bims-lymeca Biomed News
on Lysosome metabolism in cancer
Issue of 2022–04–03
eight papers selected by
Harilaos Filippakis, Harvard University
  1. ESCRT-I fuels lysosomal degradation to restrict TFEB/TFE3 signaling via the Rag-mTORC1 pathway.
  2. Quantitative phosphoproteomic analyses identify STK11IP as a lysosome-specific substrate of mTORC1 that regulates lysosomal acidification.
  3. Current methods to analyse lysosome morphology, positioning, motility and function.
  4. Folliculin promotes substrate-selective mTORC1 activity by activating RagC to recruit TFE3.
  5. Organelle transporters and inter-organelle communication as drivers of metabolic regulation and cellular homeostasis.
  6. Ca2+ regulation of constitutive vesicle trafficking.
  7. EWI2 promotes endolysosome-mediated turnover of growth factor receptors and integrins to suppress lung cancer.
  8. TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis.
  1. Life Sci Alliance. 2022 Jul;pii: e202101239. [Epub ahead of print]5(7):
    ESCRT-I fuels lysosomal degradation to restrict TFEB/TFE3 signaling via the Rag-mTORC1 pathway.
    Marta Wróbel, Jarosław Cendrowski, Ewelina Szymańska, Malwina Grębowicz-Maciukiewicz, Noga Budick-Harmelin, Matylda Macias, Aleksandra Szybińska, Michał Mazur, Krzysztof Kolmus, Krzysztof Goryca, Michalina Dąbrowska, Agnieszka Paziewska, Michał Mikula, Marta Miączyńska.
      Within the endolysosomal pathway in mammalian cells, ESCRT complexes facilitate degradation of proteins residing in endosomal membranes. Here, we show that mammalian ESCRT-I restricts the size of lysosomes and promotes degradation of proteins from lysosomal membranes, including MCOLN1, a Ca2+ channel protein. The altered lysosome morphology upon ESCRT-I depletion coincided with elevated expression of genes annotated to biogenesis of lysosomes due to prolonged activation of TFEB/TFE3 transcription factors. Lack of ESCRT-I also induced transcription of cholesterol biosynthesis genes, in response to inefficient delivery of cholesterol from endolysosomal compartments. Among factors that could possibly activate TFEB/TFE3 signaling upon ESCRT-I deficiency, we excluded lysosomal cholesterol accumulation and Ca2+-mediated dephosphorylation of TFEB/TFE3. However, we discovered that this activation occurs due to the inhibition of Rag GTPase-dependent mTORC1 pathway that specifically reduced phosphorylation of TFEB at S112. Constitutive activation of the Rag GTPase complex in cells lacking ESCRT-I restored S112 phosphorylation and prevented TFEB/TFE3 activation. Our results indicate that ESCRT-I deficiency evokes a homeostatic response to counteract lysosomal nutrient starvation, that is, improper supply of nutrients derived from lysosomal degradation.
    DOI:  https://doi.org/10.26508/lsa.202101239
  2. Nat Commun. 2022 Apr 01. 13(1): 1760
    Quantitative phosphoproteomic analyses identify STK11IP as a lysosome-specific substrate of mTORC1 that regulates lysosomal acidification.
    Zhenzhen Zi, Zhuzhen Zhang, Qiang Feng, Chiho Kim, Xu-Dong Wang, Philipp E Scherer, Jinming Gao, Beth Levine, Yonghao Yu.
      The evolutionarily conserved serine/threonine kinase mTORC1 is a central regulator of cell growth and proliferation. mTORC1 is activated on the lysosome surface. However, once mTORC1 is activated, it is unclear whether mTORC1 phosphorylates local lysosomal proteins to regulate specific aspects of lysosomal biology. Through cross-reference analyses of the lysosome proteome with the mTORC1-regulated phosphoproteome, we identify STK11IP as a lysosome-specific substrate of mTORC1. mTORC1 phosphorylates STK11IP at Ser404. Knockout of STK11IP leads to a robust increase of autophagy flux. Dephosphorylation of STK11IP at Ser404 represses the role of STK11IP as an autophagy inhibitor. Mechanistically, STK11IP binds to V-ATPase, and regulates the activity of V-ATPase. Knockout of STK11IP protects mice from fasting or Methionine/Choline-Deficient Diet (MCD)-induced fatty liver. Thus, our study demonstrates that STK11IP phosphorylation represents a mechanism for mTORC1 to regulate lysosomal acidification and autophagy, and points to STK11IP as a promising therapeutic target for the amelioration of diseases with aberrant autophagy signaling.
    DOI:  https://doi.org/10.1038/s41467-022-29461-8
  3. Traffic. 2022 Mar 28.
    Current methods to analyse lysosome morphology, positioning, motility and function.
    Duarte C Barral, Leopoldo Staiano, Cláudia Guimas Almeida, Dan F Cutler, Emily R Eden, Clare E Futter, Antony Galione, André R A Marques, Diego Luis Medina, Gennaro Napolitano, Carmine Settembre, Otília V Vieira, Johannes M F G Aerts, Peace Atakpa-Adaji, Gemma Bruno, Antonella Capuozzo, Elvira De Leonibus, Chiara Di Malta, Cristina Escrevente, Alessandra Esposito, Paolo Grumati, Michael J Hall, Rita O Teodoro, Susana S Lopes, J Paul Luzio, Jlenia Monfregola, Sandro Montefusco, Frances M Platt, Roman Polishuck, Maria De Risi, Irene Sambri, Chiara Soldati, Miguel C Seabra.
      Since the discovery of lysosomes more than 70 years ago, much has been learned about the functions of these organelles. Lysosomes were regarded as exclusively degradative organelles, but more recent research has revealed that they play essential roles in several other cellular functions, such as nutrient sensing, intracellular signalling, and metabolism. Methodological advances played a key part in generating our current knowledge about the biology of this multifaceted organelle. In this review, we cover current methods used to analyse lysosome morphology, positioning, motility, and function. We highlight the principles behind these methods, the methodological strategies, and their advantages and limitations. To extract accurate information and avoid misinterpretations, we discuss the best strategies to identify lysosomes and assess their characteristics and functions. With this review, we aim to stimulate an increase in the quantity and quality of research on lysosomes and further ground-breaking discoveries on an organelle that continues to surprise and excite cell biologists.
    Keywords:  Endolysosomes; Lysosomal storage diseases; Lysosome biogenesis; Lysosome exocytosis; Lysosome-related organelles; Lysosomes; Membrane contact sites; TFEB; mTOR
    DOI:  https://doi.org/10.1111/tra.12839
  4. PLoS Biol. 2022 Mar 31. 20(3): e3001594
    Folliculin promotes substrate-selective mTORC1 activity by activating RagC to recruit TFE3.
    Kristina Li, Shogo Wada, Bridget S Gosis, Chelsea Thorsheim, Paige Loose, Zolt Arany.
      Mechanistic target of rapamycin complex I (mTORC1) is central to cellular metabolic regulation. mTORC1 phosphorylates a myriad of substrates, but how different substrate specificity is conferred on mTORC1 by different conditions remains poorly defined. Here, we show how loss of the mTORC1 regulator folliculin (FLCN) renders mTORC1 specifically incompetent to phosphorylate TFE3, a master regulator of lysosome biogenesis, without affecting phosphorylation of other canonical mTORC1 substrates, such as S6 kinase. FLCN is a GTPase-activating protein (GAP) for RagC, a component of the mTORC1 amino acid (AA) sensing pathway, and we show that active RagC is necessary and sufficient to recruit TFE3 onto the lysosomal surface, allowing subsequent phosphorylation of TFE3 by mTORC1. Active mutants of RagC, but not of RagA, rescue both phosphorylation and lysosomal recruitment of TFE3 in the absence of FLCN. These data thus advance the paradigm that mTORC1 substrate specificity is in part conferred by direct recruitment of substrates to the subcellular compartments where mTORC1 resides and identify potential targets for specific modulation of specific branches of the mTOR pathway.
    DOI:  https://doi.org/10.1371/journal.pbio.3001594
  5. Mol Metab. 2022 Mar 25. pii: S2212-8778(22)00050-3. [Epub ahead of print] 101481
    Organelle transporters and inter-organelle communication as drivers of metabolic regulation and cellular homeostasis.
    Aakriti Jain, Roberto Zoncu.
      Spatial compartmentalization of metabolic pathways within membrane-separated organelles is key to the ability of eukaryotic cells to precisely regulate their biochemical functions. Membrane-bound organelles such as mitochondria, endoplasmic reticulum (ER) and lysosomes enable the concentration of metabolic precursors within optimized chemical environments, greatly accelerating the efficiency of both anabolic and catabolic reactions, enabling division of labor and optimal utilization of resources. However, metabolic compartmentalization also poses a challenge to cells because it creates spatial discontinuities that must be bridged for reaction cascades to be connected and completed. To do so, cells employ different methods to coordinate metabolic fluxes occurring in different organelles, such as membrane-localized transporters to facilitate regulated metabolite exchange between mitochondria and lysosomes, non-vesicular transport pathways via physical contact sites connecting the ER with both mitochondria and lysosomes, as well as localized regulatory signaling processes that coordinately regulate the activity of all these organelles. Effective communication among these systems is essential to cellular health and function, whereas disruption of inter-organelle communication is an emerging driver in a multitude of diseases, from cancer to neurodegeneration.
    Keywords:  Contact sites; Lysosome; Metabolism; Mitochondria; Transporters; mTORC1
    DOI:  https://doi.org/10.1016/j.molmet.2022.101481
  6. Fac Rev. 2022 ;11 6
    Ca2+ regulation of constitutive vesicle trafficking.
    John Sargeant, Jesse C Hay.
      Constitutive vesicle trafficking is the default pathway used by all cells for movement of intracellular cargoes between subcellular compartments and in and out of the cell. Classically, constitutive trafficking was thought to be continuous and unregulated, in contrast to regulated secretion, wherein vesicles are stored intracellularly until undergoing synchronous membrane fusion following a Ca2+ signal. However, as shown in the literature reviewed here, many continuous trafficking steps can be up- or down-regulated by Ca2+, including several steps associated with human pathologies. Notably, we describe a series of Ca2+ pumps, channels, Ca2+-binding effector proteins, and their trafficking machinery targets that together regulate the flux of cargo in response to genetic alterations as well as baseline and agonist-dependent Ca2+ signals. Here, we review the most recent advances, organized by organellar location, that establish the importance of these components in trafficking steps. Ultimately, we conclude that Ca2+ regulates an expanding series of distinct mechanistic steps. Furthermore, the involvement of Ca2+ in trafficking is complex. For example, in some cases, the same Ca2+ effectors regulate surprisingly distinct trafficking steps, or even the same trafficking step with opposing influences, through binding to different target proteins.
    Keywords:  Golgi; apoptosis-linked gene 2 (ALG-2); calcium; calcium channel; calcium signaling; endoplasmic reticulum; late endosomes; lysosomes; secretion; vesicle coat; vesicle trafficking
    DOI:  https://doi.org/10.12703/r/11-6
  7. Cancer Lett. 2022 Mar 23. pii: S0304-3835(22)00124-0. [Epub ahead of print] 215641
    EWI2 promotes endolysosome-mediated turnover of growth factor receptors and integrins to suppress lung cancer.
    Jie Wang, Jonathan D Wren, Yingjun Ding, Junxiong Chen, Nikhil Mittal, Chao Xu, Xing Li, Cengxi Zeng, Meng Wang, Jing Shi, Yanhui H Zhang, Sangyoon J Han, Xin A Zhang.
      As a partner of tetraspanins, EWI2 suppresses glioblastoma, melanoma, and prostate cancer; but its role in lung cancer has not been investigated. Bioinformatics analysis reveals that EWI2 gene expression is up regulated in lung adenocarcinoma and higher expression of EWI2 mRNA may predict poorer overall survival. However, experimental analysis shows that EWI2 protein is actually downregulated constantly in the tissues of lung adenocarcinoma and lung squamous cell carcinoma. Forced expression of EWI2 in human lung adenocarcinoma cells reduces total cellular and cell surface levels of various integrins and growth factor receptors, which initiates the outside-in motogenic and mitogenic signaling. These reductions result in the decreases in 1) cell-matrix adhesion, cell movement, and cell transformation in vitro and 2) tumor growth, burden, and metastasis in vivo, and result from the increases in lysosomal trafficking and proteolytic degradation of theses membrane receptors. EWI2 elevates lysosome formation by promoting nuclear retention of TFEB, the master transcription factor driving lysosomogenesis. In conclusion, EWI2 as a lung cancer suppressor attenuates lung cancer cells in a comprehensive fashion by inhibiting both tumor growth and tumor metastasis; EWI2 as an endolysosome regulator promotes lysosome activity to enhance lysosomal degradation of growth factor receptors and integrins and then reduce their levels and functions; and EWI2 can become a promising therapeutic candidate given its accessibility at the cell surface, dual inhibition on growth factor receptors and integrins, and broad-spectrum anti-cancer activity. More importantly, our observations also provide a novel therapeutic strategy to bypass the resistance to EGFR inhibitors.
    Keywords:  EGFR; Integrin; Lysosome; TFEB; Tumor metastasis
    DOI:  https://doi.org/10.1016/j.canlet.2022.215641
  8. Life Sci Alliance. 2022 Jul;pii: e202101283. [Epub ahead of print]5(7):
    TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis.
    Audrey Laurent, Thierry Madigou, Maud Bizot, Marion Turpin, Gaëlle Palierne, Elise Mahé, Sarah Guimard, Raphaël Métivier, Stéphane Avner, Christine Le Péron, Gilles Salbert.
      Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression by controlling the chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs, and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. The TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC-binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease-like state that contributes to an exacerbated sensitivity to autophagy inducers.
    DOI:  https://doi.org/10.26508/lsa.202101283
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