Published OnlineFirst August 29, 2017; DOI: 10.1158/1541-7786.MCR-17-0320 Review Molecular Cancer Research The MiTF/TFE Family of Transcription Factors: Master Regulators of Organelle Signaling, Metabolism, and Stress Adaptation Logan Slade and Thomas Pulinilkunnil Abstract The microphthalmia family (MITF, TFEB, TFE3, and TFEC) of mote tumorigenesis is reviewed. Likewise, the emerging function transcription factors is emerging as global regulators of cancer cell of the Folliculin (FLCN) tumor suppressor in negatively regulat- survival and energy metabolism, both through the promotion of ing the MiT/TFE family and how loss of this pathway promotes lysosomal genes as well as newly characterized targets, such as cancer is examined. Recent reports are also presented that relate to oxidative metabolism and the oxidative stress response. In addi- the role of MiT/TFE–driven lysosomal biogenesis in sustaining tion, MiT/TFE factors can regulate lysosomal signaling, which cancer cell metabolism and signaling in nutrient-limiting condi- includes the mTORC1 and Wnt/b-catenin pathways, which are tions. Finally, a discussion is provided on the future directions and both substantial contributors to oncogenic signaling. This review unanswered questions in the field. In summary, the research describes recent discoveries in MiT/TFE research and how they surrounding the MiT/TFE family indicates that these transcription impact multiple cancer subtypes. Furthermore, the literature factors are promising therapeutic targets and biomarkers for relating to TFE-fusion proteins in cancers and the potential cancers that thrive in stressful niches. Mol Cancer Res; 1–7. Ó2017 mechanisms through which these genomic rearrangements pro- AACR. Introduction Lysosomal Expression and Regulation (CLEAR) elements are recognized by the MITF family, which in turn promotes gene MITF is an evolutionarily conserved transcription factor with transcription (9, 10). Genome-wide chromatin immunoprecip- homologs identified in C. elegans and Drosophila (1). The MITF itation sequencing analysis demonstrated direct binding of family encodes four distinct genes; MITF, TFEB, TFE3,and TFEB to CLEAR elements with concomitant increment in lyso- TFEC. Structurally, MITF genes constitute a double helix leucine somalproteins(11).GenesthataremostassociatedwithTFEB zipper motif, a transactivating zone, and a domain responsible regulation contain clusters of multiple CLEAR sequences. for DNA contact and binding. The MiT/TFE family of basic Genome-wide analysis for clustered CLEAR sequences identi- helix-loop-helix (bHLH) transcription factors recognizes the fied 471 direct TFEB targets, which include lysosomal acidifi- transcription initiation or E-box (Ephrussi boxes) sites cation and degradation enzymes along with autophagy, exo-, (CANNTG) in the genome (2). The initial identification of the endo-, and phagocytosis genes. Surprisingly, several gene tar- microphthalmia family of transcription factors revealed that gets of TFEB also included those executing glucose and lipid MiT/TFEs must homodimerize or heterodimerize with another metabolism, perhaps underscoring the direct connection member of the MiT/TFE family to activate transcription (3–6). between lysosomal function and metabolism (Fig. 1; ref. 11). Early studies into the function of these transcription factors Subsequent reports have also identified that both TFE3 and identified that mutations in MITF led to Waardenburg syn- MITF are capable of binding CLEAR sequence elements to drome type II, characterized by hypopigmentation and defects induce lysosomal biogenesis and autophagy in a comparable in ectodermal development (7), while murine homozygous manner (12, 13). TFEB knockouts fail to develop due to lack of placental vas- The autophagy–lysosome system is a catabolic cellular process cularization (8). More recently, MITF, TFEB, and TFE3 were for whole organelles, protein aggregates, and other macromole- identified as regulators of lysosomal function and metabolism. cules (14). During carcinogenesis, autophagy exerts an antitu- Numerous lysosomal and autophagy genes with one or more morigenic effect by degrading and/or recycling damaged cellular 10 base pair motifs (GTCACGTGAC) termed as Coordinated organelles, thereby blocking the accumulation of endogenous mutagens, and preventing further genomic alterations. However, following tumor induction, cancer cells coopt autophagy as a cell Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dal- survival mechanism to promote nutrient reallocation for diverse housie University, Dalhousie Medicine New Brunswick, New Brunswick, Canada. cellular needs. Therefore, autophagy can suppress cancer devel- Corresponding Author: Thomas Pulinilkunnil, Department of Biochemistry and opment through its cytoprotective properties; however, once Molecular Biology, Dalhousie University, Dalhousie Medicine New Brunswick, cancer has developed, these same properties sustain survival of 100 Tucker Park Road, Saint John, New Brunswick E2L4L5, Canada. Phone: 1- the tumor (15). Cytoprotective and oncoprotective properties of 506-636-6973; Fax: 1-506-636-6001; E-mail: [email protected] autophagy include managing oxidative stress, preventing DNA doi: 10.1158/1541-7786.MCR-17-0320 damage, and supporting metabolism under nutrient-depleted Ó2017 American Association for Cancer Research. conditions (15, 16). Adaptive metabolic reprogramming of www.aacrjournals.org OF1 Downloaded from mcr.aacrjournals.org on September 26, 2021. © 2017 American Association for Cancer Research. Published OnlineFirst August 29, 2017; DOI: 10.1158/1541-7786.MCR-17-0320 Slade and Pulinilkunnil Figure 1. Regulation and downstream targets of the Microphthalmia family of transcription factors: TFEB, TFE3, and MITF are negatively regulated through phosphorylation by mTORC1, where they are then restricted to the cytosol by chaperone protein 14-3-3. Phosphorylation is reversed by calcineurin (CaN), although no reports have yet investigated whether this is true for MITF, and the dephosphorylated proteins are free to enter the nucleus, where they bind to E-boxes, CLEAR sequences, and M-boxes to promote transcription of associated genes. Genes regulated by TFEB, TFE3, and MITF promote autophagy and lysosomal catabolism, along with mitochondrial biogenesis. Cell processes regulated by the microphthalmia TFs sustain cell metabolism through ensuring a supply of amino acids, which feed protein and nucleotide biosynthesis, while also regulating to supply of energy via mitochondrial oxidative phosphorylation. Gene targets downstream of CLEAR sequences also include those that respond to oxidative stress, such as key components of the glutathione system. cancer cells provides them with the ability to utilize diverse fusion, places TFEB under the control of a more active promoter substrates as the building blocks for molecules necessary for resulting in a 60-fold higher expression (20). Crucially, the proliferation. Indeed, autophagy participates in this program resulting protein products from the gene fusion events still have through degradation of lipids and proteins within lysosomes functional basic helix-loop-helix domains and nuclear localiza- to derive substrates for nucleic acid and membrane biosynthe- tion signals, keeping the transcriptional activation function sis (14, 16). The microphthalmia family of transcription factors intact (18). It has been reported that lysosomal localization, are regulators of the autophagy–lysosome system (Fig. 1), and and thus inhibition, of MiT/TFEs requires the first 30 amino increasing evidence suggests that they also directly regulate acids, corresponding to exon 1 (21). All reported gene fusions metabolic and growth signaling pathways, and as such, re- eliminate exon 1 from the resulting protein, indicating that the present an attractive therapeutic target with wide potential fusion proteins are unlikely to be able to localize to the lyso- cancer. This review will discuss the prospect of MITF, TFEB, and some, suggesting a mechanism of constitutive activation (18). TFE3 as necessary elements for the viability of several cancer Further associating MiT/TFEs in renal neoplasia is a kidney- types with specific emphasis on changes in cellular autophagy specific TFEB overexpression mouse model that developed severe and metabolism. kidney enlargement with multiple cysts at 30 days following birth, while Ki-67–positive neoplastic lesions were detected as soon as 12 days after birth (22). Renal-specific TFEB overexpres- Role of TFEB and TFE3 as Oncogenes sion also resulted in liver metastasis in 23% of mice (22). There A number of studies have determined TFE3 and TFEB as being are no reports about the activity of TFE fusion proteins; however, oncogenes. Chromosomal translocations resulting in gene a case study has identified strong nuclear staining of the TFE3 fusions involving TFE3 or TFEB are implicated in the develop- fusion protein, and a cell line and xenograft model generated ment of sporadic renal cell carcinomas (RCC) and soft tissue from the patient maintained this nuclear localization (23), a sarcomas. These genetic rearrangements cause overexpression of result that has been reproduced in several other IHC screens of the TFE proteins (17–19), and in the case of TFEB-MALAT1 TFE3 and TFEB translocation cancers (17, 24, 25). OF2 Mol Cancer Res; 2017 Molecular Cancer Research Downloaded from mcr.aacrjournals.org on September 26, 2021. © 2017 American Association for Cancer Research. Published OnlineFirst