The lysosome as a central executioner: orchestrating multiple modalities of programmed cell death

1 Introduction

Since their discovery in the 1950s (De Duve et al., 1955), lysosomes have been defined as cytoplasmic organelles that mediate the degradation of intracellular biomacromolecules, damaged cellular components, and redundant subcellular structures via endocytic, autophagic, or phagocytic pathways (Lawrence and Zoncu, 2019). Over 7 decades, this understanding has triggered a paradigm shift-from viewing lysosomes as mere “cellular janitors” to recognizing them as intricate signaling hubs essential for life (Inpanathan and Botelho, 2019). By sensing luminal macromolecules, lysosomes integrate diverse signaling cascades, regulating interorganellar communication, metabolic homeostasis, and immune responses (Ballabio and Bonifacino, 2020; Settembre and Perera, 2024; Jain and Zoncu, 2026). This signaling capacity is exemplified by key nutrient-sensing pathways such as mTORC1 and AMPK, whose activation status is tightly regulated at the lysosomal surface (Shin and Zoncu, 2020; Goul et al., 2023). Consequently, lysosomes have emerged as central hubs that not only maintain cellular homeostasis but also actively orchestrate cell fate decisions.

Programmed cell death (PCD) is an actively initiated, highly ordered cellular process tightly governed by genetic programs in multicellular organisms. This biological process is indispensable for growth and development, maintenance of tissue homeostasis, and efficient elimination of damaged or harmful cells (Chen et al., 2024; Yuan and Ofengeim, 2024). Major PCD modalities include apoptosis, necroptosis, pyroptosis, and ferroptosis, each defined by distinct molecular features. Emerging evidence now positions lysosomes as critical executors in these PCD pathways (Radulovic et al., 2026). Beyond their degradative functions, lysosomes actively participate in cell death signaling through multiple mechanisms. For example, partial lysosomal membrane permeabilization triggers cathepsin leakage into the cytosol, initiating both caspase-dependent and independent apoptotic pathways (Boya and Kroemer, 2008). In ferroptosis, lysosomes contribute to iron accumulation via ferritin degradation through lysosomal hydrolases and the autophagy pathway. Lysosomal dysfunction and impaired autophagic flux sensitize cells to necroptosis and pyroptosis, underscoring its regulatory role in inflammatory cell death. Collectively, these discoveries highlight the lysosome as a central hub that not only maintains cellular homeostasis but also actively orchestrates multiple cell death pathways (Bonam et al., 2019). Despite this growing recognition, a comprehensive synthesis of how lysosomal mechanisms govern distinct PCD modalities remains lacking. Given that cancer cells exhibit heightened lysosomal biogenesis and vulnerability to lysosomal membrane permeabilization (LMP), understanding how lysosomes govern distinct PCD modalities offers new opportunities for cancer therapy, particularly in overcoming apoptosis resistance. In this review, we will systematically recapitulate the pivotal regulatory roles of lysosomes in diverse PCD modalities, emphasizing the underlying molecular mechanisms and their implications in health and disease.

2 The core event: lysosomal membrane permeabilization (LMP)

Lysosomal membrane permeabilization (LMP) is a critical event in cellular dysfunction (Figure 1), resulting in the release of cathepsins and other hydrolases into the cytosol, thereby activating cell death pathways. LMP is implicated in various pathologies, including neurodegenerative diseases, cancer, and autoimmunity (Boya and Kroemer, 2008; Radulovic et al., 2026).

2.1 Oxidative stress and fenton chemistry: the core endogenous driver of LMP

Among inducers of LMP, reactive oxygen species (ROS) are the most extensively investigated. In this scenario, oxidative stress and Fenton chemistry serve as the core endogenous drivers of LMP (Chen et al., 2023). Physiologically or pathologically, the mitochondrial respiratory chain constitutes a primary endogenous source of ROS (Bedard and Krause, 2007). Lysosomes inherently lack antioxidant enzymes and feature an intraluminal environment enriched with iron ions and oxidizable lipids, rendering them exquisitely vulnerable to oxidative damage (Terman et al., 2010). Upon diffusion into the lysosomal lumen, excess H₂O₂ reacts with Fe²⁺ via Fenton chemistry to generate highly reactive hydroxyl radicals (•OH). These radicals directly attack unsaturated fatty acids within the lipid bilayer, initiating a chain reaction of lipid peroxidation that alters membrane fluidity and integrity, thereby forming “leaks” (Höhn et al., 2010; Sies et al., 2022; Voronina et al., 2024). Consequently, mitochondrial dysfunction or lysosomal dysfunction leading to iron overload directly compromises lysosomal stability (Dixon et al., 2012; Ren et al., 2025). Furthermore, ROS generated by exogenous photosensitizers such as NPe6 upon light irradiation, and oxidative stress induced during the metabolism of chemotherapeutic agents like doxorubicin, fundamentally induce LMP through excessive ROS production, exacerbating lipid peroxidation (Kessel et al., 2000; Yamashita et al., 2022). ROS can also induce lipofuscin accumulation within lysosomes, further promoting oxidative stress and membrane disruption, thus establishing a vicious cycle (Pan et al., 2021).

2.2 Aberrant metabolic substrate accumulation and exogenous particles: dual physicochemical disruption mechanisms

Physicochemical stress resulting from the accumulation of undegraded materials constitutes another key endogenous cause of LMP (Platt et al., 2012). At the endogenous level, impaired cellular clearance capacity or metabolic defects lead to the accumulation of various substrates within lysosomes. For instance, protein aggregates (Aβ, α-synuclein) in neurodegenerative diseases can physically rupture the lysosomal membrane from within (Kakuda et al., 2024; Rose et al., 2024). Undegraded lipids, such as sphingomyelin and ceramide in lysosomal storage disorders, alter membrane composition chemically: the conical shape of ceramide induces negative curvature stress, directly increasing membrane permeability (López-Montero et al., 2010; Hannun and Obeid, 2018; Breiden and Sandhoff, 2021). Moreover, sphingosine generated from aberrant sphingolipid metabolism, owing to its protonable amino group (pKa 6.7–8.4), becomes enriched in the acidic lysosomal lumen via proton trapping. Its amphipathic structure confers detergent-like activity in acidic environments, enabling direct insertion into and disruption of the lipid bilayer integrity, thereby triggering apoptosis or necrosis (Kågedal et al., 2001; Cheng et al., 2026). This “inside-out” physicochemical disruption mirrors the mechanism by which internalized exogenous particles, such as silica crystals or asbestos fibers, mechanically perforate the lysosomal membrane from within due to their sharp morphology (Hornung et al., 2008). Additionally, certain pathogens can disrupt membrane stability by interfering with lipid metabolism: mycobacterial sulfolipids (SL-1) competitively bind host NOD2 protein, blocking autolysosomal function and indirectly compromising membrane integrity (Nabatov et al., 2013); the neuraminidase of H5N1 influenza virus degrades the glycosylation of LAMP1, disrupting the protective glycocalyx layer on the membrane surface and rendering the membrane susceptible to hydrolase attack (Ju et al., 2015).

2.3 Membrane structural disruption: the core structural basis for LMP occurrence

Destabilization of lysosomal membrane integrity constitutes the structural foundation for LMP, with calcium homeostasis imbalance triggering degradation of the membrane scaffold. As an intracellular calcium store, lysosomal membrane stability relies on the integrity of structural proteins such as LAMP2. Aberrant elevation of cytosolic Ca²⁺ activates calpain, which translocates to the lysosomal membrane and cleaves LAMP2, leading to loss of lysosomal membrane integrity and subsequent cathepsin B leakage and cell death (Villalpando Rodriguez and Torriglia, 2013; Yamashima, 2013; Gerónimo-Olvera et al., 2017). Calpain can also cleave the membrane-stabilizing protein Hsp70.1, abolishing its protection of the lipid bilayer and rendering the membrane more susceptible to oxidative injury (Sahara and Yamashima, 2010; Zhu et al., 2014). These processes form a positive feedback loop involving “ion leakage-structural degradation-oxidative stress.” Exogenous agents such as monensin, nigericin, and listeriolysin O toxin artificially induce such leakage and activate the calpain pathway by perturbing ion gradients or direct pore formation, ultimately triggering LMP (Shaughnessy et al., 2006; Malet et al., 2017).

Concurrently, within PCD signaling pathways, death effector proteins can directly target the lysosomal membrane. BAX has been demonstrated to regulate LMP through multiple mechanisms. In a Parkinson’s disease model, BAX translocates to the lysosomal membrane at an early stage, forming channel-like structures that directly mediate LMP (Bové et al., 2014). In autophagic cell death, monomeric BAX and BAK localize to the lysosomal membrane and enhance its permeability (Karch et al., 2017). In an alcoholic liver disease model, free fatty acids induce BAX translocation to the lysosomal membrane and promote MLKL phosphorylation and membrane localization, with both synergistically inducing LMP (Dong et al., 2023). In TNF-induced necroptosis, activated MLKL forms multimers on the lysosomal membrane, thereby disrupting membrane integrity through altered membrane tension or pore formation (Liu S. et al., 2024). These pathways operate in a cooperative manner, as degradation of membrane scaffolds sensitizes the lysosomal membrane to physical insults, while insertion of BAX and MLKL may exacerbate local ion leakage, collectively facilitating the occurrence of LMP.

2.4 Dysregulation of pH and enzymatic homeostasis: the fundamental regulatory basis of LMP

Dysregulation of pH and enzymatic homeostasis represents the fundamental basis for LMP. The functional integrity of the v-ATPase proton pump is essential for maintaining the acidic lysosomal environment and enzyme activity. Impairment of v-ATPase function or dysregulation of the proton efflux channel TMEM175 leads to elevated intraluminal pH, which not only directly inhibits hydrolase activity but also indirectly affects membrane stability and fusion capacity with other organelles (Zhang et al., 2023). Furthermore, aberrant pH changes trigger cellular stress responses, sensitizing the lysosomal membrane to external pressures (Song and Hwang, 2020). Exogenous lysosomotropic agents, such as chloroquine, become protonated and trapped, not only directly elevating pH but also inducing osmotic swelling due to the accumulation of charged molecules, leading to physical rupture (de Duve et al., 1974). The VepA toxin secreted by Vibrio parahaemolyticus directly targets and disrupts the v-ATPase complex, precisely attacking a core component maintaining internal environment homeostasis (Matsuda et al., 2012). The envelope protein of SARS-CoV-2 can act as a proton channel, reducing lysosomal acidity, indirectly compromising membrane stability in order to facilitate viral escape (Wang et al., 2023).

3 Lysosomal regulation in different forms of PCD

3.1 Apoptosis

Apoptosis is a morphologically distinct form of PCD characterized by cell shrinkage, chromatin condensation, and membrane blebbing (Yuan and Ofengeim, 2024). It is primarily mediated by two core signaling pathways: the death receptor-dependent extrinsic pathway and the mitochondria-dependent intrinsic pathway (Kerr et al., 1972; Hengartner, 2000). In the intrinsic pathway, the release of cytochrome c from mitochondria serves as the initiating signal for apoptosis, subsequently activating the caspase cascade (Riedl and Salvesen, 2007). Lysosomes regulate apoptosis specifically through this intrinsic pathway, with LMP and the ensuing release of cathepsins constituting the central regulatory mechanism (Figure 2; Table 1).

TABLE 1. Lysosomal mediators and associated cell death modalities.

Cathepsin B is the most extensively studied lysosomal protease in the context of apoptosis regulation. Following lysosomal membrane permeabilization or complete rupture, cathepsin B is released from the lysosomal lumen into the cytoplasm. This protease specifically cleaves the BH3-interacting domain death agonist (BID), generating its proapoptotic truncated fragment tBid, which in turn induces oligomerization of Bcl-XL, a member of the B-cell lymphoma-2 (Bcl-2) protein family (Stoka et al., 2001; de Castro et al., 2016). The resulting Bcl-XL oligomeric complexes are directionally translocated to the outer mitochondrial membrane, where they trigger aberrant and excessive opening of the mitochondrial permeability transition pore (MPTP) (Zhu et al., 2017). MPTP opening facilitates the release of cytochrome c from the mitochondrial intermembrane space into the cytoplasm, where it assembles with Apaf-1 and procaspase-9 to form the apoptosome. This complex activates caspase-9 and subsequently the downstream effector caspase-3, initiating the caspase cascade and ultimately driving apoptotic cell death (Zhu et al., 2017).

In addition to regulating the Bcl-2-mitochondria pathway, cathepsins can directly target caspases to modulate apoptotic signaling. In vitro studies have shown that cathepsins are capable of processing and activating proinflammatory procaspase-1 and procaspase-11 (Schotte et al., 1998; Vancompernolle et al., 1998). Notably, cathepsin B exerts its proteolytic function by cleaving procaspase-2, generating an active fragment that potently induces the release of cytochrome c from mitochondria, which contributes to hepatic injury and fibrosis in a mouse model of cholestatic liver disease (Guicciardi et al., 2004). In addition, during bacterial infection and septic shock, cathepsin D directly activates caspase-8 through a death receptor-independent pathway in neutrophils, triggering downstream effector caspases and initiating apoptosis to facilitate the resolution of inflammation (Conus et al., 2008). Together, these findings indicate that lysosomes regulate apoptosis through multiple molecular mechanisms, with cathepsin-mediated crosstalk between lysosomes and mitochondria representing the core axis of lysosome-dependent apoptosis.

3.2 Necroptosis

Necroptosis is a lytic form of PCD characterized morphologically by organelle swelling, plasma membrane rupture, and the subsequent release of intracellular contents (Yuan and Ofengeim, 2024). This highly regulated process is primarily orchestrated by the RIPK1-RIPK3-MLKL signaling axis. The initiation of necroptosis can be activated by signals derived from death receptors of the tumor necrosis factor (TNF) superfamily, Toll-like receptors (TLRs), interferon receptors (IFNAR), or Z-DNA binding protein 1 (ZBP1) (Vanden Berghe et al., 2014; Wallach et al., 2016; Rohde et al., 2017; Tang et al., 2019). Upon death ligand stimulation and caspase-8 inhibition, RIPK1 associates with RIPK3 to form the necrosome. Activated RIPK3 phosphorylates MLKL. MLKL subsequently oligomerizes and disrupts the plasma membrane. These sequential events lead to cell death and the release of damage-associated molecular patterns (DAMPs) (Cai et al., 2014; Chen et al., 2019; Wu et al., 2024).

Beyond the core signaling axis, lysosomes play a pivotal regulatory role in necroptosis. Specifically, LMP, cathepsin release, and calpain mediated lysosomal damage establish a positive feedback loop with the core necroptotic machinery (Ferri and Kroemer, 2001; Serrano-Puebla and Boya, 2016) (Figure 2; Table 1). Among the lysosomal effectors, cathepsin B and cathepsin D have been identified as key mediators. For instance, granulysin induced LMP leads to cathepsin B release, which then cleaves BID to trigger mitochondrial damage and amplify necroptosis (Zhang et al., 2009). Similarly, in dendritic cells, polyinosinic-polycytidylic acid induces cathepsin D release via LMP. This released cathepsin D cleaves caspase eight at the mitochondrial IPS-1 platform, thereby relieving its inhibition of RIPK1 and RIPK3 and promoting RIPK1 K63-linked polyubiquitination and activation (Zou et al., 2013). Of note, cathepsin D activation in this context occurs either downstream of or in concert with the necrosome (Wang et al., 2016). The functional relevance of these cathepsins is further supported by pharmacological evidence. In cytotoxin 1 induced leukemia cell necroptosis, the cathepsin B inhibitor CA-074-Me enhances the cytoprotective effect of the RIPK1 inhibitor Nec-1, confirming their synergistic regulation (Liu et al., 2019). Importantly, while single inhibition of cathepsin B or cathepsin D only partially attenuates necroptosis, combined inhibition completely abrogates it, underscoring their cooperative and essential roles in this form of cell death (Moriwaki et al., 2015; Yashin et al., 2016; Sharapova et al., 2018).

Additionally, calpains function as key upstream regulators of LMP during necroptosis. This regulation is closely linked to calcium dynamics. Upon MLKL activation, intracellular calcium levels rise, leading to the activation of lysosomal calpains. Activated calpains directly induce LMP in post-ischemic primate hippocampal neurons and in a mouse lung transplant model, leading to the release of cathepsins, which in turn trigger mitochondrial depolarization and ROS generation, thereby amplifying necroptotic signaling (Yamashima et al., 2003; Yashin et al., 2016; Cheng et al., 2018; Kim et al., 2018). Consistent with this cascade, calpain inhibitors markedly reduce the incidence of necroptosis (Yamashima et al., 2003; Kim et al., 2018). This calpainLMP–cathepsin axis is also operational in cancer cells. In this context, extralysosomal accumulation of cathepsin B drives caspase-independent necrosis-like cell death, whereas direct lysosomal membrane damage induced by gold nanorods triggers RIP1 activation and necrosome formation (Zhang et al., 2017; Josen et al., 2026). Beyond this direct pathway, calpains also regulate necroptosis through multiple feedback loops. For example, they can modulate RIPK3 expression and MLKL phosphorylation via STAT3, inducing endoplasmic reticulum stress and mitochondrial calcium dyshomeostasis. Additionally, calpains promote LMP through the sphingosine JNK signaling pathway (Andón and Fadeel, 2013).

Another critical regulator in this process is ROS. Accumulation of ROS is a hallmark of necroptosis that precedes LMP and plasma membrane disruption (Vanden Berghe et al., 2010). As upstream inducers, ROS can trigger LMP and cathepsin release to initiate necroptosis (Cai et al., 2018). Nevertheless, direct evidence for ROS mediated lysosomal membrane damage specifically within the context of necroptosis remains insufficient. Finally, beyond these canonical regulatory mechanisms, accumulating insoluble aggregates such as lipofuscin can physically disrupt the lysosomal membrane. In retinal pigment epithelium of Stargardt disease and age-related macular degeneration, lipofuscin accumulation induces LMP and triggers atypical necroptosis, with MLKL phosphorylation observed in aged human AMD retinas (Pan et al., 2021). Collectively, these findings highlight the central role of lysosomal dysfunction and protease activation in both canonical and noncanonical necroptotic across multiple pathological conditions—including cerebral ischemia, lung transplantation injury, retinal degeneration, and cancer. They reveal a sophisticated regulatory network featuring interconnected feedback loops that converge on lysosomal integrity to control the execution of this cell death program.

3.3 Pyroptosis

Pyroptosis is a lytic and inherently proinflammatory form of regulated cell death, characterized by cellular swelling, plasma membrane rupture, and the active secretion of inflammatory mediators (Yu et al., 2021; Rao et al., 2022; Wei et al., 2022). This process is primarily executed by gasdermin family proteins, notably gasdermin D (GSDMD) and gasdermin E (GSDME). Upon cleavage of GSDMD or GSDME, their N-terminal domains insert into the plasma membrane. These inserted domains form pores that disrupt ionic homeostasis. This disruption ultimately leads to cell lysis and allow the efflux of inflammatory mediators (Shi et al., 2015; Broz and Dixit, 2016; Tang et al., 2019). Canonical pyroptosis is initiated by inflammasome assembly in the cytosol. Pattern recognition receptors, including NLR family members (NLRP1, NLRP3, NLRC4) and non-NLR receptors such as AIM2, sense pathogen-associated or damage-associated signals, as well as bacterial or host double-stranded DNA (Fernandes-Alnemri et al., 2010; Rathinam et al., 2010; Broz and Dixit, 2016; He et al., 2016; Jorgensen et al., 2017). ASC bridges the interaction between pattern recognition receptors and procaspase-1 to facilitate inflammasome activation, leading to the maturation of caspase-1. Activated caspase-1 cleaves GSDMD, releasing its N-terminal fragments to form plasma membrane pores (Broz and Dixit, 2016). Concurrently, caspase-1 processes pro-IL-1β and pro-IL-18 into their mature and secreted forms, thereby driving both the inflammatory response and cell death (Chen et al., 2016; Liu et al., 2016; Rathkey et al., 2018).

Lysosomes play a dual regulatory role in pyroptosis, acting as both an executor of non-classical pyroptosis and an amplifier of the classical pathway, with cathepsin B and cathepsin D identified as core regulatory molecules (Galluzzi et al., 2012; Orlowski et al., 2017) (Figure 2; Table 1). Lysosomal injury triggers inflammasome assembly through multiple pathways, among which the release of cathepsins represents a primary mechanism. Mitochondrial ROS induce NLRP3-dependent LMP to release the cathepsins, leading to inflammasome activation, IL-1β secretion, and pyroptosis (Heid et al., 2013). The critical function of these enzymes is further demonstrated by the cathepsin B inhibitor CA-074-Me, which significantly reduces NLRC4 inflammasome mediated IL-1β processing and secretion. This finding indicates that the lysosomal pathway acts as an amplifier for classical pyroptosis rather than solely as an executor of non-classical pyroptosis (Lage et al., 2013). The regulatory roles of lysosomes in pyroptosis are also exemplified in various pathological conditions. In age-related macular degeneration, lysosomal instability in retinal pigment epithelial cells triggers the release of cathepsin B and cathepsin L, leading to NLRP3 inflammasome activation and subsequent pyroptotic cell death. Additionally, NLRP3 upregulation was observed in the RPE of patients with geographic atrophy or neovascular AMD (Tseng et al., 2013). Similarly, cholesterol crystals disrupt the phagolysosomal membrane to activate the NLRP3 inflammasome. Cholesterol crystal-induced pyroptosis and acute inflammation is impaired in mice deficient in cathepsin B or NLRP3 components, and LDLR (low-density lipoprotein receptor)-deficient mice transplanted with NLRP3-deficient bone marrow showed markedly decreased early atherosclerosis (Duewell et al., 2010). Together, these findings confirm the critical role of lysosomal cathepsins in pyroptosis regulation.

In addition to cathepsin mediated signaling, lysosomal injury also triggers inflammasome assembly through ionic pathways. One such mechanism involves the release of intralysosomal calcium into the cytoplasm following lysosomal rupture. This calcium flux activates calcium/calmodulin-dependent protein kinase II (CaMKII). Subsequently, CaMKII promotes ASC oligomerization via the TAK1-JNK pathway, leading to inflammasome activation and pyroptosis (Okada et al., 2014). Additionally, the leakage of lysosomal contents caused by agents like particulate matter and lysosomal-damaging dipeptide LLOMe triggers potassium efflux, which subsequently activates the NLRP3 inflammasome (Muñoz-Planillo et al., 2013). These ionic pathways function in parallel with cathepsin dependent mechanisms to collectively orchestrate inflammasome activation. Emerging evidence has extended lysosomal damage-induced pyroptosis to cancer settings. In the tumor microenvironment, lysosomal dysfunction in immune or cancer cells can trigger inflammasome activation and pyroptotic cell death. In non-small cell lung cancer, lysosomal dysfunction in macrophages drives NLRP3-dependent pyroptosis via TRPML1-mediated calcium efflux (Yu et al., 2025). In anaplastic thyroid cancer, lysosomal over-acidification and LMP trigger GSDME-dependent pyroptosis via V-ATPase upregulation (Liu Y. et al., 2024). Moreover, a lysosome-targeting nanoparticle induces lysosomal-to-mitochondrial ROS stress, leading to GSDME cleavage and pyroptosis in multiple tumor models (Liu J. et al., 2024).

Collectively, these findings establish lysosomes as central hubs that integrate proteolytic events, ionic signals, and redox stress to orchestrate inflammasome activation and drive pyroptotic cell death across diverse pathological contexts.

3.4 Ferroptosis

Ferroptosis is a regulated form of cell death driven by iron-dependent accumulation of lethal lipid peroxides (Dixon et al., 2012; Conrad and Pratt, 2019). Its execution fundamentally relies on the interplay between dysregulated iron metabolism and the peroxidation of polyunsaturated fatty acid-containing phospholipids (PUFA-PLs). This process is initiated by the incorporation of free PUFAs into membrane phospholipids. These lipids are then oxidized via iron-catalyzed Fenton reactions and autocatalytic radical chain propagation, ultimately compromising membrane integrity. As a negative regulator of this pathway, glutathione peroxidase 4 (GPX4) reduces phospholipid hydroperoxides (PL-OOH) to the corresponding phospholipid alcohols (PL-OH), thereby suppressing lipid peroxidation (Galluzzi et al., 2018). Consequently, ferroptosis is characterized by iron overload, glutathione (GSH) depletion, and GPX4 inactivation. As critical organelles governing multiple cellular homeostatic processes, lysosomes serve as central regulatory hubs in ferroptosis through three core mechanisms. These include acting as the primary intracellular iron reservoir, mediating lipid peroxidation-induced LMP, and regulating ferritinophagy to precisely control labile iron levels (Figure 3; Table 1).

Lysosomes play a central role in cellular iron homeostasis by governing the import, storage, and release of iron (Yambire et al., 2019; Weber et al., 2020; Rizzollo et al., 2021). Transferrin-bound iron is internalized via TFRC-mediated endocytosis and delivered to lysosomes, where STEAP3 reduces Fe³⁺ to Fe²⁺ in the acidic environment. Fe²⁺ is then exported into the cytosol via DMT1 or TRPML1, contributing to the labile iron pool (Turcu et al., 2020). The acidic lysosomal lumen harbors the highest cellular concentration of labile Fe²⁺, making it a primary site for Fenton reaction-driven ROS generation during ferroptosis (Toyokuni et al., 2017). In erastin-induced ferroptosis, lysosomal Fe²⁺ levels rise markedly, coincident with ROS production (Hirayama et al., 2019). Accordingly, pharmacological blockade of lysosomal iron export using ironomycin or DMT1 inhibitors induces lysosomal iron overload and triggers ferroptosis in therapy-resistant cancer cells. These findings highlight the therapeutic potential of targeting lysosomal iron retention (Turcu et al., 2020).

Beyond its role as an iron reservoir, the lysosome also serves as the initial site for lipid peroxidation during ferroptosis, which corresponds to the second core mechanism involving LMP. Early lipid peroxidation in ferroptosis originates within lysosomes (Torii et al., 2016; Saimoto et al., 2025). Ferroptosis inducer RSL3 initiates membrane lipid oxidation predominantly in this compartment, with lipid peroxidation subsequently propagating to the endoplasmic reticulum, indicating that lysosomal iron serves as the initial trigger for the radical chain reaction (Cañeque et al., 2025). The resulting burst of ROS promotes lysosomal membrane lipid peroxidation, exacerbates membrane damage, depletes glutathione, and induces LMP, thereby establishing a positive feedback loop that amplifies ferroptosis (Gao et al., 2018; Zhou et al., 2020). Lysosomal destabilizers such as siramesine and lapatinib disrupt this loop by raising lysosomal pH, impairing membrane stability, and increasing labile iron and ROS, ultimately inducing ferroptosis and suppressing breast tumor growth in mice (Petersen et al., 2013; Ma et al., 2017). Conversely, lysosome targeted iron chelators such as deferoxamine (DFO) and the ferroptosis inhibitor liproxstatin 1 confer protection by chelating accumulated lysosomal iron and preventing LMP (Homma and Fujii, 2015; Gaschler et al., 2018; Cañeque et al., 2025).

Ferritinophagy, a selective form of autophagy mediated by the cargo receptor nuclear receptor coactivator 4 (NCOA4), represents another critical lysosomal mechanism for fine tuning intracellular labile iron levels (Mancias et al., 2014; Gao et al., 2016; Hou et al., 2016). NCOA4 binds to ferritin and delivers it to autophagosomes, which fuse with lysosomes. Ferritin is then degraded by lysosomal hydrolases including cathepsin B, and Fe2+ is released into the cytoplasm. Overexpression of NCOA4 enhances ferritinophagy and facilitates ferroptosis, whereas lysosomal dysfunction leads to ferritin accumulation and labile iron deficiency, conferring ferroptosis resistance in cancer cells (Masaldan et al., 2018; Saimoto et al., 2025). In addition to ferritinophagy, lysosomal degradation of other iron-related cargos can also promote ferroptosis, including mitochondria via mitophagy, lipid droplets via lipophagy, and GPX4 via chaperone mediated autophagy (Basit et al., 2017; Bai et al., 2019; Wu et al., 2019).

Emerging evidence further implicates lysosome-mitochondria crosstalk and polyamine metabolism in fine-tuning ferroptosis sensitivity. Membrane contact sites and iron-dependent pathways mediate the interplay between lysosomes and mitochondria, which plays a critical role in maintaining cellular iron homeostasis. Disruption of lysosomal acidification or mitochondrial function leads to iron dysregulation, oxidative stress, and enhanced susceptibility to ferroptosis (Weber et al., 2020). Additionally, polyamine metabolism intersects with iron homeostasis through lysosomal transporters such as ATP13A2, exerting metal-chelating and antioxidant effects. Loss of ATP13A2 function results in lysosomal iron accumulation and increased oxidative stress, heightening vulnerability to iron-induced cell death (van Veen et al., 2020; Vrijsen et al., 2020). These findings underscore that lysosome-mitochondria communication and polyamine-mediated iron buffering are integral to the regulation of ferroptosis, offering new therapeutic entry points for diseases characterized by iron dysregulation (Tsunemi and Krainc, 2014; Rinaldi et al., 2015; Vara-Pérez et al., 2021).

In summary, lysosomes integrate iron metabolism and redox signaling to modulate ferroptosis sensitivity, a mechanism implicated in cancer, aging, and neurodegeneration. Targeting lysosomal iron metabolism offers therapeutic opportunities for refractory malignancies and neurodegenerative disorders.

3.5 Autophagic cell death

Autophagy is a vital cellular process that maintains homeostasis by degrading and recycling unnecessary or damaged components. In this tightly regulated pathway, the cell sequesters materials such as damaged organelles and aged proteins into double-membrane vesicles known as autophagosomes. These vesicles subsequently fuse with lysosomes, where enzymatic degradation of the contents occurs (Bialik et al., 2018). Autophagy proceeds through a series of sequential steps, including initiation, nucleation, elongation, and closure, which are governed by key regulators such as mTOR and ATG proteins (Lin et al., 2021). The underlying mechanism relies on the ULK complex, the class III-PI3K-VPS34 complex, and the Atg ubiquitin-like conjugation system (Geng and Klionsky, 2008; Mizushima, 2010; Russell et al., 2013). Given that lysosomes serve as the principal site of autophagic degradation, they have emerged as critical regulators in autophagy-mediated processes. Notably, accumulating evidence indicates that lysosomal membrane permeabilization and the consequent release of lysosomal contents, particularly cathepsins, can shift autophagy from a cytoprotective mechanism toward a pro-death process (Aits and Jäättelä, 2013) (Table 1).

During this transition, lysosomes orchestrate autophagic cell death through multiple interconnected mechanisms. LMP triggers the release of cathepsins, which degrade essential cellular structures and disrupt ion homeostasis. These events shift the balance from cytoprotective autophagy to cell death execution (Mahapatra et al., 2021). Lysosomal membrane integrity, preserved by LAMP1, LAMP2, and HSP70, determines whether autophagic flux results in cellular adaptation or cell death (Mahapatra et al., 2021). In parallel, cells possess repair mechanisms to counteract lysosomal damage. The endosomal sorting complexes required for transport (ESCRT) machinery can repair minor lysosomal membrane injuries. When the damage exceeds the repair capacity, however, lysophagy is triggered, ultimately culminating in autophagic cell death (Papadopoulos et al., 2020). In glioblastoma, DRAM-1 overexpression impairs lysosomal function and autophagic flux stability, leading to ER stress-induced apoptosis and increased tumor cell mortality in vitro and in vivo (Zhang et al., 2024). Lysosomal destabilization can tip this balance, offering a strategy to eliminate tumor cells that rely on high autophagic flux for survival under metabolic stress.

Beyond these core mechanisms, various upstream signals and lysosome-associated proteins further modulate this regulatory process. For instance, the apoptotic regulators Bax and Bak can directly act on the lysosomal membrane to promote its permeabilization and rupture, thereby initiating autophagic cell death. Accordingly, Bax/Bak double-knockout cells exhibit enhanced lysosomal stability and resistance, whereas reconstitution with lysosome-targeted Bax restores susceptibility (Karch et al., 2017). Additionally, DRAM1 facilitates LMP and subsequent mitochondrial outer membrane permeabilization (MOMP) to promote autophagic cell death (Mahapatra et al., 2021). In contrast, eva-1 homolog A (EVA1A), also known as TMEM166 (transmembrane protein 166), drives autophagic cell death under conditions of impaired autophagosome-lysosome fusion (Hu et al., 2016). Lysosomal functional homeostasis also depends on its own regenerative capacity. Sustained mTORC1 inhibition disrupts autophagic lysosome reformation (ALR), leading to autolysosome accumulation and eventual cell death. In hereditary spastic paraplegia SPG11 and SPG15, mutations in Spastizin and Spatacsin impair ALR, resulting in lysosomal depletion and autophagosome accumulation; pharmacological restoration of ALR by naringenin or SMER28 rescues locomotor deficits in Drosophila models (Yu et al., 2018; Mahapatra et al., 2021).

Evidence from multiple models underscores the essential role of lysosomes in this form of cell death. In A549 cells infected with respiratory syncytial virus (RSV), a pathogen that causes lower respiratory tract infections in infants and immunocompromised adults, the massive accumulation of autolysosomes degrades mitochondria and the ER, demonstrating that excessive autophagic flux directly drives cell death (Dasari et al., 2017). Likewise, during Drosophila metamorphosis, a canonical model of physiological cell death, blocking lysosomal acidification suppresses autophagic progression and midgut clearance. This finding highlights the indispensable role of lysosomal hydrolytic activity in the execution of autophagic cell death (Denton et al., 2019). In Alzheimer’s disease, autolysosome acidification failure leads to intraneuronal Aβ accumulation within enlarged de-acidified autolysosomes, a pathological pattern termed PANTHOS, which triggers lysosomal membrane permeabilization, cathepsin release, and lysosomal-dependent neuronal death (Nixon, 2024). Together, lysosomal-dependent autophagic cell death has been implicated in diverse disease contexts, including respiratory syncytial virus infection, glioblastoma, hereditary spastic paraplegia, and Alzheimer’s disease, highlighting the translational relevance of this pathway. However, the precise nature of autophagic cell death remains controversial, including whether it arises from selective organelle degradation or nonspecific cytoplasmic clearance. Further elucidation is needed to define the precise regulatory role of lysosomes in orchestrating these distinct scenarios.

3.6 The crosstalk among lysosome-mediated cell death pathways

Accumulating evidence indicates that different forms of PCD are not isolated, but share upstream signals and regulatory nodes (Yuan and Ofengeim, 2024). LMP and the subsequent release of cathepsins, particularly cathepsin B, serve as a central hub integrating multiple PCD pathways (Boya and Kroemer, 2008; Serrano-Puebla and Boya, 2016). The extent of LMP determines the outcome: mild LMP tends to trigger apoptosis or pyroptosis, whereas severe LMP leads to necrosis (Galluzzi et al., 2012). Depending on the upstream stimulus, cathepsin B either cleaves Bid to induce MOMP and caspase-dependent apoptosis, or activates the NLRP3 inflammasome to promote pyroptosis. This highlights how cellular context dictates whether lysosomal damage results in silent apoptosis or inflammatory pyroptosis (Stoka et al., 2001; Duewell et al., 2010; Heid et al., 2013; de Castro et al., 2016). Apoptosis and pyroptosis also interact via the caspase family. Caspase-1 inhibits certain apoptotic pathways, while caspase-8 participates in inflammasome assembly, enabling a functional switch between the two programs (Moriwaki et al., 2015; Orlowski et al., 2017).

Ferroptosis is closely linked to LMP. As major intracellular iron storage organelles, lysosomes release iron upon LMP, which catalyzes Fenton reactions and promotes lipid peroxidation (Torii et al., 2016; Cañeque et al., 2025). This process is attenuated by iron chelation or lysosomal inhibition (Homma and Fujii, 2015). Positive feedback loops amplify the crosstalk. Pyroptosis-derived IL-1β generates ROS, which together with lysosomal iron exacerbates lipid peroxidation and ferroptosis; conversely, ferroptotic lipid peroxides act as DAMPs to activate inflammasomes and enhance pyroptosis (Zhou et al., 2020; Rao et al., 2022).

Autophagic cell death is tightly integrated into this network. Following LMP, autophagy switches from cytoprotection to death execution (Mahapatra et al., 2021). It crosstalks with apoptosis via Bax and Bak. These proteins directly promote LMP to initiate autophagic cell death (Karch et al., 2017). Autophagy also intersects with ferroptosis through ferritinophagy. In this process, NCOA4 delivers ferritin to lysosomes. This releases iron that fuels lipid peroxidation (Mancias et al., 2014; Hou et al., 2016). Additionally, autophagy promotes pyroptosis by activating the NLRP3 inflammasome upon lysosomal damage (Duewell et al., 2010). When autophagic flux is overwhelmed, cells shift toward necrosis. They then release DAMPs to propagate death signals to neighboring cells (Pan et al., 2021).

Lysosomes and mitochondria can communicate bidirectionally. LMP-induced cathepsin release triggers MOMP, while mitochondrial ROS further destabilizes lysosomal membranes, forming a positive amplification loop that accelerates cell death (Heid et al., 2013; Zhu et al., 2017). When apoptosis, pyroptosis, or ferroptosis are compromised, cells activate necrosis as a backup program and release DAMPs to engage adjacent cells (Vanden Berghe et al., 2014).

In summary, LMP acts as a central hub orchestrating crosstalk among apoptosis, pyroptosis, ferroptosis, necrosis, and autophagic cell death. This network refines cell death classification and provides a therapeutic rationale for targeting lysosomes in cancer, neurodegeneration, and chronic inflammation. The engagement of multiple lysosome-dependent death pathways in cancer offers opportunities to combat therapy resistance.

4 Concluding remarks and future perspectives

The lysosome has emerged as a decisive regulator of cellular fate. Beyond its classical degradative role, it functions as a central signaling hub that integrates stress signals and orchestrates PCD. Upon lysosomal membrane permeabilization, the lysosome releases cathepsins and disrupts ion homeostasis, thereby activating or amplifying distinct death pathways, including apoptosis, ferroptosis, and pyroptosis. This multifunctional organelle therefore serves as a critical decision point, decoding the nature and intensity of stress inputs into specific death outputs to preserve cellular and organismal homeostasis. Dysregulation of this lysosomal death machinery has been implicated in diverse disease contexts, including cancer, neurodegeneration, atherosclerosis, age-related macular degeneration, and respiratory viral infections, highlighting the broad translational relevance of lysosomal PCD regulation.

However, key questions remain regarding the specificity and spatiotemporal control of LMP. The same initial event of lysosomal leakage can lead to different PCD modalities depending on cellular context, suggesting that selectivity involves differential activation of downstream effectors and crosstalk with other organelles. Moreover, LMP can occur as a graded event, where partial permeabilization may allow limited content release and signaling without immediate cell lysis. Elucidating how LMP initiation, propagation, and containment are regulated through lipid composition, membrane repair, and protein interactions will be crucial for understanding how cells interpret lysosomal damage.

Advances in lysosome-targeted technologies are accelerating the dissection of these unresolved mechanisms. Techniques such as lysosome-specific immunoprecipitation, genetically encoded fluorescent probes, super-resolution microscopy, and CRISPR-based screening enable real-time visualization and systematic identification of LMP regulators and lysosome-centric signaling networks. These tools lay the foundation for translating lysosome biology into precision therapeutics. In cancer, lysosome-destabilizing agents such as siramesine and lapatinib have entered early-phase clinical trials, either alone or in combination with standard chemotherapies. Ironomycin and other lysosomal iron export inhibitors are being optimized for improved selectivity and reduced off-target toxicity. Combining lysosomal destabilizers with immune checkpoint inhibitors may further enhance therapeutic efficacy by exploiting the multifaceted role of lysosomes in PCD, particularly in converting “cold” tumors into “hot” tumors amenable to immunotherapy.

Meanwhile, in neurodegenerative disorders, enhancing lysosomal membrane stability through pharmacological activation of the ESCRT machinery or inhibition of calpain-mediated LMP represents a promising neuroprotective strategy. The development of lysosome-targeted delivery systems, including pH-responsive nanoparticles and antibody-drug conjugates directed against lysosomal membrane proteins, further enables cell type-specific intervention. Future interventions must address the dual role of lysosomes by developing cell type- and context-specific approaches that harness the death-executing potential of lysosomes while preserving their essential homeostatic functions. Deeper mechanistic insights will pave the way for novel targeted treatments, grounded in a mechanistic understanding of lysosomal PCD regulation, poised to translate basic discoveries into clinical benefit across a spectrum of human diseases.

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Glossary

AIM2 Absent in melanoma 2 ALR Autophagic lysosome reformation AMPK AMP-activated protein kinase ASC Apoptosis-associated speck-like protein containing a CARD ATG Autophagy-related gene ATP13A2 ATPase cation transporting 13A2 BAX BCL2-associated X protein BAK BCL2-antagonist/killer 1 Bcl-2 B-cell lymphoma 2 BID BH3-interacting domain death agonist CaMKII Calcium/calmodulin-dependent protein kinase II DAMP Damage-associated molecular pattern DFO Deferoxamine DMT1 Divalent metal transporter 1 DRAM1 DNA damage-regulated autophagy modulator 1 ESCRT Endosomal sorting complexes required for transport EVA1A Eva-1 homolog A GPX4 Glutathione peroxidase 4 GSDMD Gasdermin D GSDME Gasdermin E GSH Glutathione HSP70 Heat shock protein 70 IFN Interferon IL Interleukin JNK c-Jun N-terminal kinase LAMP Lysosome-associated membrane protein LMP Lysosomal membrane permeabilization MLKL Mixed lineage kinase domain-like protein MOMP Mitochondrial outer membrane permeabilization MPTP Mitochondrial permeability transition pore mTORC1 Mechanistic target of rapamycin complex 1 NCOA4 Nuclear receptor coactivator 4 NLRP NLR family pyrin domain-containing protein NOD2 Nucleotide-binding oligomerization domain-containing protein 2 PCD Programmed cell death PI3K Phosphoinositide 3-kinase PUFA-PL Polyunsaturated fatty acid-containing phospholipid RIPK Receptor-interacting protein kinase ROS Reactive oxygen species STAT3 Signal transducer and activator of transcription 3 STEAP3 Six-transmembrane epithelial antigen of prostate 3 TAK1 Transforming growth factor-β-activated kinase 1 TFRC Transferrin receptor TMEM175 Transmembrane protein 175 TNF Tumor necrosis factor TRPML1 Transient receptor potential mucolipin 1 ULK1 Unc-51-like autophagy-activating kinase 1 v-ATPase Vacuolar-type ATPase VPS34 Vacuolar protein sorting 34

Footnotes

Edited by: Zhenggang Liu, National Institutes of Health (NIH), United States

Reviewed by: Siriporn Jitkaew, Chulalongkorn University, Thailand

Michael Joseph Morgan, Northeastern State University, United States