Quick Guide: TFEB

What is TFEB?

TFEB (Transcription Factor EB) is a member of the MiT/TFE family of basic helix-loop-helix leucine zipper transcription factors that orchestrates cellular responses against a variety of stress conditions.

What does it do?

Upon stress, TFEB translocates from the cytosol to the nucleus and binds to specific sequences in the promoter of multiple lysosomal and autophagic genes, thus inducing their upregulation. As a result, the degradative capacity of the cell is enhanced, facilitating the elimination of waste material and favoring catabolic processes that restore energy homeostasis.

Is that all?

Nope, there is more. TFEB activates in response to many different types of stress conditions, including, nutrient deprivation, oxidative stress, mitochondrial malfunction, lysosomal rupture, accumulation of unfolded proteins in the endoplasmic reticulum, bacterial and viral infection, DNA damage, and physical exercise, among others. In the nucleus, TFEB upregulates not only autophagy and lysosomal biogenesis, but also expression of key genes that facilitate stress-specific responses. These include the unfolded protein response, DNA repair, expression of antioxidant genes and inflammatory cytokines, cell cycle control, carbohydrate and lipid metabolic regulation, mitochondrial biogenesis, mitophagy and lysophagy (Figure 1). Furthermore, TFEB participates in several developmental processes, such as monocyte and stem cell differentiation, bone resorption, circadian cycles, vascular development, induction of hepatic bile acid synthesis, restoration of the intestinal epithelial barrier and myelinization repression.

Figure 1. TFEB global picture.

(A) Phosphorylation of TFEB by different cellular kinases regulates its shuttling between cytosol (inactive) and nucleus (active). (B) TFEB promotes autophagy, lysosomal biogenesis, and stress responses upon activation. (C) Tissue-specific functions of TFEB. (D) TFEB involvement in human diseases.

Does TFEB do all of that by itself?

TFEB can heterodimerize with other members of the MiT/TFE family, which includes TFE3, MITF, and TFEC. There is also evidence of a high level of redundancy and cooperation between TFEB and TFE3 in multiple tissues.

Who has MiT/TFE transcription factors, and how many?

The four members of the MiT/TFE family are present in most metazoan organisms, including humans. In some cases, like zebrafish, gene duplication resulted in a total of six genes encoding MiT/TFE proteins (Tfeb, Tfe3a, Tfe3b, Mitfa, Mitfb, and Tfec). In contrast, only one member of the family is present in Drosophila melanogaster (Mitf) and Caenorhabditis elegans (HLH-30).

How is TFEB regulated?

Despite being a transcription factor, TFEB spends most of its time sequestered in the cytosol. This retention requires binding of TFEB to active Rags, a family of heterodimeric small GTPases that undergo conformational changes in response to cellular cues, such as changes in nutrient levels. In basal conditions, Rags recruit both TFEB and the serine/threonine kinase mTORC1 to the limiting membrane of the lysosome, facilitating Rheb-dependent activation of the kinase. Active mTORC1 phosphorylates TFEB in several resides, including serine 211 (S211), generating a binding site for 14-3-3, a cytosolic chaperone that keeps TFEB retained in the cytosol. Stress conditions that cause inactivation of mTORC1 or Rags, as well as activation of specific phosphatases, such as calcineurin and PP2A, lead to dephosphorylation of TFEB-S211, preventing its interaction with 14-3-3 and inducing translocation of the transcription factor to the nucleus.

Additional post-translational modifications further contribute to the fine-tune regulation of TFEB cellular localization, stability, and conformation. These include phosphorylation by other cellular kinases, such as AMPK, AKT, p38 MAPK, CDK4/6, ERK1/2, GSK3β, MAP4K3, and PKCβ, as well as modifications like acetylation, SUMOylation, oxidation, glutathionylation, PARsylation, oxidation, and itaconatylation. It is also intriguing how some pathogens directly modify TFEB for their own benefit. For example, Legionella pneumophila effector SetA glucosylates TFEB in several residues to prevent 14-3-3 interaction and facilitate nuclear retention. Active TFEB enhances catabolic processes, such as autophagy, promoting generation of free amino acids required for bacteria survival and replication. In contrast, some viruses reduce TFEB activity to damper immune response. Coxsackievirus B3 proteinase 3 cleavages TFEB, attenuating its transcriptional response, while beta-coronaviruses, including SARS-CoV2 and MHV, induce TFEB ubiquitination and proteasomal degradation.

Is TFEB implicated in human diseases?

Excessive TFEB activation, as well as TFE3 and MITF, contribute to the pathogenesis of different types of cancer by promoting tumor progression, chemoresistance, and metastasis. These include renal cell carcinoma, alveolar soft part sarcoma, pancreatic ductal adenocarcinoma, melanoma, breast, prostate, and colorectal cancer. In most cases, chromosomal translocations and other rearrangements result in gene fusions that lack the regulatory region of TFEB implicated in cytosolic retention, causing constitutive activation of the protein. Loss-of-function mutations in folliculin, a TFEB and TFE3 negative regulator, also result in accumulation of the transcription factors in the nucleus, contributing to tumorigenesis in Birt-Hogg-Dube syndrome, a hereditary cancer condition characterized by numerous renal and lung cysts, skin tumors, and increased risk of kidney cancer. Increased TFEB expression and lysosomal biogenesis have also been reported in Systemic Lupus Erythematosus, suggesting that enhanced TFEB activity may promote autoimmune disorders. Quite interesting is the recent identification of a X-linked neurodevelopmental disorder characterized by intellectual disability, coarse facial dysmorphism, and pigmentary anomalies, linked to de novo missense mutations in the TFE3 Rag binding domain. These mutations result in TFE3 constitutive misslocalization in the nucleus, suggesting an important link between TFE3 signaling and development.

Reduced TFEB activity is also associated to disease. TFEB plays a critical role facilitating elimination of protein aggregates via its ability to induce autophagy, lysosomal biogenesis, and lysosomal exocytosis. Reduced TFEB expression and activation leads to impaired autophagy and accumulation of protein aggregates, impacting kidney disease pathogenesis in diverse conditions, such as cystinosis, diabetic nephropathy, and acute kidney disease, as well as pancreatitis, osteoarthritis, and liver disease. Defective TFEB function also contributes to several neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, X-linked spinal & bulbar muscular atrophy, and amyotrophic lateral sclerosis. Different aspects of TFEB regulation are dysfunctional in neurodegenerative diseases, including increased cytoplasmic retention, enhanced nuclear exit, and transcriptional incompetence.

What are some key questions that remain unanswered?

While the essential role of TFEB and TFE3 in cellular response to stress is well established, we still need to better understand how these transcription factors orchestrate cell type- and stress-specific transcriptional responses. It will be also important to identify chromatin modifications, as well as transcriptional activators and repressors, that may help adjusting the strength and extent of TFEB and TFE3-mediated responses. In this regard, it has been recently described that the histone arginine methyltransferase CARM1 and the histone chaperone FACT facilitate expression of TFEB targets. At the same time, TFEB modulates epigenetic programs by regulating expression of genes implicated in DNA demethylation. These studies emphasize the role of TFEB linking changes in environmental cues, chromatin remodeling, and gene expression.

Finally, is likely that the design of new pharmacological strategies aimed to enhance or mitigate TFEB-transcriptional responses may help alleviate the symptoms of a variety of immune, metabolic, and neurodegenerative diseases. Once again, ensuring specificity for particular cell types and transcriptional networks will be key to achieve positive outcomes.