bims-auttor 2026-04-05 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2026–04–05
thirty-two papers selected by
Viktor Korolchuk, Newcastle University

Dual pathways of TFEB activation under lysosomal stress: ATG conjugation-dependent and -independent modes.
The snare protein SYP22 in Arabidopsis interacts with ATG8 to promote the autophagosome-vacuole fusion.
Lysosome: a critical hub for ferroptosis regulation.
Isoginkgetin protects against degeneration of ALS motor neurons via regulating the GSK-3β-TFEB signaling axis.
Loss of Lamp2a-dependent chaperone-mediated autophagy drives dry AMD-like retinal pathology in mice and is rescued by BK channel activation.
A pathogenic Tau mutation drives autophagy-lysosome dysfunction that limits Tau degradation in a model of frontotemporal dementia.
Molecular and structural mechanisms of nutrient sensing in the mTORC1 pathway.
PINK1 and STUB1 pathway orchestrates peroxisomal selective autophagy by PEX13 depletion.
Cell-intrinsic regulation of epilepsy-associated pathology by mTORC1 and mTORC2.
STUB1-VCP/p97 complex regulates mitophagy via fine-tuning of PINK1 levels.
Autophagy-Independent Function of ATG-18 Is Essential for Gonadal Longevity in Caenorhabditis elegans.
Signal peptide-directed proteins generated in the endoplasmic reticulum are secreted or degraded via the autophagic pathway.
Lysosomal homeostasis at the crossroads of neurodegeneration.
Activation of the protective arm of renin-angiotensin system enhances mitochondrial turnover improving respiration and decreasing integrated stress response in a human Complex III deficiency model.
Mechanosensory channels mediate ER Ca2+ transients to trigger assembly of autophagosome initiation sites for degradation of ER subdomains.
Fluorescence microscopic quantification of lysosomal cholesterol accumulation induced by cationic amphiphilic drugs.
A nature-inspired nanoplatform for multi-protein targeted degradation via the autophagy-lysosome pathway.
Dysregulation of a novel autophagosome-mitochondria contact contributes to autophagy dysfunction and neurodegeneration in tauopathy.
Molecular mechanisms underlying exercise-enhanced autophagy in improving neuroplasticity in Alzheimer's disease.
Nucleophagy is promoted by two autophagy receptors and inhibited by chromatin-nuclear envelope tethering in fission yeast.
Regulation of STK38 by autophagy governs YAP1 activity during paligenosis.
Revitalizing mitochondrial quality control: targeting mitochondria-derived vesicles in Parkinson's disease.
NRF2 controls a diverse network of antiviral effectors with p62 acting as a central restriction factor effective across virus families.
Purifying selection during maternal inheritance of mammalian mtDNA depends on autophagy and bottleneck size.
Discovery of Autophagy Modulators that Increase I1061T NPC1 Expression and Promote Cholesterol Efflux in Niemann-Pick Type C Patient-Derived Fibroblasts.
Identification of potential autophagy inducers through high-throughput and high-content imaging analysis.
Autophagy dysfunction in iPSCs-derived neurons and midbrain organoids carrying a SNCA triplication.
TFEB degradation is regulated by an IKK/β-TrCP2 phosphorylation-ubiquitination cascade.
HR3/RORα-mediated cholesterol sensing regulates TOR signaling.
Mitochondrial IRF3 drives pulmonary fibrosis by impairing mitophagy and triggering ferroptosis.
Cytosolic AcCoA: a metabolic signal bridging nutrient sensing and mitophagy.
RANKL-inducible Arl8b effector RUFY4 drives HOPS-mediated lysosomal maturation and trafficking in osteoclasts.

Autophagy. 2026 Mar 30. 1-3

Dual pathways of TFEB activation under lysosomal stress: ATG conjugation-dependent and -independent modes.

Takayuki Shima, Shuhei Nakamura.

  TFEB (transcription factor EB) regulates the expression of autophagy and lysosomal genes, is activated by various cellular stresses, and plays a key role in maintaining cellular homeostasis. Recent work demonstrates that TFEB is activated during lysosomal damage through two distinct mechanisms: ATG conjugation-dependent and -independent. TFEB activation proceeds sequentially through two modes. In the early ATG conjugation-independent mode (Mode I), APEX1 interacts with TFEB in the nucleus, maintaining its transcriptional activity and protein stability. In the later ATG conjugation-dependent mode (Mode II), CCT7 and TRIP6 translocate to lysosomes and interact with TFEB, modulating its phosphorylation and nuclear localization. Moreover, TFEB regulation induced by other cellular stresses-such as oxidative stress, proteasome inhibition, mitochondrial damage, and DNA damage-also involves either Mode I or Mode II. Our findings provide new insights into a unified understanding of TFEB regulation under diverse cellular stress conditions.

Keywords:  Damage; TFEB; lysosome; mitochondria; organelle

DOI:  https://doi.org/10.1080/15548627.2026.2642336
Autophagy. 2026 Mar 30.

The snare protein SYP22 in Arabidopsis interacts with ATG8 to promote the autophagosome-vacuole fusion.

Hyera Jung, Wenlong Ma, Jeong Hun Kim, Chian Kwon, Byung-Ho Kang, Taijoon Chung.

  In eukaryotic cells, excess or damaged cytoplasmic constituents are targeted into lytic compartments via autophagosomal membrane trafficking. Biogenesis of autophagosomes in fungi, metazoans, and plants relies on the conserved ATG (autophagy related) proteins. The machinery responsible for autophagosome turnover has been elucidated in yeast and metazoans, but not in plants. Here we examined 14 soluble N-ethylmaleimide-sensitive-factor attachment protein receptors (SNAREs) in Arabidopsis thaliana by autophagy marker and genetic analyses. We identified SYP22 (Syntaxin of Plants 22) as a SNARE that is necessary for the efficient fusion of autophagosomes with the vacuole. Genetic disruption of SYP22 led to a reduction in autophagic flux and the accumulation of autophagosomes. The vacuolar Qa-SNARE SYP22 interacted with autophagosomal proteins, such as ATG8 and the R-SNARE VAMP724. Overall, our molecular and genetic analyses of Arabidopsis SNAREs underscore the importance of autophagosome-vacuole fusion in autophagic flux, and provide an insight into how plant vacuolar SNARE proteins recognize the autophagosome and mediate its fusion. As a unique mutant defective in the turnover of autophagosomes, syp22 will be useful for overcoming bottlenecks in plant autophagy research.

Keywords:  ALPHA-SNAP2; GFP-ATG8; phagophore; proteinase protection assay; starvation; tonoplast

DOI:  https://doi.org/10.1080/15548627.2026.2653789
Trends Cell Biol. 2026 Mar 30. pii: S0962-8924(26)00038-3. [Epub ahead of print]

Lysosome: a critical hub for ferroptosis regulation.

Xin Chen.

  Ferroptosis is an iron-dependent programmed cell death that involves lipid peroxidation. Ferroptosis represents a critical process underlying tumorigenesis and multiple pathological disorders. Recently, lysosomes have been found to orchestrate ferroptotic signaling, linking iron metabolism, oxidative homeostasis, and selective autophagy. Furthermore, lysosomal membrane disruption leads to the release of intraluminal iron and cathepsins, thereby facilitating ferroptotic damage, whereas lysosomal exocytosis acts in the opposite direction to limit ferroptosis. Therefore, pharmacological modulation of lysosomal activities could be used to treat drug-resistant tumors or protect normal tissues against ferroptosis-related injuries. In this review, we summarize how lysosomes control ferroptosis, focusing on the regulation through lysosomal contents, pH, degradation processes, and exocytosis. We also discuss possible therapeutics that target lysosomes to modulate ferroptosis-associated diseases.

Keywords:  LMP; autophagy; ferritinophagy; ferroptosis; iron; lysosome

DOI:  https://doi.org/10.1016/j.tcb.2026.03.007
Pharmacol Res. 2026 Mar 28. pii: S1043-6618(26)00087-3. [Epub ahead of print]227 108172

Isoginkgetin protects against degeneration of ALS motor neurons via regulating the GSK-3β-TFEB signaling axis.

Ang Li, Xianglu Xiao, Guopan Liu, Krinos Li, Yixia Ling, Shenglong Deng, Chunzuan Xu, Shu-Qin Cao, Jing Wen, Guang Lu, Guang Yang, Evandro F Fang, Dajiang Qin, Huanxing Su.

  Lysosomal dysfunction is a core pathological driver of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). Transcription factor EB (TFEB) serves as a master regulator of lysosomal biogenesis, and its pharmacological activation represents a strategy to restore lysosomal function in disease and aging. Here, using a series of artificial intelligence-powered computational virtual screening workflows, we have identified isoginkgetin (ISO), a small-molecule compound, as a potent TFEB activator that promotes mechanistic target of rapamycin complex 1 (mTORC1)-independent TFEB nuclear translocation to enhance lysosomal biogenesis and function. Mechanistically, ISO functions as an ATP-competitive inhibitor that binds to the key Lys85 residue within the ATP-binding pocket of glycogen synthase kinase 3β (GSK-3β), thereby regulating the GSK-3β-TFEB signaling axis to activate TFEB nuclear translocation. Functionally, ISO improves lysosomal function and protects motor neurons differentiated from induced pluripotent stem cells derived from patients with ALS from degeneration. Collectively, these results support the hypothesis that lysosomal dysfunction is a druggable target for ALS.

Keywords:  Amyotrophic lateral sclerosis; Artificial intelligence; GSK-3β–TFEB axis; Isoginkgetin; Lysosome

DOI:  https://doi.org/10.1016/j.phrs.2026.108172
bioRxiv. 2026 Mar 23. pii: 2026.03.19.712761. [Epub ahead of print]

Loss of Lamp2a-dependent chaperone-mediated autophagy drives dry AMD-like retinal pathology in mice and is rescued by BK channel activation.

Hilal Ahmad Mir, Gaddam Mahesh, Arunan Palanimuthu, Christopher L Cioffi, Konstantin Petrukhin.

Age-related macular degeneration (AMD) is the leading cause of irreversible visual loss in elderly individuals for which no effective treatments are currently available. The photoreceptor loss in dry AMD is secondary to the demise of the retinal pigment epithelium (RPE) cells. The accumulation of extracellular deposits, known as drusen, resulting in part from deficient lysosomal and autophagosomal degradation, is a key feature of dry AMD pathogenesis. Chaperone-mediated autophagy (CMA) is a selective lysosomal degradation pathway that maintains proteostasis by targeting specific cytosolic proteins for lysosomal translocation and degradation. LAMP2A (lysosome-associated membrane protein 2A) functions as the key lysosomal receptor required for CMA. Using Lamp2a knockout mouse, we show that selective CMA dysfunction recapitulates AMD-like pathologies, including sub-RPE lipid and protein deposits, RPE atrophy, Bruch's membrane thickening, and impaired autophagic activity. Furthermore, we identify large-conductance Ca²⁺-activated K⁺ (BK) channels as a therapeutic target for restoring autophagic activity. Mechanistically, pharmacological activation of BK channels with the small-molecule agonist GLA-1-1 enhances macroautophagy and stimulates autophagic flux by promoting autophagosome-lysosome fusion. Importantly, oral administration of GLA-1-1 in markedly attenuates structural, functional, and molecular retinal abnormalities in Lamp2a -deficient mice, suggesting that pharmacological activation of macroautophagy through facilitating autophagosome-lysosome fusion can partially compensate for CMA deficiency. Together, these findings demonstrate that pharmacological activation of macroautophagy can ameliorate the retinal phenotype resulting from CMA dysfunction and support BK channel activation by GLA-1-1 as a promising therapeutic strategy for dry AMD.

DOI: https://doi.org/10.64898/2026.03.19.712761
Nat Commun. 2026 Mar 31. pii: 2699. [Epub ahead of print]17(1):

A pathogenic Tau mutation drives autophagy-lysosome dysfunction that limits Tau degradation in a model of frontotemporal dementia.

Farzaneh S Mirfakhar, Jacob A Marsh, Chihiro Sato, Kylie J Schache, Miguel A Minaya, Roland E Dolle, Stephen C Pak, Gary A Silverman, David H Perlmutter, Shannon L Macauley, Celeste M Karch.

Tau accumulates in a group of neurodegenerative diseases known as tauopathies. A prevailing hypothesis has been that Tau degradation is impaired due to an age-related imbalance in the autophagy-lysosome pathway, but whether these defects are a cause or consequence of Tau accumulation remains unclear. Here we show that a disease-causing mutation in the MAPT gene, which encodes Tau, p.R406W, is sufficient to disrupt multiple steps of the autophagy-lysosome pathway in human neurons. Using Airyscan super-resolution imaging, we find that mutant Tau neurons accumulate Tau and phosphorylated Tau in dysfunctional lysosomes, exhibit reduced lysosome motility, impaired fusion of autophagosomes and lysosomes, and increased undegraded cellular cargo. Pharmacological enhancement of autophagy improves cargo clearance and lowers Tau levels, without restoring defects in lysosomal motility. Together, these findings demonstrate that mutant Tau directly perturbs cellular clearance pathways and suggest that boosting autophagy may help restore Tau homeostasis in tauopathies.

DOI: https://doi.org/10.1038/s41467-026-70473-5
Trends Biochem Sci. 2026 Mar 30. pii: S0968-0004(26)00037-X. [Epub ahead of print]

Molecular and structural mechanisms of nutrient sensing in the mTORC1 pathway.

Serim Yang, Tong Bian, Roberto Zoncu.

  Primary nutrient sensors directly bind metabolites and undergo conformational changes that signal through core pathways to coordinate metabolic and cellular outcomes. Sensing of amino acids, lipids, sugars, and nucleotides is critical for the master growth regulatory Ser/Thr kinase, mechanistic target of rapamycin complex 1 (mTORC1), to promote growth and proliferation. Systematic proteomic and bioinformatic studies have accelerated the discovery of primary nutrient sensors upstream of mTORC1, whereas structural biology has shed light on how binding to their cognate metabolites triggers mTORC1-dependent signaling responses. This review focuses on recently reported amino acid and lipid sensors upstream of mTORC1 and highlights structural and functional features of these sensors that illuminate fundamental principles of nutrient detection and signal transduction.

Keywords:  CASTOR1; LYCHOS; amino acid sensors; cholesterol sensors; metabolites; primary nutrient sensor

DOI:  https://doi.org/10.1016/j.tibs.2026.02.009
Cell Death Differ. 2026 Apr 02.

PINK1 and STUB1 pathway orchestrates peroxisomal selective autophagy by PEX13 depletion.

Doo Sin Jo, Na Yeon Park, Ae-Kyeong Kim, Sunhoe Bang, Yong Hwan Kim, Ji-Eun Bae, Kyunghee Noh, Jeong-Hoon Kim, Min Jae Lee, Seong-Kyu Choe, Peter K Kim, Jongkyeong Chung, Kyu-Sun Lee, Dong-Hyung Cho.

Peroxisomes are dynamic organelles essential for lipid metabolism, oxidative balance, and cellular stress responses. Their dysfunction contributes to various diseases, including metabolic and neurodegenerative disorders. Selective autophagy, or pexophagy, preserves peroxisomal quality by removing damaged or excess peroxisomes. Here, we propose a novel ATM-PINK1-STUB1-ABCD3-SQSTM1 signaling cascade that orchestrates pexophagy in response to peroxisomal impairment. Through siRNA screening, we find that PINK1 is a key regulator of pexophagy induced by PEX13 depletion. PINK1 phosphorylates STUB1, enhancing its E3 ligase activity to ubiquitinate ABCD3, which in turn recruits SQSTM1 for peroxisomal degradation. We further identify that ATM activates PINK1 under peroxisomal stress, linking cellular stress signaling to organelle quality control. These findings provide new insights into the molecular mechanisms underlying peroxisome turnover and may have implications for therapeutic strategies targeting diseases related to peroxisomal dysfunction.

DOI: https://doi.org/10.1038/s41418-026-01726-5
J Neurosci. 2026 Mar 31. pii: e1211252026. [Epub ahead of print]

Cell-intrinsic regulation of epilepsy-associated pathology by mTORC1 and mTORC2.

Christin M Godale, Sarah Yaser, Austin W Drake, Kimberly L Kraus, Natasha Mayer, Mary R Dusing, Candi L LaSarge, Christina Gross, Steve C Danzer.

Mechanistic target of rapamycin (mTOR) signaling is mediated through mTORC1 and mTORC2. mTORC1 signaling requires the regulatory protein Raptor, while mTORC2 signaling requires Rictor. mTOR signaling is increased during epileptogenesis, and manipulations to inhibit mTOR have been shown to reduce seizure incidence in some epilepsy models. Inhibiting mTOR signaling is hypothesized to prevent epileptogenic changes. To test this hypothesis, and to assess how mTORC1 and mTORC2 might modulate epileptogenesis, we deleted Raptor or Rictor from a subset of hippocampal dentate granule cells in male and female mice to cell-autonomously inhibit mTORC1 or mTORC2, respectively. Gene deletion effects were examined in healthy mice and following status epilepticus, which leads to the development of epilepsy. Raptor and Rictor knockout cells had fewer dendritic spines than neighboring wildtype cells, and Raptor knockout cells had reduced presynaptic terminal volume and contributed less to mossy fiber axon sprouting. Raptor deletion decreased somatic contact with parvalbumin inhibitory neuron puncta and reduced soma area, while Rictor knockout cells were more likely to be c-Fos immunoreactive. Findings demonstrate that Raptor and Rictor deletion exert mixed effects on morphological changes associated with epilepsy, implying that mTORC1 and mTORC2 have both overlapping and distinct neuroanatomical targets. In addition, the magnitude of gene deletion effects was similar in saline and SE-exposed animals. The observation implies that rather than specifically blocking epileptogenic circuit rewiring in acquired epilepsy, mTOR inhibition acts similarly on granule cells in healthy and epileptic mice to produce mixed changes on structures underlying excitatory and inhibitory synaptic transmission.Significance Statement The mTOR signaling pathway is a critical regulator of cell growth and metabolism, and is implicated in the development of numerous diseases, including cancer, autism and epilepsy. mTOR signaling is mediated through two arms, mTORC1 and mTORC2. Here, we manipulated signaling through the two arms to assess the impact on neuronal structure in control and epileptic brains. Manipulating mTORC1 and mTORC2 signaling produced both overlapping and distinct effects on neuronal structure - in some cases offsetting changes associated with epilepsy, but in most cases producing similar effects in healthy and epileptic animals. Findings provide new insights into the role of mTOR signaling in epilepsy, and guidance for predicting off target effects of mTOR antagonism.

DOI: https://doi.org/10.1523/JNEUROSCI.1211-25.2026
Cell Rep. 2026 Mar 27. pii: S2211-1247(26)00261-5. [Epub ahead of print]45(4): 117183

STUB1-VCP/p97 complex regulates mitophagy via fine-tuning of PINK1 levels.

Jin-Yi Lin, Ze-Bo Huang, Shi-Qi Zhang, Yong Wu, Ling-Jun Cheng, Xiangzheng Gao, Sofie Lautrup, Shu-Qin Cao, Junping Pan, Dade Rong, Ruixue Ai, Hayden Weng Siong Tan, Liming Wang, Haihe Wang, Han-Ming Shen, Evandro F Fang, Guang Lu.

  PINK1 is a master regulator of PINK1-parkin-mediated mitophagy, a key process for maintaining mitochondrial homeostasis. The precise regulation of PINK1 is therefore essential for orchestrating mitophagy. While proteolytic processing of PINK1 and degradation of cleaved PINK1 via the N-end rule under basal conditions have been extensively characterized, the mechanisms governing full-length PINK1 degradation upon mitochondrial damage remain enigmatic. Here, we demonstrate that PINK1 undergoes ubiquitination and proteasomal degradation during mitophagy through the coordinated action of STUB1 and VCP/p97. Depletion of STUB1 stabilizes full-length PINK1, which paradoxically impairs mitophagy through the acceleration of parkin degradation. At the organismal level, the STUB1-VCP axis plays an important role in neuronal mitophagy-related memory and learning capacities in the roundworm C. elegans. Congruently, this axis is impaired in the postmortem brain tissues from patients with Alzheimer's disease compared with cognitively normal controls. Collectively, our findings support STUB1-VCP as a molecular calibrator that fine-tunes full-length PINK1 levels to enable efficient mitophagy and maintain mitochondrial homeostasis.

Keywords:  Alzheimer’s disease; CP: metabolism; CP: molecular biology; PINK1; STUB1; VCP/p97; autophagy; mitophagy; parkin; ubiquitination-proteasome system

DOI:  https://doi.org/10.1016/j.celrep.2026.117183
Aging Cell. 2026 Apr;25(4): e70454

Autophagy-Independent Function of ATG-18 Is Essential for Gonadal Longevity in Caenorhabditis elegans.

Tatsuya Shioda, Ittetsu Takahashi, Makoto Horikawa, Taiichi Osumi, Takayuki Shima, Akiyo Yamauchi, Kayo Nakamura, Taeko Sasaki, Tatsuya Kaminishi, Harunori Yoshikawa, Miyuki Sato, Hidetaka Kosako, Tamotsu Yoshimori, Shuhei Nakamura.

Autophagy, a highly conserved cellular degradation process, plays essential roles in various physiological processes including aging. Though autophagy is required for lifespan extension in multiple longevity paradigms, the tissue-specific roles of autophagy-related genes (atgs) in longevity remain incompletely understood. Here, we investigate the tissue-specific requirements of atgs to promote longevity conferred by germline ablation (called gonadal longevity) using C. elegans. Remarkably, we discovered that neuronal or intestinal knockdown of atg-18, but not other atgs, specifically abolished gonadal longevity, although knockdown of all tested atgs effectively inhibited autophagic activity in these targeted tissues, implying the presence of an autophagy-independent function of ATG-18 in gonadal longevity. We demonstrated that germline deficiency triggered significant upregulation of ATG-18 in neurons and the intestine. From the proteomics analysis and subsequent screening, we found ATG-18 interacts with PCK-2, a phosphoenolpyruvate carboxykinase. PCK-2 is upregulated within the intestine of germline-deficient animals, but this depends on the non-autophagic function of ATG-18. Consistently, we showed that PCK-2 overexpression mediated longevity required ATG-18 but not its potential interacting partner to regulate autophagy, ATG-2. These findings reveal a previously unrecognized autophagy-independent role for ATG-18 in regulating lifespan in response to germline signals, expanding our understanding of how this evolutionarily conserved protein coordinates organism-wide responses to promote longevity.

DOI: https://doi.org/10.1111/acel.70454
Biochim Biophys Acta Mol Cell Res. 2026 Mar 27. pii: S0167-4889(26)00037-6. [Epub ahead of print]1873(4): 120140

Signal peptide-directed proteins generated in the endoplasmic reticulum are secreted or degraded via the autophagic pathway.

Taek-Yeong Kim, Ye-Jin Cho, Kwon-Yul Ryu.

  Signal peptides (SPs) are short N-terminal sequences that direct proteins to the endoplasmic reticulum (ER). After cleavage of the SP, these proteins are mostly trafficked to the Golgi apparatus for secretion. Lipocalin-2 (LCN2), a neurotoxic secretory protein, was recently identified as a target of autophagy. The presence of an SP is a prerequisite for secretion and autophagic degradation. Based on these observations, we investigated whether the SP of LCN2 is sufficient to enable proteins to be secreted or degraded via autophagy. We fused the SP of LCN2 to a non-secretory green fluorescent protein (GFP) and found that this ER-generated GFP was either secreted or degraded via autophagy. These results indicate that the LCN2-derived SP alone is sufficient to direct proteins to the ER and subsequent secretion or autophagic degradation. This dual regulation was abolished when the SP was deleted from LCN2. Notably, the effect was preserved even when the LCN2 SP was replaced with the SP from brain-derived neurotrophic factor, another secretory protein. These results suggest that SPs with different sequences can similarly direct proteins to the ER and subsequent secretion or autophagic degradation. Furthermore, we found that even when LCN2 reached the Golgi apparatus for secretion, it could also be degraded via autophagy. Thus, we propose that SP-directed and ER-generated secretory proteins can undergo autophagic degradation during ER-Golgi transport, including at the ER, the ER-Golgi intermediate compartment, or the Golgi apparatus. Taken together, degradation of secretory proteins via autophagy suggests implications for the potential control of secretory protein homeostasis.

Keywords:  Autophagy; Brain-derived neurotrophic factor; Green fluorescent protein; Lipocalin-2; Secretion; Signal peptide

DOI:  https://doi.org/10.1016/j.bbamcr.2026.120140
J Clin Invest. 2026 Apr 01. pii: e199845. [Epub ahead of print]136(7):

Lysosomal homeostasis at the crossroads of neurodegeneration.

Stefano De Tito, Sharon A Tooze.

Lysosomes function as metabolic control centers that integrate degradation, nutrient sensing, and stress signaling. In neurons, which must maintain proteostasis and energetic balance throughout life, lysosomal homeostasis determines cellular resilience. Emerging evidence identifies lysosomal injury and defective repair as common denominators across neurodegenerative diseases. Damage to the lysosomal membrane caused by oxidative stress, lipid imbalance, or genetic mutations triggers a hierarchical quality control cascade. Early lesions recruit the endosomal sorting complex required for transport (ESCRT) machinery for mechanical resealing, while larger ruptures activate lipid-centered recovery modules. When repair fails, lysophagy eliminates irreparable organelles and a TFEB-dependent transcriptional program regenerates the lysosomal pool. These tightly coupled responses safeguard neurons from catastrophic proteostatic collapse. Their impairment, through mutations in lysosomal proteins, or through aging, produces the lysosomal fragility that underlies Alzheimer disease, Parkinson disease, amyotrophic lateral sclerosis/frontotemporal dementia, and Huntington disease. Crosstalk between lysosomes, mitochondria, and ER integrates local damage with systemic metabolic adaptation, while dysregulated lysosomal exocytosis and inflammation propagate pathology. Understanding how ESCRT complexes, lipid transport, and transcriptional renewal cooperate to preserve lysosomal integrity reveals unifying principles of neurodegeneration and defines molecular targets for intervention. Restoring lysosomal repair and renewal offers a rational path toward preventing neuronal loss.

DOI: https://doi.org/10.1172/JCI199845
bioRxiv. 2026 Mar 25. pii: 2026.03.20.711686. [Epub ahead of print]

Activation of the protective arm of renin-angiotensin system enhances mitochondrial turnover improving respiration and decreasing integrated stress response in a human Complex III deficiency model.

Lucía Fernández-Del-Río, Andrea Eastes, David Rincón Fernández Pacheco, Nikole Scillitani, Jasmine Garza, Matthew Dugan, Matheus Pinto de Oliveira, Pradnya Kadam, Iman Gauhar, Karel Erion, Kathleen Rodgers, Kevin Gaffney, Amy Wang, Marc Liesa, Cristiane Benincá, Orian Shaul Shirihai.

Primary mitochondrial diseases are clinically and genetically heterogeneous disorders, commonly caused by defects in the oxidative phosphorylation system. This heterogeneity presents major challenges for therapeutic development; however, a shared hallmark across these diseases is the accumulation of dysfunctional mitochondria. Enhancing mitochondrial turnover, by activating the selective degradation of dysfunctional mitochondria via mitophagy, concurrently with the activation of mitochondrial biogenesis, could represent a shared therapeutic strategy for mitochondrial diseases. Here, we describe a novel mitophagy inducer, CAP-1902. CAP-1902 is a new agonist of the MAS G-Protein Coupled Receptor (MasR). In fibroblasts from patients carrying a BCS1L mutation that impairs complex III (CIII) assembly, CAP-1902 increased mitochondrial turnover by promoting both mitophagy and biogenesis. Specifically, MasR activation triggered the AMPK/ULK1/FUNDC1 mitophagy pathway. Knockdown of FUNDC1 blocked mitophagy but not AMPK activation, confirming pathway specificity. Additionally, a decrease in the occurrence of depolarized mitochondria with treatment indicated the selective targeting of accumulated damaged mitochondria in the disease context. MasR activation by CAP-1902 also stimulated the nuclear translocation of PGC-1α, promoting increased expression of transcripts associated with mitochondrial biogenesis, respiratory chain components, and mitochondrial translation. Remarkably, CAP-1902 was ultimately able to restore key defects in CIII-deficient fibroblasts by rescuing bioenergetics and correcting both the aberrant lysosomal distribution and the elevated integrated stress response markers, which is consistent with a shift toward a healthier mitochondrial population. In summary, we describe the first potential GPCR-mediated treatment of mitochondrial diseases and demonstrate that MasR activation by CAP-1902 induces mitochondrial turnover and improves mitochondrial function.

DOI: https://doi.org/10.64898/2026.03.20.711686
Mol Cell. 2026 Apr 02. pii: S1097-2765(26)00158-9. [Epub ahead of print]86(7): 1377-1396.e6

Mechanosensory channels mediate ER Ca2+ transients to trigger assembly of autophagosome initiation sites for degradation of ER subdomains.

Xiaoli Ma, Zhiyang Cheng, Hongyu Zhao, Huan Zhang, Ke Xiao, Jiali Xie, Yun Feng, Chun Yang, Yujie Feng, Xi Wang, Yaozu Xiang, Junjie Hu, Qiaoxia Zheng, Wei Ji, Hong Zhang.

  ER-phagy involves the selective autophagosomal engulfment of ER fragments, but the signaling events, selection mechanisms, and membrane source of ER-phagic autophagosomes remain elusive. Here, using state-of-the-art super-resolution multi-SIM imaging, we reveal that stresses (prolonged starvation, cholesterol dyshomeostasis, and high-Ca2+ insults) trigger the expansion of sheet ER subdomains containing high levels of luminal Ca2+ in mammalian cells, which are subsequently degraded by ER-phagy. Autophagosome formation and sequestration of ER sheets require the concerted actions of FAM134B and lipidated LC3, whereas the autophagy proteins ATG14 and ATG9 are partially dispensable. Electron microscopy and cryo-electron tomography show that the membranes of autophagosomes enclosing high-Ca2+-containing ER sheets are directly remodeled from the ER. The ER-localized cation channels PIEZO1 and TRPV1 are enriched at and mediate Ca2+ transients from high-Ca2+-containing ER sheets, triggering liquid-liquid phase separation of the autophagosome-initiating FIP200 complex to initiate ER-phagy. Thus, distinct mechanisms are employed for the formation of high-Ca2+-containing ER-enclosing autophagosomes and non-selective autophagosomes.

Keywords:  Ca(2+); ER-phagy; FAM134B; FIP200; PIEZO1; TRPV1

DOI:  https://doi.org/10.1016/j.molcel.2026.03.002
Methods Cell Biol. 2026 ;pii: S0091-679X(25)00197-9. [Epub ahead of print]204 285-299

Fluorescence microscopic quantification of lysosomal cholesterol accumulation induced by cationic amphiphilic drugs.

Karla Alvarez-Valadez, Samy Dehissi, Lucille Ferret, Guido Kroemer, Mojgan Djavaheri-Mergny.

  Lysosomes are involved in the transport, degradation, and recycling of macromolecules through the autophagy and endocytosis pathways. Cholesterol is taken up by cells through the internalization of low-density lipoprotein (LDL) via LDL receptor-mediated endocytosis or micropinocytosis. Free cholesterol generated by the action of acid lipases contained in lysosomes can be transferred to other organelles. Dysfunctions in either cholesterol uptake or release from lysosomes can compromise the function and integrity of these organelles, thereby contributing to the pathogenesis of lysosomal storage disorders. We previously showed that some cationic amphiphilic drugs (CADs) mimic the phenotype of lysosomal storage disorders by inducing lysosomal cholesterol accumulation followed by lysosomal damage. Here, we describe two fluorescence microscopic methods for the visualization of cholesterol accumulation in lysosomes in response to the CAD leelamine. In the first method, the cell-permeable cholesterol analog labeled with the fluorophore BODIPY is used. In the second method, endogenous cholesterol-rich microdomains are labeled with filipin complex. Both methods imply the additional visualization of the lysosomal associated membrane protein 2 (LAMP2) by immunofluorescence. Finally, the role of lysosomal cholesterol accumulation in the induction of lysosomal membrane permeabilization (LMP) was assessed through a method based on the recruitment of Galectin-3 on damaged lysosomes.

Keywords:  BODIPY-cholesterol; Cancer; Filipin complex; Galectin-3; High-throughput fluorescence microscopy; LAMP2; Lysosomal membrane permeabilization

DOI:  https://doi.org/10.1016/bs.mcb.2025.09.009
Cell Chem Biol. 2026 Apr 02. pii: S2451-9456(26)00077-2. [Epub ahead of print]

A nature-inspired nanoplatform for multi-protein targeted degradation via the autophagy-lysosome pathway.

Bide Tong, Yulei Wang, Junyu Wei, Zixuan Ou, Huaizhen Liang, Jie Lei, Dingchao Zhu, Hanpeng Xu, Lei Tan, Zhiwei Liao, Cao Yang.

  Extracellular vesicles (EVs) have emerged as key mediators of intercellular communication. However, the mechanisms governing their degradation remain poorly understood. In this study, we demonstrated that EVs are predominantly degraded via the lysosomal pathway. Mechanistically, MAP1LC3B recognizes SNX18 on the surface of endosome-escaped EVs to facilitate their sorting into the autolysosomal pathway for degradation. Leveraging this mechanism, we optimized the lysosomal sorting efficiency of EVs by surface display of LIR motifs and constructed an EV-based targeted protein degradation nanoplatform. The EV-based nanoplatform is highly modular and can be combined with monoclonal antibodies in a plug-and-play manner. It demonstrated remarkable efficiency and selectivity in degrading EGFR, PD-L1, and VEGF. Moreover, the nanoplatform demonstrated multi-targeting capability by simultaneously degrading EGFR and VEGF. Our findings uncover a previously unrecognized mechanism of EVs degradation and provide a novel strategy to harness the EVs degradation machinery as a nature-inspired nanoplatform for the degradation of multiple targeted proteins.

Keywords:  autophagy; extracellular vesicles; lysosome; nanopartcles; targeted protein degradation

DOI:  https://doi.org/10.1016/j.chembiol.2026.03.007
bioRxiv. 2026 Mar 25. pii: 2026.03.23.713823. [Epub ahead of print]

Dysregulation of a novel autophagosome-mitochondria contact contributes to autophagy dysfunction and neurodegeneration in tauopathy.

Nuo Jia, Hongyuan Guan, Yantao Zuo, Yu Young Jeong, Niharika Amireddy, Gavesh Rajapaksha, Cuauhtemoc Ulises Gonzalez, Nora Jaber, Yun-Kyung Lee, Marialaina Nissenbaum, David J Margolis, Wei Dai, Alexander W Kusnecov, Qian Cai.

Mitochondria engage in extensive communication with other organelles through membrane contacts. Perturbed mitochondria-organelle interactions are indicated in a variety of neurodegenerative diseases, but the underlying mechanisms remain poorly understood. Here, we report a new class of mitochondria-organelle communication: autophagosome/autophagic vacuole (AV)-mitochondria (Mito) contact, which exhibits hyper-tethering in tauopathy neurons, consequently hampering AV retrograde transport. Such defects are attributed to accelerated turnover of the contact release factor TBC1D15, triggered by mitochondrial bioenergetic deficit-induced hyperactivity of the AMP-activated protein kinase (AMPK). Increasing TBC1D15 levels or repressing AMPK activity normalizes AV-Mito contact release and restores retrograde transport of AVs, thereby increasing autophagic cargo clearance and reducing tau burden in tauopathy axons. Furthermore, overexpression of TBC1D15 enhances autophagic clearance and attenuates tau pathology, alleviating neurodegeneration and cognitive dysfunction in tauopathy mice. Taken together, our study provides new insights into AV-Mito contact dysregulation in tauopathy-related autophagy failure, laying the groundwork for the development of potential therapeutics to combat tauopathy diseases.

DOI: https://doi.org/10.64898/2026.03.23.713823
Front Aging Neurosci. 2026 ;18 1780247

Molecular mechanisms underlying exercise-enhanced autophagy in improving neuroplasticity in Alzheimer's disease.

Qian Li, Renqing Zhao, Xin Tian, Haocheng Xu.

  Alzheimer's disease (AD), the most prevalent form of dementia, is characterized by progressive memory impairment and cognitive dysfunction. The neuropathological hallmarks of this neurodegenerative disorder encompass two principal pathological features: extracellular deposition of amyloid-β (Aβ) plaques due to abnormal protein aggregation, and intracellular accumulation of neurofibrillary tangles (NFTs) caused by hyperphosphorylation of tau proteins (p-Tau). These pathological changes induce synaptic loss and neuronal apoptosis, which leads to impaired neuroplasticity and progressive deterioration of cognitive function. Autophagy, a critical mechanism in the central nervous system (CNS) responsible for clearing misfolded protein aggregates and damaged organelles, plays a pivotal role in maintaining neuronal homeostasis and synaptic plasticity. However, AD is associated with autophagy impairment, resulting in the accumulation of toxic protein aggregates and damaged organelles. These pathological changes disrupt protein homeostasis, thereby exacerbating neurodegenerative processes. Currently, AD therapeutic strategies remain limited. Emerging evidence indicates that exercise intervention mitigates cognitive decline and enhances synaptic plasticity, potentially through reducing Aβ deposition and pathological phosphorylation of tau proteins. However, the precise mechanisms through which these interventions act remain to be fully elucidated. Recent studies have shown that exercise can promote autophagosome formation, fusion, and lysosomal hydrolytic function, thereby ameliorating the pathological progression of AD. Despite these promising findings, the precise molecular targets and underlying signaling mechanisms through which exercise modulates autophagy in AD remain to be fully elucidated. The purpose of this study is to establish innovative therapeutic targets while identifying mechanistically actionable pharmacological targets to advance therapeutic development against AD pathogenesis.

Keywords:  Alzheimer’s disease; autophagy; cognitive functions; exercise; neuroplasticity

DOI:  https://doi.org/10.3389/fnagi.2026.1780247
Nat Commun. 2026 Mar 31.

Nucleophagy is promoted by two autophagy receptors and inhibited by chromatin-nuclear envelope tethering in fission yeast.

Zhu-Hui Ma, Zhao-Qian Pan, Zhao-Di Jiang, Guang-Can Shao, Yu Hua, Fang Suo, Chen-Xi Zou, Yi-Feng Jiang, Meng-Qiu Dong, Li-Lin Du.

Selective autophagy of the nucleus, known as nucleophagy, targets nuclear components for degradation. The molecular mechanisms underlying nucleophagy remain inadequately understood. In this study, we identify a nucleophagy receptor, Npr1, in the fission yeast Schizosaccharomyces pombe. Npr1 is an Atg8-binding multi-transmembrane protein localized to the outer nuclear membrane. It functions redundantly with another autophagy receptor, Epr1, to promote nitrogen starvation-induced nucleophagy. In the absence of both Npr1 and Epr1, starved cells exhibit abnormal nuclear morphology and reduced survival. During nucleophagy, the nuclear envelope (NE) forms outward protrusions where Atg8 co-localizes with Npr1 and/or Epr1. These protrusions subsequently detach from the NE, resulting in the formation of autophagosomes that contain nucleophagy cargo. Notably, artificially enhancing chromatin association with the inner nuclear membrane leads to NE protrusions that fail to detach, thereby aborting nucleophagy. Our findings provide mechanistic insights into nucleophagy and suggest that abortive nucleophagy protects chromatin from degradation.

DOI: https://doi.org/10.1038/s41467-026-71237-x
Proc Natl Acad Sci U S A. 2026 Apr 07. 123(14): e2517488123

Regulation of STK38 by autophagy governs YAP1 activity during paligenosis.

Yongji Zeng, Yang-Zhe Huang, Qing Kay Li, Raymond Ho, Steven J Bark, Spencer G Willet, Richard J DiPaolo, Jason C Mills.

  Paligenosis is a conserved cellular plasticity program that allows mature cells to reenter the cell cycle in response to tissue injury. Paligenosis progresses via three stages: autodegradation (with dramatic increase in autophagy and lysosomes), induction of metaplastic or fetal-like genes, and cell cycle entry. Hippo signaling, particularly the downstream effector YAP1, regulates cellular plasticity, but its role in paligenosis has not been studied. Here, we examine YAP1 dynamics during paligenosis in digestive-enzyme-secreting chief cells from the mouse stomach. We identified Serine/Threonine Kinase 38 (STK38) as a noncanonical YAP1 kinase that phosphorylates and deactivates YAP1 in uninjured chief cells. During paligenosis, STK38 was degraded by autophagy in stage 1, dephosphorylating and activating YAP1. YAP1 activation was necessary and sufficient for paligenosis-driven conversion of chief cells into metaplastic, proliferating progenitors. Additionally, we show that STK38, like canonical Hippo kinases, interacts with Neurofibromatosis Type 2 (Merlin), a scaffold that recruits Hippo kinases to phosphorylate YAP1. We also observed the same pattern of YAP1 induction via autophagic destruction of STK38 in other tissues and cell types, suggesting injury-induced activation of autophagy in differentiated cells during tissue damage may be a more general feature by which Hippo effectors induce plasticity for regeneration.

Keywords:  Hippo pathway; redifferentiation; reprogramming

DOI:  https://doi.org/10.1073/pnas.2517488123
Biochem Pharmacol. 2026 Mar 29. pii: S0006-2952(26)00268-6. [Epub ahead of print] 117935

Revitalizing mitochondrial quality control: targeting mitochondria-derived vesicles in Parkinson's disease.

Jimna Mohamed Ameer, Sneha Mary Alexander, K Navya, Rajesh A Shenoi, Goutam Chandra.

  Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by the selective loss of dopaminergic neurons in the midbrain substantia nigra, resulting in debilitating motor and non-motor symptoms. No disease modifying therapy is currently available for PD patients. Mounting evidence implicates impaired mitochondrial quality control (MQC) as a central driver of PD pathogenesis. MQC maintains mitochondrial integrity and function through coordinated mechanisms such as mitochondrial biogenesis, dynamics, mitophagy, the ubiquitin-proteasome system, and the formation of mitochondria-derived vesicles (MDVs). MDVs are small vesicular structures that selectively sequester and transport damaged mitochondrial components to lysosomes for degradation, representing a rapid and localized quality control pathway distinct from mitophagy. Beyond their degradative role, MDVs also participate in inter-organelle signalling and intercellular communication, suggesting a broader influence on neuronal homeostasis. Disruption of MDV biogenesis, trafficking, or clearance has been emerging as a key contributor of mitochondrial dysfunction and neurodegeneration in PD. This review synthesizes current understanding of MDV biology, its integration within the MQC network, role in PD pathogenesis and explores how targeting MDV pathways may offer novel diagnostic and therapeutic strategies to modify disease progression in PD.

Keywords:  Endolysosome; Mitochondrial dynamics; Mitophagy; SNARE proteins; Transport vesicles; Ubiquitin-protein ligases

DOI:  https://doi.org/10.1016/j.bcp.2026.117935
Redox Biol. 2026 Apr 01. pii: S2213-2317(26)00133-3. [Epub ahead of print]93 104135

NRF2 controls a diverse network of antiviral effectors with p62 acting as a central restriction factor effective across virus families.

Alice Pedersen, Julia Blay-Cadanet, Jacob Storgaard, Bruno Hernaez, Jacob Thyrsted, Cecilie S Bach-Nielsen, Krishna Twayana, Sofie E Jørgensen, Clàudia Rio-Bergé, Cecilie Poulsen, Anne L Thielke, Emil A Thomsen, Joanna Kalucka, David Olagnier, Yonglun Luo, Fulvio Reggiori, Trine H Mogensen, Antonio Alcamí, Anne Louise Hansen, Christian K Holm.

The transcription factor erythroid 2 (NFE2)-related factor 2 (NRF2) is a key regulator of cellular homeostasis. Recent discoveries have identified agonists of NRF2 as inducers of broad cellular resistance to viral infection including SARS-CoV-2. Nevertheless, it is still unclear to what extent NRF2 itself is an inducer of anti-viral immunity and its downstream antiviral effectors have not been mapped. Here, we first demonstrate through specific genetic activation and silencing that NRF2 restricts SARS-CoV-2 replication. We then used a focused CRISPR-activation screen to map antiviral NRF2-inducible effector genes that restrict replication of SARS-CoV-2, Influenza A virus (IAV), Herpes Simplex virus 1 (HSV1) and Vaccinia virus (VACV). This approach allowed us to identify a range of antiviral effectors each of which restrict members of one or more virus families. Importantly, we identified the NRF2-inducible selective autophagy receptor p62/SQSTM1 as a broadly effective restriction factor across all the tested viruses. Importantly, p62 inhibited SARS-CoV-2 replication in cells treated with the lysosomal inhibitor bafilomycin A1, as well as in cells deficient in the autophagy protein ATG5. Similarly, p62 inhibited replication of HSV1 and IAV independently of ATG5 and ATG16L1 respectively. Thus, NRF2 restricts viral replication through a hitherto underappreciated network of antiviral restriction factors effective across multiple virus families. Importantly, we identify p62 as a broadly acting antiviral effector that restricts viral replication independently of canonical autophagy.

DOI: https://doi.org/10.1016/j.redox.2026.104135
Autophagy. 2026 Mar 31. 1-3

Purifying selection during maternal inheritance of mammalian mtDNA depends on autophagy and bottleneck size.

Polyxeni Papadea, Nils-Göran Larsson.

  Mammalian mitochondrial DNA (mtDNA) is transmitted asexually without recombination and accumulates mutations at a high rate, which eventually should cause a mutational meltdown. Two processes operating in the maternal germline, the genetic bottleneck and purifying selection, are counteracting this decline but the exact molecular mechanisms and their possible link remain incompletely understood. To address this, we investigated the role of autophagy and mtDNA copy number in shaping purifying selection during maternal mtDNA transmission. Using a carefully designed breeding strategy in mice expressing a proofreading-deficient mitochondrial DNA polymerase, we generated animals carrying random mtDNA mutations and simultaneously introduced moderately decreased or increased mtDNA copy number, or impaired autophagy. Mutation patterns in control animals closely resembled those observed in humans, showing strong purifying selection against non-synonymous mutations, particularly in oxidative phosphorylation (OXPHOS) genes. Our recent work provides new insight by identifying autophagy as a key mediator of germline purifying selection of mtDNA. Moreover, we demonstrate that mtDNA copy number directly influences the efficiency of purifying selection, revealing that these two processes are functionally interconnected.

Keywords:  Bottleneck; maternal transmission; mitochondria; mitophagy; mtDNA mutations

DOI:  https://doi.org/10.1080/15548627.2026.2650772
ACS Chem Biol. 2026 Apr 03.

Discovery of Autophagy Modulators that Increase I1061T NPC1 Expression and Promote Cholesterol Efflux in Niemann-Pick Type C Patient-Derived Fibroblasts.

Maryna Salkovski, Andrea Arrieche Suarez, Qiwen Gao, Ryan S Hippman, Zoe A Petros, Melissa A Korkmaz-Vaisys, Erica M Gerlach, Yaneris M Alvarado-Cartagena, Thu T A Nguyen, Ivan Pavlinov, Olga Ilnytska, Judith Storch, Stephanie M Cologna, Leslie N Aldrich.

Autophagy, an evolutionarily conserved catabolic process, has been implicated as a potential therapeutic target in Niemann-Pick Type C (NPC) disease, a fatal lysosomal storage disorder. Our goal was to identify autophagy modulators that positively impact NPC-relevant phenotypes to further evaluate the role of autophagy in this disease. Using a phenotypic high-throughput screen for autophagy modulation and a subsequent secondary assay in homozygous I1061T NPC1 patient-derived fibroblasts, two compounds, 1 and 2, were identified that induced autophagy and reduced unesterified cholesterol accumulation to a level comparable to the reduction achieved by 2-hydroxypropyl-β-cyclodextrin. Global protein expression changes were evaluated in I1061T NPC1 fibroblasts following treatment with compounds 1 and 2 to identify affected pathways, and we observed a significant reduction of lysosomal hydrolase levels induced by compound 2. Additional mechanistic studies revealed that the expression of NPC1 protein is required for compound-induced amelioration of cholesterol accumulation and that compound 2 increases expression levels of I1061T NPC1 without broadly inhibiting proteasomal activity or exacerbating ER stress. These results have led to the hypothesis that compound 2 may serve as a proteostasis modulator or small-molecule chaperone that upregulates autophagy to a level that is predominantly cytoprotective and increases the proportion of properly folded mutant NPC1, thus increasing NPC1 expression levels and alleviating cholesterol accumulation and associated phenotypes. This work, along with future mechanistic studies, contributes to the development of novel strategies to modulate autophagy and proteostasis with potentially broad therapeutic applications.

DOI: https://doi.org/10.1021/acschembio.6c00039
Mol Pharmacol. 2026 Mar 04. pii: S0026-895X(26)00016-7. [Epub ahead of print]108(4): 100116

Identification of potential autophagy inducers through high-throughput and high-content imaging analysis.

Masato Ooka, Leah Mitchell, Jinghua Zhao, Zhengxi Wei, Li Zhang, Danielle Bougie, Hsiu-Ling Lin, Yuhong Fang, Dingyin Tao, Kelli Wilson, Wen-Xing Ding, Ruili Huang, Menghang Xia.

  Autophagy is a cellular degradation process that plays a critical role in maintaining homeostasis and preventing stress-induced damage, making it a promising therapeutic target for cancer and neurodegenerative diseases. In this study, we utilized mouse embryonic fibroblasts expressing GFP-labeled microtubule-associated protein 1 light chain 3, a widely used biomarker of autophagy activation, to screen 3733 clinically approved or investigational drugs using a high-throughput and high-content screening platform. From the primary screening, 117 compounds were identified as potential autophagy inducers. Subsequent confirmation studies narrowed this group to 5 previously uncharacterized autophagy-inducing candidates for further investigation. Follow-up studies assessed the mechanisms underlying autophagy modulation by these compounds, with a focus on key pathways such as mechanistic target of rapamycin inhibition, endoplasmic reticulum stress activation, and p53 activation. To further explore their therapeutic potential in cancer, we conducted an angiogenesis inhibition assay. This study successfully identified several autophagy inducers that may be repurposed for the treatment of cancer, highlighting their potential for future therapeutic development. SIGNIFICANT STATEMENT: This study identifies novel autophagy inducers from high-throughput screening of approved and investigational drugs. The findings highlight key pathways such as mechanistic target of rapamycin inhibition and endoplasmic reticulum stress activation, and demonstrate the ability of these compounds to inhibit angiogenesis, suggesting their potential for repurposing in cancer therapy.

Keywords:  Autophagy; Drug repurposing; High-content screening; LC3

DOI:  https://doi.org/10.1016/j.molpha.2026.100116
NPJ Parkinsons Dis. 2026 Mar 31.

Autophagy dysfunction in iPSCs-derived neurons and midbrain organoids carrying a SNCA triplication.

Catarina Serra-Almeida, Javier Jarazo, Gemma Gomez-Giro, Isabel Rosety, Alise Zagare, Daniele Ferrante, Cláudia Saraiva, Daniela Frangenberg, Jennifer Modamio-Chamarro, Elisa Zuccoli, Ana Clara Cristóvão, Liliana Bernardino, Jens Christian Schwamborn.

Parkinson's disease (PD), characterized by α-Synuclein aggregation and dopaminergic neuronal loss, has no current cure. Autophagy is critical for α-Synuclein clearance, yet its real-time dynamics remain challenging to assess in human-relevant systems. Here, we used live-cell imaging to assess autophagy within human neuronal cultures and midbrain organoids (hMOs) derived from induced pluripotent stem cells (iPSCs) of PD patients carrying a triplication of the α-Synuclein gene (3xSNCA). Using the LC3-Rosella dual-fluorescent reporter, we quantified autolysosomes dynamics in real time. In 3xSNCA neuronal cultures, we detected early autophagy defects. In 3xSNCA hMOs, reduced autolysosome area, increased total and phosphorylated α-Synuclein (pS129), and decreased electrophysiological activity were observed at 50 days of differentiation (DoD). By 70 DoD, autophagy impairment became more pronounced, overlapping with dopaminergic neuron dysfunction. These findings support the use of human iPSCs-derived models to study autophagy dysfunction in PD and demonstrate a temporal correlation between impaired autophagy, α-Synuclein pathology and neuronal degeneration.

DOI: https://doi.org/10.1038/s41531-026-01330-x
Nat Commun. 2026 Apr 01.

TFEB degradation is regulated by an IKK/β-TrCP2 phosphorylation-ubiquitination cascade.

Yan Xiong, Jaiprakash Sharma, Meggie N Young, Wen Xiong, Ali Jazayeri, Karl F Poncha, Ma Xenia G Ilagan, Qing Wang, Bei Gao, Hui Zheng, Nicolas L Young, Marco Sardiello.

Transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis and cellular clearance pathways. TFEB activity is tightly controlled by multiple post-translational mechanisms, but the exact molecular mechanism controlling its stability has remained elusive. Here, we identify the IκB kinase (IKK) complex as a key regulator of TFEB protein stability through a phosphorylation-ubiquitination cascade. A high-content kinase inhibitor screen reveals that IKK inhibition increases TFEB protein levels, and genetic ablation of IKK components increases TFEB stability, upregulates lysosomal genes, and enhances lysosomal biogenesis and degradative capacity. Mechanistically, we show that IKK phosphorylates TFEB on a cluster of serine residues (423SPFPSLS429), generating a phosphodegron recognized by the E3 ligase β-TrCP2, which in turn targets TFEB for proteasomal degradation via ubiquitination of adjacent lysine residues (K430 and K431). Mutation of either the phosphosites or the ubiquitination sites stabilizes TFEB without impairing its ability to translocate to the nucleus, activate target gene expression, or promote tau clearance in a cell model of tauopathy. These findings establish IKK-β-TrCP2 as a core regulatory axis controlling TFEB protein turnover and levels and reveal a mechanistically distinct layer of TFEB regulation that may be leveraged to enhance lysosomal function in disease contexts.

DOI: https://doi.org/10.1038/s41467-026-71001-1
Nat Commun. 2026 Mar 30.

HR3/RORα-mediated cholesterol sensing regulates TOR signaling.

Mette Lassen, Keith Pardee, Ivan Bradic, Lisa H Pedersen, Olga Kubrak, Nadja Ahrentløv, Sebastian Clancy, Takashi Koyama, Aleksandar Necakov, Suya Liu, Arnis Kuksis, Gilles Lajoie, Aled Edwards, Aurelio A Teleman, Martin R Larsen, Henry M Krause, Michael J Texada, Kim Rewitz.

Cells and organisms adjust their growth based on the availability of cholesterol, which is essential for cellular functions. However, the mechanisms by which cells sense cholesterol levels and translate these into growth signals are not fully understood. We report that cholesterol rapidly activates the master growth-regulatory TOR pathway in Drosophila tissues. We identify the nuclear receptor HR3, an ortholog of mammalian RORα, as an essential factor in cholesterol-induced TOR activation. We demonstrate that HR3 binds cholesterol and promotes TOR-pathway activation through a non-genomic mechanism acting upstream of the Rag GTPases while also restraining longer-term responses through genomic regulation. We also find that RORα is necessary for cholesterol-mediated TOR activation in human cells, suggesting that HR3/RORα-mediated signaling represents a conserved mechanism for cholesterol sensing that couples cholesterol availability to TOR-pathway activity. These findings advance our understanding of how cholesterol influences cell growth, with implications for cholesterol-related diseases and cancer.

DOI: https://doi.org/10.1038/s41467-026-71059-x
Cell Signal. 2026 Apr 01. pii: S0898-6568(26)00169-5. [Epub ahead of print] 112517

Mitochondrial IRF3 drives pulmonary fibrosis by impairing mitophagy and triggering ferroptosis.

Zhang Jiashu, Liu Jingbao, Fang Hua, Sun Meiqi, Liu Jing, Wang Mengyao, Zhang Wei.

   BACKGROUND: Pulmonary fibrosis (PF) is a progressive, lethal lung disease with limited treatments. Although inflammation is involved, how it triggers specific oxidative cell death in epithelial cells remains unclear. The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway is active in PF, but research has focused on its upstream inflammatory role. The function of its key effector, interferon regulatory factor 3 (IRF3), especially through non-canonical mechanisms, is largely unknown. We hypothesized that activated IRF3 translocates to mitochondria to disrupt quality control and promote ferroptosis, linking inflammation to fibrosis.
METHODS: We employed a bleomycin-induced mouse PF model and TGF-β-stimulated A549 cells. Techniques included molecular analyses (western blot, RT-qPCR, Co-IP), imaging (TEM, immunofluorescence), mitophagy flux assays, and measurement of ferroptosis markers (Fe2+, MDA). Interventions involved H151, si-IRF3, Ferrostatin-1, and Mdivi-1.
RESULTS: In PF, phosphorylated IRF3 translocated to mitochondria, interacting with PINK1 to impair mitophagy, shown by decreased PINK1, accumulated p62, and reduced LC3-II/LC3-I ratio. This triggered ferroptosis, evidenced by upregulated ACSL4, downregulated GPX4, elevated Fe2+/MDA, and mitochondrial damage. In TGF-β-stimulated A549 cells, IRF3 knockdown or STING inhibition restored mitophagy and suppressed ferroptosis. Mdivi-1 reversed si-IRF3's protection. In vivo, H151 treatment suppressed the IRF3-mitophagy-ferroptosis axis and alleviated PF.
CONCLUSIONS: Mitochondrial IRF3 integrates cGAS-STING signaling with mitophagic dysfunction and ferroptosis to drive PF, revealing a novel therapeutic target.

Keywords:  Alveolar epithelial cells; Ferroptosis; IRF3; Mitophagy; Pulmonary fibrosis

DOI:  https://doi.org/10.1016/j.cellsig.2026.112517
Trends Biochem Sci. 2026 Mar 28. pii: S0968-0004(26)00007-1. [Epub ahead of print]

Cytosolic AcCoA: a metabolic signal bridging nutrient sensing and mitophagy.

Jiayi Chen, Xin Pan.

  How cells sense energy status to precisely regulate organelle fate is a central question in life sciences. Recent work by Zhang et al. reframes cytosolic acetyl-coenzyme A (AcCoA) from a metabolic substrate into a signaling metabolite that directly regulates mitophagy, thereby establishing a molecular link between nutrient sensing and mitochondrial homeostasis.

Keywords:  NLRX1; cytosolic AcCoA; mitophagy

DOI:  https://doi.org/10.1016/j.tibs.2026.01.007
Mol Biol Cell. 2026 Apr 02. mbcE25080412

RANKL-inducible Arl8b effector RUFY4 drives HOPS-mediated lysosomal maturation and trafficking in osteoclasts.

Kshitiz Walia, Gaurav Kumar, Subhash B Arya, Priya Chouhan, Arshdeep Kaur, Medha Gupta, Amit Tuli.

Osteoclast-mediated bone resorption depends on the secretion of lysosomal hydrolases via the fusion of secretory lysosomes with the ruffled border, yet the molecular mechanisms governing lysosomal trafficking and fusion remain incompletely understood. Here, we demonstrate that the small GTPase Arl8b regulates the processing of osteoclast-specific lysosomal hydrolase, cathepsin K, and the positioning of secretory lysosomes toward the actin ring. Accordingly, depletion of Arl8b led to defects in lysosome-mediated bone resorption in osteoclasts. We identify RUFY4 as a RANKL-inducible Arl8b effector that promotes lysosome clustering and maturation by linking Arl8b to Rab7 through the adaptor PLEKHM1 and recruiting the multi-subunit tethering factor HOPS complex to drive late endosome-lysosome fusion. Depletion of RUFY4 or HOPS subunits impairs cathepsin K processing and disrupts lysosome positioning, leading to reduced bone resorption activity. These findings suggest that Arl8b and its interaction partners play essential roles in biogenesis and positioning of secretory lysosomes, essential for osteoclast function in bone remodeling. [Media: see text] [Media: see text] [Media: see text].

DOI: https://doi.org/10.1091/mbc.E25-08-0412