Ballabio's Lab

Our laboratory is focused on the study of the lysosome and its role in the control of cell metabolism in health and disease. The lysosome has always been viewed as a cellular "incinerator" that performs “housekeeping” functions. Discoveries from our laboratory, as well as from other labs, have challenged this view and postulated that the lysosome is a dynamic structure that controls cell metabolism.

The lysosome as control center of cell metabolism

We discovered that lysosomal function is subject to a global transcriptional control exerted by TFEB, a master regulator of lysosomal genes (Science 2009, 325:473-7). We also found that TFEB also controls autophagy by regulating genes involved in several steps of the autophagic pathway (Science 2011, 332:1429-33.)

TFEB, a remote control that modulates the expression levels of lysosomal and autophagic genes

We showed that induction of lysosomal biogenesis and autophagy via TFEB is a potent tool to promote intra-cellular clearance (Dev Cell 2011, 21:421-30). This approach has been used by several groups to rescue the phenotype of mouse models of human diseases, such as lysosomal storage disorders and neurodegenerative diseases.

Further studies showed that the activity of TFEB is regulated by the mechanistic Target Of Rapamycin Complex 1 (mTORC1), a central hub of cell metabolism, which inhibits TFEB cytoplasm-to-nucleus translocation.

We identified a feedback loop mechanism by which TFEB is not only a substrate but also a regulator of mTORC1 (Science 2017, 356:1188-1192). This feedback loop enables adaptation of cell metabolism to nutrient availability.

TFEB-mTORC1 feedback loop

More recently, we produced the first evidence that mTORC1 can mediate specific responses to several environmental cues by differential substrate phosphorylation (Nature 2020 585:597-602). We identified a non-canonical, substrate-specific, mTORC1 signalling pathway by which mTORC1 phosphorylates TFEB (as well as TFE3, another member of the MiT-TFE family), differently from S6K and 4EBP1.

Recently, through a collaborative effort with Jim Hurley's and Lukas Huber's groups we obtained structural evidence for the co-existence of canonical and non-canonical mTORC1 signalling pathways (Nature 2023, 614:572-579.)

Cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator megacomplex. (Hurley’s, Huber’s and Ballabio’s labs, Nature,2023).

We also discovered that in Birt-Hogg-Dube' (BHD) inherited cancer syndrome, FLCN gene mutations lead to dysregulation of non-canonical mTORC1 pathway, resulting in constitutive activation of TFEB/TFE3. This causes imbalance of cell metabolism and impaired switch between anabolism and catabolism.

TFEB-mTORC1 feedback loop as a switch between catabolism and anabolism.

Constitutive activation of TFEB/TFE3 leads to imbalance of cell metabolism

By studying transgenic mice and mouse xenografts we demonstrated that TFEB and TFE3 are the main drivers of the renal cystic and tumorigenic phenotype observed in BHD syndrome (Nature 2023; 614, 572–579 and EMBO Mol Med. 2023;15(5):e16877). Remarkably, deletion of TFEB completely rescued renal cystogenesis and tumorigenesis, as well as mTORC1 hyperactivation, in a kidney-specific BHD mouse model. Recently, in collaboration with the group of Lisa Henske at Harvard, we obtained evidence that TFEB also plays a crucial role in kidney tumorigenesis in Tuberous Sclerosis Complex (TSC).

The TFEB/mTORC1 pathway promotes kidney cystogenesis and tumorigenesis.

Lab Projects

Based on these exciting discoveries and on recently funded grants, including an Advanced ERC grant that is due to start in 2023, our lab will start new projects focused on the identification of key components of the lysosomal non-canonical mTORC1 signaling pathway and the characterization of its role in the control of TFEB and TFE3 transcription factors.

We are also studying the consequences of TFEB and TFE3 dysregulation in inherited cancer syndromes. These are a group of autosomal dominant diseases in which affected individuals are at risk for developing multiple types of tumors, which are caused by somatic, “second-hit”, mutations of the normal allele, resulting in loss-of-heterozygosity (LOH).

In particular, our lab will focus on two inherited cancer syndromes: Birt-Hogg-Dube' (BHD) syndrome and Tuberous Sclerosis Complex (TSC), both associated to kidney cancer and caused by mutations of the FLCN and TSC1/2 genes, respectively.

Indeed we and others recently discovered that loss of function of the FLCN and TSC1/2 genes in BHD and TSC leads to constitutive activation of TFEB and TFE3, members of the MiT-TFE family of transcription factors, which were found to be the main drivers of disease phenotype.

Objectives

1) Identify novel components of non-canonical mTORC1 pathway and key regulators of MiT-TFE factors.

2) Elucidate the pathogenic role of MiT-TFE factors in kidney and brain.

3) Develop new disease models of inherited cancer syndromes, which better recapitulate the corresponding human diseases.

4) Determine the cascade of events leading from LOH of the FLCN and TSC2 genes to kidney cystogenesis and tumorigenesis.

5) Develop novel therapeutic strategies to prevent/suppress the oncogenic activity of MiT-TFE factoirs.

Approaches

To achieve these aims we are going to use a variety of approaches, such as molecular and cell biology, biochemistry, genomic-transcriptomic-proteomic analyses, mouse genetic models and mouse xenografts, organoids, viral mediated gene transfer, and CRISPR-siRNA-drug screenings.

Selected Publications

Sambri I, Ferniani M, Campostrini G, Testa M, Meraviglia V, de Araujo MEG, Dokládal L, Vilardo C, Monfregola J, Zampelli N, Vecchio Blanco FD, Torella A, Ruosi C, Fecarotta S, Parenti G, Staiano L, Bellin M, Huber LA, De Virgilio C, Trepiccione F, Nigro V, Ballabio A. RagD auto-activating mutations impair MiT/TFE activity in kidney tubulopathy and cardiomyopathy syndrome. Nat Commun. 2023 May 15;14(1):2775. doi: 10.1038/s41467-023-38428-2. PMID: 37188688.
Di Malta C, Zampelli A, Granieri L, Vilardo C, De Cegli R, Cinque L, Nusco E, Pece S, Tosoni D, Sanguedolce F, Sorrentino NC, Merino MJ, Nielsen D, Srinivasan R, Ball MW, Ricketts CJ, Vocke CD, Lang M, Karim B, Lanfrancone L, Schmidt LS, Linehan WM, Ballabio A. TFEB and TFE3 drive kidney cystogenesis and tumorigenesis. EMBO Mol Med. 2023 May 8;15(5):e16877. doi: 10.15252/emmm.202216877. Epub 2023 Mar 29. PMID: 36987696; PMCID: PMC10165358.
Cui Z, Napolitano G, de Araujo MEG, Esposito A, Monfregola J, Huber LA, Ballabio A, Hurley JH. Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. Nature. 2023 Feb;614(7948):572-579. doi: 10.1038/s41586-022-05652-7. Epub 2023 Jan 25. PMID: 36697823; PMCID: PMC9931586.
Napolitano G, Di Malta C, Esposito A, de Araujo MEG, Pece S, Bertalot G, Matarese M, Benedetti V, Zampelli A, Stasyk T, Siciliano D, Venuta A, Cesana M, Vilardo C, Nusco E, Monfregola J, Calcagnì A, Di Fiore PP, Huber LA, Ballabio A. A substrate-specific mTORC1 pathway underlies Birt-Hogg-Dubé syndrome. Nature. 2020 Sep;585(7826):597-602. doi: 10.1038/s41586-020-2444-0. Epub 2020 Jul 1. PMID: 32612235; PMCID: PMC7610377.
Di Malta C, Siciliano D, Calcagni A, Monfregola J, Punzi S, Pastore N, Eastes AN, Davis O, De Cegli R, Zampelli A, Di Giovannantonio LG, Nusco E, Platt N, Guida A, Ogmundsdottir MH, Lanfrancone L, Perera RM, Zoncu R, Pelicci PG, Settembre C, Ballabio A. Transcriptional activation of RagD GTPase controls mTORC1 and promotes cancer growth. Science. 2017 Jun 16;356(6343):1188-1192. doi: 10.1126/science.aag2553. PMID: 28619945; PMCID: PMC5730647.
Mansueto G, Armani A, Viscomi C, D'Orsi L, De Cegli R, Polishchuk EV, Lamperti C, Di Meo I, Romanello V, Marchet S, Saha PK, Zong H, Blaauw B, Solagna F, Tezze C, Grumati P, Bonaldo P, Pessin JE, Zeviani M, Sandri M, Ballabio A. Transcription Factor EB Controls Metabolic Flexibility during Exercise. Cell Metab. 2017 Jan 10;25(1):182-196. doi: 10.1016/j.cmet.2016.11.003. Epub 2016 Dec 20. PMID: 28011087; PMCID: PMC5241227.
Medina DL, Di Paola S, Peluso I, Armani A, De Stefani D, Venditti R, Montefusco S, Scotto-Rosato A, Prezioso C, Forrester A, Settembre C, Wang W, Gao Q, Xu H, Sandri M, Rizzuto R, De Matteis MA, Ballabio A. Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. Nat Cell Biol. 2015 Mar;17(3):288-99. doi: 10.1038/ncb3114. PMID: 25720963; PMCID: PMC4801004.
Settembre C, Zoncu R, Medina DL, Vetrini F, Erdin S, Erdin S, Huynh T, Ferron M, Karsenty G, Vellard MC, Facchinetti V, Sabatini DM, Ballabio A. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. EMBO J. 2012 Mar 7;31(5):1095-108. doi: 10.1038/emboj.2012.32. Epub 2012 Feb 17. PMID: 22343943; PMCID: PMC3298007.
Settembre C, Di Malta C, Polito VA, Garcia Arencibia M, Vetrini F, Erdin S, Erdin SU, Huynh T, Medina D, Colella P, Sardiello M, Rubinsztein DC, Ballabio A. TFEB links autophagy to lysosomal biogenesis. Science. 2011 Jun 17;332(6036):1429-33. doi: 10.1126/science.1204592. Epub 2011 May 26. PMID: 21617040; PMCID: PMC3638014.
Sardiello M, Palmieri M, di Ronza A, Medina DL, Valenza M, Gennarino VA, Di Malta C, Donaudy F, Embrione V, Polishchuk RS, Banfi S, Parenti G, Cattaneo E, Ballabio A. A gene network regulating lysosomal biogenesis and function. Science. 2009 Jul 24;325(5939):473-7. doi: 10.1126/science.1174447. Epub 2009 Jun 25. PMID: 19556463.

Selected Reviews

Napolitano G, Di Malta C, Ballabio A. Non-canonical mTORC1 signaling at the lysosome. Trends Cell Biol. 2022 Nov;32(11):920-931. doi: 10.1016/j.tcb.2022.04.012. Epub 2022 May 30. PMID: 35654731.

Parenti G, Medina DL, Ballabio A. The rapidly evolving view of lysosomal storage diseases. EMBO Mol Med. 2021 Feb 5;13(2):e12836. doi: 10.15252/emmm.202012836. Epub 2021 Jan 18. PMID: 33459519; PMCID: PMC7863408.

Ballabio A, Bonifacino JS. Lysosomes as dynamic regulators of cell and organismal homeostasis. Nat Rev Mol Cell Biol. 2020 Feb;21(2):101-118. doi: 10.1038/s41580-019-0185-4. Epub 2019 Nov 25. PMID: 31768005.

Perera RM, Di Malta C, Ballabio A. MiT/TFE Family of Transcription Factors, Lysosomes, and Cancer. Annu Rev Cancer Biol. 2019 Mar;3:203-222. doi: 10.1146/annurev-cancerbio-030518-055835. Epub 2018 Nov 28. PMID: 31650096; PMCID: PMC6812561.

Pastore N, Ballabio A. Keeping the autophagy tempo. Autophagy. 2019 Oct;15(10):1854-1856. doi: 10.1080/15548627.2019.1645545. Epub 2019 Jul 24. PMID: 31318631; PMCID: PMC6735489.

Napolitano G, Ballabio A. TFEB at a glance. J Cell Sci. 2016 Jul 1;129(13):2475-81. doi: 10.1242/jcs.146365. Epub 2016 Jun 1. PMID: 27252382; PMCID: PMC4958300.

Ballabio A. The awesome lysosome. EMBO Mol Med. 2016 Feb 1;8(2):73-6. doi: 10.15252/emmm.201505966. PMID: 26787653; PMCID: PMC4734841.

Open Positions

We are hiring !

We are looking for bright and motivated Post-Docs and PhD students to work on the above-listed projects

To Join the Lab please send an email with your CV, a motivational letter and the name and contact info of two referees to Floriana Forzati: f.forzati@tigem.it

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