bims-lycede 2026-09-20 papers

Proc Natl Acad Sci U S A. 2026 Sep 22. 123(38): e2616684123

Lipids regulate export of lysosomal enzymes from the endoplasmic reticulum.

Baolong Xia, Myeonghoon Han, Isaac Park, Norbert Perrimon.

Lysosomal enzymes are synthesized in the Endoplasmic Reticulum (ER) and transported to lysosomes to execute their functions. Deficiencies in lysosomal enzymes or components of the lysosomal transport machinery result in lysosomal storage disorders. While mannose-6-phosphate mediated lysosomal enzymes sorting in the Golgi has been extensively characterized, the mechanisms governing their export from the ER remain elusive. Here, we show that de novo lipogenesis, a metabolic pathway responsible for fatty acid synthesis, regulates lysosomal enzyme transport. Inhibition of de novo lipogenesis leads to the retention of lysosomal enzymes within the ER. Mechanistically, fatty acid derived from de novo lipogenesis is used for Arf1 myristoylation. Myristoylated Arf1 promotes retrograde vesicle trafficking from the Golgi to the ER, thereby maintaining the homeostatic bidirectional flux required for efficient ER export of lysosomal enzymes. Our findings uncover a critical functional link between lipid metabolism and lysosomal enzyme trafficking.

Keywords: SREBP; de novo lipogenesis; lysosomal enzyme transport; protein myristoylation; proximity labeling

DOI: https://doi.org/10.1073/pnas.2616684123

Eur J Pharmacol. 2026 Sep 18. pii: S0014-2999(26)00850-2. [Epub ahead of print] 179368

Multidimensional Roles of the Transcription Factor EB-Regulated Autophagy-Lysosomal Network in Tumor Drug Resistance.

Yue Lu, Yuewen Wang, Daying Sun, Zhangwei Qiao, Zhengchao Wang, Shuliang Song, Junfeng Hou.

Chemotherapy resistance is a key factor in tumor recurrence and mortality and a barrier to durable therapeutic effectiveness. Besides canonical mechanisms, including target alterations and drug efflux, tumor cells integrate chemotherapy-induced DNA damage, oxidative stress, and metabolic stress into persistent adaptive stress-response programs in which the autophagy-lysosomal pathway (ALP) plays a pivotal role. Transcription factor EB (TFEB), a master transcriptional regulator of the ALP, undergoes stress-responsive nuclear translocation under chemotherapeutic conditions through mechanistic target of rapamycin complex 1 (mTORC1) inhibition, lysosomal Ca2+-calcineurin-mediated dephosphorylation, and related signaling cascades. Nuclear TFEB activates the canonical coordinated lysosomal expression and regulation (CLEAR) network while also engaging broader context-dependent transcriptional programs. Within the autophagy-lysosomal system, CLEAR-dependent regulation promotes autophagosome biogenesis and maturation, autophagosome-lysosome fusion, and lysosomal biogenesis, resulting in enhanced autophagic flux. TFEB-driven enhancement of ALP flux generates multiple adaptive functional outputs, including clearance of damaged cellular substrates, buffering of reactive oxygen species (ROS), recycling of metabolic substrates to meet bioenergetic demands, modulation of cell death thresholds, and reduced effective intracellular drug exposure via lysosomal sequestration, storage, efflux, and intracellular redistribution. This review presents an integrated conceptual platform linking stress-induced TFEB activation, enhanced autophagic flux, downstream functional adaptations, and the emergence of chemotherapeutic resistance. By focusing on the TFEB-ALP axis, this review further identifies a stratified therapeutic intervention model comprising upstream suppression, intermediate pathway blockade, and downstream functional counteraction. These perspectives provide a more systematic and mechanistic understanding for developing precision strategies to overcome chemotherapy resistance by targeting the TFEB-ALP axis.

Keywords: Drug resistance; autophagic flux; lysosomes; transcription factor EB (TFEB); tumor stress adaptation

DOI: https://doi.org/10.1016/j.ejphar.2026.179368

Nat Cell Biol. 2026 Sep 15.

DFCP1-containing ER microdomains mediate lysosomal membrane repair.

Maja Radulovic, Sascha Pust, Athanasios Kournoutis, Di Chen, M Isabel Giner, Qijian Liang, Santosh Phuyal, Thomas J Böddeker, Katy McCarron, Eric Herrmann, Kevin Rose, Sebastian W Schultz, Andreas Brech, James H Hurley, Claudio Bussi, Luis Bonet-Ponce, Maximiliano G Gutierrez, Camilla Raiborg, Harald Stenmark.

Lysosomal membrane integrity is essential for preserving cellular homeostasis in response to different stressors. Upon lysosomal membrane permeabilization, cells activate several mechanisms for lysosomal membrane repair, including ESCRT proteins, phosphatidylinositol 4-phosphate (PI4P)-dependent lipid transfer from the endoplasmic reticulum (ER) and conjugation of ATG8 family proteins to single membranes (CASM). The interplay between these pathways and the regulation of the lipid transfer machinery remain incompletely understood. Here we show that phosphatidylinositol 3-phosphate (PI3P)-containing ER domains play a major role in lysosomal membrane repair. PI3P is formed on lysosome-proximal ER domains by the phosphatidylinositol 3-kinase PIK3C3/VPS34 in response to membrane damage, and inhibition or depletion of PIK3C3 inhibits lysosome repair. Mechanistically, the ATPase DFCP1/ZFYVE1 accumulates on lysosome-proximal ER domains by its PI3P binding, triggered by Ca2+ efflux from lysosomes and requiring the ULK1 kinase complex and ER proteins of the VAP family. Downstream of CASM, PI4P, ESCRTs and PI3P, DFCP1 promotes focal accumulation of the lipid channel VPS13C on ER domains proximal to damaged lysosomes to promote their repair. The function and dynamics of DFCP1 depend on its ability to bind and hydrolyse ATP, and absence of DFCP1 compromises cellular resistance to vacuolar damage induced by Listeria monocytogenes. We conclude that DFCP1 mediates concentration of the ER-associated lipid transport machinery at damaged lysosomes to promote their sealing in response to Ca2+ flux and PIK3C3 activation.

DOI: https://doi.org/10.1038/s41556-026-02062-z

STAR Protoc. 2026 Sep 17. pii: S2666-1667(26)00499-5. [Epub ahead of print]7(4): 104846

Protocol for designing and evaluating antibody-drug conjugates to promote endocytosis and lysosomal trafficking.

Xinlei Zhuang, Li Lin, Liqiang Pan.

Receptor endocytosis and lysosomal delivery are critical for efficient intracellular delivery of antibody-drug conjugates (ADCs), yet many cancer targets exhibit limited internalization. Here, we present a protocol for engineering and evaluating ADCs to induce receptor ubiquitination, thereby promoting receptor uptake and transport toward lysosomal compartments. We describe steps for designing antibodies fused with E3 ligase-binding modules, drug conjugation, and cellular assays to quantify ubiquitination-dependent internalization and lysosomal accumulation in cancer cell models. For complete details on the use and execution of this protocol, please refer to Zhuang et al.1.

Keywords: Biotechnology and bioengineering; Flow Cytometry; Microscopy; Protein expression and purification; SPR; Surface plasmon resonance; antibody

DOI: https://doi.org/10.1016/j.xpro.2026.104846

ACS Nano Med. 2026 Sep 09. 1(8): 2071-2090

Intracellular Nanopharmacology of Trastuzumab Deruxtecan Reveals Lysosome-Centered Organelle Vulnerabilities in HER2-Positive Breast Cancer Cells.

Trastuzumab-deruxtecan (T-DXd) is a clinically effective antibody-drug conjugate (ADC) with activity across HER2-amplified, HER2-low, and ultralow breast cancers. Despite its clinical success, how its nanoscale intracellular trafficking and processing shape therapeutic outcomes remains incompletely defined. Given the central role of HER2 internalization and lysosomal processing in ADC pharmacology, we investigated the spatiotemporal intracellular response to T-DXd in human HER2-positive breast cancer cell models. By integrating biochemical analyses with light and electron microscopy-based nanoscale imaging, and employing orthogonal nanoscale probes, including BSA-gold nanoparticles and nanogold-based labeling, together with proteomic profiling, we reconstructed the temporal sequence of T-DXd action over 72 h. An early phase (2-24 h) was characterized by rapid HER2 phosphorylation, sustained ERK signaling, metabolic activation, and TFEB-driven lysosomal engagement, consistent with active drug processing. Nanoscale probing of the endocytic pathway using BSA-gold nanoparticles demonstrated a marked expansion of the lysosomal compartment, with increased lysosome number and size, supporting the concept that T-DXd actively remodels lysosomal architecture rather then passively exploiting it as a delivery site. A transitional phase at 48 h revealed pronounced lysosomal accumulation of T-DXd and extensive organelle remodeling. By 72 h, cells entered a late phase marked by mitochondrial dysfunction, nuclear envelope stress, and DNA damage, accompanied by the emergence of nanoscale contacts among lysosomes, mitochondria, and the nucleus, suggestive of coordinated organelle failure. Proteomic analysis indicated activation of inflammatory and stress-associated pathways, including TNFα/NF-κB signaling, supported by increased release of IL-6, IL-8, and TNF-α. Collectively, this spatiotemporal framework identifies compartment-specific nanoscale vulnerabilities engaged by T-DXd and highlights ERK-dependent signaling and lysosomal function as potential targets for rational combination strategies in HER2-positive breast cancer.

Keywords: HER2-positive breast cancer; antibody−drug conjugates; electron microscopy; lysosomal remodeling; nanoscale drug trafficking; trastuzumab deruxtecan (T-DXd)

DOI: https://doi.org/10.1021/acsnanomed.6c00097