Figures & data
Table 1. Known and predicted phosphoinositide-regulatory enzyme and effector protein functions in ALR.
Table 2. Disorders showing inhibition of autophagic lysosome reformation.
McGrath MJ, Eramo MJ, Gurung R, et al. Defective lysosome reformation during autophagy causes skeletal muscle disease. J Clin Invest. 2021 Jan 4;131(1):e135124. PubMed PMID: 33119550. Khundadze M, Ribaudo F, Hussain A, et al. Mouse models for hereditary spastic paraplegia uncover a role of PI4K2A in autophagic lysosome reformation. Autophagy. 2021 Nov;17(11):3690–3706. PubMed PMID: 33618608. Sridhar S, Patel B, Aphkhazava D, et al. The lipid kinase PI4KIIIbeta preserves lysosomal identity. EMBO J. 2013 Feb 6;32(3):324–339. PubMed PMID: 23258225. Rong Y, Liu M, Ma L, et al. Clathrin and phosphatidylinositol-4,5-bisphosphate regulate autophagic lysosome reformation. Nat Cell Biol. 2012 Sep;14(9):924–934. PubMed PMID: 22885770. Du W, Su QP, Chen Y, et al. Kinesin 1 drives autolysosome tubulation. Dev Cell. 2016 May 23;37(4):326–336. PubMed PMID: 27219061. Dai A, Yu L, Wang HW. WHAMM initiates autolysosome tubulation by promoting actin polymerization on autolysosomes. Nat Commun. 2019 Aug 16;10(1):3699. PubMed PMID: 31420534. Schulze RJ, Weller SG, Schroeder B, et al. Lipid droplet breakdown requires dynamin 2 for vesiculation of autolysosomal tubules in hepatocytes. J Cell Biol. 2013 Oct 28;203(2):315–326. PubMed PMID: 24145164. Eramo MJ, Gurung R, Mitchell CA, et al. Bidirectional interconversion between PtdIns4P and PtdIns(4,5)P2 is required for autophagic lysosome reformation and protection from skeletal muscle disease. Autophagy. 2021 May;17(5):1287–1289. PubMed PMID: 33879025. Munson MJ, Allen GF, Toth R, et al. mTOR activates the VPS 34– UVRAG complex to regulate autolysosomal tubulation and cell survival. EMBO J. 2015 Sep 2;34(17):2272–2290. PubMed PMID: 26139536. Hirst J, Hesketh GG, Gingras AC, et al. Rag GTPases and phosphatidylinositol 3-phosphate mediate recruitment of the AP-5/SPG11/SPG15 complex. J Cell Biol. 2021 Feb 1;220(2):e202002075. PubMed PMID: 33464297. Chang J, Lee S, Blackstone C. Spastic paraplegia proteins spastizin and spatacsin mediate autophagic lysosome reformation. J Clin Invest. 2014 Dec;124(12):5249–5262. PubMed PMID: 25365221. Yu L, McPhee CK, Zheng L, et al. Termination of autophagy and reformation of lysosomes regulated by mTOR. Nature. 2010 Jun 17;465(7300):942–946. PubMed PMID: 20526321. Hampe CS, Wesley J, Lund TC, et al. Mucopolysaccharidosis type I: current treatments, limitations, and prospects for improvement. Biomolecules. 2021;11(2):189. PubMed PMID: 33572941. Dinu IR, Ş G Firu. Fabry disease - current data and therapeutic approaches. Rom J Morphol Embryol. 2021 Jan-Mar;62(1):5–11. PubMed PMID: 34609404. Arvio M, Mononen I. Aspartylglycosaminuria: a review. Orphanet J Rare Dis. 2016 Dec 1;11(1):162. PubMed PMID: 27906067. Magalhaes J, Gegg ME, Migdalska-Richards A, et al. Autophagic lysosome reformation dysfunction in glucocerebrosidase deficient cells: relevance to parkinson disease. Hum Mol Genet. 2016 Aug 15;25(16):3432–3445. PubMed PMID: 27378698. Ginns EI, Brady RO, Pirruccello S, et al. Mutations of glucocerebrosidase: discrimination of neurologic and non-neurologic phenotypes of gaucher disease. Proc Natl Acad Sci U S A. 1982 Sep;79(18):5607–5610. PubMed PMID: 6957882. Roh J, Subramanian S, Weinreb NJ, et al. Gaucher disease - more than just a rare lipid storage disease. J Mol Med (Berl). 2022 Apr;100(4):499–518. PubMed PMID: 35066608. Yanagisawa H, Ishii T, Endo K, et al. L-Leucine and SPNS1 coordinately ameliorate dysfunction of autophagy in mouse and human niemann-pick type C disease. Sci Rep. 2017 Nov 21;7(1):15944. PubMed PMID: 29162837. Avenali M, Blandini F, Cerri S. Glucocerebrosidase defects as a major risk factor for Parkinson’s disease. Front Aging Neurosci. 2020 Apr;12:97. PubMed PMID: 32372943. Latourelle JC, Pankratz N, Dumitriu A, et al. Genomewide association study for onset age in Parkinson disease. BMC Med Genet. 2009 Sep 22;10(1):98. PubMed PMID: 19772629. Do CB, Tung JY, Dorfman E, et al. Web-Based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson’s disease. PLoS Genet. 2011 Jun 23;7(6):e1002141. PubMed PMID: 21738487. Miyazaki M, Hiramoto M, Takano N, et al. Targeted disruption of GAK stagnates autophagic flux by disturbing lysosomal dynamics. Int J Mol Med. 2021 Oct;48(4):195. PubMed PMID: 34468012. Varga RE, Khundadze M, Damme M, et al. In vivo evidence for lysosome depletion and impaired autophagic clearance in hereditary spastic paraplegia type SPG11. PLoS Genet. 2015 Aug 15;11(8):e1005454. PubMed PMID: 26284655. Hanein S, Martin E, Boukhris A, et al. Identification of the SPG15 gene, encoding spastizin, as a frequent cause of complicated autosomal-recessive spastic paraplegia, including kjellin syndrome. Am J Hum Genet. 2008 Apr;82(4):992–1002. PubMed PMID: 18394578. Vantaggiato C, Panzeri E, Castelli M, et al. ZFYVE26/SPASTIZIN and SPG11/SPATACSIN mutations in hereditary spastic paraplegia types AR-SPG15 and AR-SPG11 have different effects on autophagy and endocytosis. Autophagy. 2019 Jan;15(1):34–57. PubMed PMID: 30081747. Khundadze M, Ribaudo F, Hussain A, et al. A mouse model for SPG48 reveals a block of autophagic flux upon disruption of adaptor protein complex five. Neurobiol Dis. 2019 Jul;127:419–431. PubMed PMID: 30930081. Boutry M, Branchu J, Lustremant C, et al. Inhibition of lysosome membrane recycling causes accumulation of gangliosides that contribute to neurodegeneration. Cell Rep. 2018 Jun 26;23(13):3813–3826. PubMed PMID: 29949766. Stevanin G, Santorelli FM, Azzedine H, et al. Mutations in SPG11, encoding spatacsin, are a major cause of spastic paraplegia with thin corpus callosum. Nat Genet. 2007 Mar;39(3):366–372. PubMed PMID: 17322883. Słabicki M, Theis M, Krastev DB, et al. A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. PLoS Biol. 2010 Jun 29;8(6):e1000408. PubMed PMID: 20613862. Bouchard JP, Barbeau A, Bouchard R, et al. Autosomal recessive spastic ataxia of Charlevoix-Saguenay. Can J Neurol Sci. 1978 Feb;5(1):61–69. PubMed PMID: 647499. Engert JC, Bérubé P, Mercier J, et al. ARSACS, a spastic ataxia common in northeastern québec, is caused by mutations in a new gene encoding an 11.5-kb ORF. Nat Genet. 2000 Feb;24(2):120–125. PubMed PMID: 10655055. Bagaria J, Bagyinszky E, An SSA Genetics of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) and role of sacsin in neurodegeneration. Int J Mol Sci. 2022 Jan 4;23(1):552. PubMed PMID: 35008978. Francis V, Alshafie W, Kumar R, et al. The ARSACS disease protein sacsin controls lysosomal positioning and reformation by regulating microtubule dynamics. J Biol Chem. 2022 Sep; 298(9):102320. PubMed PMID: 35933016. Wiessner M, Roos A, Munn CJ, et al. Mutations in INPP5K, encoding a phosphoinositide 5-phosphatase, cause congenital muscular dystrophy with cataracts and mild cognitive impairment. Am J Hum Genet. 2017 Mar 2;100(3):523–536. PubMed PMID: 28190456. Osborn DPS, Pond HL, Mazaheri N, et al. Mutations in INPP5K cause a form of congenital muscular dystrophy overlapping Marinesco-Sjogren syndrome and dystroglycanopathy. Am J Hum Genet. 2017 Mar 2;100(3):537–545. PubMed PMID: 28190459. D’Amico A, Fattori F, Nicita F, et al. A recurrent pathogenic variant of INPP5K underlies autosomal recessive congenital muscular dystrophy with cataracts and intellectual disability: evidence for a founder effect in Southern Italy. Front Genet. 2020 Sep 18;11:565868. PubMed PMID: 33193651. Rasineni K, Donohue TM Jr., Thomes PG, et al. Ethanol-Induced steatosis involves impairment of lipophagy, associated with reduced dynamin2 activity. Hepatol Commun. 2017 Aug;1(6):501–512. PubMed PMID: 29152606. Lazarus JV, Mark HE, Anstee QM, et al. Advancing the global public health agenda for NAFLD: a consensus statement. Nat Rev Gastroenterol Hepatol 2021. Jan;19(1):60–78. PubMed PMID: 34707258. Priest C, Tontonoz P. Inter-Organ cross-talk in metabolic syndrome. Nat Metab. 2019 Dec 9;1(12):1177–1188. PubMed PMID: 32694672. Jahng JWS, Alsaadi RM, Palanivel R, et al. Iron overload inhibits late stage autophagic flux leading to insulin resistance. EMBO Rep. 2019 Oct 4;20(10):e47911. PubMed PMID: 31441223. Gu Z, Cui X, Sun P, et al. Regulatory roles of tumor necrosis factor-α-induced protein 8 like-protein 2 in inflammation, immunity and cancers: a review. Cancer Manag Res. 2020 Dec 14;12:12735–12746. PubMed PMID: 33364825. Li W, Li Y, Guan Y, et al. TNFAIP8L2/TIPE2 impairs autolysosome reformation via modulating the RAC1-MTORC1 axis. Autophagy. 2021 Jun;17(6):1410–1425. PubMed PMID: 32460619.