and Rab5 and Rab7 positive endosomes localise around the entire spermatogonium, indicating that the interconnected germ cells are engulfed as a single unit. RNAi knockdown of Rab5 in cyst cells completely arrests germ cell death, a necessary qualifier for phagoptosis. The receptors Draper and Croquemort play complementary roles: draper and ced-12 are essential for engulfment but not acidification, whereas crq affects acidification without disrupting engulfment. Loss of engulfment causes hyperplasia at the testis apex, where live spermatogonia accumulate, a phenotype mirrored in p53 null mutants, pointing to the tumour suppressor as an intrinsic inducer of germ cell death, a role conserved in mice under mild heat shock.

The conservation extends to mammals. In the fetal mouse ovary, nurse cells in germline cysts of up to 32 cells are eliminated by the surrounding pregranulosa cells. LysoTracker activity rises in nurse cells during late oogenesis, and inhibition of V-ATPase activity with bafilomycin A1 abolishes this signal and leaves nurse cell nuclei persisting. Single-cell RNA sequencing shows late-oogenesis pregranulosa cells expressing multiple V-ATPase subunits and cathepsins Ctsb, Ctsd, Ctsl and Ctsz, the orthologue of Drosophila Cp1. Apoptosis also occurs simultaneously, albeit at far lower levels, apparently to remove non-viable germ cells, suggesting that specific cues deterministically activate one pathway or the other.

Why would evolution place a destructive acid bath so close to a precariously incubated gamete? The authors speculate that acidification may harm nurse cells without impairing the oocyte, and may even benefit gamete competence; the rodent male reproductive tract maintains an acidic luminal environment, by V-ATPase proton secretion, to help nascent sperm mature. Extracellular proton secretion by plasma membrane V-ATPases is known in kidney intercalated cells and osteoclasts, but its involvement in cell killing thus far appears confined to gametogenesis. Many questions remain: how the nurse cell plasma membrane is disposed of, whether trogocytosis or cellular nibbling precedes acidification, what eat-me signals mark live germ cells for recognition when phosphatidylserine appears only after engulfment, and how the Toll pathway and single-cell gene expression programmes shape the phagocytic fate of these somatic cells. What is already clear is that somatic cells across the animal kingdom share a conserved, non-apoptotic mechanism for pruning the germline, one that turns the protective envelope of the cyst into its executioner.

Subject of Research: Non-apoptotic germline cyst cell death via somatic cell acidification

Article Title: Sacrificing cells of the cyst: non-apoptotic cell death in germline cysts via acidification

Article References: Bandyadka, S., Tohline, L., Wandji, G.-V., Toledano, H., & McCall, K. (2025). Sacrificing cells of the cyst: non-apoptotic cell death in germline cysts via acidification. Frontiers in Cell Death, 4, Article 1677498. https://doi.org/10.3389/fceld.2025.1677498

Image Credits: AI Generated

DOI: 10.3389/fceld.2025.1677498

Keywords: germline cyst, phagoptosis, Drosophila, cell death, acidification, V-ATPase, oogenesis, spermatogenesis, Sacrificing, cells, cyst, non-apoptotic

Primary angle-closure glaucoma, or PACG, is particularly prevalent in East Asian populations and arises when the iris physically blocks the drainage angle of the eye, driving up intraocular pressure. Because the lens sits directly behind the iris and a thickened or enlarged lens can itself promote closure of the angle, ophthalmologists have suspected for decades that lens biology and PACG are intertwined. What has been missing is a molecular account of that relationship. The anterior lens capsule is not merely packaging; it is a biologically active interface through which nutrients, signaling molecules, and waste products pass, and it houses the lens epithelial cells that maintain lens transparency throughout life. Until now, its protein landscape in PACG had remained essentially uncharted.

To build that map, the team turned to data-independent acquisition mass spectrometry, a proteomic technique that systematically measures thousands of proteins in a sample with high reproducibility. They compared anterior lens capsule specimens from patients undergoing cataract surgery who had age-related cataract alone against those who had cataract combined with PACG. After rigorous quality control, the analysis included 13 capsules from the cataract-only group and 10 from the PACG group. The comparison yielded a striking result: 1,262 proteins were differentially expressed between the two conditions, a scale of molecular remodeling far beyond what anyone had anticipated in this thin sheet of tissue.

The direction of the changes proved as informative as their number. Proteins that were reduced in PACG-associated capsules were enriched for networks governing proteostasis — the cell’s system for maintaining properly folded, functional proteins — including molecular chaperones and the neddylation pathway, a modification cascade that regulates protein degradation machinery. When the researchers ran these depleted proteins through enrichment and protein-protein interaction network analyses, they converged on a common hub: lysosome-related dysfunction. Lysosomes are the cell’s acidic recycling compartments, and their proper function depends on the vacuolar-type H+-ATPase, or V-ATPase, the proton pump that acidifies them. In the PACG capsules, ATP6V1A — a major subunit of that pump — was coordinately decreased alongside additional V-ATPase subunits, the lysosomal membrane protein LAMP2, and members of the Rag GTPase family, which regulate lysosomal signaling and nutrient sensing.

On the other side of the ledger, proteins that were increased in the PACG capsules were enriched for extracellular matrix remodeling and lipid and glycan metabolic pathways. That pattern suggests the capsule in PACG eyes is not simply degenerating; it is actively restructuring, with potential consequences for the mechanical relationships between the lens, iris, and drainage angle that define angle-closure disease. The researchers also performed receiver operating characteristic analyses to evaluate how well the differential proteins distinguished the two patient groups, an early step toward assessing whether such markers could eventually support clinical classification.

A single proteomic comparison, however compelling, cannot establish mechanism. So the team pursued ATP6V1A through an unusually thorough series of validation experiments. They confirmed reduced ATP6V1A in human anterior lens capsule flat mounts — whole-mount preparations that preserve the spatial architecture of the tissue. They then applied pressure stress to lens epithelial cells in culture, mimicking the mechanical environment of elevated intraocular pressure, and again observed ATP6V1A reduction. Retinal stress models, including ischemia-reperfusion paradigms, reproduced the signal, and — critically — so did peripheral blood mononuclear cells drawn from an additional small clinical cohort of patients with PACG. The consistency of the ATP6V1A decrease across human tissue, cell culture, animal models, and circulating immune cells lent substantial weight to the finding.

To test whether the loss of this proton pump actually matters functionally, the researchers used pharmacologic inhibition of the V-ATPase. The result was telling: disrupting the pump disturbed lysosomal homeostasis before any overt loss of cell viability could be detected. In other words, lysosomal dysfunction is not merely a late consequence of dying cells; it is an early event that precedes cell death, positioning it as a plausible upstream driver of lens epithelial injury rather than a passive byproduct. This temporal ordering is what elevates ATP6V1A from a correlational marker to a candidate mechanistic link between elevated intraocular pressure, lens epithelial damage, and the coexistence of PACG with age-related cataract.

The study also looked outward, to an independent population-scale dataset. The team examined an exploratory plasma proteomic dataset from the UK Biobank, a large-scale biomedical resource containing health data from hundreds of thousands of participants. Notably, the ATP6V1A signal itself did not reappear in circulating plasma, a reminder that tissue-resident protein changes do not always translate to the bloodstream and that plasma proteomics has inherent limitations for detecting organ-specific molecular events. Yet the UK Biobank analysis did provide external support for glaucoma-associated lens-related and metabolic alterations, independently corroborating the broader biological themes — if not the specific protein — that emerged from the capsule analysis.

The implications reach in several directions at once. Clinically, the findings suggest that the lens capsule could serve as a readout of molecular stress in glaucoma, and that ATP6V1A-associated lysosomal dysfunction might eventually inform how ophthalmologists understand and stratify patients whose cataract and glaucoma travel together. Mechanistically, the work reframes the lens as an active participant in PACG pathogenesis: pressure stress appears to erode the very machinery that lens epithelial cells need to recycle damaged proteins and maintain transparency, and that erosion is detectable in the capsule before cells die. If lysosomal failure is indeed an early, targetable event, it opens a conceptual window for interventions aimed at preserving proteostasis in the stressed lens — though the authors are careful to frame ATP6V1A as a candidate link, not a proven therapeutic target.

There are, of course, limits to what any single study can establish. The clinical cohorts were small — 13 and 10 capsules in the primary comparison, plus a modest validation cohort — and the UK Biobank plasma analysis failed to recapitulate the central signal. The study was conducted in accordance with the Declaration of Helsinki, approved by the Ethics Committee of Xiangya Hospital, and registered with the Chinese Clinical Trial Registry, with animal work separately approved by the institution’s animal care committee, but replication in larger and more diverse populations will be essential before these molecular signatures enter clinical practice. Even so, the scale of the proteomic remodeling documented here — more than 1,200 differential proteins converging on a single lysosomal hub — makes a persuasive case that the anterior lens capsule has been telling a molecular story all along, and that researchers are only now learning to read it. For the millions of people, particularly across Asia, who face the double burden of cataract and angle-closure glaucoma, that story may ultimately point toward new ways of protecting both the clarity of the lens and the survival of the sight it helps deliver.

Subject of Research: Proteomic identification of ATP6V1A-associated lysosomal dysregulation in the anterior lens capsule in age-related cataract with primary angle-closure glaucoma

Article Title: Comparative proteomics of human anterior lens capsules reveals ATP6V1A-associated lysosomal dysregulation in age-related cataract with primary angle-closure glaucoma

Article References: Liu, J., Wang, J., Zeng, Y., Zhao, Z., Zhu, P., Liu, Y., Dong, Q., Zhao, J., Xia, X., Rong, R., & Ding, L. (2026). Comparative proteomics of human anterior lens capsules reveals ATP6V1A-associated lysosomal dysregulation in age-related cataract with primary angle-closure glaucoma. Journal of Translational Medicine. https://doi.org/10.1186/s12967-026-08934-0

Image Credits: AI Generated

DOI: 10.1186/s12967-026-08934-0

Keywords: primary angle-closure glaucoma, age-related cataract, anterior lens capsule, proteomics, ATP6V1A, lysosomal dysfunction, V-ATPase, lens epithelial cells, intraocular pressure, proteostasis, UK Biobank, mass spectrometry

The promise of TFEB has never been in doubt. The transcription factor controls the expression of hundreds of genes involved in lysosomal biogenesis and autophagy, the twin processes by which cells build new recycling machinery and degrade damaged components. When TFEB is active, it migrates into the nucleus and switches on the genetic program that keeps cellular clearance running. Boosting TFEB activity, researchers reasoned, could help cells cope with the buildup of toxic material that characterizes many diseases. The idea has attracted enormous attention: nearly 3,000 scientific publications now focus on TFEB, more than 90 percent of them appearing in the last decade alone. Experimental studies have explored TFEB activation as a strategy in lysosomal storage disorders, Parkinson’s disease, obesity and cancer, and the protein ranks among the priority targets of the Michael J. Fox Foundation’s Targets to Therapies initiative for Parkinson’s disease.

Yet a stubborn obstacle has kept TFEB from the clinic. Transcription factors as a class are notoriously difficult to target with drugs. They operate inside the nucleus, lack the well-defined enzymatic pockets that medicinal chemists prefer to bind, and are embedded in dense regulatory networks that are hard to manipulate selectively. No therapy specifically designed to activate TFEB has reached patients, despite years of effort. What was missing, essentially, was a handle: an upstream control point that could be pharmacologically tuned to dial TFEB activity up or down. The new study, coordinated by Gennaro Napolitano at TIGEM, provides exactly that. Rather than attacking TFEB itself, the researchers mapped the molecular machinery that senses lysosomal stress and switches TFEB on, revealing several proteins along the way that are far more amenable to drug development.

The scientific lineage of the work runs through Andrea Ballabio, former scientific director of TIGEM, whose research in 2009 first established TFEB as the master regulator of lysosomal function and cellular clearance. That discovery transformed lysosomal biology, recasting the lysosome from a static waste bin into a dynamically regulated system with its own genetic control hub. But one fundamental question remained open: how do cells actually detect that their lysosomes are malfunctioning, and how do they translate that signal into TFEB activation? The sensing step, the molecular bridge between lysosomal perturbation and the nuclear response, had never been fully described. Closing that gap was the central achievement of the new research, which involved collaborators at the University of Fribourg in Switzerland, UC Berkeley in the United States, the University of Rome Tor Vergata in Italy and the German Cancer Research Center (DKFZ) in Germany, with primary support from Fondazione Telethon and Fondazione AIRC.

The answer the team uncovered is a signaling cascade that begins at the lysosome itself. When lysosomal function is disturbed, the lysosomal proton pump known as v-ATPase, a molecular machine that acidifies the organelle’s interior, initiates the response. The stress signal is then transmitted through the adaptor protein TAX1BP1 to two enzymes, TBK1 and ULK1, which become activated. Once switched on, these kinases modify a protein called FNIP1, and this modification sets off a chain of events that releases TFEB to move from the cytoplasm into the nucleus. There, TFEB activates the genes that drive cellular recycling and lysosomal biogenesis. In effect, the cell possesses a dedicated alarm system for lysosomal trouble, wired through TBK1 and ULK1, and TFEB is the responder that answers the call.

“Researchers have known for years that TFEB plays a fundamental role in helping cells maintain their recycling machinery and adapt to stress,” says Alessandra Esposito, first author of the study. “What remained unclear was how cells sense lysosomal dysfunction and translate that signal into TFEB activation. Our work identifies the molecular players involved in this process and reveals a signaling pathway that had never been described before.” The identification of this axis, running from v-ATPase through TAX1BP1 and the TBK1 and ULK1 kinases to FNIP1 and finally TFEB, gives researchers a complete wiring diagram of the lysosomal stress response, and every component in that diagram is a potential point of pharmacological intervention.

The discovery is not only about boosting cellular recycling. The researchers also examined the pathway in the context of follicular lymphoma, a blood cancer in which mutations affecting ATP6V1B2, a component of the v-ATPase proton pump, are relatively common. They showed that these mutations cause persistent activation of TFEB, which in turn helps tumor cells survive and proliferate in nutrient-poor environments, a hallmark of the tumor microenvironment in lymphoma. In this setting, the newly mapped pathway works against the patient: cancer cells exploit the lysosomal stress response to adapt to scarcity and keep growing. That finding suggests a second therapeutic strategy, one of inhibition rather than activation. Drugs that block the TBK1-ULK1 signaling axis might deprive such tumors of their survival advantage, opening a potential avenue for treating follicular lymphoma and possibly other malignancies that depend on lysosomal reprogramming.

“Rather than targeting TFEB itself, our study identifies molecular regulators that control its activation,” Esposito explains. “This provides new entry points for the development of therapeutic strategies aimed at harnessing TFEB activity in disease.” The distinction matters enormously for drug development. Kinases such as TBK1 and ULK1 are enzymes with well-characterized active sites, and potent inhibitors of both already exist in the chemical biology toolkit. A pathway made of kinases and adaptor proteins is, from a medicinal chemistry standpoint, a far more tractable target than a transcription factor. By identifying the regulators upstream of TFEB, the study converts an aspirational goal, pharmacological control of the cell’s recycling master switch, into a concrete set of engineering problems that pharmaceutical researchers know how to approach.

“The identification of the TBK1/ULK1 pathway expands the therapeutic opportunities for modulating TFEB,” says Napolitano, the study’s lead investigator. “Because this mechanism acts upstream of TFEB, it could offer new opportunities not only in TFEB-dependent cancers but also in a broader spectrum of diseases where improving lysosomal function may be beneficial.” That broader spectrum is large. Lysosomal dysfunction lies at the heart of dozens of rare genetic diseases, collectively affecting a substantial number of patients worldwide, and has been implicated in common neurodegenerative disorders, metabolic conditions and aging itself. A single druggable pathway that modulates lysosomal clearance could therefore have applications that span from ultra-rare pediatric storage diseases to some of the most prevalent illnesses of old age.

The study, published under the title describing a TBK1-ULK1 signaling axis that couples lysosomal stress to TFEB activation, marks a turning point in a research story that began in 2009. For fifteen years, the field has known what TFEB does; now it knows how cells control it, and the control points are druggable. Translating that knowledge into medicines will take years of further work, from developing selective modulators of the pathway to testing them in disease models and, eventually, patients. But the direction is clear. By uncovering the molecular sensors and kinases that stand between lysosomal stress and the master regulator of cellular recycling, the TIGEM-led team has brought researchers a decisive step closer to turning one of lysosomal biology’s most celebrated discoveries into real therapies for rare genetic diseases, cancer and beyond.

Subject of Research: The TBK1-ULK1 signaling pathway that regulates TFEB activation in response to lysosomal stress

Article Title: Newly discovered pathway unlocks the therapeutic potential of TFEB

Article References: Newly discovered pathway unlocks the therapeutic potential of TFEB. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: TFEB, lysosomes, TBK1, ULK1, FNIP1, autophagy, lysosomal storage diseases, follicular lymphoma, v-ATPase, TAX1BP1, drug targets, TIGEM