bims-lymeca Biomed News
on Lysosome metabolism in cancer
Issue of 2022‒02‒20
seventeen papers selected by
Harilaos Filippakis
Harvard University


  1. J Cell Biol. 2022 Apr 04. pii: e202107148. [Epub ahead of print]221(4):
      The lysosome is the major catabolic organelle in the cell that has been established as a key metabolic signaling center. Mutations in many lysosomal proteins have catastrophic effects and cause neurodegeneration, cancer, and age-related diseases. The vacuole is the lysosomal analog of Saccharomyces cerevisiae that harbors many evolutionary conserved proteins. Proteins reach vacuoles via the Vps10-dependent endosomal vacuolar protein sorting pathway, via the alkaline phosphatase (ALP or AP-3) pathway, and via the cytosol-to-vacuole transport (CVT) pathway. A systematic understanding of the cargo spectrum of each pathway is completely lacking. Here, we use quantitative proteomics of purified vacuoles to generate the yeast lysosomal biogenesis map. This dataset harbors information on the cargo-receptor relationship of almost all vacuolar proteins. We map binding motifs of Vps10 and the AP-3 complex and identify a novel cargo of the CVT pathway under nutrient-rich conditions. Our data show how organelle purification and quantitative proteomics can uncover fundamental insights into organelle biogenesis.
    DOI:  https://doi.org/10.1083/jcb.202107148
  2. Autophagy. 2022 Feb 15. 1-3
      Several cytotoxic agents used in cancer therapy cause DNA damage and replication stress. Understanding the metabolic determinants of the cell response to replication stress-inducing agents could have relevant implications for cancer treatment. In a recent study, we showed that cell survival during replication stress is influenced by the availability of amino acids, as well as by TORC1 and Gcn2-mediated amino acid sensing pathways. Amino acid starvation, or TORC1 inhibition, sensitizes cells to replication stress conditions, whereas Gcn2 ablation promotes cell survival by stimulating protein synthesis. The Vps34-Vps15-Vps30/Atg6/BECN1-Vps38/UVRAG phosphatidylinositol-3-phosphate (PtdIns3P) complex at the endosomes sets the balance between survival and death signals during replication stress and amino acid starvation. The Vps34-Vps15-Vps30/Atg6/BECN1-Vps38/UVRAG axis promotes the degradation of amino acid transporters, thus sensitizing cells to amino acid starvation, while Vps34-Vps15-Vps30/Atg6/BECN1-Vps38/UVRAG inactivation promotes cell survival by enabling synthesis of stress response proteins mediating survival under replication stress conditions. Our study unravels an autophagy-independent mechanism through which Vps34-Vps30/Atg6/BECN1 promotes lethal events during replication stress.
    Keywords:  Amino acids; Atg6; DNA damage; Gcn2; TORC1; autophagy; endosomal trafficking; phosphatidylinositol-3 phosphate; replication stress
    DOI:  https://doi.org/10.1080/15548627.2022.2038502
  3. Cell Rep. 2022 02 15. pii: S2211-1247(22)00086-9. [Epub ahead of print]38(7): 110365
      AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin complex 1 (mTORC1) are metabolic kinases that co-ordinate nutrient supply with cell growth. AMPK negatively regulates mTORC1, and mTORC1 reciprocally phosphorylates S345/7 in both AMPK α-isoforms. We report that genetic or torin1-induced loss of α2-S345 phosphorylation relieves suppression of AMPK signaling; however, the regulatory effect does not translate to α1-S347 in HEK293T or MEF cells. Dephosphorylation of α2-S345, but not α1-S347, transiently targets AMPK to lysosomes, a cellular site for activation by LKB1. By mass spectrometry, we find that α2-S345 is basally phosphorylated at 2.5-fold higher stoichiometry than α1-S347 in HEK293T cells and, unlike α1, phosphorylation is partially retained after prolonged mTORC1 inhibition. Loss of α2-S345 phosphorylation in endogenous AMPK fails to sustain growth of MEFs under amino acid starvation conditions. These findings uncover an α2-specific mechanism by which AMPK can be activated at lysosomes in the absence of changes in cellular energy.
    Keywords:  AMPK; energy homeostasis; kinase; lysosome; mTORC1; metabolic signaling; phosphorylation
    DOI:  https://doi.org/10.1016/j.celrep.2022.110365
  4. Science. 2022 Feb 18. 375(6582): eabc4203
      Adaptation to nutrient scarcity involves an orchestrated response of metabolic and signaling pathways to maintain homeostasis. We find that in the fat body of fasting Drosophila, lysosomal export of cystine coordinates remobilization of internal nutrient stores with reactivation of the growth regulator target of rapamycin complex 1 (TORC1). Mechanistically, cystine was reduced to cysteine and metabolized to acetyl-coenzyme A (acetyl-CoA) by promoting CoA metabolism. In turn, acetyl-CoA retained carbons from alternative amino acids in the form of tricarboxylic acid cycle intermediates and restricted the availability of building blocks required for growth. This process limited TORC1 reactivation to maintain autophagy and allowed animals to cope with starvation periods. We propose that cysteine metabolism mediates a communication between lysosomes and mitochondria, highlighting how changes in diet divert the fate of an amino acid into a growth suppressive program.
    DOI:  https://doi.org/10.1126/science.abc4203
  5. EMBO Rep. 2022 Feb 15. e53477
      The vacuole/lysosome plays essential roles in the growth and proliferation of many eukaryotic cells via the activation of target of rapamycin complex 1 (TORC1). Moreover, the yeast vacuole/lysosome is necessary for progression of the cell division cycle, in part via signaling through the TORC1 pathway. Here, we show that an essential cyclin-dependent kinase, Bur1, plays a critical role in cell cycle progression in cooperation with TORC1. A mutation in BUR1 combined with a defect in vacuole inheritance shows a synthetic growth defect. Importantly, the double mutant, as well as a bur1-267 mutant on its own, has a severe defect in cell cycle progression from G1 phase. In further support that BUR1 functions with TORC1, mutation of bur1 alone results in high sensitivity to rapamycin, a TORC1 inhibitor. Mechanistic insight for Bur1 function comes from the findings that Bur1 directly phosphorylates Sch9, a target of TORC1, and that both Bur1 and TORC1 are required for the activation of Sch9. Together, these discoveries suggest that multiple signals converge on Sch9 to promote cell cycle progression.
    Keywords:   SCH9 ; SGV1 ; lysosome; rapamycin; yeast
    DOI:  https://doi.org/10.15252/embr.202153477
  6. Proc Natl Acad Sci U S A. 2022 Feb 22. pii: e2200788119. [Epub ahead of print]119(8):
      
    DOI:  https://doi.org/10.1073/pnas.2200788119
  7. Cells. 2022 Jan 31. pii: 496. [Epub ahead of print]11(3):
      Charcot-Marie-Tooth type 2B (CMT2B) disease is a dominant axonal peripheral neuropathy caused by five mutations in the RAB7A gene. Autophagy and late endocytic trafficking were already characterized in CMT2B. Indeed, impairment of autophagy and an increase in lysosomal degradative activity were found in cells expressing the mutant proteins. Recently, we described a novel RAB7 mutation associated with predominantly motor CMT2 and impaired EGFR trafficking. With the aim to analyze the autophagy process and lysosomal activity in CMT2B fibroblasts carrying the p.K126R RAB7 novel mutation and to investigate further the causes of the different phenotype, we have performed Western blot, immunofluorescence and cytometric analyses monitoring autophagic markers and endocytic proteins. Moreover, we investigated lipophagy by analyzing accumulation of lipid droplets and their co-localization with endolysosomal degradative compartments. We found that cells expressing the RAB7K126R mutant protein were characterized by impairment of autophagy and lipophagy processes and by a moderate increase in lysosomal activity compared to the previously studied cells carrying the RAB7V162M mutation. Thus, we concluded that EGFR trafficking alterations and a moderate increase in lysosomal activity with concomitant impairment of autophagy could induce the specific predominantly motor phenotype observed in K126R patients.
    Keywords:  Charcot-Marie-Tooth; RAB7A; autophagy; lipid droplets; lipophagy; lysosome
    DOI:  https://doi.org/10.3390/cells11030496
  8. Int J Mol Sci. 2022 Jan 20. pii: 1131. [Epub ahead of print]23(3):
      Rab21 is a GTPase protein that is functional in intracellular trafficking and involved in the pathologies of many diseases, such as Alzheimer's disease (AD), glioma, cancer, etc. Our previous work has reported its interaction with the catalytic subunit of gamma-secretase, PS1, and it regulates the activity of PS1 via transferring it from the early endosome to the late endosome/lysosome. However, it is still unknown how Rab21 protein itself is regulated. This work revealed that Rab21 protein, either endogenously or exogenously, can be degraded by the ubiquitin-proteasome pathway and the autophagy-lysosome pathway. It is further observed that the ubiquitinated Rab21 is increased, but the total protein is unchanged in AD model mice. We further observed that overexpression of Rab21 leads to increased expression of a series of genes involved in the autophagy-lysosome pathway. We speculated that even though the ubiquitinated Rab21 is increased due to the impaired proteasome function in the AD model, the autophagy-lysosome pathway functions in parallel to degrade Rab21 to keep its protein level in homeostasis. In conclusion, understanding the characters of Rab21 protein itself help explore its potential as a target for therapeutic strategy in diseases.
    Keywords:  Rab21 protein; autophagy-lysosome pathway; ubiquitin-proteasome pathway
    DOI:  https://doi.org/10.3390/ijms23031131
  9. Biochem Soc Trans. 2022 Feb 15. pii: BST20210813. [Epub ahead of print]
      Autophagy is an evolutionally conserved cytoplasmic degradation pathway in which the double membrane structure, autophagosome sequesters cytoplasmic material and delivers them to lysosomes for degradation. Many autophagy related (ATG) proteins participate in the regulation of the several steps of autophagic process. Among ATGs, ubiquitin-like protein, ATG8 plays a pivotal role in autophagy. ATG8 is directly conjugated on lipid in autophagosome membrane upon induction of autophagy thus providing a good marker to monitor and analyze autophagy process. However, recent discoveries suggest that ATG8 has autophagy independent non-canonical functions and ATG8 positive structures are not always autophagosomes. This review briefly overviews canonical and non-canonical roles of ATG8 and introduce novel function of ATG8 to activate Transcriptional Factor EB(TFEB), a master transcription factor of autophagy and lysosome function during lysosomal damage.
    Keywords:  ATG8; TFEB; autophagy; lysosomes
    DOI:  https://doi.org/10.1042/BST20210813
  10. Int J Mol Sci. 2022 Jan 21. pii: 1155. [Epub ahead of print]23(3):
      Cancer has long been considered a genetic disease characterized by a myriad of mutations that drive cancer progression. Recent accumulating evidence indicates that the dysregulated metabolism in cancer cells is more than a hallmark of cancer but may be the underlying cause of the tumor. Most of the well-characterized oncogenes or tumor suppressor genes function to sustain the altered metabolic state in cancer. Here, we review evidence supporting the altered metabolic state in cancer including key alterations in glucose, glutamine, and fatty acid metabolism. Unlike genetic alterations that do not occur in all cancer types, metabolic alterations are more common among cancer subtypes and across cancers. Recognizing cancer as a metabolic disorder could unravel key diagnostic and treatments markers that can impact approaches used in cancer management.
    Keywords:  cancer; fatty acids; glucose; glutamine; metabolism
    DOI:  https://doi.org/10.3390/ijms23031155
  11. Brain Commun. 2022 ;4(1): fcab310
      Haploinsufficiency of the progranulin protein is a leading cause of frontotemporal lobar degeneration. Accumulating evidence support a crucial role of progranulin in the lysosome. Progranulin comprises 7.5 granulin repeats and is known to traffic to lysosomes via direct interactions with prosaposin or sortilin. Within the lysosome, progranulin gets processed into granulin peptides. Here, we report that sortilin and prosaposin independently regulate lysosomal trafficking of progranulin in vivo. The deletion of either prosaposin or sortilin alone results in a significant decrease in the ratio of granulin peptides versus full-length progranulin in mouse brain lysates. This decrease is further augmented by the deficiency of both prosaposin and sortilin. A concomitant increase in the levels of secreted progranulin in the serum was observed. Interestingly, while the deletion of both prosaposin and sortilin totally abolishes lysosomal localization of progranulin in neurons, it has a limited effect on lysosomal trafficking of progranulin in microglia, suggesting the existence of a novel sortilin and prosaposin independent pathway mediating progranulin lysosomal trafficking. In summary, our studies shed light on the regulation of lysosomal trafficking and processing of progranulin in vivo.
    Keywords:  frontotemporal lobar degeneration; lysosome; progranulin; prosaposin; sortilin
    DOI:  https://doi.org/10.1093/braincomms/fcab310
  12. Theranostics. 2022 ;12(3): 1132-1147
      Rationale: Employing in situ bioorthogonal catalysis within subcellular organelles, such as lysosomes, remains a challenge. Lysosomal membranes pose an intracellular barrier for drug sequestration, thereby greatly limiting drug accumulation and concentrations at intended targets. Here, we provide a proof-of-concept report of a nanozyme-based strategy that mediates in situ bioorthogonal uncaging reactions within lysosomes, followed by lysosomal escape and the release of uncaged drugs into the cytoplasm. Methods: A model system composed of a protein-based nanozyme platform (based on the transition metals Co, Fe, Mn, Rh, Ir, Pt, Au, Ru and Pd) and caged compound fluorophores was designed to screen for nanozyme/protecting group pairings. The optimized nanozyme/protecting group pairing was then selected for utilization in the design of anti-cancer pro-drugs and drug delivery systems. Results: Our screening system identified Pd nanozymes that mimic mutant P450BM3 activity and specifically cleave propargylic ether groups. We found that the intrinsic peroxidase-like activity of Pd nanozymes induced the production of free radicals under acid conditions, resulting in lysosomal membrane leakage of uncaged molecules into the cytoplasm. Using a multienzyme synergistic approach, our Pd nanozymes achieved in situ bioorthogonal catalysis and nanozyme-mediated lysosomal membrane leakage, which were successfully applied to the design of model pro-drugs for anti-cancer therapy. The extension of our nanozyme system to the construction of a liposome-based "all-in-one" delivery system offers promise for realizing efficacious in vivo tumor-targeted therapies. Conclusions: This strategy shows a promising new direction by utilizing nanotechnology for drug development through in situ catalyzing bioorthogonal chemistry within specific subcellular organelles.
    Keywords:  Bioorthogonal catalysis; Lysosome; Nanozyme; Pro-drug; Targeted delivery; Tumor
    DOI:  https://doi.org/10.7150/thno.66325
  13. Spectrochim Acta A Mol Biomol Spectrosc. 2022 Feb 05. pii: S1386-1425(22)00150-0. [Epub ahead of print]272 121002
      Lysosomes are the acidic organelles in the cells that play an important role in intracellular degradation and other various cellular functions. The pH disturbance of lysosomes will result in the lysosomal dysfunction and many lysosomal related diseases. In this work, we reported a methoxy-based covalent organic framework (TAPB-DMTP-COF) that a novel pH-responsive fluorescent probe for lysosomal pH imaging in cells. The prepared TAPB-DMTP-COF presented regular crystal structure, low toxicity and good pH responsive property. The rich imine structure in the material enabled pH-responsive properties of the TAPB-DMTP-COF and made it exhibited pH-dependent fluorescence response. Good detection linearity for pH measurements in aqueous solution was achieved by this probe. Moreover, the TAPB-DMTP-COF can be used for the selective lysosomal pH imaging. Confocal fluorescence imaging results demonstrated that the pH fluctuations (from 4.0 to 7.4) and the pH changes in lysosomes can be effectively monitored in situ by the developed probe. This study may provide a new avenue for the intracellular pH sensing, deep study and understanding about the mechanism of diseases related to abnormal lysosomal pH.
    Keywords:  Covalent organic framework; Fluorescence intensity; Subcellular imaging; pH sensitive
    DOI:  https://doi.org/10.1016/j.saa.2022.121002
  14. J Agric Food Chem. 2022 Feb 18.
      Autophagy, an evolutionarily conserved process, is intricately involved in many aspects of human health and a variety of human diseases, including cancer. Discovery of small-molecule autophagy modulators with potent anticancer effect would be of great significance. To this end, a natural product library consisting of 170 natural compounds were screened as autophagy modulators with potent cytotoxicity in our present study. Among these compounds, gossypol acetate (GAA), the mostly used medicinal form of gossypol, was identified. GAA effectively increased the number of autophagic puncta in GFP-LC3B-labeled 293T cells and significantly decreased cell viability in different cancer cells. In A549 cells, GAA at concentrations below 10 μM triggered caspase-independent cell death via targeting autophagy, as evidenced by elevated LC3 conversion and decreased p62/SQSTM1 levels. Knocking down of LC3 significantly attenuated GAA-induced cell death. Mechanistically, GAA at low concentrations induced autophagy through targeting AMPK-mTORC1-ULK1 signaling. Interestingly, high concentrations of GAA induced LC3 conversion, p62 accumulation, and yellow autophagosome formation, indicating that GAA at high concentrations blocked autophagic flux. Mechanistically, GAA decreased intracellular ATP level and suppressed lysosome activity. Exogenous ATP partially reversed the inhibitory effect of GAA on autophagy, suggesting that decreased ATP level and lysosome activity might be involved in the blocking of autophagy flux by GAA. Collectively, our present study reveals the mechanisms by which GAA modulates autophagy and illustrates whether autophagy regulation by GAA is functionally involved in GAA-induced cancer cell death.
    Keywords:  ATP; adenosine 5′-monophosphate (AMP)-activated protein kinase (AMPK); apoptosis; autophagy; cancer cell death; gossypol acetate; lysosome; mammalian target of rapamycin complex-1 (mTORC1); unc-51-like autophagy-activating kinase 1 (ULK1)
    DOI:  https://doi.org/10.1021/acs.jafc.1c06399
  15. Aging (Albany NY). 2022 Feb 15. 14(undefined):
      The protein kinase R (PKR)-like endoplasmic reticulum (ER) kinase (PERK), a key ER stress sensor of the unfolded protein response (UPR), can confer beneficial effects by facilitating the removal of cytosolic aggregates through the autophagy-lysosome pathway (ALP). In neurodegenerative diseases, the ALP ameliorates the accumulation of intracellular protein aggregates in the brain. Transcription factor-EB (TFEB), a master regulator of the ALP, positively regulates key genes involved in the cellular degradative pathway. However, in neurons, the role of PERK activation in mitigating amyloidogenesis by ALP remains unclear. In this study, we found that SB202190 selectively activates PERK independently of its inhibition of p38 mitogen-activated protein kinase, but not inositol-requiring transmembrane kinase/endoribonuclease-1α (IRE1α) or activating transcription factor 6 (ATF6), in human neuroblastoma cells. PERK activation by SB202190 was dependent on mitochondrial ROS production and promoted Ca2+-calcineurin activation. The activation of the PERK-Ca2+-calcineurin axis by SB202190 positively affects TFEB activity to increase ALP in neuroblastoma cells. Collectively, our study reveals a novel physiological mechanism underlying ALP activation, dependent on PERK activation, for ameliorating amyloidogenesis in neurodegenerative diseases.
    Keywords:  PERK; amyloidogenesis; autophagy-lysosome pathway; mitochondrial reactive oxygen species; transcription factor-EB
    DOI:  https://doi.org/10.18632/aging.203899
  16. Front Oncol. 2022 ;12 820173
      Metabolic reprogramming is one of the hallmarks of tumor. Growing evidence suggests metabolic changes that support oncogenic progression may cause selective vulnerabilities that can be exploited for cancer treatment. Increasing demands for certain nutrients under genetic determination or environmental challenge enhance dependency of tumor cells on specific nutrient, which could be therapeutically developed through targeting such nutrient dependency. Various nutrients including several amino acids and glucose have been found to induce dependency in genetic alteration- or context-dependent manners. In this review, we discuss the extensively studied nutrient dependency and the biological mechanisms behind such vulnerabilities. Besides, existing applications and strategies to target nutrient dependency in different cancer types, accompanied with remaining challenges to further exploit these metabolic vulnerabilities to improve cancer therapies, are reviewed.
    Keywords:  cancer; dependency; metabolism; nutrient; therapy
    DOI:  https://doi.org/10.3389/fonc.2022.820173
  17. Nat Commun. 2022 Feb 16. 13(1): 904
      Targeted protein degradation allows targeting undruggable proteins for therapeutic applications as well as eliminating proteins of interest for research purposes. While several degraders that harness the proteasome or the lysosome have been developed, a technology that simultaneously degrades targets and accelerates cellular autophagic flux is still missing. In this study, we develop a general chemical tool and platform technology termed AUTOphagy-TArgeting Chimera (AUTOTAC), which employs bifunctional molecules composed of target-binding ligands linked to autophagy-targeting ligands. AUTOTACs bind the ZZ domain of the otherwise dormant autophagy receptor p62/Sequestosome-1/SQSTM1, which is activated into oligomeric bodies in complex with targets for their sequestration and degradation. We use AUTOTACs to degrade various oncoproteins and degradation-resistant aggregates in neurodegeneration at nanomolar DC50 values in vitro and in vivo. AUTOTAC provides a platform for selective proteolysis in basic research and drug development.
    DOI:  https://doi.org/10.1038/s41467-022-28520-4