Autophagy

Wen, Xin; Klionsky, Daniel J.

doi: 10.1080/15548627.2025.2555048pmid: 41450005

Although KRAS-driven tumors exhibit elevated macroautophagy/autophagy, the extent to which this process diverges from canonical regulatory pathways has not been well characterized. In a recent study published in Cell Research, Wang et al. unveil a novel form of non-canonical autophagy driven by oncogenic RAS mutations, which they termed RAS-induced non-canonical autophagy via ATG8ylation (RINCAA). This pathway operates through a unique MAPK/p38-ULK1-PI4KB axis, diverging significantly from canonical starvation-induced autophagy. The research not only elucidates a new regulatory mechanism but also identifies a potential, highly specific therapeutic target for RAS-mutant cancers.Abbreviations: PI4KB, phosphatidylinositol 4-kinase beta; PtdIns4P, phosphatidylinositol-4-phosphate; RINCAA, RAS-induced non-canonical autophagy via Atg8ylation; ULK1, unc-51 like autophagy activating kinase 1; WIPI2, WD repeat domain phosphoinositide-interacting protein 2

Li, Yankun; Ma, Tongtong; Liang, Xinhua; Jin, Tingting; Zhao, Xingqi; Huang, Junmin; Hao, Junfeng; Liu, Huafeng; Wang, Peng

doi: 10.1080/15548627.2025.2551683pmid: 40851276

Macroautophagy/autophagy is a conserved cellular process that degrades misfolded proteins and damaged organelles to regulate cell survival and division. Normal levels of autophagy are observed in healthy kidney cells. In contrast, excessive or insufficient autophagy is observed during kidney disease progression. However, canonical treatments that regulate autophagy using chemical reagents may induce unexpected side effects in other organs. This necessitates the development of therapeutic approaches with fewer adverse effects. Non-coding RNAs, which are highly tissue-specific, regulate autophagy and accurately modulate the expression of related genes. This review presents evidence of the effects of non-coding RNAs on the progression of kidney diseases and their responses to treatment in vitro, in vivo, and in clinical trials. Our analyses and interpretations of key findings elucidate the pathogenesis of kidney diseases and explore potential new therapeutic approaches. Abbreviations: 3' UTR: 3' untranslated region; 3-MA: 3-methyladenine; ADPKD: autosomal dominant polycystic kidney disease; AKI: acute kidney injury; ccRCC: clear cell RCC; ATG: autophagy related gene; ceRNA: competing endogenous RNA; circRNA: circular RNA; CKD: chronic kidney disease; DKD: diabetic kidney disease; HG: high glucose; IRI: ischemia-reperfusion injury; lncRNA: long non-coding RNA; LPS: lipopolysaccharide; miRNA: microRNA; MTOR: mechanistic target of rapamycin kinase; ncRNA: non-coding RNA; PI3K: phosphoinositide 3-kinase; RCC: renal cell carcinoma; ROS: reactive oxygen species; RTEC: renal tubular epithelial cells; ULK1: unc-51 like autophagy activating kinase 1; UUO: unilateral ureteral obstruction; VHL: von Hippel-Lindau tumor suppressor.

Du, Fang; Yu, Qing; Hu, Gang; Lin, Chyuan-Sheng; ShiDu Yan, Shirley

doi: 10.1080/15548627.2025.2463322pmid: 40320714

Mitochondrial dysfunction plays a preponderant role in the development of Alzheimer disease (AD). We have demonstrated that activation of PINK1 (PTEN induced kinase 1)-dependent mitophagy ameliorates amyloid pathology, attenuates mitochondrial and synaptic dysfunction, and improves cognitive function. However, the underlying mechanisms remain largely unknown. Using a newly generated PINK1-AD transgenic mouse model and AD neuronal cell lines, we provide substantial evidence supporting the contribution of PINK1-mediated mitochondrial ROS (reactive oxygen species) and NFKB/NF-κB (nuclear factor kappa B) signaling to altering APP (amyloid beta precursor protein) processing and Aβ metabolism. Enhancing neuronal PINK1 is sufficient to suppress Aβ-induced activation of NFKB signal transduction in PINK1-overexpressed Aβ-AD mice and Aβ-producing neurons. Blocking PINK1-mediated NFKB activation inhibits activities of BACE1 (beta-secretase 1) and γ-secretase, which are key enzymes for cleavage of APP processing to produce Aβ. Conversely, loss or knockdown of PINK1 produces excessive ROS, along with increased phosphorylated NFKB1/p50 and RELA/p65 subunits, APP-related BACE1 and γ-secretase, and Aβ accumulation. Importantly, these detrimental effects were robustly blocked by the addition of scavenging PINK1 Aβ-induced mitochondrial ROS, leading to the suppression of NFKB activation, restoration of normal APP processing, and limitation of Aβ accumulation. Thus, our findings highlight a novel mechanism underlying PINK1-mediated modulation of Aβ metabolism via a ROS-NFKB-APP processing nexus. Activation of PINK1 signaling could be a potential therapeutic avenue for the early stages of AD by combining improving mitochondrial quality control with limiting amyloid pathology in AD.

Wang, Lin; Hou, Peili; Ma, Wenqing; Jin, Rong; Wei, Xinxin; Li, Xingyu; He, Hongbin; Wang, Hongmei

doi: 10.1080/15548627.2025.2511077pmid: 40413753

As a core aptamer for anti-DNA viral immunity, STING1 (stimulator of interferon response cGAMP interactor 1) is tightly regulated to ensure the proper functioning of the natural antiviral immune response. However, many mechanisms underlying the regulation of STING1 remain largely unknown. In this study, we identify EXOC4/SEC8 (exocyst complex component 4) as a novel positive regulator of DNA virus-triggered type I interferon signaling responses through stabilizing STING1, thereby inhibiting DNA viral replication. Mechanistically, EXOC4 suppresses K27-linked ubiquitination of STING1 at K338, K347, and K370 catalyzed by the E3 ligase FBXL19 (F-box and leucine rich repeat protein 19), thereby preventing ubiquitinated-STING1 from recognition by SQSTM1 (sequestosome 1) for autophagic degradation. Importantly, mice conditionally knocked out for Exoc4/Sec8 are more susceptible to herpes simplex virus type 1 (HSV-1) infection and exhibit more severe lung pathology compared to control mice. This further confirms the important role of EXOC4/SEC8 in antiviral natural immunity. Taken together, our study reveals the importance of EXOC4/SEC8 in promoting STING1-centered antiviral natural immunity and highlights its potential as an anti-DNA viral therapeutic target.Abbreviations: ACTB/β-actin: actin beta; BMDMs: bone marrow-derived macrophages; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; cGAMP: cyclic GMP-AMP; CQ: chloroquine; ER: endoplasmic reticulum; EXOC4/SEC8: exocyst complex component 4; CGAS: cyclic GMP-AMP synthase; HAdV-4: human adenovirus type 4; HSV-1: herpes simplex virus type 1; IFIT1: interferon induced protein with tetratricopeptide repeats 1; IFIT2: interferon induced protein with tetratricopeptide repeats 2; IFNB1: interferon beta 1; IRF3: interferon regulatory factor 3; IFN-I: type I interferon; ISGs: IFN-stimulated genes; ISRE: IFN-stimulated response element; MG132/Z-LLL-CHO: carbobenzoxy-Leu-Leu-leucinal; MOI: multiplicity of infection; MST: microscale thermophoresis; PMs: peritoneal macrophages; Poly(dA:dT): polydeoxyadenylic-thymidylic acid; qPCR: quantitative real-time PCR; shRNAs: short hairpin RNAs; siRNA: small interfering RNA; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TBK1: TANK binding kinase 1; TCID50: 50% tissue culture infectious dose; WT: wild-type.

Zhou, Qiongqiong; Shi, Deshi; Tang, Yan-Dong; Zhang, Longfeng; Liu, Hongyang; Ye, Guangqiang; Zhang, Zhaoxia; Hu, Boli; Huang, Li; Weng, Changjiang

doi: 10.1080/15548627.2025.2511584pmid: 40462306

Macroautophagy/autophagy is a biological process that sequesters and degrades cytoplasmic material, damaged organelles, and infectious pathogens in eukaryotic cells via lysosomes. Autophagy is involved in different phases of the viral life cycle and regulates viral replication. Here, we demonstrated that pseudorabies virus (PRV) infection induced incomplete autophagy, and blocking the autophagosome-lysosome fusion facilitated PRV replication. Mechanistically, PRV late envelope glycoprotein M (gM) triggered SQSTM1/p62-dependent selective autophagy. Meanwhile, gM protein was found to inhibit the fusion between autophagosomes and lysosomes by activating CASP3 (caspase 3) to degrade SNAP29, resulting in increased viral replication. Interestingly, we confirmed that the gM homologs from several herpesviruses (herpes simplex virus-1, human cytomegalovirus, equine herpesvirus-1, and varicella-zoster virus) shared the same function of activating CASP3 and inhibiting autophagic flux. Deletion of the CASP3 gene led to an intact autophagic pathway and the increased formation of autolysosomes. Collectively, our results illustrated that blockage of autophagosome-lysosome fusion mediated by PRV gM and its homologs in other herpesviruses protected viral proteins from host autophagic signaling, thus facilitating herpesvirus replication. Abbreviations: 3-MA: 3-methyladenine; Baf A1: bafilomycin A1; CASP3: caspase 3; cl-CASP3: cleaved-CASP3; co-IP: co-immunoprecipitation; CQ: chloroquine; DAPI: 4’,6-diamidino-2-phenylindole; DMSO: dimethyl sulfoxide; EHV-1: equine herpesvirus 1; gM: glycoprotein M; HCMV: human cytomegalovirus; HSV-1: herpes simplex virus 1; LAMP1: lysosomal associated membrane protein 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; OD: optical density; PCR: polymerase chain reaction; PFU: plaque forming units; PRV: pseudorabies virus; Rap: rapamycin; SNAP29; synaptosome associated protein 29; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TCID: 50% tissue culture infectious doses; UBA: ubiquitin-binding domain; VAMP8: vesicle associated membrane protein 8; µm, micrometer; VZV: varicella-zoster virus; WT: wild type.

Jin, Suwei; Yan, Mingzhu; Liu, Yongguang; Zhang, Shanshan; Song, Hongbin; Cao, Chenxi; Li, Yujia; Sun, Guibo; Ye, Linhu; Chen, Jianzhi; Han, Wen; Li, Lingyu; Chang, Qi

doi: 10.1080/15548627.2025.2512884

Jang, Yunyeong; Ko, Minjeong; Lee, Ju Yeon; Kim, Jin Young; Lee, Eun-Woo; Kwon, Ho Jeong

doi: 10.1080/15548627.2025.2519054pmid: 40548398

Metabolic dysfunction-associated fatty liver disease (MAFLD) is a serious metabolic disorder characterized by fat accumulation in the liver, which can trigger liver inflammation and fibrosis, potentially leading to cirrhosis or liver cancer. Despite many studies, effective treatments for MAFLD remain elusive due to its complex etiology. In this study, we have focused on the discovery of therapeutic agents and molecular targets for MAFLD treatment. We demonstrated that the natural compound acacetin (ACA) alleviates MAFLD by regulating macroautophagy/autophagy in a CDAHFD mouse model of rapidly induced steatohepatitis. In addition, ACA inhibits lipid accumulation in 3T3-L1 adipocytes through autophagy induction. To identify the target responsible for the autophagy activity induced by ACA, we performed drug affinity responsive target stability (DARTS) combined with LC-MS/MS proteomic analysis. This led to the identification of LAMTOR1 (late endosomal/lysosomal adaptor, MAPK and MTOR activator 1), a lysosomal membrane adaptor protein. We found that binding of ACA to LAMTOR1 induces its release from the LAMTOR complex, leading to inhibition of MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1), thereby increasing autophagy. This process helps ameliorate metabolic disorders by modulating the MTORC1-AMPK axis. Genetic knockdown of LAMTOR1 phenocopies the effects of ACA treatment, further supporting the role of LAMTOR1 as a target of ACA. These findings suggest LAMTOR1 plays a crucial role in ACA’s therapeutic effects on MAFLD. In summary, our study identifies LAMTOR1 as a key protein target of ACA, revealing a potential therapeutic avenue for MAFLD by modulating autophagy via the LAMTOR1-MTORC1-AMPK signaling pathway. Abbreviations: ACA: acacetin; ADGRE1/EMR1/F4/80: adhesion G protein-coupled receptor E1; AMPK: AMP-activated protein kinase; CDAHFD: choline-deficient amino acid-defined, high-fat diet; CETSA: cellular thermal shift assay; CQ: chloroquine; DARTS: drug affinity responsive target stability; DQ-BSA: dye quenched-bovine serum albumin; GOT1/AST: glutamic-oxaloacetic transaminase 1; GPT/ALT: glutamic-pyruvic transaminase; LAMP2: lysosomal associated membrane protein 2; LAMTOR1: late endosomal/lysosomal adaptor, MAPK and MTOR activator 1; LC-MS/MS: liquid chromatography-tandem mass spectrometry; MAFLD: metabolic dysfunction-associated fatty liver disease; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MASH: metabolic dysfunction-associated steatohepatitis; mRFP-GFP-MAP1LC3B: tandem fluorescent-tagged MAP1LC3B; MTORC1: mechanistic target of rapamycin complex 1; PA: palmitic acid; PRKAA: protein kinase AMP-activated catalytic subunit alpha; PLA: proximity ligation assay; Rapa: rapamycin; RPS6KB1/p70S6K: ribosomal protein S6 kinase B1; RRAG: Ras-related GTP-binding; SQSTM1: sequestosome 1; TFEB: transcription factor EB; VMP1: vacuole membrane protein 1.

Xie, Fei; Fan, Jia-Xin; Wang, Hao; Song, Qi-Long; Xu, Yan-Song; Lan, Qing-Su; Jiang, Xiu-Mei; Cheng, Jie; Hou, Ya-Min; Yang, Hong-Rui; Zhang, Xu; Zhang, Qiu-Ting; Wang, Peng; Liu, Long-Hao; Qian, Ju-Ying; Qin, Wei-Dong;

Wang, Huina; Yi, Xiuli; Qu, Di; Wang, Xiangxu; Wang, Hao; Zhang, Hengxiang; Yang, Yuqi; Gao, Tianwen; Guo, Weinan; Li, Chunying

doi: 10.1080/15548627.2025.2519066pmid: 40509568

Enhanced cholesterol biosynthesis is a hallmark metabolic characteristic of cancer, exerting an oncogenic role by supplying intermediate metabolites that regulate intracellular signaling pathways. The pharmacological blockade of cholesterol biosynthesis has been well documented as a promising therapeutic approach in cancer. Particularly, cholesterol biosynthesis is linked to macroautophagy/autophagy and lysosome metabolism, with the engagement of the critical autophagy regulators like MTOR to be fully activated by lysosomal cholesterol trafficking and accumulation. Previous studies have primarily focused on the role of cholesterol biosynthesis in tumor cell-intrinsic biological processes, whereas its involvement in tumor immune evasion and the underlying mechanisms related to autophagy or lysosome metabolism remain elusive. Herein, through bioinformatics analysis we discovered a negative correlation between cholesterol biosynthesis and the score of tumor-infiltrating lymphocytes in cancers. Inhibition of tumor cell cholesterol biosynthesis leads to increased infiltration and activation of CD8+ T cells in the tumor microenvironment, which is largely responsible for the impairment of tumor growth. Mechanistically, cholesterol biosynthesis inhibition impairs the activation of MTOR at lysosomes, thereby promoting the nuclear translocation of TFEB and downstream lysosome biosynthesis, facilitating the degradation of CD274/PD-L1 within lysosomes in tumor cells. Ultimately, the HMGCR-MTOR-LAMP1 axis that connects cholesterol, lysosome and tumor immunology, predicts poor response to immunotherapy and worse prognosis of patients with melanoma. These findings unveil an immunomodulatory role of tumorous cholesterol biosynthesis via the regulation of CD274 lysosomal degradation. Targeting cholesterol biosynthesis holds promise as a potential therapeutic strategy in cancer, particularly when combined with immune checkpoint blockade. Abbreviations: ATG5, autophagy related 5; CD274/PD-L1, CD274 molecule; CQ, chloroquine; CTLA4, cytotoxic T-lymphocyte associated protein 4; CHX, cycloheximide; EIF4EBP1, eukaryotic translation initiation factor 4E binding protein 1; GSVA, gene set variation analysis; GZMB, granzyme B; HMGCR, 3-hydroxy-3-methylglutaryl-CoA reductase; IFNG/IFN-γ, Interferon gamma; IHC, Immunohistochemistry; LAMP1, lysosomal associated membrane protein 1; MITF, melanocyte inducing transcription factor; MTOR, mechanistic target of rapamycin kinase; NK, natural killer; NSCLC, non-small cell lung cancer; PBMC, peripheral blood mononuclear cell; PDCD1/PD-1, programmed cell death 1; qRT-PCR, quantitative real-time polymerase chain reaction; SKCM, skin cutaneous melanoma; TCGA, The Cancer Genome Atlas; TFE3, transcription factor binding to IGHM enhancer 3; TFEB, transcription factor EB; TIL, tumor infiltrated lymphocyte; TME, tumor microenvironment; Treg, regulatory T.

Wang, Wei; Wang, Xufeng; Zhou, Xiaoqi; Jiang, Lu; Shang, Weina; Wang, Liquan; Tong, Chao

doi: 10.1080/15548627.2025.2522124pmid: 40568837

Lipophagy engulfs lipid droplets and delivers them to lysosomes for degradation. We found that lipophagy levels were low in most fly tissues, except for the prothoracic gland (PG) during larval development. Therefore, we performed a small-scale screening in the PG to identify regulators of lipophagy. We discovered that the loss of nmd, a gene encoding a mitochondrial AAA-ATPase, led to developmental failure and reduced lipophagy in the PG. Further studies indicated that nmd was not only required for lipophagy but also essential for general macroautophagy/autophagy in both PG and fat body tissues. Autophagy was induced but blocked at the autophagosome-lysosome fusion stage upon nmd reduction. Additionally, nmd interacted with mitochondrial protein import machinery, such as Tom20, Tom40, and the import cargo, such as Idh. Loss of nmd decreased protein import into mitochondria. Similar to the loss of nmd, reduction of Tom20 or Tom40 also resulted in reduced lipophagy in the PG. In adult flies, reducing nmd expression in the eyes caused lipid droplet accumulation and severe degeneration during aging. Overexpression of bmm, a triglyceride lipase, reduced lipid droplets in the eye but did not rescue the eye degeneration caused by the reduction of nmd. Abbreviation: ATAD1: ATPase family AAA domain containing 1; Atg8a: Autophagy-related 8a; Atg9: Autophagy-related 9; Atg14: Autophagy-related 14; Atg18a: Autophagy-related 18a; ATP: adenosine triphosphate; bmm: brummer; CtsL1: Cathepsin L1; Idh: isocitrate dehydrogenase (NADP+); Cis1: CItrinin Sensitive knockout; GFP: green fluorescent protein; LDs: lipid droplets; LIRs:LC3-interacting regions; Lsd-1: Lipid storage droplet-1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; Marf: Mitochondrial assembly regulatory factor; Miga: Mitoguardin; Msp1: Mitochondrial Sorting of Proteins 1; nmd: no mitochondrial derivative; PG: prothoracic gland; phtm: phantom; PNPLA2/ATGL: patatin like domain 2, triacylglycerol lipase; RFP: red fluorescent protein; RNAi: RNA interference; Syx17: Syntaxin 17; TA: tail-anchored; TEM: transmission electron microscopy; TOMM: translocase of outermitochondrial membrane; Tom20: Translocase of outer membrane 20; Tom40: Translocase of outer membrane 40.