bims-lymeca 2023-03-12 papers

bims-lymeca

Biomed News

on Lysosome metabolism in cancer

Issue of 2023–03–12
nine papers selected by
Harilaos Filippakis, University of New England

EGR1 drives cell proliferation by directly stimulating TFEB transcription in response to starvation.
The role of lysosomes in metabolic and autoimmune diseases.
Lysosomal function and intracellular position determine the malignant phenotype in malignant melanoma.
Lysosomal Ion Channels and Lysosome-Organelle Interactions.
Lysosome-targeted multifunctional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor.
Rapamycin-Induced Feedback Activation of eIF4E-EIF4A Dependent mRNA Translation in Pancreatic Cancer.
What Is the Significance of Lysosomal-Mediated Resistance to Imatinib?
Repurposing Itraconazole and Hydroxychloroquine to Target Lysosomal Homeostasis in Epithelial Ovarian Cancer.
Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase.

PLoS Biol. 2023 Mar;21(3): e3002034

EGR1 drives cell proliferation by directly stimulating TFEB transcription in response to starvation.

Marcella Cesana, Gennaro Tufano, Francesco Panariello, Nicolina Zampelli, Susanna Ambrosio, Rossella De Cegli, Margherita Mutarelli, Lorenzo Vaccaro, Micheal J Ziller, Davide Cacchiarelli, Diego L Medina, Andrea Ballabio.

The stress-responsive transcription factor EB (TFEB) is a master controller of lysosomal biogenesis and autophagy and plays a major role in several cancer-associated diseases. TFEB is regulated at the posttranslational level by the nutrient-sensitive kinase complex mTORC1. However, little is known about the regulation of TFEB transcription. Here, through integrative genomic approaches, we identify the immediate-early gene EGR1 as a positive transcriptional regulator of TFEB expression in human cells and demonstrate that, in the absence of EGR1, TFEB-mediated transcriptional response to starvation is impaired. Remarkably, both genetic and pharmacological inhibition of EGR1, using the MEK1/2 inhibitor Trametinib, significantly reduced the proliferation of 2D and 3D cultures of cells displaying constitutive activation of TFEB, including those from a patient with Birt-Hogg-Dubé (BHD) syndrome, a TFEB-driven inherited cancer condition. Overall, we uncover an additional layer of TFEB regulation consisting in modulating its transcription via EGR1 and propose that interfering with the EGR1-TFEB axis may represent a therapeutic strategy to counteract constitutive TFEB activation in cancer-associated conditions.

DOI: https://doi.org/10.1371/journal.pbio.3002034
Nat Rev Nephrol. 2023 Mar 09.

The role of lysosomes in metabolic and autoimmune diseases.

Frédéric Gros, Sylviane Muller.

Lysosomes are catabolic organelles that contribute to the degradation of intracellular constituents through autophagy and of extracellular components through endocytosis, phagocytosis and macropinocytosis. They also have roles in secretory mechanisms, the generation of extracellular vesicles and certain cell death pathways. These functions make lysosomes central organelles in cell homeostasis, metabolic regulation and responses to environment changes including nutrient stresses, endoplasmic reticulum stress and defects in proteostasis. Lysosomes also have important roles in inflammation, antigen presentation and the maintenance of long-lived immune cells. Their functions are tightly regulated by transcriptional modulation via TFEB and TFE3, as well as by major signalling pathways that lead to activation of mTORC1 and mTORC2, lysosome motility and fusion with other compartments. Lysosome dysfunction and alterations in autophagy processes have been identified in a wide variety of diseases, including autoimmune, metabolic and kidney diseases. Deregulation of autophagy can contribute to inflammation, and lysosomal defects in immune cells and/or kidney cells have been reported in inflammatory and autoimmune pathologies with kidney involvement. Defects in lysosomal activity have also been identified in several pathologies with disturbances in proteostasis, including autoimmune and metabolic diseases such as Parkinson disease, diabetes mellitus and lysosomal storage diseases. Targeting lysosomes is therefore a potential therapeutic strategy to regulate inflammation and metabolism in a variety of pathologies.

DOI: https://doi.org/10.1038/s41581-023-00692-2
J Invest Dermatol. 2023 Mar 03. pii: S0022-202X(23)00171-9. [Epub ahead of print]

Lysosomal function and intracellular position determine the malignant phenotype in malignant melanoma.

Ida Eriksson, Linda Vainikka, Petra Wäster, Karin Öllinger.

  Lysosomes are central in cell homeostasis and participate in macromolecular degradation, plasma membrane repair, exosome release, cell adhesion/migration and apoptosis. In cancer, alterations in lysosomal function and spatial distribution may facilitate disease progression. In this study we show enhanced lysosomal activity in malignant melanoma cells compared to normal human melanocytes. Most lysosomes show perinuclear location in melanocytes, while they are more dispersed in melanoma, with retained proteolytic activity and low pH also in the peripheral population. Rab7a expression is lower in melanoma cells than in melanocytes and, by increasing Rab7a, lysosomes are relocated to the perinuclear region in melanoma. Exposure to the lysosome destabilizing drug LLOMe (L-leucyl-L-leucine methyl ester) causes higher damage in the perinuclear subset of lysosomes in melanomas, while difference in subpopulation susceptibility cannot be found in melanocytes. Interestingly, melanoma cells recruit the ESCRT-III core protein CHMP4B, involved in lysosomal membrane repair, rather than initiate lysophagy. However, when the perinuclear lysosomal position is promoted by Rab7a overexpression or kinesore treatment, lysophagy is increased. In addition, Rab7a-overexpression is accompanied by reduced migration capacity. Taken together, the study emphasizes that alterations in lysosomal properties facilitate the malignant phenotype and declares the targeting of lysosomal function as a future therapeutic approach.

Keywords:  LMP; lysosomal positioning; lysosome; malignant melanoma; melanocytes

DOI:  https://doi.org/10.1016/j.jid.2023.01.036
Handb Exp Pharmacol. 2023 Mar 08.

Lysosomal Ion Channels and Lysosome-Organelle Interactions.

Weijie Cai, Ping Li, Mingxue Gu, Haoxing Xu.

  Intracellular organelles exchange their luminal contents with each other via both vesicular and non-vesicular mechanisms. By forming membrane contact sites (MCSs) with ER and mitochondria, lysosomes mediate bidirectional transport of metabolites and ions between lysosomes and organelles that regulate lysosomal physiology, movement, membrane remodeling, and membrane repair. In this chapter, we will first summarize the current knowledge of lysosomal ion channels and then discuss the molecular and physiological mechanisms that regulate lysosome-organelle MCS formation and dynamics. We will also discuss the roles of lysosome-ER and lysosome-mitochondria MCSs in signal transduction, lipid transport, Ca 2+ transfer, membrane trafficking, and membrane repair, as well as their roles in lysosome-related pathologies.

Keywords:  ER; Lysosomes; Membrane contact sites; Mitochondria; TRPML1

DOI:  https://doi.org/10.1007/164_2023_640
Proc Natl Acad Sci U S A. 2023 Mar 14. 120(11): e2213886120

Lysosome-targeted multifunctional lipid probes reveal the sterol transporter NPC1 as a sphingosine interactor.

Janathan Altuzar, Judith Notbohm, Frank Stein, Per Haberkant, Pia Hempelmann, Saskia Heybrock, Jutta Worsch, Paul Saftig, Doris Höglinger.

  Lysosomes are catabolic organelles involved in macromolecular digestion, and their dysfunction is associated with pathologies ranging from lysosomal storage disorders to common neurodegenerative diseases, many of which have lipid accumulation phenotypes. The mechanism of lipid efflux from lysosomes is well understood for cholesterol, while the export of other lipids, particularly sphingosine, is less well studied. To overcome this knowledge gap, we have developed functionalized sphingosine and cholesterol probes that allow us to follow their metabolism, protein interactions, and their subcellular localization. These probes feature a modified cage group for lysosomal targeting and controlled release of the active lipids with high temporal precision. An additional photocrosslinkable group allowed for the discovery of lysosomal interactors for both sphingosine and cholesterol. In this way, we found that two lysosomal cholesterol transporters, NPC1 and to a lesser extent LIMP-2/SCARB2, bind to sphingosine and showed that their absence leads to lysosomal sphingosine accumulation which hints at a sphingosine transport role of both proteins. Furthermore, artificial elevation of lysosomal sphingosine levels impaired cholesterol efflux, consistent with sphingosine and cholesterol sharing a common export mechanism.

Keywords:  lysosomal storage diseases; organelle-targeted probes; photocrosslinking; protein–lipid interaction; sphingolipids

DOI:  https://doi.org/10.1073/pnas.2213886120
Cancers (Basel). 2023 Feb 24. pii: 1444. [Epub ahead of print]15(5):

Rapamycin-Induced Feedback Activation of eIF4E-EIF4A Dependent mRNA Translation in Pancreatic Cancer.

Trang Uyen Nguyen, Harrison Hector, Eric Nels Pederson, Jianan Lin, Zhengqing Ouyang, Hans-Guido Wendel, Kamini Singh.

  Pancreatic cancer cells adapt molecular mechanisms to activate the protein synthesis to support tumor growth. This study reports the mTOR inhibitor rapamycin's specific and genome-wide effect on mRNA translation. Using ribosome footprinting in pancreatic cancer cells that lack the expression of 4EBP1, we establish the effect of mTOR-S6-dependent mRNAs translation. Rapamycin inhibits the translation of a subset of mRNAs including p70-S6K and proteins involved in the cell cycle and cancer cell growth. In addition, we identify translation programs that are activated following mTOR inhibition. Interestingly, rapamycin treatment results in the translational activation of kinases that are involved in mTOR signaling such as p90-RSK1. We further show that phospho-AKT1 and phospho-eIF4E are upregulated following mTOR inhibition suggesting a feedback activation of translation by rapamycin. Next, targeting eIF4E and eIF4A-dependent translation by using specific eIF4A inhibitors in combination with rapamycin shows significant growth inhibition in pancreatic cancer cells. In short, we establish the specific effect of mTOR-S6 on translation in cells lacking 4EBP1 and show that mTOR inhibition leads to feedback activation of translation via AKT-RSK1-eIF4E signals. Therefore, targeting translation downstream of mTOR presents a more efficient therapeutic strategy in pancreatic cancer.

Keywords:  CR-1-31B; eIF4A; eIF4E; mTOR; p70-RSK1; ribosome footprinting

DOI:  https://doi.org/10.3390/cancers15051444
Cells. 2023 Feb 23. pii: 709. [Epub ahead of print]12(5):

What Is the Significance of Lysosomal-Mediated Resistance to Imatinib?

Petr Mlejnek.

  The lysosomal sequestration of hydrophobic weak-base anticancer drugs is one proposed mechanism for the reduced availability of these drugs at target sites, resulting in a marked decrease in cytotoxicity and consequent resistance. While this subject is receiving increasing emphasis, it is so far only in laboratory experiments. Imatinib is a targeted anticancer drug used to treat chronic myeloid leukaemia (CML), gastrointestinal stromal tumours (GISTs), and a number of other malignancies. Its physicochemical properties make it a typical hydrophobic weak-base drug that accumulates in the lysosomes of tumour cells. Further laboratory studies suggest that this might significantly reduce its antitumor efficacy. However, a detailed analysis of published laboratory studies shows that lysosomal accumulation cannot be considered a clearly proven mechanism of resistance to imatinib. Second, more than 20 years of clinical experience with imatinib has revealed a number of resistance mechanisms, none of which is related to its accumulation in lysosomes. This review focuses on the analysis of salient evidence and raises a fundamental question about the significance of lysosomal sequestration of weak-base drugs in general as a possible resistance mechanism both in clinical and laboratory settings.

Keywords:  STI571; cancer; drug resistance mechanisms; hydrophobic weak-base drugs; lysosomal drug sequestration; tyrosine kinase inhibitors

DOI:  https://doi.org/10.3390/cells12050709
Cancer Res Commun. 2022 May;2(5): 293-306

Repurposing Itraconazole and Hydroxychloroquine to Target Lysosomal Homeostasis in Epithelial Ovarian Cancer.

Stefano Marastoni, Ainhoa Madariaga, Aleksandra Pesic, Sree Narayanan Nair, Zhu Juan Li, Zvi Shalev, Troy Ketela, Ilaria Colombo, Victoria Mandilaras, Michael Cabanero, Jeff P Bruce, Xuan Li, Swati Garg, Lisa Wang, Eric X Chen, Sarbjot Gill, Neesha C Dhani, Wenjiang Zhang, Melania Pintilie, Valerie Bowering, Marianne Koritzinsky, Robert Rottapel, Bradly G Wouters, Amit M Oza, Anthony M Joshua, Stephanie Lheureux.

Drug repurposing is an attractive option for oncology drug development. Itraconazole is an antifungal ergosterol synthesis inhibitor that has pleiotropic actions including cholesterol antagonism, inhibition of Hedgehog and mTOR pathways. We tested a panel of 28 epithelial ovarian cancer (EOC) cell lines with itraconazole to define its spectrum of activity. To identify synthetic lethality in combination with itraconazole, a whole-genome drop-out genome-scale clustered regularly interspaced short palindromic repeats sensitivity screen in two cell lines (TOV1946 and OVCAR5) was performed. On this basis, we conducted a phase I dose-escalation study assessing the combination of itraconazole and hydroxychloroquine in patients with platinum refractory EOC (NCT03081702). We identified a wide spectrum of sensitivity to itraconazole across the EOC cell lines. Pathway analysis showed significant involvement of lysosomal compartments, the trans-golgi network and late endosomes/lysosomes; similar pathways are phenocopied by the autophagy inhibitor, chloroquine. We then demonstrated that the combination of itraconazole and chloroquine displayed Bliss defined synergy in EOC cancer cell lines. Furthermore, there was an association of cytotoxic synergy with the ability to induce functional lysosome dysfunction, by chloroquine. Within the clinical trial, 11 patients received at least one cycle of itraconazole and hydroxychloroquine. Treatment was safe and feasible with the recommended phase II dose of 300 and 600 mg twice daily, respectively. No objective responses were detected. Pharmacodynamic measurements on serial biopsies demonstrated limited pharmacodynamic impact. In vitro, itraconazole and chloroquine have synergistic activity and exert a potent antitumor effect by affecting lysosomal function. The drug combination had no clinical antitumor activity in dose escalation.
Significance: The combination of the antifungal drug itraconazole with antimalarial drug hydroxychloroquine leads to a cytotoxic lysosomal dysfunction, supporting the rational for further research on lysosomal targeting in ovarian cancer.

DOI: https://doi.org/10.1158/2767-9764.CRC-22-0037
Science. 2023 Mar 10. 379(6636): 996-1003

Protein-metabolite interactomics of carbohydrate metabolism reveal regulation of lactate dehydrogenase.

Kevin G Hicks, Ahmad A Cluntun, Heidi L Schubert, Sean R Hackett, Jordan A Berg, Paul G Leonard, Mariana A Ajalla Aleixo, Youjia Zhou, Alex J Bott, Sonia R Salvatore, Fei Chang, Aubrie Blevins, Paige Barta, Samantha Tilley, Aaron Leifer, Andrea Guzman, Ajak Arok, Sarah Fogarty, Jacob M Winter, Hee-Chul Ahn, Karen N Allen, Samuel Block, Iara A Cardoso, Jianping Ding, Ingrid Dreveny, William C Gasper, Quinn Ho, Atsushi Matsuura, Michael J Palladino, Sabin Prajapati, Pengkai Sun, Kai Tittmann, Dean R Tolan, Judith Unterlass, Andrew P VanDemark, Matthew G Vander Heiden, Bradley A Webb, Cai-Hong Yun, Pengkai Zhao, Bei Wang, Francisco J Schopfer, Christopher P Hill, Maria Cristina Nonato, Florian L Muller, James E Cox, Jared Rutter.

Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS) to identify such interactions. Analysis of 33 enzymes from human carbohydrate metabolism identified 830 protein-metabolite interactions, including known regulators, substrates, and products as well as previously unreported interactions. We functionally validated a subset of interactions, including the isoform-specific inhibition of lactate dehydrogenase by long-chain acyl-coenzyme A. Cell treatment with fatty acids caused a loss of pyruvate-lactate interconversion dependent on lactate dehydrogenase isoform expression. These protein-metabolite interactions may contribute to the dynamic, tissue-specific metabolic flexibility that enables growth and survival in an ever-changing nutrient environment.

DOI: https://doi.org/10.1126/science.abm3452