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Article ; Online: Beating the ER: novel insights into FAM134B function and regulation.

De Leonibus, Chiara / Cinque, Laura / Settembre, Carmine

2020 Volume 39, Issue 5, Page(s) e104546

Abstract: To maintain cellular homeostasis, the endoplasmic reticulum (ER) necessitates a continuous removal of ER fragments via a selective, receptor-mediated, form of autophagy known as ER-phagy. In this issue of The EMBO Journal, Jiang et al (2020) shed light ... ...

Abstract	To maintain cellular homeostasis, the endoplasmic reticulum (ER) necessitates a continuous removal of ER fragments via a selective, receptor-mediated, form of autophagy known as ER-phagy. In this issue of The EMBO Journal, Jiang et al (2020) shed light on how the best characterized autophagy receptor FAM134B mediates ER membrane fragmentation, the earliest event during ER-phagy. They propose a dynamic model for FAM134B protein oligomerization and ER membrane scission, which are driven by CAMK2B-mediated phosphorylation of the receptor and are altered in sensory neuropathy.
MeSH term(s)	Autophagy ; Carrier Proteins ; Endoplasmic Reticulum ; Homeostasis ; Membrane Proteins
Chemical Substances	Carrier Proteins ; Membrane Proteins
Language	English
Publishing date	2020-02-19
Publishing country	England
Document type	Journal Article ; Comment
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2020104546
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Article: Transcriptional Regulation of Autophagy: Mechanisms and Diseases.

Di Malta, Chiara / Cinque, Laura / Settembre, Carmine

Frontiers in cell and developmental biology

2019 Volume 7, Page(s) 114

Abstract: Macro (Autophagy) is a catabolic process that relies on the cooperative function of two organelles: the lysosome and the autophagosome. The recent discovery of a transcriptional gene network that co-regulates the biogenesis and function of these two ... ...

Abstract	Macro (Autophagy) is a catabolic process that relies on the cooperative function of two organelles: the lysosome and the autophagosome. The recent discovery of a transcriptional gene network that co-regulates the biogenesis and function of these two organelles, and the identification of transcription factors, miRNAs and epigenetic regulators of autophagy, demonstrated that this catabolic process is controlled by both transcriptional and post-transcriptional mechanisms. In this review article, we discuss the nuclear events that control autophagy, focusing particularly on the role of the MiT/TFE transcription factor family. In addition, we will discuss evidence suggesting that the transcriptional regulation of autophagy could be targeted for the treatment of human genetic diseases, such as lysosomal storage disorders (LSDs) and neurodegeneration.
Language	English
Publishing date	2019-07-02
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2019.00114
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Article ; Online: Emerging lysosomal pathways for quality control at the endoplasmic reticulum.

De Leonibus, Chiara / Cinque, Laura / Settembre, Carmine

FEBS letters

2019 Volume 593, Issue 17, Page(s) 2319–2329

Abstract: Protein misfolding occurring in the endoplasmic reticulum (ER) might eventually lead to aggregation and cellular distress, and is a primary pathogenic mechanism in multiple human disorders. Mammals have developed evolutionary-conserved quality control ... ...

Abstract	Protein misfolding occurring in the endoplasmic reticulum (ER) might eventually lead to aggregation and cellular distress, and is a primary pathogenic mechanism in multiple human disorders. Mammals have developed evolutionary-conserved quality control mechanisms at the level of the ER. The best characterized is the ER-associated degradation (ERAD) pathway, through which misfolded proteins translocate from the ER to the cytosol and are subsequently proteasomally degraded. However, increasing evidence indicates that additional quality control mechanisms apply for misfolded ER clients that are not eligible for ERAD. This review focuses on the alternative, ERAD-independent, mechanisms of clearance of misfolded polypeptides from the ER. These processes, collectively referred to as ER-to-lysosome-associated degradation, involve ER-phagy, microautophagy or vesicular transport. The identification of the underlying molecular mechanisms is particularly important for developing new therapeutic approaches for human diseases associated with protein aggregate formation.
MeSH term(s)	Animals ; Autophagy ; Disease ; Endoplasmic Reticulum/metabolism ; Humans ; Lysosomes/metabolism
Language	English
Publishing date	2019-08-13
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.13571
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Article: Emerging lysosomal pathways for quality control at the endoplasmic reticulum

De Leonibus, Chiara / Cinque, Laura / Settembre, Carmine

FEBS letters. 2019 Sept., v. 593, no. 17

2019

Abstract	Protein misfolding occurring in the endoplasmic reticulum (ER) might eventually lead to aggregation and cellular distress, and is a primary pathogenic mechanism in multiple human disorders. Mammals have developed evolutionary‐conserved quality control mechanisms at the level of the ER. The best characterized is the ER‐associated degradation (ERAD) pathway, through which misfolded proteins translocate from the ER to the cytosol and are subsequently proteasomally degraded. However, increasing evidence indicates that additional quality control mechanisms apply for misfolded ER clients that are not eligible for ERAD. This review focuses on the alternative, ERAD‐independent, mechanisms of clearance of misfolded polypeptides from the ER. These processes, collectively referred to as ER‐to‐lysosome–associated degradation, involve ER‐phagy, microautophagy or vesicular transport. The identification of the underlying molecular mechanisms is particularly important for developing new therapeutic approaches for human diseases associated with protein aggregate formation.
Keywords	cytosol ; distress ; endoplasmic reticulum ; humans ; polypeptides ; protein folding ; quality control ; therapeutics
Language	English
Dates of publication	2019-09
Size	p. 2319-2329.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1002/1873-3468.13571
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Article ; Online: Autophagy gets to the bone.

Cinque, Laura / Forrester, Alison / Settembre, Carmine

Cell cycle (Georgetown, Tex.)

2016 Volume 15, Issue 7, Page(s) 871–872

MeSH term(s)	Autophagy ; Bone and Bones ; Cartilage ; Chondrocytes ; Collagen ; Humans
Chemical Substances	Collagen (9007-34-5)
Language	English
Publishing date	2016-03-03
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	2146183-1
ISSN	1551-4005 ; 1538-4101 ; 1554-8627
ISSN (online)	1551-4005
ISSN	1538-4101 ; 1554-8627
DOI	10.1080/15384101.2016.1151724
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Article ; Online: Defective collagen proteostasis and matrix formation in the pathogenesis of lysosomal storage disorders.

Settembre, Carmine / Cinque, Laura / Bartolomeo, Rosa / Di Malta, Chiara / De Leonibus, Chiara / Forrester, Alison

Matrix biology : journal of the International Society for Matrix Biology

2018 Volume 71-72, Page(s) 283–293

Abstract: The lysosome is a catabolic organelle devoted to the degradation of cellular components, such as protein complexes and whole or portion of organelles that reach the lysosomes through (macro)autophagy. The lysosomes also function as signaling organelles ... ...

Abstract	The lysosome is a catabolic organelle devoted to the degradation of cellular components, such as protein complexes and whole or portion of organelles that reach the lysosomes through (macro)autophagy. The lysosomes also function as signaling organelles by controlling the activity of key metabolic kinases, such as the mechanistic target of Rapamycin complex 1 (mTORC1). Lysosome dysfunction has dramatic consequences on cellular homeostasis and causes lysosomal storage disorders (LSDs). Here we review the recently proposed mechanisms by which impairment of lysosome/autophagy pathway affects extracellular matrix formation and skeletal development and growth. In particular, we will highlight the role of autophagy as a collagen quality control pathway in collagen-producing cells. An impairment of autophagy, such as the one observed in LSDs, leads to a collagen proteostatic defects and can explain, at least in part, the skeletal phenotypes characterizing patients with lysosomal storage disorders.
MeSH term(s)	Animals ; Autophagy ; Collagen/metabolism ; Extracellular Matrix/metabolism ; Humans ; Lysosomal Storage Diseases/metabolism ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Phenotype ; Proteostasis
Chemical Substances	Collagen (9007-34-5) ; Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1)
Language	English
Publishing date	2018-06-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1183793-7
ISSN	1569-1802 ; 0945-053X
ISSN (online)	1569-1802
ISSN	0945-053X
DOI	10.1016/j.matbio.2018.06.001
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Article ; Online: TFEB and TFE3 drive kidney cystogenesis and tumorigenesis.

Di Malta, Chiara / Zampelli, Angela / Granieri, Letizia / Vilardo, Claudia / De Cegli, Rossella / Cinque, Laura / Nusco, Edoardo / Pece, Salvatore / Tosoni, Daniela / Sanguedolce, Francesca / Sorrentino, Nicolina Cristina / Merino, Maria J / Nielsen, Deborah / Srinivasan, Ramaprasad / Ball, Mark W / Ricketts, Christopher J / Vocke, Cathy D / Lang, Martin / Karim, Baktiar /

Lanfrancone, Luisa / Schmidt, Laura S / Linehan, W Marston / Ballabio, Andrea

EMBO molecular medicine

2023 Volume 15, Issue 5, Page(s) e16877

Abstract: Birt-Hogg-Dubé (BHD) syndrome is an inherited familial cancer syndrome characterized by the development of cutaneous lesions, pulmonary cysts, renal tumors and cysts and caused by loss-of-function pathogenic variants in the gene encoding the tumor- ... ...

Abstract	Birt-Hogg-Dubé (BHD) syndrome is an inherited familial cancer syndrome characterized by the development of cutaneous lesions, pulmonary cysts, renal tumors and cysts and caused by loss-of-function pathogenic variants in the gene encoding the tumor-suppressor protein folliculin (FLCN). FLCN acts as a negative regulator of TFEB and TFE3 transcription factors, master controllers of lysosomal biogenesis and autophagy, by enabling their phosphorylation by the mechanistic Target Of Rapamycin Complex 1 (mTORC1). We have previously shown that deletion of Tfeb rescued the renal cystic phenotype of kidney-specific Flcn KO mice. Using Flcn/Tfeb/Tfe3 double and triple KO mice, we now show that both Tfeb and Tfe3 contribute, in a differential and cooperative manner, to kidney cystogenesis. Remarkably, the analysis of BHD patient-derived tumor samples revealed increased activation of TFEB/TFE3-mediated transcriptional program and silencing either of the two genes rescued tumorigenesis in human BHD renal tumor cell line-derived xenografts (CDXs). Our findings demonstrate in disease-relevant models that both TFEB and TFE3 are key drivers of renal tumorigenesis and suggest novel therapeutic strategies based on the inhibition of these transcription factors.
MeSH term(s)	Humans ; Mice ; Animals ; Kidney/pathology ; Kidney Neoplasms/genetics ; Kidney Neoplasms/pathology ; Birt-Hogg-Dube Syndrome/genetics ; Birt-Hogg-Dube Syndrome/pathology ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Transcription Factors ; Carcinogenesis/genetics ; Cysts
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Transcription Factors ; TFE3 protein, human ; TFEB protein, human
Language	English
Publishing date	2023-03-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.15252/emmm.202216877
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Article ; Online: Phosphorylation of FAM134C by CK2 controls starvation-induced ER-phagy.

Science advances

2022 Volume 8, Issue 35, Page(s) eabo1215

Abstract: Selective degradation of the endoplasmic reticulum (ER) via autophagy (ER-phagy) is initiated by ER-phagy receptors, which facilitate the incorporation of ER fragments into autophagosomes. FAM134 reticulon family proteins (FAM134A, FAM134B, and FAM134C) ... ...

Abstract	Selective degradation of the endoplasmic reticulum (ER) via autophagy (ER-phagy) is initiated by ER-phagy receptors, which facilitate the incorporation of ER fragments into autophagosomes. FAM134 reticulon family proteins (FAM134A, FAM134B, and FAM134C) are ER-phagy receptors with structural similarities and nonredundant functions. Whether they respond differentially to the stimulation of ER-phagy is unknown. Here, we describe an activation mechanism unique to FAM134C during starvation. In fed conditions, FAM134C is phosphorylated by casein kinase 2 (CK2) at critical residues flanking the LIR domain. Phosphorylation of these residues negatively affects binding affinity to the autophagy proteins LC3. During starvation, mTORC1 inhibition limits FAM134C phosphorylation by CK2, hence promoting receptor activation and ER-phagy. Using a novel tool to study ER-phagy in vivo and FAM134C knockout mice, we demonstrated the physiological relevance of FAM134C phosphorylation during starvation-induced ER-phagy in liver lipid metabolism. These data provide a mechanistic insight into ER-phagy regulation and an example of autophagy selectivity during starvation.
Language	English
Publishing date	2022-08-31
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.abo1215
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Article ; Online: mTORC1 hyperactivation arrests bone growth in lysosomal storage disorders by suppressing autophagy.

Bartolomeo, Rosa / Cinque, Laura / De Leonibus, Chiara / Forrester, Alison / Salzano, Anna Chiara / Monfregola, Jlenia / De Gennaro, Emanuela / Nusco, Edoardo / Azario, Isabella / Lanzara, Carmela / Serafini, Marta / Levine, Beth / Ballabio, Andrea / Settembre, Carmine

The Journal of clinical investigation

2017 Volume 127, Issue 10, Page(s) 3717–3729

Abstract: The mammalian target of rapamycin complex 1 (mTORC1) kinase promotes cell growth by activating biosynthetic pathways and suppressing catabolic pathways, particularly that of macroautophagy. A prerequisite for mTORC1 activation is its translocation to the ...

Abstract	The mammalian target of rapamycin complex 1 (mTORC1) kinase promotes cell growth by activating biosynthetic pathways and suppressing catabolic pathways, particularly that of macroautophagy. A prerequisite for mTORC1 activation is its translocation to the lysosomal surface. Deregulation of mTORC1 has been associated with the pathogenesis of several diseases, but its role in skeletal disorders is largely unknown. Here, we show that enhanced mTORC1 signaling arrests bone growth in lysosomal storage disorders (LSDs). We found that lysosomal dysfunction induces a constitutive lysosomal association and consequent activation of mTORC1 in chondrocytes, the cells devoted to bone elongation. mTORC1 hyperphosphorylates the protein UV radiation resistance-associated gene (UVRAG), reducing the activity of the associated Beclin 1-Vps34 complex and thereby inhibiting phosphoinositide production. Limiting phosphoinositide production leads to a blockage of the autophagy flux in LSD chondrocytes. As a consequence, LSD chondrocytes fail to properly secrete collagens, the main components of the cartilage extracellular matrix. In mouse models of LSD, normalization of mTORC1 signaling or stimulation of the Beclin 1-Vps34-UVRAG complex rescued the autophagy flux, restored collagen levels in cartilage, and ameliorated the bone phenotype. Taken together, these data unveil a role for mTORC1 and autophagy in the pathogenesis of skeletal disorders and suggest potential therapeutic approaches for the treatment of LSDs.
MeSH term(s)	Animals ; Autophagy ; Beclin-1/genetics ; Beclin-1/metabolism ; Bone Development ; Chondrocytes/metabolism ; Chondrocytes/pathology ; Lysosomal Storage Diseases/genetics ; Lysosomal Storage Diseases/metabolism ; Lysosomal Storage Diseases/pathology ; Mechanistic Target of Rapamycin Complex 1 ; Mice ; Mice, Knockout ; Multiprotein Complexes/genetics ; Multiprotein Complexes/metabolism ; Phosphatidylinositols/genetics ; Phosphatidylinositols/metabolism ; Phosphorylation/genetics ; Phosphorylation/radiation effects ; TOR Serine-Threonine Kinases/genetics ; TOR Serine-Threonine Kinases/metabolism ; Ultraviolet Rays
Chemical Substances	Beclin-1 ; Becn1 protein, mouse ; Multiprotein Complexes ; Phosphatidylinositols ; TOR Serine-Threonine Kinases (EC 2.7.1.1) ; Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1)
Language	English
Publishing date	2017-10-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	3067-3
ISSN	1558-8238 ; 0021-9738
ISSN (online)	1558-8238
ISSN	0021-9738
DOI	10.1172/JCI94130
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Article ; Online: MiT/TFE factors control ER-phagy via transcriptional regulation of FAM134B.

Cinque, Laura / De Leonibus, Chiara / Iavazzo, Maria / Krahmer, Natalie / Intartaglia, Daniela / Salierno, Francesco Giuseppe / De Cegli, Rossella / Di Malta, Chiara / Svelto, Maria / Lanzara, Carmela / Maddaluno, Marianna / Wanderlingh, Luca Giorgio / Huebner, Antje K / Cesana, Marcella / Bonn, Florian / Polishchuk, Elena / Hübner, Christian A / Conte, Ivan / Dikic, Ivan /

Mann, Matthias / Ballabio, Andrea / Sacco, Francesca / Grumati, Paolo / Settembre, Carmine

The EMBO journal

2020 Volume 39, Issue 17, Page(s) e105696

Abstract: Lysosomal degradation of the endoplasmic reticulum (ER) via autophagy (ER-phagy) is emerging as a critical regulator of cell homeostasis and function. The recent identification of ER-phagy receptors has shed light on the molecular mechanisms underlining ... ...

Abstract	Lysosomal degradation of the endoplasmic reticulum (ER) via autophagy (ER-phagy) is emerging as a critical regulator of cell homeostasis and function. The recent identification of ER-phagy receptors has shed light on the molecular mechanisms underlining this process. However, the signaling pathways regulating ER-phagy in response to cellular needs are still largely unknown. We found that the nutrient responsive transcription factors TFEB and TFE3-master regulators of lysosomal biogenesis and autophagy-control ER-phagy by inducing the expression of the ER-phagy receptor FAM134B. The TFEB/TFE3-FAM134B axis promotes ER-phagy activation upon prolonged starvation. In addition, this pathway is activated in chondrocytes by FGF signaling, a critical regulator of skeletal growth. FGF signaling induces JNK-dependent proteasomal degradation of the insulin receptor substrate 1 (IRS1), which in turn inhibits the PI3K-PKB/Akt-mTORC1 pathway and promotes TFEB/TFE3 nuclear translocation and enhances FAM134B transcription. Notably, FAM134B is required for protein secretion in chondrocytes, and cartilage growth and bone mineralization in medaka fish. This study identifies a new signaling pathway that allows ER-phagy to respond to both metabolic and developmental cues.
MeSH term(s)	Active Transport, Cell Nucleus ; Animals ; Autophagy ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Endoplasmic Reticulum/genetics ; Endoplasmic Reticulum/metabolism ; HeLa Cells ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Mechanistic Target of Rapamycin Complex 1/genetics ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Mice ; Oryzias ; Signal Transduction
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Fam134b protein, mouse ; Intracellular Signaling Peptides and Proteins ; Membrane Proteins ; RETREG1 protein, human ; TFE3 protein, human ; TFEB protein, human ; Tcfeb protein, mouse ; Tcfe3 protein, mouse (136896-33-8) ; Mechanistic Target of Rapamycin Complex 1 (EC 2.7.11.1)
Language	English
Publishing date	2020-07-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.15252/embj.2020105696
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