Lysosomal Repair in Health and Disease

Abstract

Lysosomes are essential organelles degrading a wide range of substrates, maintaining cellular homeostasis, and regulating cell growth through nutrient and metabolic signaling. A key vulnerability of lysosomes is their membrane permeabilization (LMP), a process tightly linked to diseases including aging, neurodegeneration, lysosomal storage disorders, and cardiovascular disease. Research progress in the past few years has greatly improved our understanding of lysosomal repair mechanisms. Upon LMP, cells activate multiple membrane remodeling processes to restore lysosomal integrity, such as membrane invagination, tubulation, lipid patching, and membrane stabilization. These repair pathways are critical in preserving cellular stress tolerance and preventing deleterious inflammation and cell death triggered by lysosomal damage. This review focuses on the expanding mechanistic insights of lysosomal repair, highlighting its crucial role in maintaining cellular health and the implications for disease pathogenesis and therapeutic strategies.

Keywords: Atg8ylation; CASM; ESCRT; Lysosomal repair; PITT; annexins; lysosomal membrane permeabilization; microlysophagy; stress granules.

Figure 1

Overview of cellular strategies in lysosomal repair. In theory, lysosomal membrane damage can be repaired through at least four distinct strategies: (1) invagination of the damaged membrane segment into the lysosomal lumen for degradation, also known as microlysophagy; (2) tubulation and budding of damaged membrane segments for removal; (3) patching of damaged membranes with lipids; (4) stabilization of damaged membranes by protein assemblies, which may facilitate membrane recovery. Reports in the literature support the existence of lysosomal repair mechanisms corresponding to each of these categories, although some of these mechanisms require more in‐depth investigation.

Figure 2

Lysosomal repair by ESCRT‐mediated membrane invagination or microlysophagy. (1) Ca²⁺ leakage from damaged lysosomes triggers ESCRT recruitment through the Ca²⁺ effector ALG2. (2) There are also ALG2‐independent mechanisms for ESCRT recruitment to damaged lysosomes. Lysosomal protein ubiquitination may be one such mechanism, which recruits ESCRT‐0 or ‐I subunits through their ubiquitin‐binding motifs. Once assembled, ESCRT‐III forms oligomers that seal damaged lysosomal membranes through membrane remodeling or intraluminal membrane invagination (microlysophagy). (3) ESCRT‐independent membrane invagination has also been proposed through Ca²⁺‐dependent sphingomyelin (SM) exposure and subsequent SM conversion to ceramide. (4) CASM/lysosomal membrane Atg8ylation through the ATG5‐ATG12 E3‐like complex also plays a role in ESCRT recruitment. It is yet to be determined if ALG2 recruits ESCRT independently of CASM. (5) The lipid conjugation of ATG8 proteins, particularly GABARAPs, is critical for ALIX recruitment in response to lysosomal membrane damage. (6) The ESCRT recruitment and function are further regulated by STK38 and LRRK2. LAPTM4A, lysosomal associated protein transmembrane 4A; RNF152, Ring Finger Protein 152; ALG2, apoptosis‐linked gene 2; ALIX, ALG2‐interacting protein X; VPS4, vacuolar protein sorting 4; STK38, serine/threonine‐protein kinase 38; DOK1, docking protein 1; PS, phosphatidylserine; PE, phosphatidylethanolamine.

Figure 3

LMP‐induced lysosomal membrane tubulation. Lysosomal membrane damage triggers the tubulation of both LAMP1‐positive and ‐negative membranes. (1) CASM/lysosomal membrane Atg8ylation plays a key role in recruiting LRRK2 to damaged lysosomes, which in turn triggers JIP4‐mediated lysosomal tubulation, known as lysosomal tubulation/sorting driven by LRRK2 (LYTL). (2) CASM also associates with LRRK2‐independent tubulation of LC3‐positive, LAMP1‐negative lysosomal membranes. The exact function of these CASM‐related lysosomal tubulation is yet to be determined. (3) Another lysosomal tubulation pathway is mediated by the RAB7 GTPase‐activating protein TBC1D15 and contributes to lysosomal reformation. In response to severe lysosomal damage, macroautophagy‐related ATG8 recruits TBC1D15 to the lysosome independent of CASM. TBC1D15 then recruits multiple proteins from the autophagic lysosomal reformation pathway, including clathrin and dynamin2. TBC1D15‐dependent lysosomal tubulation recycles lysosomal components before autophagic turnover of overly damaged lysosomes. JIP4, c‐Jun N‐terminal kinase (JNK)–interacting protein 4; PS, phosphatidylserine; PE, phosphatidylethanolamine; LRRK2, leucine‐rich repeat kinase 2. LAMP1, lysosomal‐associated membrane protein 1.

Figure 4

The PITT pathway – patching damaged lysosomes through lipid transfer. The phosphoinositide‐initiated membrane tethering and lipid transport (PITT) pathway mediates rapid lysosomal repair through ER‐to‐lysosome lipid transfer. (1) PI4P signaling: Ca²⁺ leakage from damaged lysosomes triggers lysosomal recruitment of PI4K2A which generates prominent levels of phosphatidylinositol‐4‐phosphate (PI4P) on the lysosomal membrane as a signaling messenger. (2) Membrane tethering and lipid exchanging: PI4P serves as a damage signal to recruit oxysterol‐binding protein (OSBP) and OSBP‐related proteins (ORP9/10/11) which tether damaged lysosomes to the ER membrane via simultaneous interactions with the lysosomal PI4P and ER‐anchored adapter proteins vesicle‐associated membrane protein (VAMP)‐associated protein A and B (VAPA/VAPB); at the membrane contacts, OSBP and ORPs mediate PI4P/cholesterol and PI4P/phosphatidylserine (PS) exchanging between ER and lysosomes, leading to lysosomal accumulation of both cholesterol and PS. Increased cholesterol levels improve lysosomal membrane rigidity and stability. (3) Lysosomal repair via large‐scale lipid transfer: lysosomal PS activates ATG2‐mediated lipid delivery to repair damaged membranes. Additional bridge‐like lipid transfer proteins such as VPS13C and BLTP3A are also recruited to damaged lysosomes. The lipid scramblase ATG9 may also regulate lysosomal membrane remodeling. (4) Damaged lysosomes undergo retrograde transport to the ER‐extensive perinuclear region, which may facilitate lysosome‐ER membrane contact formation. Multiple mechanisms promote lysosomal retrograde trafficking upon membrane damage. Chol, cholesterol; PS, phosphatidylserine; SAC1, ER‐anchored PI4P phosphatase; RILP, Rab‐interacting lysosomal protein; JIP4, c‐Jun‐amino‐terminal kinase‐interacting protein 4; ER, endoplasmic reticulum; ALG2, apoptosis‐linked gene 2; BLTP3A, bridge‐like lipid transfer protein family member 3A.

Figure 5

Lysosomal membrane stabilization by multiple pathways. The lysosomal membrane is stabilized by multiple mechanisms that may contribute to lysosomal repair. (1) Stress granules are triggered both on lysosomes and in the cytosol during lysosomal membrane damage, which involves protein kinase R (PKR, EIF2AK2) phosphorylation facilitated by Ca²⁺‐dependent ALIX assembly on the lysosome. PKR subsequently phosphorylates eIF2α to activate stress granule formation. (2) Annexin A1, A2, and A7 (ANXAs) promote lysosomal repair by localizing to large membrane pores where ANXAs may oligomerize to stabilize and repair the membrane. (3) Myoferlin localization to lysosomes in cancers can increase lysosomal membrane stability, which may be driven by Ca²⁺‐ and PS‐stimulated Myoferlin oligomerization. (4) The heat shock chaperone protein Hsp70 promotes lysosomal membrane stability by binding to bis‐(monoacylglycero)‐phosphate (BMP) on intraluminal vesicles (ILVs) in the lysosomal lumen, which in turn activates acid sphingomyelinase (ASM) to convert sphingomyelin (SM) into ceramide. The latter may increase lysosomal membrane stability indirectly through improved lysosomal lipid metabolism. ALG2, apoptosis‐linked gene 2; ALIX, ALG2‐interacting protein X; ILV, intraluminal vesicle; PACT, protein activator of the interferon‐induced protein kinase; PS, phosphatidylserine.

Figure 6

CASM/Membrane Atg8ylation coordinates multiple lysosomal repair/quality control pathways. Conjugation of ATG8 to single membranes (CASM) or lysosomal membrane Atg8ylation is a robust response triggered by lysosomal stress including membrane damage. CASM is redundantly activated by either the V‐ATPase‐ATG16L1 axis or sphingomyelin (SM)‐TECPR1 axis. CASM cross‐talks with multiple lysosomal repair/quality control pathways through ATG8 interactions with different proteins, such as ATG2 (PITT), BLTP3A, ALIX and VPS37A (ESCRT), LRRK2 (LYTL), and FNIP/FLCN (TFEB). Most of the interactions have been clearly defined by the presence of ATG8‐interacting motifs (AIM) in these proteins. BLTP3A, bridge‐like lipid transfer protein family member 3A; LYTL: lysosomal tubulation/sorting driven by LRRK2; PS, phosphatidylserine; PE, phosphatidylethanolamine; TECPR1, tectonin beta‐propeller repeat‐containing protein 1; TFEB, transcription factor EB.