% Bibliography for hypothesis h-51e7234f
% Title: APOE-Dependent Autophagy Restoration
% Generated: 2026-04-28T15:13:03Z

@article{pmid41445190,
  title = {Metabolic dysregulation reshapes the immune landscape: The gut microbiota-mTOR axis in respiratory viral infection immunity.},
  author = {Li J, Li J, Chen K},
  journal = {Mol Ther},
  year = {2026},
  pmid = {41445190},
  doi = {doi: 10.1016/j.ymthe.2025.12.033},
  url = {https://pubmed.ncbi.nlm.nih.gov/41445190/},
}

@article{pmid41479169,
  title = {Senecavirus a VP2 protein orchestrates PRDX1 degradation through dual autophagy pathways: macroautophagy and chaperone-mediated autophagy.},
  author = {Li Z, Yang X, Mao J, Zeng P, Qi Y et al.},
  journal = {Autophagy},
  year = {2026},
  pmid = {41479169},
  doi = {doi: 10.1080/15548627.2025.2610449},
  url = {https://pubmed.ncbi.nlm.nih.gov/41479169/},
}

@article{pmid41529091,
  title = {Inhibition of mTOR Enhances the Efficacy of Proteasome-Dependent Targeted Protein Degradation Approaches.},
  author = {Liu Y, Sun Y, Song TY, Ni SY, Pu YS et al.},
  journal = {Cancer Res},
  year = {2026},
  pmid = {41529091},
  doi = {doi: 10.1158/0008-5472.CAN-25-3941},
  url = {https://pubmed.ncbi.nlm.nih.gov/41529091/},
}

@article{pmid41651180,
  title = {Microglial metabolic reprogramming in Alzheimer's disease: Pathways, mechanisms, and therapeutic implications.},
  author = {Yang FG, Yang H, Han SW, Wang JT, Gao W et al.},
  journal = {Ageing Res Rev},
  year = {2026},
  pmid = {41651180},
  doi = {doi: 10.1016/j.arr.2026.103050},
  url = {https://pubmed.ncbi.nlm.nih.gov/41651180/},
}

@article{pmid41789635,
  title = {mTOR signaling pathway in primary Sjögren's syndrome: Pathogenesis and potential therapeutic targets (Review).},
  author = {Huo R, Yang Y, Wei C, Yang Y, Meng D et al.},
  journal = {Int J Mol Med},
  year = {2026},
  pmid = {41789635},
  doi = {pii: 104. doi: 10.3892/ijmm.2026.5775},
  url = {https://pubmed.ncbi.nlm.nih.gov/41789635/},
}

@article{pmid41846138,
  title = {Microcystin-LR-induced phosphorylation imbalance and organelle stress: An integrative review of autophagy dysregulation and cross-species toxicity.},
  author = {Teng Z, Shahzad A, Xu Z, Xia J, Zhang J et al.},
  journal = {J Hazard Mater},
  year = {2026},
  pmid = {41846138},
  doi = {doi: 10.1016/j.jhazmat.2026.141768},
  url = {https://pubmed.ncbi.nlm.nih.gov/41846138/},
}

@article{pmid41865874,
  title = {Targeting of the PI3K/AKT/mTOR signaling pathway in the neurovascular interface in both Alzheimer's disease and atherosclerosis: The potential nexus.},
  author = {Alameen AAM, Al-Kuraishy HM, Al-Gareeb AI, Shokr MM, Batiha GE},
  journal = {Microvascular research},
  year = {2026},
  pmid = {41865874},
  doi = {10.1016/j.mvr.2026.104947},
  url = {https://pubmed.ncbi.nlm.nih.gov/41865874/},
}

@article{pmid41876253,
  title = {Replating Induces mTOR-Dependent Rescue of Protein Synthesis in Charcot-Marie-Tooth Diseased Neurons.},
  author = {Koenig J, McGuire A, Homedan Y, Alberhasky J, Summers DW},
  journal = {eNeuro},
  year = {2026},
  pmid = {41876253},
  doi = {10.1523/ENEURO.0337-25.2026},
  url = {https://pubmed.ncbi.nlm.nih.gov/41876253/},
}

@article{pmid41904574,
  title = {Platelet proteomic signatures of amyloid β-positive mild cognitive impairment and Alzheimer's disease.},
  author = {Cho YE, Kim A, Lee HM, Oh JW, Son SJ, Roh HW, Jung YS, Hong CH, Lee SY, Kim KP},
  journal = {Molecular brain},
  year = {2026},
  pmid = {41904574},
  doi = {10.1186/s13041-026-01294-2},
  url = {https://pubmed.ncbi.nlm.nih.gov/41904574/},
}

@article{pmid41918200,
  title = {Neuroinflammation, Autophagy, and Neurodegeneration: Mechanisms and Therapeutic Insights.},
  author = {["Khanal P", "Balmik A"]},
  journal = {CNS & neurological disorders drug targets},
  year = {2026},
  pmid = {41918200},
  doi = {10.2174/0118715273440234260304000039},
}

@article{pmid41920999,
  title = {Copper deficiency impairs oligodendrocyte maturation and social behavior via mitophagy and mTOR suppression in ASD.},
  author = {Usui N, Doi M, Berto S, Matsuoka K, Ishida R et al.},
  journal = {Sci Adv},
  year = {2026},
  pmid = {41920999},
  doi = {doi: 10.1126/sciadv.adz3398},
  url = {https://pubmed.ncbi.nlm.nih.gov/41920999/},
}

@article{pmid41921697,
  title = {iPSC-NPC transplantation alleviates brain injury after intracerebral hemorrhage in mice by downregulating autophagy via AMPK/ mTOR signaling pathway.},
  author = {Zhong Z, Wang S, Xu C, Liu Q, Chen X, Lin D, Bian L},
  journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
  year = {2026},
  pmid = {41921697},
  doi = {10.1016/j.jstrokecerebrovasdis.2026.108628},
  url = {https://pubmed.ncbi.nlm.nih.gov/41921697/},
}

@article{pmid41922823,
  title = {Targeting the GSK-3β/mTOR axis: a novel pharmacological strategy for preeclampsia prevention and treatment.},
  author = {Alshaikh ABA, Al-Kuraishy HM, Abdelaziz AM, Hepishy IM, Albar M, Batiha GE},
  journal = {Naunyn-Schmiedeberg's archives of pharmacology},
  year = {2026},
  pmid = {41922823},
  doi = {10.1007/s00210-026-05202-2},
  url = {https://pubmed.ncbi.nlm.nih.gov/41922823/},
}

@article{pmid41924135,
  title = {Targeting the AKT/mTOR axis: pectolinarigenin induces autophagy and apoptosis in human cervical cancer cells.},
  author = {Fang Y, Bai J, Bo S, Cui X, Song H, Guo L, Luan Z, Sui Q, Zheng Y, Sun L},
  journal = {Frontiers in pharmacology},
  year = {2026},
  pmid = {41924135},
  doi = {10.3389/fphar.2026.1544170},
  url = {https://pubmed.ncbi.nlm.nih.gov/41924135/},
}

@article{pmid41925800,
  title = {S-equol promotes ferroptosis in triple negative breast cancer by coordinating NCOA4-mediated ferritinophagy and PPARγ-mediated lipid metabolism.},
  author = {Ni F, Huang Z, Cui Y, Huang P, Xue Z, Huang G, Zhao Y},
  journal = {Molecular and cellular biochemistry},
  year = {2026},
  pmid = {41925800},
  doi = {10.1007/s11010-026-05524-y},
  url = {https://pubmed.ncbi.nlm.nih.gov/41925800/},
}

@article{pmid41925978,
  title = {Aromatic amino acid metabolism shapes autophagy-mediated adaptation to iron deprivation in glioblastoma cells.},
  author = {Zhao K, Ludwig-Radtke L, Wang Y, Rusch T, Nimsky C, Taudte RV, Bartsch JW},
  journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine},
  year = {2026},
  pmid = {41925978},
  doi = {10.1007/s10534-026-00809-7},
  url = {https://pubmed.ncbi.nlm.nih.gov/41925978/},
}

@article{pmid41933042,
  title = {Crosstalk between inflammation and autophagy in CeD organoids.},
  author = {Bellomo C, Furone F, Auricchio R, D'Aniello G, Pennacchio R et al.},
  journal = {Sci Rep},
  year = {2026},
  pmid = {41933042},
  doi = {doi: 10.1038/s41598-026-42642-5},
  url = {https://pubmed.ncbi.nlm.nih.gov/41933042/},
}

@article{pmid39779911,
  title = {Modulating mTOR-dependent astrocyte substate transitions to alleviate neurodegeneration.},
  author = {Zhang L, Xu Z, Jia Z, Cai S, Wu Q, Liu X, Hu X, Bai T, Chen Y, Li T, Liu Z, Wu B, Zhu J, Zhou H},
  journal = {Nature aging},
  year = {2025},
  pmid = {39779911},
  doi = {10.1038/s43587-024-00792-z},
  url = {https://pubmed.ncbi.nlm.nih.gov/39779911/},
}

@article{pmid35740927,
  title = {The Translational Regulation in mTOR Pathway.},
  author = {Yang M, Lu Y, Piao W, Jin H},
  journal = {Biomolecules},
  year = {2022},
  pmid = {35740927},
  doi = {10.3390/biom12060802},
  url = {https://pubmed.ncbi.nlm.nih.gov/35740927/},
}

@article{pmid35948010,
  title = {Lactate is an epigenetic metabolite that drives survival in model systems of glioblastoma.},
  author = {Torrini C, Nguyen TTT, Shu C, Mela A, Humala N, Mahajan A, Seeley EH, Zhang G, Westhoff MA, Karpel-Massler G, Bruce JN, Canoll P, Siegelin MD},
  journal = {Molecular cell},
  year = {2022},
  pmid = {35948010},
  doi = {10.1016/j.molcel.2022.06.030},
  url = {https://pubmed.ncbi.nlm.nih.gov/35948010/},
}

@article{pmid36104566,
  title = {Brain-restricted mTOR inhibition with binary pharmacology.},
  author = {Zhang Z, Fan Q, Luo X, Lou K, Weiss WA, Shokat KM},
  journal = {Nature},
  year = {2022},
  pmid = {36104566},
  doi = {10.1038/s41586-022-05213-y},
  url = {https://pubmed.ncbi.nlm.nih.gov/36104566/},
}

@article{pmid33432245,
  title = {Cryo-EM structures of Toll-like receptors in complex with UNC93B1.},
  author = {Ishida H, Asami J, Zhang Z, Nishizawa T, Shigematsu H, Ohto U, Shimizu T},
  journal = {Nature structural & molecular biology},
  year = {2021},
  pmid = {33432245},
  doi = {10.1038/s41594-020-00542-w},
  url = {https://pubmed.ncbi.nlm.nih.gov/33432245/},
}

@article{pmid33692541,
  title = {A high-resolution protein architecture of the budding yeast genome.},
  author = {Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, Kellogg GD, Mahony S, Pugh BF},
  journal = {Nature},
  year = {2021},
  pmid = {33692541},
  doi = {10.1038/s41586-021-03314-8},
  url = {https://pubmed.ncbi.nlm.nih.gov/33692541/},
}

@article{pmid34031601,
  title = {Partial recovery of visual function in a blind patient after optogenetic therapy.},
  author = {Sahel JA, Boulanger-Scemama E, Pagot C, Arleo A, Galluppi F, Martel JN, Esposti SD, Delaux A, de Saint Aubert JB, de Montleau C, Gutman E, Audo I, Duebel J, Picaud S, Dalkara D, Blouin L, Taiel M, Roska B},
  journal = {Nature medicine},
  year = {2021},
  pmid = {34031601},
  doi = {10.1038/s41591-021-01351-4},
  url = {https://pubmed.ncbi.nlm.nih.gov/34031601/},
}

@article{pmid34192655,
  title = {Investigating the forensic pathological characteristics of systemic vasculitis: A retrospective study of 20 deaths caused by systemic vasculitis.},
  author = {Zheng Z, Xiong H, Zhang L, Zhao C, Li Y, Li J},
  journal = {Journal of forensic and legal medicine},
  year = {2021},
  pmid = {34192655},
  doi = {10.1016/j.jflm.2021.102204},
  url = {https://pubmed.ncbi.nlm.nih.gov/34192655/},
}

@article{pmid34215308,
  title = {Mammalian/mechanistic target of rapamycin (mTOR) complexes in neurodegeneration.},
  author = {["Querfurth H", "Lee H"]},
  journal = {Molecular neurodegeneration},
  year = {2021},
  pmid = {34215308},
  doi = {10.1186/s13024-021-00428-5},
}

@article{pmid34788101,
  title = {Re-identification of individuals in genomic datasets using public face images.},
  author = {Venkatesaramani R, Malin BA, Vorobeychik Y},
  journal = {Science advances},
  year = {2021},
  pmid = {34788101},
  doi = {10.1126/sciadv.abg3296},
  url = {https://pubmed.ncbi.nlm.nih.gov/34788101/},
}

@article{pmid31937935,
  title = {mTOR at the nexus of nutrition, growth, ageing and disease.},
  author = {["Liu G", "Sabatini D"]},
  journal = {Nature reviews. Molecular cell biology},
  year = {2020},
  pmid = {31937935},
  doi = {10.1038/s41580-019-0199-y},
}

@article{pmid30636564,
  title = {Brain MR Radiomics to Differentiate Cognitive Disorders.},
  author = {Ranjbar S, Velgos SN, Dueck AC, Geda YE, Mitchell JR, Alzheimer's Disease Neuroimaging Initiative},
  journal = {The Journal of neuropsychiatry and clinical neurosciences},
  year = {2019},
  pmid = {30636564},
  doi = {10.1176/appi.neuropsych.17120366},
  url = {https://pubmed.ncbi.nlm.nih.gov/30636564/},
}

@article{pmid31235664,
  title = {[Surgical Anatomy and Techniques for the Endoscopic Endonasal Skull Base Surgery].},
  author = {Yudo Ishii; Ryosuke Mori; Kazuhiro Omura; Nobuyoshi Otori; Yuichi Murayama},
  journal = {No shinkei geka. Neurological surgery},
  year = {2019},
  pmid = {31235664},
  doi = {10.11477/mf.1436203996},
  url = {https://pubmed.ncbi.nlm.nih.gov/31235664/},
}

@article{pmid31578018,
  title = {Assessment of Capacity Impairment in Patients with Mental Disorders by Routine Clinical Assessment and by Structured Assessment with the Mini-ICF-APP.},
  author = {Muschalla B, Poguntke KJ, Linden M},
  journal = {Psychopathology},
  year = {2019},
  pmid = {31578018},
  doi = {10.1159/000502123},
  url = {https://pubmed.ncbi.nlm.nih.gov/31578018/},
}

@article{pmid29566236,
  title = {Is disability in leprosy still a burden? A cross-sectional study in a rural block in Tamil Nadu, India.},
  author = {Ganesan DK, Muthunarayanan L},
  journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
  year = {2018},
  pmid = {29566236},
  doi = {10.1093/trstmh/try021},
  url = {https://pubmed.ncbi.nlm.nih.gov/29566236/},
}

@article{pmid28178527,
  title = {An Intrinsic Transcriptional Program Underlying Synaptic Scaling during Activity Suppression.},
  author = {Schaukowitch K, Reese AL, Kim SK, Kilaru G, Joo JY, Kavalali ET, Kim TK},
  journal = {Cell reports},
  year = {2017},
  pmid = {28178527},
  doi = {10.1016/j.celrep.2017.01.033},
  url = {https://pubmed.ncbi.nlm.nih.gov/28178527/},
}

@article{pmid26024166,
  title = {Evidence of soft dipole resonance in ^{11}li with isoscalar character.},
  author = {Kanungo R, Sanetullaev A, Tanaka J, Ishimoto S, Hagen G, Myo T, Suzuki T, Andreoiu C, Bender P, Chen AA, Davids B, Fallis J, Fortin JP, Galinski N, Gallant AT, Garrett PE, Hackman G, Hadinia B, Jansen G, Keefe M, Krücken R, Lighthall J, McNeice E, Miller D, Otsuka T, Purcell J, Randhawa JS, Roger T, Rojas A, Savajols H},
  journal = {Physical review letters},
  year = {2015},
  pmid = {26024166},
  doi = {10.1103/PhysRevLett.114.192502},
  url = {https://pubmed.ncbi.nlm.nih.gov/26024166/},
}

@article{pmid24670762,
  title = {REST and stress resistance in ageing and Alzheimer's disease.},
  author = {["Lu Tao", "Aron Liviu", "Zullo Joseph", "Pan Ying", "Kim Haeyoung"]},
  journal = {Nature},
  year = {2014},
  pmid = {24670762},
  doi = {10.1016/j.cell.2012.08.001},
}

@article{pmid22500797,
  title = {mTOR signaling in growth control and disease.},
  author = {["Laplante M", "Sabatini D"]},
  journal = {Cell},
  year = {2012},
  pmid = {22500797},
  doi = {10.1016/j.cell.2012.03.017},
}