4,629
Views
3
CrossRef citations to date
0
Altmetric
Research Paper

Autophagy modulates cell fate decisions during lineage commitment

ORCID Icon, ORCID Icon, ORCID Icon, ORCID Icon, , ORCID Icon, , , ORCID Icon & ORCID Icon show all
Pages 1915-1931 | Received 24 Jul 2020, Accepted 15 Nov 2021, Published online: 19 Dec 2021

References

  • Dikic I, Elazar Z. Mechanism and medical implications of mammalian autophagy. Nat Rev Mol Cell Biol. 2018;19:349–364.
  • Levine B, Kroemer G. Biological functions of autophagy genes: a disease perspective. Cell. 2019;176:11–42.
  • Morishita H, Mizushima N. Diverse cellular roles of autophagy. Annu Rev Cell Dev Biol. 2019;35:453–475.
  • Mizushima N, Levine B. Autophagy in mammalian development and differentiation. Nat Cell Biol. 2010;12:823–830.
  • Galluzzi L, Baehrecke EH, Ballabio A, et al. Molecular definitions of autophagy and related processes. EMBO J. 2017;36:1811–1836.
  • Mercer TJ, Gubas A, Tooze SA. A molecular perspective of mammalian autophagosome biogenesis. J Biol Chem. 2018;293:5386–5395.
  • Dooley HC, Razi M, Polson HE, et al. WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12-5-16L1. Mol Cell. 2014;55:238–252.
  • Dudley LJ, Cabodevilla AG, Makar AN, et al. Intrinsic lipid binding activity of ATG16L1 supports efficient membrane anchoring and autophagy. EMBO J. 2019;38.
  • Lystad AH, Carlsson SR, de La Ballina LR, et al. Distinct functions of ATG16L1 isoforms in membrane binding and LC3B lipidation in autophagy-related processes. Nat Cell Biol. 2019;21:372–383.
  • Lystad AH, Simonsen A. Mechanisms and pathophysiological roles of the ATG8 conjugation machinery. Cells. 2019;8.
  • Shpilka T, Weidberg H, Pietrokovski S, et al. Atg8: an autophagy-related ubiquitin-like protein family. Genome Biol. 2011;12:226.
  • Johansen T, Lamark T. Selective autophagy: ATG8 family proteins, LIR motifs and cargo receptors. J Mol Biol. 2019;432(1):80–103.
  • Khaminets A, Behl C, Dikic I. Ubiquitin-dependent and independent signals in selective autophagy. Trends Cell Biol. 2016;26:6–16.
  • Clausen TH, Lamark T, Isakson P, et al. p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. Autophagy. 2010;6:330–344.
  • Lystad AH, Ichimura Y, Takagi K, et al. Structural determinants in GABARAP required for the selective binding and recruitment of ALFY to LC3B-positive structures. EMBO Rep. 2014;15:557–565.
  • Turco E, Witt M, Abert C, et al. FIP200 claw domain binding to p62 promotes autophagosome formation at ubiquitin condensates. Mol Cell. 2019;74:330–46 e11.
  • Mauthe M, Orhon I, Rocchi C, et al. Chloroquine inhibits autophagic flux by decreasing autophagosome-lysosome fusion. Autophagy. 2018;14:1435–1455.
  • Yamamoto A, Tagawa Y, Yoshimori T, et al. Bafilomycin A1 prevents maturation of autophagic vacuoles by inhibiting fusion between autophagosomes and lysosomes in rat hepatoma cell line, H-4-II-E cells. Cell Struct Funct. 1998;23:33–42.
  • Kiecker C, Bates T, Bell E. Molecular specification of germ layers in vertebrate embryos. Cell Mol Life Sci. 2016;73:923–947.
  • Aymard E, Barruche V, Naves T, et al. Autophagy in human keratinocytes: an early step of the differentiation? Exp Dermatol. 2011;20:263–268.
  • Tra T, Gong L, Kao LP, et al. Autophagy in human embryonic stem cells. PLoS One. 2011;6:e27485.
  • Zhao Y, Chen G, Zhang W, et al. Autophagy regulates hypoxia-induced osteoclastogenesis through the HIF-1alpha/BNIP3 signaling pathway. J Cell Physiol. 2012;227:639–648.
  • Robinton DA, Daley GQ. The promise of induced pluripotent stem cells in research and therapy. Nature. 2012;481:295–305.
  • Pera MF, Trounson AO. Human embryonic stem cells: prospects for development. Development. 2004;131:5515–5525.
  • Li C, Zhang S, Lu Y, et al. The roles of Notch3 on the cell proliferation and apoptosis induced by CHIR99021 in NSCLC cell lines: a functional link between Wnt and Notch signaling pathways. PLoS One. 2013;8:e84659.
  • Ye S, Tan L, Yang R, et al. Pleiotropy of glycogen synthase kinase-3 inhibition by CHIR99021 promotes self-renewal of embryonic stem cells from refractory mouse strains. PLoS One. 2012;7:e35892.
  • Sullivan GJ, Hay DC, Park IH, et al. Generation of functional human hepatic endoderm from human induced pluripotent stem cells. Hepatology. 2010;51:329–335.
  • Siller R, Greenhough S, Naumovska E, et al. Small-molecule-driven hepatocyte differentiation of human pluripotent stem cells. Stem Cell Reports. 2015;4:939–952.
  • Lian X, Zhang J, Azarin SM, et al. Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/beta-catenin signaling under fully defined conditions. Nat Protoc. 2013;8:162–175.
  • Chambers SM, Fasano CA, Papapetrou EP, et al. Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling. Nat Biotechnol. 2009;27:275–280.
  • Yang Z, Klionsky DJ. Mammalian autophagy: core molecular machinery and signaling regulation. Curr Opin Cell Biol. 2010;22:124–131.
  • Mizushima N, Komatsu M. Autophagy: renovation of cells and tissues. Cell. 2011;147:728–741.
  • Xia P, Wang S, Du Y, et al. WASH inhibits autophagy through suppression of Beclin 1 ubiquitination. EMBO J. 2013;32:2685–2696.
  • Teo AK, Arnold SJ, Trotter MW, et al. Pluripotency factors regulate definitive endoderm specification through eomesodermin. Genes Dev. 2011;25:238–250.
  • Baltus GA, Kowalski MP, Zhai H, et al. Acetylation of sox2 induces its nuclear export in embryonic stem cells. Stem Cells. 2009;27:2175–2184.
  • Ji J, Yu Y, Li ZL, et al. XIAP limits autophagic degradation of Sox2 and is a therapeutic target in nasopharyngeal carcinoma stem cells. Theranostics. 2018;8:1494–1510.
  • Maroof AM, Keros S, Tyson JA, et al. Directed differentiation and functional maturation of cortical interneurons from human embryonic stem cells. Cell Stem Cell. 2013;12:559–572.
  • Luo X, Wang H, Leighton J, et al. Generation of endoderm lineages from pluripotent stem cells. Regen Med. 2017;12:77–89.
  • Zorn AM, Wells JM. Vertebrate endoderm development and organ formation. Annu Rev Cell Dev Biol. 2009;25:221–251.
  • Mathapati S, Siller R, Impellizzeri AA, et al. Small-molecule-directed hepatocyte-like cell differentiation of human pluripotent stem cells. Curr Protoc Stem Cell Biol. 2016;38:1G 6 1–G 6 18.
  • Siller R, Naumovska E, Mathapati S, et al. Development of a rapid screen for the endodermal differentiation potential of human pluripotent stem cell lines. Sci Rep. 2016;6:37178.
  • Pisal RV, Suchanek J, Siller R, et al. Directed reprogramming of comprehensively characterized dental pulp stem cells extracted from natal tooth. Sci Rep. 2018;8:6168.
  • Siller R, Sullivan GJ. Rapid screening of the endodermal differentiation potential of human pluripotent stem cells. Curr Protoc Stem Cell Biol. 2017;43:1G 7 1–G 7 23.
  • Peale FV Jr., Sugden L, Bothwell M. Characterization of CMIX, a chicken homeobox gene related to the Xenopus gene mix.1. Mech Dev. 1998;75:167–170.
  • Stein S, Roeser T, Kessel M. CMIX, a paired-type homeobox gene expressed before and during formation of the avian primitive streak. Mech Dev. 1998;75:163–165.
  • Ang SL, Wierda A, Wong D, et al. The formation and maintenance of the definitive endoderm lineage in the mouse: involvement of HNF3/forkhead proteins. Development. 1993;119:1301–1315.
  • Kanai-Azuma M, Kanai Y, Gad JM, et al. Depletion of definitive gut endoderm in Sox17-null mutant mice. Development. 2002;129:2367–2379.
  • Monaghan AP, Kaestner KH, Grau E, et al. Postimplantation expression patterns indicate a role for the mouse forkhead/HNF-3 alpha, beta and gamma genes in determination of the definitive endoderm, chordamesoderm and neuroectoderm. Development. 1993;119:567–578.
  • Petherick KJ, Conway OJ, Mpamhanga C, et al. Pharmacological inhibition of ULK1 kinase blocks mammalian target of rapamycin (mTOR)-dependent autophagy. J Biol Chem. 2015;290:28726.
  • Loh KM, Ang LT, Zhang J, et al. Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations. Cell Stem Cell. 2014;14:237–252.
  • Murry CE, Keller G. Differentiation of embryonic stem cells to clinically relevant populations: lessons from embryonic development. Cell. 2008;132:661–680.
  • Gong J, Gu H, Zhao L, et al. Phosphorylation of ULK1 by AMPK is essential for mouse embryonic stem cell self-renewal and pluripotency. Cell Death Dis. 2018;9:38.
  • Wang G, Yang L, Grishin D, et al. Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies. Nat Protoc. 2017;12:88–103.
  • Callaerts P, Halder G, Gehring WJ. PAX-6 in development and evolution. Annu Rev Neurosci. 1997;20:483–532.
  • Barnes RM, Firulli BA, Conway SJ, et al. Analysis of the Hand1 cell lineage reveals novel contributions to cardiovascular, neural crest, extra-embryonic, and lateral mesoderm derivatives. Dev Dyn. 2010;239:3086–3097.
  • Zaret K. Developmental competence of the gut endoderm: genetic potentiation by GATA and HNF3/fork head proteins. Dev Biol. 1999;209:1–10.
  • Minegishi N, Suzuki N, Yokomizo T, et al. Expression and domain-specific function of GATA-2 during differentiation of the hematopoietic precursor cells in midgestation mouse embryos. Blood. 2003;102:896–905.
  • Kim J, Dalton VM, Eggerton KP, et al. Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways. Mol Biol Cell. 1999;10:1337–1351.
  • Tanida I, Mizushima N, Kiyooka M, et al. Apg7p/Cvt2p: a novel protein-activating enzyme essential for autophagy. Mol Biol Cell. 1999;10:1367–1379.
  • Ferreira A, Caceres A. Expression of the class III beta-tubulin isotype in developing neurons in culture. J Neurosci Res. 1992;32:516–529.
  • Zhang S, Cui W. Sox2, a key factor in the regulation of pluripotency and neural differentiation. World J Stem Cells. 2014;6:305–311.
  • Cho YH, Han KM, Kim D, et al. Autophagy regulates homeostasis of pluripotency-associated proteins in hESCs. Stem Cells. 2014;32:424–435.
  • He J, Kang L, Wu T, et al. An elaborate regulation of Mammalian target of rapamycin activity is required for somatic cell reprogramming induced by defined transcription factors. Stem Cells Dev. 2012;21:2630–2641.
  • Gouon-Evans V, Boussemart L, Gadue P, et al. BMP-4 is required for hepatic specification of mouse embryonic stem cell-derived definitive endoderm. Nat Biotechnol. 2006;24:1402–1411.
  • Tada S, Era T, Furusawa C, et al. Characterization of mesendoderm: a diverging point of the definitive endoderm and mesoderm in embryonic stem cell differentiation culture. Development. 2005;132:4363–4374.
  • Cimadamore F, Fishwick K, Giusto E, et al. Human ESC-derived neural crest model reveals a key role for SOX2 in sensory neurogenesis. Cell Stem Cell. 2011;8:538–551.
  • Dou Z, Xu C, Donahue G, et al. Autophagy mediates degradation of nuclear lamina. Nature. 2015;527:105–109.
  • Kvam E, Goldfarb DS. Nucleus-vacuole junctions and piecemeal microautophagy of the nucleus in S cerevisiae. Autophagy. 2007;3:85–92.
  • Pan X, Roberts P, Chen Y, et al. Nucleus-vacuole junctions in Saccharomyces cerevisiae are formed through the direct interaction of Vac8p with Nvj1p. Mol Biol Cell. 2000;11:2445–2457.
  • Roberts P, Moshitch-Moshkovitz S, Kvam E, et al. Piecemeal microautophagy of nucleus in Saccharomyces cerevisiae. Mol Biol Cell. 2003;14:129–141.
  • Kaitsuka T, Kobayashi K, Otsuka W, et al. Erythropoietin facilitates definitive endodermal differentiation of mouse embryonic stem cells via activation of ERK signaling. Am J Physiol Cell Physiol. 2017;312:C573–C82.
  • Thomson JA, Itskovitz-Eldor J, Shapiro SS, et al. Embryonic stem cell lines derived from human blastocysts. Science. 1998;282:1145–1147.
  • Wang S, Xia P, Ye B, et al. Transient activation of autophagy via Sox2-mediated suppression of mTOR is an important early step in reprogramming to pluripotency. Cell Stem Cell. 2013;13:617–625.