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Article: Lysosomal calcium and autophagy.

Medina, Diego L

International review of cell and molecular biology

2021 Volume 362, Page(s) 141–170

Abstract: Lysosomal calcium is emerging as a modulator of autophagy and lysosomal compartment, an obligatory partner to complete the autophagic pathway. A variety of specific signals such as nutrient deprivation or oxidative stress can trigger lysosomal calcium- ... ...

Abstract	Lysosomal calcium is emerging as a modulator of autophagy and lysosomal compartment, an obligatory partner to complete the autophagic pathway. A variety of specific signals such as nutrient deprivation or oxidative stress can trigger lysosomal calcium-mediated nuclear translocation of the transcription factor EB (TFEB), a master regulator of global lysosomal function. Also, lysosomal calcium can promote the formation of autophagosome vesicles (AVs) by a mechanism that requires the production of the phosphoinositide PI3P by the VPS34 autophagic complex and the activation of the energy-sensing kinase AMPK. Additionally, lysosomal calcium plays a role in membrane fusion and fission events involved in cellular processes such as endocytic maturation, autophagosome-lysosome fusion, lysosomal exocytosis, and lysosomal reformation upon autophagy completion. Lysosomal calcium-dependent functions are defective in cellular and animal models of the non-selective cation channel TRPML1, whose mutations in humans cause the neurodegenerative lysosomal storage disease mucolipidosis type IV (MLIV). Lysosomal calcium is not only acting as a positive regulator of autophagy, but it is also responsible for turning-off this process through the reactivation of the mTOR kinase during prolonged starvation. More recently, it has been described the role of lysosomal calcium on an elegant sequence of intracellular signaling events such as membrane repair, lysophagy, and lysosomal biogenesis upon the induction of different grades of lysosomal membrane damage. Here, we will discuss these novel findings that re-define the importance of the lysosome and lysosomal calcium signaling at regulating cellular metabolism.
MeSH term(s)	Animals ; Autophagy ; Calcium/metabolism ; Calcium Channels/metabolism ; Endosomes/metabolism ; Humans ; Lysosomes/metabolism ; Models, Biological
Chemical Substances	Calcium Channels ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2021-04-20
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2427220-6
ISSN	1937-6448 ; 0074-7696
ISSN	1937-6448 ; 0074-7696
DOI	10.1016/bs.ircmb.2021.03.002
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Article ; Online: The rapidly evolving view of lysosomal storage diseases.

Parenti, Giancarlo / Medina, Diego L / Ballabio, Andrea

EMBO molecular medicine

2021 Volume 13, Issue 2, Page(s) e12836

Abstract: Lysosomal storage diseases are a group of metabolic disorders caused by deficiencies of several components of lysosomal function. Most commonly affected are lysosomal hydrolases, which are involved in the breakdown and recycling of a variety of complex ... ...

Abstract	Lysosomal storage diseases are a group of metabolic disorders caused by deficiencies of several components of lysosomal function. Most commonly affected are lysosomal hydrolases, which are involved in the breakdown and recycling of a variety of complex molecules and cellular structures. The understanding of lysosomal biology has progressively improved over time. Lysosomes are no longer viewed as organelles exclusively involved in catabolic pathways, but rather as highly dynamic elements of the autophagic-lysosomal pathway, involved in multiple cellular functions, including signaling, and able to adapt to environmental stimuli. This refined vision of lysosomes has substantially impacted on our understanding of the pathophysiology of lysosomal disorders. It is now clear that substrate accumulation triggers complex pathogenetic cascades that are responsible for disease pathology, such as aberrant vesicle trafficking, impairment of autophagy, dysregulation of signaling pathways, abnormalities of calcium homeostasis, and mitochondrial dysfunction. Novel technologies, in most cases based on high-throughput approaches, have significantly contributed to the characterization of lysosomal biology or lysosomal dysfunction and have the potential to facilitate diagnostic processes, and to enable the identification of new therapeutic targets.
MeSH term(s)	Autophagy ; Humans ; Lysosomal Storage Diseases ; Lysosomes ; Metabolic Diseases
Language	English
Publishing date	2021-01-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.15252/emmm.202012836
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Article ; Online: The Regulation of MiTF/TFE Transcription Factors Across Model Organisms: from Brain Physiology to Implication for Neurodegeneration.

Agostini, Francesco / Agostinis, Rossella / Medina, Diego L / Bisaglia, Marco / Greggio, Elisa / Plotegher, Nicoletta

Molecular neurobiology

2022 Volume 59, Issue 8, Page(s) 5000–5023

Abstract: The microphthalmia/transcription factor E (MiTF/TFE) transcription factors are responsible for the regulation of various key processes for the maintenance of brain function, including autophagy-lysosomal pathway, lipid catabolism, and mitochondrial ... ...

Abstract	The microphthalmia/transcription factor E (MiTF/TFE) transcription factors are responsible for the regulation of various key processes for the maintenance of brain function, including autophagy-lysosomal pathway, lipid catabolism, and mitochondrial homeostasis. Among them, autophagy is one of the most relevant pathways in this frame; it is evolutionary conserved and crucial for cellular homeostasis. The dysregulation of MiTF/TFE proteins was shown to be involved in the development and progression of neurodegenerative diseases. Thus, the characterization of their function is key in the understanding of the etiology of these diseases, with the potential to develop novel therapeutics targeted to MiTF/TFE proteins and to the autophagic process. The fact that these proteins are evolutionary conserved suggests that their function and dysfunction can be investigated in model organisms with a simpler nervous system than the mammalian one. Building not only on studies in mammalian models but also in complementary model organisms, in this review we discuss (1) the mechanistic regulation of MiTF/TFE transcription factors; (2) their roles in different regions of the central nervous system, in different cell types, and their involvement in the development of neurodegenerative diseases, including lysosomal storage disorders; (3) the overlap and the compensation that occur among the different members of the family; (4) the importance of the evolutionary conservation of these protein and the process they regulate, which allows their study in different model organisms; and (5) their possible role as therapeutic targets in neurodegeneration.
MeSH term(s)	Animals ; Humans ; Autophagy/physiology ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Brain/metabolism ; Lysosomes/metabolism ; Mammals/metabolism ; Microphthalmia-Associated Transcription Factor/genetics ; Microphthalmia-Associated Transcription Factor/metabolism ; Microphthalmos/metabolism
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Microphthalmia-Associated Transcription Factor ; MITF protein, human
Language	English
Publishing date	2022-06-04
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	645020-9
ISSN	1559-1182 ; 0893-7648
ISSN (online)	1559-1182
ISSN	0893-7648
DOI	10.1007/s12035-022-02895-3
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Article ; Online: TRPML1-/TFEB-Dependent Regulation of Lysosomal Exocytosis.

Di Paola, Simone / Medina, Diego L

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1925, Page(s) 143–144

Abstract: Emerging experimental evidences indicate that the lysosome can trigger a calcium signaling, via TRPML1/calcineurin/TFEB pathway, that promotes lysosomal exocytosis and clearance of lysosomal accumulation in various cellular models of lysosomal storage ... ...

Abstract	Emerging experimental evidences indicate that the lysosome can trigger a calcium signaling, via TRPML1/calcineurin/TFEB pathway, that promotes lysosomal exocytosis and clearance of lysosomal accumulation in various cellular models of lysosomal storage disorders (LSDs). Here, we described methods to determine TFEB activation and lysosomal exocytosis that may represent innovative tools to study lysosomal function and to develop novel therapeutic approaches to promote clearance in LSDs.
MeSH term(s)	Animals ; Autophagy ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Calcium/metabolism ; Exocytosis ; Humans ; Lysosomal Storage Diseases/metabolism ; Lysosomes/metabolism ; Signal Transduction ; Transient Receptor Potential Channels/metabolism
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; MCOLN1 protein, human ; TFEB protein, human ; Transient Receptor Potential Channels ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2019-01-23
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9018-4_12
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Article ; Online: Ca

Di Paola, Simone / Medina, Diego L

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1925, Page(s) 145–155

Abstract: Lysosomes are emerging as calcium store organelles that can modulate various intracellular processes such as the regulation of nutrient signaling through the activation of TFEB, a master gene for lysosomal function, or very specialized functions like ... ...

Abstract	Lysosomes are emerging as calcium store organelles that can modulate various intracellular processes such as the regulation of nutrient signaling through the activation of TFEB, a master gene for lysosomal function, or very specialized functions like lysosomal exocytosis. Here, we describe two different techniques that can be used to study these processes. In the case report, we described two studies where these methodologies allowed us to unravel the role of calcineurin in the dephosphorylation of TFEB as well as the involvement of TFEB in lysosomal exocytosis, respectively.
MeSH term(s)	Animals ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Calcineurin/metabolism ; Calcium/metabolism ; Cations, Divalent/metabolism ; Cell Culture Techniques/methods ; Cell Line ; Exocytosis ; HeLa Cells ; Humans ; Immunoblotting/methods ; Immunoprecipitation/methods ; Lysosomes/genetics ; Lysosomes/metabolism ; Mice ; Phosphorylation ; Transfection/methods
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Cations, Divalent ; TFEB protein, human ; Calcineurin (EC 3.1.3.16) ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2019-01-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9018-4_13
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Article ; Online: Investigation on lysosomal accumulation by a quantitative analysis of 2D phase-maps in digital holography microscopy.

Giugliano, Giusy / Schiavo, Michela / Pirone, Daniele / Běhal, Jaromír / Bianco, Vittorio / Montefusco, Sandro / Memmolo, Pasquale / Miccio, Lisa / Ferraro, Pietro / Medina, Diego L

Cytometry. Part A : the journal of the International Society for Analytical Cytology

2024

Abstract: Lysosomes are the terminal end of catabolic pathways in the cell, as well as signaling centers performing important functions such as the recycling of macromolecules, organelles, and nutrient adaptation. The importance of lysosomes in human health is ... ...

Abstract	Lysosomes are the terminal end of catabolic pathways in the cell, as well as signaling centers performing important functions such as the recycling of macromolecules, organelles, and nutrient adaptation. The importance of lysosomes in human health is supported by the fact that the deficiency of most lysosomal genes causes monogenic diseases called as a group Lysosomal Storage Diseases (LSDs). A common phenotypic hallmark of LSDs is the expansion of the lysosomal compartment that can be detected by using conventional imaging methods based on immunofluorescence protocols or overexpression of tagged lysosomal proteins. These methods require the alteration of the cellular architecture (i.e., due to fixation methods), can alter the behavior of cells (i.e., by the overexpression of proteins), and require sample preparation and the accurate selection of compatible fluorescent markers in relation to the type of analysis, therefore limiting the possibility of characterizing cellular status with simplicity. Therefore, a quantitative and label-free methodology, such as Quantitative Phase Imaging through Digital Holographic (QPI-DH), for the microscopic imaging of lysosomes in health and disease conditions may represent an important advance to study and effectively diagnose the presence of lysosomal storage in human disease. Here we proof the effectiveness of the QPI-DH method in accomplishing the detection of the lysosomal compartment using mouse embryonic fibroblasts (MEFs) derived from a Mucopolysaccharidosis type III-A (MSP-IIIA) mouse model, and comparing them with wild-type (WT) MEFs. We found that it is possible to identify label-free biomarkers able to supply a first pre-screening of the two populations, thus showing that QPI-DH can be a suitable candidate to surpass fluorescent drawbacks in the detection of lysosomes dysfunction. An appropriate numerical procedure was developed for detecting and evaluate such cellular substructures from in vitro cells cultures. Results reported in this study are encouraging about the further development of the proposed QPI-DH approach for such type of investigations about LSDs.
Language	English
Publishing date	2024-02-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2099868-5
ISSN	1552-4930 ; 0196-4763 ; 1552-4922
ISSN (online)	1552-4930
ISSN	0196-4763 ; 1552-4922
DOI	10.1002/cyto.a.24833
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Article ; Online: Cellular and Gene Expression Response to the Combination of Genistein and Kaempferol in the Treatment of Mucopolysaccharidosis Type I.

Węsierska, Magdalena / Kloska, Anna / Medina, Diego L / Jakóbkiewicz-Banecka, Joanna / Gabig-Cimińska, Magdalena / Radzińska, Marta / Moskot, Marta / Malinowska, Marcelina

International journal of molecular sciences

2022 Volume 23, Issue 3

Abstract: Flavonoids are investigated as therapeutics for mucopolysaccharidosis, a metabolic disorder with impaired glycosaminoglycan degradation. Here we determined the effects of genistein and kaempferol, used alone or in combination, on cellular response and ... ...

Abstract	Flavonoids are investigated as therapeutics for mucopolysaccharidosis, a metabolic disorder with impaired glycosaminoglycan degradation. Here we determined the effects of genistein and kaempferol, used alone or in combination, on cellular response and gene expression in a mucopolysaccharidosis type I model. We assessed the cell cycle, viability, proliferation, subcellular localization of the translocation factor EB (TFEB), number and distribution of lysosomes, and glycosaminoglycan synthesis after exposure to flavonoids. Global gene expression was analysed using DNA microarray and quantitative PCR. The type and degree of flavonoid interaction were determined based on the combination and dose reduction indexes. The combination of both flavonoids synergistically inhibits glycosaminoglycan synthesis, modulates TFEB localization, lysosomal number, and distribution. Genistein and kaempferol in a 1:1 ratio regulate the expression of 52% of glycosaminoglycan metabolism genes. Flavonoids show synergy, additivity, or slight antagonism in all analysed parameters, and the type of interaction depends on the concentration and component ratios. With the simultaneous use of genistein and kaempferol in a ratio of 4:1, even a 10-fold reduction in the concentration of kaempferol is possible. Flavonoid mixtures, used as the treatment of mucopolysaccharidosis, are effective in reducing glycosaminoglycan production and storage and show a slight cytotoxic effect compared to single-flavonoid usage.
MeSH term(s)	Flavonoids/pharmacology ; Gene Expression ; Genistein/pharmacology ; Glycosaminoglycans/metabolism ; Humans ; Kaempferols ; Mucopolysaccharidoses ; Mucopolysaccharidosis I ; Oligonucleotide Array Sequence Analysis
Chemical Substances	Flavonoids ; Glycosaminoglycans ; Kaempferols ; kaempferol (731P2LE49E) ; Genistein (DH2M523P0H)
Language	English
Publishing date	2022-01-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23031058
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Article: TFEB and the CLEAR network.

Settembre, Carmine / Medina, Diego L

Methods in cell biology

2015 Volume 126, Page(s) 45–62

Abstract: The general view of the lysosome as the terminal end of cellular catabolic pathways, has started to change due to the recent discoveries of a lysosomal nutrient sensing machinery and of a lysosome-to-nucleus signaling mechanism that modulate lysosomal ... ...

Abstract	The general view of the lysosome as the terminal end of cellular catabolic pathways, has started to change due to the recent discoveries of a lysosomal nutrient sensing machinery and of a lysosome-to-nucleus signaling mechanism that modulate lysosomal function by way of the master transcriptional regulator TFEB. Lysosomal biogenesis and autophagy are coordinated by TFEB, whose function is regulated by phosphorylation. TFEB interacts with and is phosphorylated by mTORC1 at the lysosomal surface. Thus, conditions resulting in inhibition of mTOR, such as starvation and lysosomal stress, promote TFEB nuclear translocation. Preliminary evidences showing that the TFEB activation are able to ameliorate the phenotype of lysosomal storage disorders and more common neurodegenerative diseases have opened an extraordinary possibility for the development of innovative therapies. Research in TFEB and lysosomal function has continued to advance and attract interest due to increased understanding of the mechanisms behind lysosomal function. In this paper, we present a set of procedures that facilitate examination of TFEB function and its related processes.
MeSH term(s)	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/physiology ; Gene Expression ; Gene Expression Regulation ; Gene Regulatory Networks ; HeLa Cells ; Humans ; Lysosomes/metabolism ; Phosphorylation ; Protein Processing, Post-Translational ; Protein Transport ; Proteins/genetics ; Proteins/metabolism
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Proteins ; TFEB protein, human ; lysosomal proteins
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article
ISSN	0091-679X
ISSN	0091-679X
DOI	10.1016/bs.mcb.2014.11.011
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Article ; Online: Lysosomal calcium regulates autophagy.

Medina, Diego L / Ballabio, Andrea

Autophagy

2015 Volume 11, Issue 6, Page(s) 970–971

Abstract: Recent evidence has indicated that the lysosome is able to act as a signaling organelle that senses nutrient availability and generates an adaptive response that is important for cellular homeostasis. We recently discovered another example of lysosomal ... ...

Abstract	Recent evidence has indicated that the lysosome is able to act as a signaling organelle that senses nutrient availability and generates an adaptive response that is important for cellular homeostasis. We recently discovered another example of lysosomal signaling where lysosomal calcium release activates the master autophagy regulator TFEB via the phosphatase calcineurin.
MeSH term(s)	Animals ; Autophagy/physiology ; Calcium/metabolism ; Calcium Signaling/physiology ; Gene Expression Regulation/physiology ; Humans ; Lysosomes/metabolism ; Protein Transport/physiology
Chemical Substances	Calcium (SY7Q814VUP)
Language	English
Publishing date	2015-05-22
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2015.1047130
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Article ; Online: Activation of Ca

Marchesan, Elena / Nardin, Alice / Mauri, Sofia / Bernardo, Greta / Chander, Vivek / Di Paola, Simone / Chinellato, Monica / von Stockum, Sophia / Chakraborty, Joy / Herkenne, Stephanie / Basso, Valentina / Schrepfer, Emilie / Marin, Oriano / Cendron, Laura / Medina, Diego L / Scorrano, Luca / Ziviani, Elena

Cell death and differentiation

2024 Volume 31, Issue 2, Page(s) 217–238

Abstract: Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/ ... ...

Abstract	Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin-decorated mitochondria are selectively recruiting autophagy receptors, which are required to terminate the organelle via autophagy. In this work, we show a previously uncharacterized molecular pathway that correlates the activation of the Ca
MeSH term(s)	Animals ; Calcineurin/metabolism ; Protein Kinases/genetics ; Protein Kinases/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Mitophagy/genetics ; Mitochondria/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitin/metabolism ; Drosophila/metabolism ; Protein Serine-Threonine Kinases/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism
Chemical Substances	Calcineurin (EC 3.1.3.16) ; Protein Kinases (EC 2.7.-) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Ubiquitin ; PINK1 protein, Drosophila (EC 2.7.11.1) ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Drosophila Proteins
Language	English
Publishing date	2024-01-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1225672-9
ISSN	1476-5403 ; 1350-9047
ISSN (online)	1476-5403
ISSN	1350-9047
DOI	10.1038/s41418-023-01251-9
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