bims-lymeca Biomed News
on Lysosome metabolism in cancer
Issue of 2023–04–16
nine papers selected by
Harilaos Filippakis, University of New England
  1. Genome-wide CRISPR screens identify ILF3 as a mediator of mTORC1-dependent amino acid sensing.
  2. Lysosomal swelling and lysis mediate delivery of C3 toxins to their cytoplasmic targets.
  3. Mechanosensitive mTORC1 signaling maintains lymphatic valves.
  4. Lysosomal chloride transporter CLH-6 protects lysosome membrane integrity via cathepsin activation.
  5. Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells.
  6. De novo missense variants in RRAGC lead to a fatal mTORopathy of early childhood.
  7. Lysosome transporter purification and reconstitution identifies Ypq1 pH-gated lysine transport and regulation.
  8. The role of extracellular vesicles in cancer.
  9. Highlights from Recent Cancer Literature.
  1. Nat Cell Biol. 2023 Apr 10.
    Genome-wide CRISPR screens identify ILF3 as a mediator of mTORC1-dependent amino acid sensing.
    Guokai Yan, Jinxin Yang, Wen Li, Ao Guo, Jialiang Guan, Ying Liu.
      The mechanistic target of rapamycin complex 1 (mTORC1) is an essential hub that integrates nutrient signals and coordinates metabolism to control cell growth. Amino acid signals are detected by sensor proteins and relayed to the GATOR2 and GATOR1 complexes to control mTORC1 activity. Here we perform genome-wide CRISPR/Cas9 screens, coupled with an assay for mTORC1 activity based on fluorescence-activated cell sorting analysis of pS6, to identify potential regulators of mTORC1-dependent amino acid sensing. We then focus on interleukin enhancer binding factor 3 (ILF3), one of the candidate genes from the screen. ILF3 tethers the GATOR complexes to lysosomes to control mTORC1. Adding a lysosome-targeting sequence to the GATOR2 component WDR24 bypasses the requirement for ILF3 to modulate amino-acid-dependent mTORC1 signalling. ILF3 plays an evolutionarily conserved role in human and mouse cells, and in worms to regulate the mTORC1 pathway, control autophagy activity and modulate the ageing process.
    DOI:  https://doi.org/10.1038/s41556-023-01123-x
  2. Mol Microbiol. 2023 Apr 10.
    Lysosomal swelling and lysis mediate delivery of C3 toxins to their cytoplasmic targets.
    Madison Turner, Jonathan Plumb, A Rod Merrill, Sergio Grinstein, Johannes Westman.
      Unlike other cholera-like toxins that contain separate binding/translocation and catalytic subunits, C3-like mono-ADP-ribosyltransferases consist of a single subunit that serves both functions. The manner whereby C3 toxins reach the host cell cytoplasm is poorly understood and was addressed in this study by monitoring the fate of fluorescently labeled C3larvinA. Following binding to the macrophage membrane in a discontinuous punctate pattern, the toxin was internalized, traversing the endocytic pathway to reach lysosomes. Strikingly, the lysosomes of C3larvinA-treated cells underwent massive swelling over the course of 1-4 h. Lysosomal swelling preceded the extensive rearrangement of the cellular F-actin caused by ADP-ribosylation of cytosolic Rho-GTPases. This suggested that lysosome swelling might be required for the escape of the toxin into the cytoplasm where the GTPases reside. Accordingly, preventing swelling by osmotic manipulation or by arresting macropinocytosis precluded the F-actin rearrangement. Toxin-induced swelling was associated with leakage of sulforhodamine B and dextran from the lysosomes, implying membrane rupture or activation of mechano-sensitive pores, enabling the toxin itself to reach the cytosol. Finally, comparison of the cellular traffic and actin remodeling activities of C3larvinA with that of two related toxins, C3larvintrunc and Plx2A, highlighted the importance of the N-terminal α1 -helix for lysosomal swelling and successful intoxication.
    Keywords:  Rho GTPase; bacterial toxin; lysis; lysosome; macrophage
    DOI:  https://doi.org/10.1111/mmi.15063
  3. J Cell Biol. 2023 Jun 05. pii: e202207049. [Epub ahead of print]222(6):
    Mechanosensitive mTORC1 signaling maintains lymphatic valves.
    Cansaran Saygili Demir, Amélie Sabine, Muyun Gong, Olivier Dormond, Tatiana V Petrova.
      Homeostatic maintenance and repair of lymphatic vessels are essential for health. We investigated the dynamics and the molecular mechanisms of lymphatic endothelial cell (LEC) renewal in adult mesenteric quiescent lymphatic vasculature using label-retention, lineage tracing, and cell ablation strategies. Unlike during development, adult LEC turnover and proliferation was confined to the valve regions of collecting vessels, with valve cells displaying the shortest lifespan. Proliferating valve sinus LECs were the main source for maintenance and repair of lymphatic valves. We identified mechanistic target of rapamycin complex 1 (mTORC1) as a mechanoresponsive pathway activated by fluid shear stress in LECs. Depending on the shear stress level, mTORC1 activity drives division of valve cells or dictates their mechanic resilience through increased protein synthesis. Overactivation of lymphatic mTORC1 in vivo promoted supernumerary valve formation. Our work provides insights into the molecular mechanisms of maintenance of healthy lymphatic vascular system.
    DOI:  https://doi.org/10.1083/jcb.202207049
  4. J Cell Biol. 2023 Jun 05. pii: e202210063. [Epub ahead of print]222(6):
    Lysosomal chloride transporter CLH-6 protects lysosome membrane integrity via cathepsin activation.
    Qianqian Zhang, Yuan Li, Youli Jian, Meijiao Li, Xiaochen Wang.
      Lysosomal integrity is vital for cell homeostasis, but the underlying mechanisms are poorly understood. Here, we identify CLH-6, the C. elegans ortholog of the lysosomal Cl-/H+ antiporter ClC-7, as an important factor for protecting lysosomal integrity. Loss of CLH-6 affects lysosomal degradation, causing cargo accumulation and membrane rupture. Reducing cargo delivery or increasing CPL-1/cathepsin L or CPR-2/cathepsin B expression suppresses these lysosomal defects. Inactivation of CPL-1 or CPR-2, like CLH-6 inactivation, affects cargo digestion and causes lysosomal membrane rupture. Thus, loss of CLH-6 impairs cargo degradation, leading to membrane damage of lysosomes. In clh-6(lf) mutants, lysosomes are acidified as in wild type but contain lower chloride levels, and cathepsin B and L activities are significantly reduced. Cl- binds to CPL-1 and CPR-2 in vitro, and Cl- supplementation increases lysosomal cathepsin B and L activities. Altogether, these findings suggest that CLH-6 maintains the luminal chloride levels required for cathepsin activity, thus facilitating substrate digestion to protect lysosomal membrane integrity.
    DOI:  https://doi.org/10.1083/jcb.202210063
  5. Cell Rep. 2023 Apr 13. pii: S2211-1247(23)00412-6. [Epub ahead of print]42(4): 112401
    Cell-to-cell variability in Myc dynamics drives transcriptional heterogeneity in cancer cells.
    Chad Liu, Takamasa Kudo, Xin Ye, Karen Gascoigne.
      Cell-to-cell heterogeneity is vital for tumor evolution and survival. How cancer cells achieve and exploit this heterogeneity remains an active area of research. Here, we identify c-Myc as a highly heterogeneously expressed transcription factor and an orchestrator of transcriptional and phenotypic diversity in cancer cells. By monitoring endogenous c-Myc protein in individual living cells, we report the surprising pulsatile nature of c-Myc expression and the extensive cell-to-cell variability in its dynamics. We further show that heterogeneity in c-Myc dynamics leads to variable target gene transcription and that timing of c-Myc expression predicts cell-cycle progression rates and drug sensitivities. Together, our data advocate for a model in which cancer cells increase the heterogeneity of functionally diverse transcription factors such as c-Myc to rapidly survey transcriptional landscapes and survive stress.
    Keywords:  CP: Cancer; CP: Cell biology; Myc; cancer; cell-to-cell heterogeneity; gene expression; transcription
    DOI:  https://doi.org/10.1016/j.celrep.2023.112401
  6. Genet Med. 2023 Apr 10. pii: S1098-3600(23)00851-1. [Epub ahead of print] 100838
    De novo missense variants in RRAGC lead to a fatal mTORopathy of early childhood.
    Margot R F Reijnders, Annette Seibt, Melanie Brugger, Ideke J C Lamers, Torsten Ott, Oliver Klaas, Judit Horváth, Ailsa M S Rose, Isabel M Craghill, Theresa Brunet, Elisabeth Graf, Katharina Mayerhanser, Debby Hellebrekers, David Pauck, Eva Neuen-Jacob, Richard J T Rodenburg, Dagmar Wieczorek, Dirk Klee, Ertan Mayatepek, Gertjan Driessen, Robert Bindermann, Luisa Averdunk, Klaus Lohmeier, Margje Sinnema, Alexander P A Stegmann, Ronald Roepman, James A Poulter, Felix Distelmaier.
       INTRODUCTION: Mechanistic target of rapamycin complex 1 (mTORC1) regulates cell growth in response to nutritional status. Central to mTORC1 function is the Rag-GTPase heterodimer. One component of the Rag heterodimer is RagC (Ras-related GTP-binding protein C), which is encoded by the RRAGC gene.
    MATERIAL AND METHODS: Genetic testing via trio exome sequencing was applied to identify the underlying disease cause in three infants who suffered from dilated cardiomyopathy, hepatopathy and brain abnormalities including pachygyria, polymicrogyria, and septo-optic dysplasia. Studies in patient-derived skin fibroblasts and in a HEK293 cell model were performed to investigate the cellular consequences.
    RESULTS: We identified three de novo missense variants in RRAGC (NM_022157.4: c.269C>A, p.(Thr90Asn), c.353C>T, p.(Pro118Leu), and c.343T>C, p.(Trp115Arg)), which were previously reported as occurring somatically in follicular lymphoma. Studies of patient-derived fibroblasts carrying the p.(Thr90Asn) variant revealed increased cell size as well as dysregulation of mTOR-related p70S6K (ribosomal protein S6 kinase 1) and TFEB (transcription factor EB) signaling. Moreover, subcellular localization of mTOR was decoupled from metabolic state. We confirmed the key-findings for all RRAGC variants described in this study in a HEK293 cell model.
    DISCUSSION: The above results are in line with a constitutive over-activation of the mTORC1 pathway. Our study establishes de novo missense variants in RRAGC as cause of an early-onset mTORopathy with unfavorable prognosis.
    Keywords:  cardiomyopathy; cortical malformation; heart; lysosome; mTORopathy; mitochondrial
    DOI:  https://doi.org/10.1016/j.gim.2023.100838
  7. bioRxiv. 2023 Mar 31. pii: 2023.03.31.535002. [Epub ahead of print]
    Lysosome transporter purification and reconstitution identifies Ypq1 pH-gated lysine transport and regulation.
    Felichi Mae Arines, Aleksander Wielenga, Olive E Burata, Francisco Narro Garcia, Randy B Stockbridge, Ming Li.
      Lysosomes achieve their function through numerous transporters that import or export nutrients across their membrane. However, technical challenges in membrane protein overexpression, purification, and reconstitution hinder our understanding of lysosome transporter function. Here, we developed a platform to overexpress and purify the putative lysine transporter Ypq1 using a constitutive overexpression system in protease- and ubiquitination-deficient yeast vacuoles. Using this method, we purified and reconstituted Ypq1 into proteoliposomes and showed lysine transport function, supporting its role as a basic amino acid transporter on the vacuole membrane. We also found that the absence of lysine destabilizes purified Ypq1 and causes it to aggregate, consistent with its propensity to be downregulated in vivo upon lysine starvation. Our approach may be useful for the biochemical characterization of many transporters and membrane proteins to understand organellar transport and regulation.
    DOI:  https://doi.org/10.1101/2023.03.31.535002
  8. Cell. 2023 Apr 13. pii: S0092-8674(23)00263-5. [Epub ahead of print]186(8): 1610-1626
    The role of extracellular vesicles in cancer.
    Raghu Kalluri, Kathleen M McAndrews.
      Intercellular communication is a key feature of cancer progression and metastasis. Extracellular vesicles (EVs) are generated by all cells, including cancer cells, and recent studies have identified EVs as key mediators of cell-cell communication via packaging and transfer of bioactive constituents to impact the biology and function of cancer cells and cells of the tumor microenvironment. Here, we review recent advances in understanding the functional contribution of EVs to cancer progression and metastasis, as cancer biomarkers, and the development of cancer therapeutics.
    DOI:  https://doi.org/10.1016/j.cell.2023.03.010
  9. Cancer Res. 2023 Apr 14. 83(8): 1163-1164
    Highlights from Recent Cancer Literature.
      
    DOI:  https://doi.org/10.1158/0008-5472.CAN-83-8-BI
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