The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans

An Evolutionarily Conserved PLC-PKD-TFEB Pathway for Host Defense.

Cell growth is accompanied by the synthesis of macromolecules and biogenesis of organelles. The protein kinase mTOR (mechanistic or mammalian target of rapamycin) controls these processes by sensing availability of growth signals. The targeting of macromolecules and trafficking of cargo‐containing vesicles into appropriate cellular compartments are also important processes that are highly controlled during growth versus stress conditions. In this issue of The EMBO Journal , Pena‐Llopis et al demonstrate that mTOR complex 1 (mTORC1) could regulate endocytosis by controlling the expression of endosomal proteins such as the vacuolar (V)‐ATPases. mTORC1 performs this novel function by modulating the phosphorylation and activity of the transcription factor EB (TFEB), which is required for expression of genes involved in autophagosome and lysosome biogenesis. This study, along with a related study in Science by Settembre et al , reveals how growth signals mediated by mTOR and other protein kinases such as mitogen‐activated protein kinase (MAPK) can converge on TFEB to direct endosome biogenesis and trafficking.

Wnt signaling is mainly transduced by β-catenin via regulation of the β-catenin destruction complex containing Axin, APC, and GSK3β. Transcription factor EB (TFEB) is a well-known master regulator of autophagy and lysosomal biogenesis processes. TFEB’s nuclear localization and transcriptional activity are also regulated by various upstream signals. In this study, we found that Wnt signaling induces the nuclear localization of TFEB and the expression of Wnt target genes is regulated by TFEB-β-catenin-TCF/LEF1 as well as β-catenin-TCF/LEF1 complexes. Our biochemical data revealed that TFEB is a part of the β-catenin destruction complex, and destabilization of the destruction complex by knockdown of either Axin or APC causes nuclear localization of TFEB. Interestingly, RNA-sequencing analysis revealed that about 27% of Wnt3a-induced genes were TFEB dependent. However, these “TFEB mediated Wnt target genes” were different from TFEB target genes involved in autophagy and lysosomal biogenesis processes. Mechanistically, we found that Tankyrase (TNKS) PARsylates TFEB with Wnt ON signaling, and the nuclear localized PARsylated TFEB forms a complex with β-catenin-TCF/LEF1 to induce the “TFEB mediated Wnt target genes”. Finally, we found that in various types of cancer, the levels of TFEB mediated Wnt target genes exhibit strong correlations with the level of Axin2, which represents the activity of Wnt signaling. Overall, our data suggest that Wnt signaling induces the expression of a subset of genes that are distinct from previously known genes regulated by the β-catenin-TCF/LEF1 complex or TFEB, by forming a transcription factor complex consisting of PARsylated TFEB and β-catenin-TCF/LEF1.

Background: Aging-dependent decline of autophagy contributes to cardiac dysfunction and ischemic intolerance. Transcription factor EB (TFEB) is a master transcriptional regulator of the autophagy-lysosome pathway. The present study aimed to characterize the role of TFEB in the autophagic decrease with aging. Methods and Results: We analyzed age-associated autophagic changes in male C57BL/6 young (4-6 mo) and aged (22-24 mo) mice. The results demonstrated that TFEB expressed predominantly as a SUMOylated form in cardiomyocyte nuclei and this SUMOylation of TFEB declined in aged heart associated with autophagy reduction. Interestingly, SUMOylation of TFEB was unaffected by rapamycin. Rapamycin induced translocation of TFEB into nucleus but lower level of nuclear TFEB in aged hearts than that seen in young hearts (P<0.05). SUMO1 downregulation by adeno-associated-virus-mediated small hairpin RNA (rAAV9-shSUMO1) significantly reduced nuclear TFEB levels (P<0.05), depressed cardiac autophagy and accelerated cardiomyocyte contractile dysfunction with worse hypoxia/reoxygenation (H/R) injury (all P<0.05). Therefore, impaired SUMOylation decreased nuclear TFEB during aging. By contrast, SUMO1 restitution significantly augmented nuclear SUMOylated TFEB with enhanced autophagy and ultimately reduced infarct size in aged heart. However, knockdown of cardiac TFEB blocked the protective effect of upregulation of SUMO1 in aged hearts, resulted in decline of autophagy and worse in vivo I/R injury. Conclusions: The present study newly demonstrates that SUMOylation is a critical post-translational modification that regulates cardiac TFEB. Impaired SUMOylation of TFEB aggravates decline of autophagy in the senescent heart. Targeting SUMO1 may provide a novel therapeutic strategy for the treatment of aging-related loss of cardioprotection.

Comment on: Peña-Llopis S, et al. EMBO J 2011; 30:3242-58.

Mammalian target of rapamycin (mTOR) complex 1 (mTORC1) is an important, highly conserved, regulator of cell growth. Ancient among the signals that regulate mTORC1 are nutrients. Amino acids direct mTORC1 to the surface of the late endosome/lysosome, where mTORC1 becomes receptive to other inputs. However, the interplay between endosomes and mTORC1 is poorly understood. Here, we report the discovery of a network that links mTORC1 to a critical component of the late endosome/lysosome, the V-ATPase. In an unbiased screen, we found that mTORC1 regulated the expression of, among other lysosomal genes, the V-ATPases. mTORC1 regulates V-ATPase expression both in cells and in mice. V-ATPase regulation by mTORC1 involves a transcription factor translocated in renal cancer, TFEB. TFEB is required for the expression of a large subset of mTORC1 responsive genes. mTORC1 coordinately regulates TFEB phosphorylation and nuclear localization and in a manner dependent on both TFEB and V-ATPases, mTORC1 promotes endocytosis. These data uncover a regulatory network linking an oncogenic transcription factor that is a master regulator of lysosomal biogenesis, TFEB, to mTORC1 and endocytosis.

<b>Background:</b> LDL receptor-related protein 5 (LRP5) triggers the canonical Wnt pathway which participates in cell function regulation, including lipoprotein metabolism, macrophage mobility and phagocytosis, but its function in the heart is unknown. <b>Purpose:</b> The aim of this study was to investigate LRP5 and the canonical Wnt signalling pathway in myocardial injury after acute-myocardial infarction (MI). <b>Methods:</b> MI was induced in WT and LRP5-/- mice by coronary ligation. Infarct size, LRP5 and Wnt signalling proteins were measured. LRP5 and the different metabolic pathways involved in myocardial damage post-MI were analyzed in isolated cardiomyocytes, myofibroblasts and endothelial cells. <b>Results:</b> LRP5-/- mice have significantly larger infarcts than WT mice (20.8 vs 9.9 p<0.5) suggesting a protective role of LRP5/Wnt in injured myocardium. Furthermore, administration of a GSK3 inhibitor that activates the Wnt pathway downstream LRP5, induced smaller infarcts in LRP5-/- mice indicating that an active Wnt pathway plays a protective role in the myocardium. Hypoxia induced LRP5 overexpression in isolated cardiomyocytes and endothelial cells indicating that a defensive and protective expression of LRP5 is triggered in both cell types. Induction of MI in WT and in LRP5-/- hypercholesterolemic animals, common risk factor in patients with ACS, induced larger infarcts in both genotypes. In isolated cardiomyocytes, LDL induced LRP5 overexpression and Wnt pathway activation whereas LRP5-silencing blocked the pathway. <b>Conclusions:</b> LRP5 and the canonical Wnt pathway activation is a defensive pro-survival process triggered to protect the ischemic myocardium against different injury triggers, such as hypoxia and hypercholesterolemia to favour and restore cell viability.

Transcription factor EB (TFEB), a well-known master regulator of autophagy and lysosomal biogenesis, is a member of the microphthalmia family of transcription factors (MiT family). Over the years, TFEB has been shown to have diverse roles in various physiological processes such as clearance for intracellular pathogenic factors and having developmental functions such as dendritic maturation, as well as osteoclast, and endoderm differentiation. However, in the present study, we propose a novel mechanism for TFEB governing pluripotency of mouse ESCs (mESCs) by regulating the pluripotency transcriptional network (PTN) in these cells. We observed high levels of TFEB mRNA and protein levels in undifferentiated mESCs. Interestingly, we found a reduction of Nanog and Sox2 levels in TFEB knockout (KO) mESCs while pluripotency was maintained as there was an upregulation of TFE3, a potent stem cell maintenance factor. In consistent, double knockout of TFEB/TFE3 (TFEB/3 DKO) reduced mESC pluripotency, as indicated by the loss of ESC morphology, reduction of ESC markers, and the emergence of differentiation markers. We further discovered that Nanog was a TFEB target gene in undifferentiated mESCs. TFEB also promoted sex-determining region Y-box2 (Sox2) transcription by forming a heterodimer with Sox2 in mESCs. Notably, Sox2, Oct4, and Nanog were also binding to the TFEB promoter and thus generating a feed-forward loop in relation to TFEB. Although high levels of nuclear TFEB are expected to enhance autophagy–lysosomal activity, undifferentiated mESC remarkably displayed low basal autophagy–lysosomal activity. Overexpression or knockout of TFEB did not affect the expression of TFEB lysosomal–autophagy target genes and TFEB also had a lesser binding affinity to its own lysosomal promoter-target genes in mESCs compared to differentiated cells. Collectively, these findings define a newly incorporative, moonlighting function for TFEB in regulating PTN, independent of its autophagy–lysosomal biogenesis roles.

TFEB (transcription factor EB) regulates multiple genes involved in the process of macroautophagy/autophagy and plays a critical role in lifespan determination. However, the detailed mechanisms that regulate TFEB activity are not fully clear. In this study, we identified a role for HSP90AA1 in modulating TFEB. HSP90AA1 was phosphorylated by CDK5 at Ser 595 under basal condition. This phosphorylation inhibited HSP90AA1, disrupted its binding to TFEB, and impeded TFEB’s nuclear localization and subsequent autophagy induction. Pro-autophagy signaling attenuated CDK5 activity and enhanced TFEB function in an HSP90AA1-dependent manner. Inhibition of HSP90AA1 function or decrease in its expression significantly attenuated TFEB’s nuclear localization and transcriptional function following autophagy induction. HSP90AA1-mediated regulation of a TFEB ortholog was involved in the extended lifespan of Caenorhabditis elegans in the absence of its food source bacteria. Collectively, these findings reveal that this regulatory process plays an important role in modulation of TFEB, autophagy, and longevity. Abbreviations: AL: autolysosome; AP: autophagosome; ATG: autophagy related; BafA1: bafilomycin A1; CDK5: cyclin-dependent kinase 5; CDK5R1: cyclin dependent kinase 5 regulatory subunit 1; CR: calorie restriction; FUDR: 5-fluorodeoxyuridine; HSP90AA1: heat shock protein 90 alpha family class A member 1; MAP1LC3: microtubule associated protein 1 light chain 3; NB: novobiocin sodium; SQSTM1: sequestosome 1; TFEB: transcription factor EB; WT: wild type.

Multiple studies suggest that autophagy is strongly dysregulated in Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS), as evidenced by accumulation of numerous autophagosomes, lysosomes with discontinuous membranes, and aggregated proteins in the patients' brains. Transcription factor EB (TFEB) was recently discovered to be a master regulator of lysosome biogenesis and autophagy. To examine whether aberrant autophagy in AD and ALS is due to alterations in TFEB expression, we systematically quantified the levels of TFEB in these brains by immunoblotting. Interestingly, cytoplasmic fractions of AD brains showed increased levels of normalized (to tubulin) TFEB only at Braak stage IV (61%, p < 0.01). Most importantly, normalized (to lamin) TFEB levels in the nuclear fractions were consistently reduced starting from Braak stage IV (52%, p < 0.01), stage V (67%, p < 0.01), and stage VI (85%, p < 0.01) when compared to normal control (NC) brains. In the ALS brains also, nuclear TFEB levels were reduced by 62% (p < 0.001). These data suggest that nuclear TFEB is selectively lost in ALS as well as AD brains, in which TFEB reduction was Braak-stage-dependent. Taken together, the observed reductions in TFEB protein levels may be responsible for the widely reported autophagy defects in these disorders.

The transcription factor EB (TFEB) was identified as a master regulator of autophagy and lysosomal biogenesis. We recently demonstrated that TFEB is aberrantly regulated in pancreatic cancer (PDAC) cells. Interference with TFEB impairs PDAC cell growth supporting an important role for TFEB in maintaining PDAC cell phenotype. Given the limited impact of chemotherapeutic drugs in the context of PDAC, we aimed at testing whether the aberrantly regulated TFEB in PDAC cells could confer resistance to DNA damage agents, commonly used in PDAC therapeutic regimens. Methods: Experiments were performed in PDAC cells (MIA PaCa2, PANC1). The DNA damage agents gemcitabine, 5-FU, cisplatin and doxorubicin were used. Autophagic flux was measured upon 4-hours treatment with bafilomycin A1. Results: Treatment with DNA damage agents 1) increased the autophagic flux in PDAC cells. This autophagic signal was associated with 2) the dephosphorylation and nuclear accumulation of TFEB. The mTORC1 pathway is well-known to regulate TFEB phosphorylation and nuclear localization of TFEB. 3) However, the impact of the DNA damage agents on TFEB appeared independent of the mTORC1 pathway since no modulation in the phosphorylation of the mTORC1 target S6K1 was observed. To delineate whether TFEB influenced the response to DNA damage agents, we generated stable populations of PDAC cells expressing a non-targeting or shRNA targeting TFEB. Interfering with TFEB function 4) prevented the autophagic response upon treatment with DNA damage agents. This correlated with 5) increased accumulation of DNA damage and 6) increased sensitivity to the DNA damage agents. Conclusion: Our results suggest that DNA damage agents can induce a pro-survival autophagic response involving TFEB. Interfering with TFEB function limits the autophagic response and leads to increased sensitivity to DNA damage agents. Altogether, our results suggest that the aberrantly expressed TFEB in PDAC cells could confer resistance to DNA damage agents by, among others, promoting autophagy and limiting DNA damage accumulation. Citation Format: Benoit Marchand, Marie-Josée Boucher. DNA damage agents promote TFEB function and induce pro-survival autophagy signals [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2619.

Transcription factor EB (TFEB) is a conserved master transcriptional activator of autophagy and lysosomal genes that modulates organismal lifespan regulation and stress resistance. As neurons can coordinate organism‐wide processes, we investigated the role of neuronal TFEB in stress resistance and longevity. To this end, the Caenorhabditis elegans TFEB ortholog, hlh‐30, was rescued panneuronally in hlh‐30 loss of function mutants. While important in the long lifespan of daf‐2 animals, neuronal HLH‐30/TFEB was not sufficient to restore normal lifespan in short‐lived hlh‐30 mutants. However, neuronal HLH‐30/TFEB rescue mediated robust improvements in the heat stress resistance of wildtype but not daf‐2 animals. Notably, these mechanisms can be uncoupled, as neuronal HLH‐30/TFEB requires DAF‐16/FOXO to regulate longevity but not thermoresistance. Through further transcriptomics profiling and functional analysis, we discovered that neuronal HLH‐30/TFEB modulates neurotransmission through the hitherto uncharacterized protein W06A11.1 by inducing peripheral mitochondrial fragmentation and organismal heat stress resistance in a non‐cell autonomous manner. Taken together, this study uncovers a novel mechanism of heat stress protection mediated by neuronal HLH‐30/TFEB.

BackgroundInduction of lysosomal function and autophagy is regarded as an adaptive mechanism in response to cellular stress. The transcription factor EB (TFEB) has been identified as a master regulator of lysosomal function and autophagy. TFEB is a member of the microphthalmia family of bHLH-LZ transcription factors that includes other members such as micropthalmia-associated transcription factor (MITF), TFE3, and TFEC. TFEB controls lysosome biogenesis and autophagy by upregulation of a family of genes belonging to the Coordinated Lysosomal Expression and Regulation (CLEAR) network. Here, we investigated the expression of TFEB in cells subjected to nutrient deprivation and lysosomal stress. We studied transcriptional induction of TFEB-regulated genes in response to nutrient deprivation and lysosomal stress in retinal pigment epithelial (RPE) cells. Furthermore, we also investigated the induction of autophagy and lysosomal genes upon overexpression of constitutively active form of TFEB.MethodsExpression of TFEB and MITF protein levels were evaluated in cells subjected to prolonged periods of nutrient deprivation. mRNA levels of the CLEAR network genes was measured by quantitative real time PCR (qRT-PCR) analysis in cells deprived of nutrients, treated with ammonium chloride and upon overexpression of constitutively active TFEB. Immunostaining with LC3 antibody was used to measure autophagy flux. Labeling with lysoTracker dye was used to assess lysosomes.ResultsOur results show that nutrient deprivation increases protein levels of TFEB and MITF in ARPE-19 cells. Nutrient stress induces the expression of lysosomal (LAMP1, CTSD MCOLN1, SGSH) and autophagy (BECN1) genes. Lysosomal stress also increases the expression of lysosomal (ATP6V0A1 and LAMP1) and autophagy (p62 and BECN1) genes. Our results show that overexpression of constitutively active TFEB also induces the expression of CLEAR network genes.ConclusionsCollectively, these observations suggest that nutrient stress induces the protein expression of both MITF and TFEB in ARPE-19 cells. TFEB-regulated transcriptional program plays an important role in adaptive response of cells during both nutrient and lysosomal stress.

Impaired TFEB-Mediated Lysosome Biogenesis and Autophagy Promote Chronic Ethanol-Induced Liver Injury and Steatosis in Mice

Rationale: Abdominal aortic aneurysm (AAA) is a vascular disease with a very high mortality rate in the case of rupture. Vascular smooth muscle cells (VSMCs) are crucial to maintaining vascular integrity and function. Transcription Factor EB (TFEB) is a master regulator of autophagy and lysosomal biogenesis in a variety of cell types via inducing the transcription of a coordinated lysosomal regulatory gene network. TFEB shows anti-inflammatory and anti-atherosclerotic effects in vascular endothelial cells and macrophages. However, the role of TFEB in vascular disease remains to be further explored. Objectives: To investigate the role of VSMC TFEB in AAA. Methods and Results: We found that TFEB was down-regulated in human aortic aneurysmal lesion compared with the non-lesion area by QRT-PCR and immunostaining. In human aortic smooth muscle cells (HASMCs), TFEB mRNA and protein abundance were decreased upon treatment with pro-inflammatory factors while adenovirus-mediated TFEB overexpression potently inhibits inflammation, apoptosis (caspase 3 cleavage and Annexin V staining) and matrix metalloproteinase activity (zymography). A consistent phenotype was observed in the TFEB knockdown HASMCs. Mechanistically, TFEB activates the PI3K-Akt pathway, and PI3K inhibitors (wortmannin and LY294002) abolished the anti-apoptotic effect of TFEB in HASMCs. Utilizing VSMC-specific TFEB deficiency mice (floxed-TFEB/myh11-ERT2 cre+), we determined the effect of TFEB on AAA formation in vivo. In the mouse aneurysm model induced by the combination of angiotensin II and 3-aminopropionitrile infusion, TFEB VSMC-deletion significantly increases aneurysm formation, rupture, and mortality (n =13-14 for each group, p&lt; 0.01). Conclusions: Our data reveal a critical protective role of TFEB in VSMC homeostasis, suggesting TFEB to be a potential target to treat aortic aneurysm.