bims-lymeca 2022-07-10 papers

bims-lymeca

Biomed News

on Lysosome metabolism in cancer

Issue of 2022–07–10
seven papers selected by
Harilaos Filippakis, University of New England

Transcription factor EB controls both motogenic and mitogenic cell activities.
Lysosomal sequestration of weak base drugs, lysosomal biogenesis, and cell cycle alteration.
Secretory autophagy during lysosome inhibition (SALI).
The Three Two-Pore Channel Subtypes from Rabbit Exhibit Distinct Sensitivity to Phosphoinositides, Voltage, and Extracytosolic pH.
Multiparameter phenotypic screening for endogenous TFEB and TFE3 translocation identifies novel chemical series modulating lysosome function.
Spatial regulation of AMPK signaling revealed by a sensitive kinase activity reporter.
Endosomal LC3C-pathway selectively targets plasma membrane cargo for autophagic degradation.

FEBS Lett. 2022 Jul 04.

Transcription factor EB controls both motogenic and mitogenic cell activities.

Elena Astanina, Federico Bussolino, Gabriella Doronzo.

  Transcription factor EB (TFEB) belongs to the microphthalmia family of bHLH-leucine zipper transcription factors and was first identified as an oncogene in a subset of renal cell carcinomas. In addition to exhibiting oncogenic activity, TFEB coordinates genetic programs connected with the cellular response to stress conditions, including roles in lysosome biogenesis, autophagy, modulation of metabolism. As is the case for other transcription factors, the activities of TFEB are not limited to a specific cellular condition such as the response to stress and recent findings indicate that TFEB has more widespread functions. Here, we review the emerging roles of TFEB in regulating cellular proliferation and motility. The well-established and emerging roles of TFEB suggest that this protein serves as a hub of signalling networks involved in many non-communicable diseases, such as cancer, ischaemic diseases and immune disorders, drug resistance mechanisms, and tissue generation.

Keywords:  TFEB; autophagy; cell motility; cell-cycle

DOI:  https://doi.org/10.1002/1873-3468.14442
Biomed Pharmacother. 2022 Jul 01. pii: S0753-3322(22)00717-X. [Epub ahead of print]153 113328

Lysosomal sequestration of weak base drugs, lysosomal biogenesis, and cell cycle alteration.

P Mlejnek, J Havlasek, N Pastvova, P Dolezel, K Dostalova.

  Lysosomes, now known to take part in multiple cellular functions, also respond to various stress stimuli. These include biogenesis in response to nanomolar concentrations of hydrophobic weak-base anticancer drugs. However, since lysosomal stress mediated by accumulation of weak-base drugs at such concentrations has never been proven and these drugs have diverse effects on malignant cells, we investigated whether the interpretation of the data was true. We found that lysosomal accumulation of the drugs daunorubicin, doxorubicin, mitoxantrone, symadex, chloroquine, clomipramine and sunitinib alone, was insufficient to induce lysosomal alkalization i.e., lysosomal stress-mediated biogenesis at nanomolar concentrations. Instead, we found that some of the drugs used induced G2 phase arrest and lysosomal biogenesis that is associated with activation of transcription factor EB (TFEB). Similarly, cantharidin, a control compound that does not belong to the weak base drugs, induced cell cycle arrest in the G2 phase associated with TFEB-driven lysosomal biogenesis. Overall none of the tested drugs caused stress-induced lysosomal biogenesis at nanomolar concentrations. However, daunorubicin, doxorubicin, mitoxantrone, symadex and cantharidin induced a massive block in the G2 phase of the cell cycle which is naturally associated with TFEB-driven lysosomal biogenesis.

Keywords:  A549 cells; Cell cycle progression; G2 arrest; K562 cells; Lysosomal biogenesis; Lysosomal sequestration; Weak base drugs

DOI:  https://doi.org/10.1016/j.biopha.2022.113328
Autophagy. 2022 Jul 04.

Secretory autophagy during lysosome inhibition (SALI).

Jayanta Debnath, Andrew M Leidal.

  Both macroautophagy/autophagy and extracellular vesicle (EV) secretion pathways converge upon the endolysosome system. Although lysosome impairment leads to defects in autophagic degradation, the impact of such dysfunction on EV secretion remains poorly understood. Recently, we uncovered a novel secretory autophagy pathway that employs EVs and nanoparticles (EVPs) for the secretion of autophagy cargo receptors outside the cell when either autophagosome maturation or lysosomal function is blocked. We term this process secretory autophagy during lysosome inhibition (SALI). SALI functionally requires multiple steps in classical autophagosome formation and the small GTPase RAB27A. Because the intracellular accumulation of autophagy cargo receptors perturbs cell signaling and quality control pathways, we propose that SALI functions as a failsafe mechanism to preserve protein and cellular homeostasis when autophagic or lysosomal degradation is impaired.

Keywords:  Autophagy cargo receptors; extracellular vesicles; lysosome; proteostasis; secretory autophagy; vesicular trafficking

DOI:  https://doi.org/10.1080/15548627.2022.2095788
Cells. 2022 Jun 23. pii: 2006. [Epub ahead of print]11(13):

The Three Two-Pore Channel Subtypes from Rabbit Exhibit Distinct Sensitivity to Phosphoinositides, Voltage, and Extracytosolic pH.

Xinghua Feng, Jian Xiong, Weijie Cai, Jin-Bin Tian, Michael X Zhu.

  Two pore channels (TPCs) are implicated in vesicle trafficking, virus infection, and autophagy regulation. As Na+- or Ca2+-permeable channels, TPCs have been reported to be activated by NAADP, PI(3,5)P2, and/or high voltage. However, a comparative study on the function and regulation of the three mammalian TPC subtypes is currently lacking. Here, we used the electrophysiological recording of enlarged endolysosome vacuoles, inside-out and outside-out membrane patches to examine the three TPCs of rabbit (Oryctolagus cuniculus, or Oc) heterologously expressed in HEK293 cells. While PI(3,5)P2 evoked Na+ currents with a potency order of OcTPC1 > OcTPC3 > OcTPC2, only OcTPC2 displayed a strict dependence on PI(3,5)P2. Both OcTPC1 and OcTPC3 were activatable by PI3P and OcTPC3 was also activated by additional phosphoinositide species. While OcTPC2 was voltage-independent, OcTPC1 and OcTPC3 showed voltage dependence with OcTPC3 depending on high positive voltages. Finally, while OcTPC2 preferred a luminal pH of 4.6-6.0 in endolysosomes, OcTPC1 was strongly inhibited by extracytosolic pH 5.0 in both voltage-dependent and -independent manners, and OcTPC3 was inhibited by pH 6.0 but potentiated by pH 8.0. Thus, the three OcTPCs form phosphoinositide-activated Na+ channels with different ligand selectivity, voltage dependence, and extracytosolic pH sensitivity, which likely are optimally tuned for function in specific endolysosomal populations.

Keywords:  TPCN1; TPCN2; TPCN3; electrophysiology; endosome; ion channel; lysosome; phosphoinositide; sodium channels; voltage dependence

DOI:  https://doi.org/10.3390/cells11132006
Autophagy. 2022 Jul 04.

Multiparameter phenotypic screening for endogenous TFEB and TFE3 translocation identifies novel chemical series modulating lysosome function.

Phillippa J Carling, Brent J Ryan, William McGuinness, Shikha Kataria, Stewart W Humble, Stefan Milde, James A Duce, Nirav Kapadia, William J Zuercher, John B Davis, Elena Di Daniel, Richard Wade-Martins.

  The accumulation of toxic protein aggregates in multiple neurodegenerative diseases is associated with defects in the macroautophagy/autophagy-lysosome pathway. The amelioration of disease phenotypes across multiple models of neurodegeneration can be achieved through modulating the master regulator of lysosome function, TFEB (transcription factor EB). Using a novel multi-parameter high-throughput screen for cytoplasmic:nuclear translocation of endogenous TFEB and the related transcription factor TFE3, we screened the Published Kinase Inhibitor Set 2 (PKIS2) library as proof of principle and to identify kinase regulators of TFEB and TFE3. Given that TFEB and TFE3 are responsive to cellular stress we have established assays for cellular toxicity and lysosomal function, critical to ensuring the identification of hit compounds with only positive effects on lysosome activity. In addition to AKT inhibitors which regulate TFEB localization, we identified a series of quinazoline-derivative compounds that induced TFEB and TFE3 translocation. A novel series of structurally-related analogs was developed, and several compounds induced TFEB and TFE3 translocation at higher potency than previously screened compounds. KINOMEscan and cell-based KiNativ kinase profiling revealed high binding for the PRKD (protein kinase D) family of kinases, suggesting good selectivity for these compounds. We describe and utilize a cellular target-validation platform using CRISPRi knockdown and orthogonal PRKD inhibitors to demonstrate that the activity of these compounds is independent of PRKD inhibition. The more potent analogs induced subsequent upregulation of the CLEAR gene network and cleared pathological HTT protein in a cellular model of proteinopathy, demonstrating their potential to alleviate neurodegeneration-relevant phenotypes.

Keywords:  High-content screening; PKIS2; TFEB; lysosome activity; lysosome biogenesis; protein aggregation

DOI:  https://doi.org/10.1080/15548627.2022.2095834
Nat Commun. 2022 Jul 05. 13(1): 3856

Spatial regulation of AMPK signaling revealed by a sensitive kinase activity reporter.

Danielle L Schmitt, Stephanie D Curtis, Anne C Lyons, Jin-Fan Zhang, Mingyuan Chen, Catherine Y He, Sohum Mehta, Reuben J Shaw, Jin Zhang.

AMP-activated protein kinase (AMPK) is a master regulator of cellular energetics which coordinates metabolism by phosphorylating a plethora of substrates throughout the cell. But how AMPK activity is regulated at different subcellular locations for precise spatiotemporal control over metabolism is unclear. Here we present a sensitive, single-fluorophore AMPK activity reporter (ExRai AMPKAR), which reveals distinct kinetic profiles of AMPK activity at the mitochondria, lysosome, and cytoplasm. Genetic deletion of the canonical upstream kinase liver kinase B1 (LKB1) results in slower AMPK activity at lysosomes but does not affect the response amplitude at lysosomes or mitochondria, in sharp contrast to the necessity of LKB1 for maximal cytoplasmic AMPK activity. We further identify a mechanism for AMPK activity in the nucleus, which results from cytoplasmic to nuclear shuttling of AMPK. Thus, ExRai AMPKAR enables illumination of the complex subcellular regulation of AMPK signaling.

DOI: https://doi.org/10.1038/s41467-022-31190-x
Nat Commun. 2022 Jul 02. 13(1): 3812

Endosomal LC3C-pathway selectively targets plasma membrane cargo for autophagic degradation.

Paula P Coelho, Geoffrey G Hesketh, Annika Pedersen, Elena Kuzmin, Anne-Marie N Fortier, Emily S Bell, Colin D H Ratcliffe, Anne-Claude Gingras, Morag Park.

Autophagy selectively targets cargo for degradation, yet mechanistic understanding remains incomplete. The ATG8-family plays key roles in autophagic cargo recruitment. Here by mapping the proximal interactome of ATG8-paralogs, LC3B and LC3C, we uncover a LC3C-Endocytic-Associated-Pathway (LEAP) that selectively recruits plasma-membrane (PM) cargo to autophagosomes. We show that LC3C localizes to peripheral endosomes and engages proteins that traffic between PM, endosomes and autophagosomes, including the SNARE-VAMP3 and ATG9, a transmembrane protein essential for autophagy. We establish that endocytic LC3C binds cargo internalized from the PM, including the Met receptor tyrosine kinase and transferrin receptor, and is necessary for their recruitment into ATG9 vesicles targeted to sites of autophagosome initiation. Structure-function analysis identified that LC3C-endocytic localization and engagement with PM-cargo requires the extended carboxy-tail unique to LC3C, the TBK1 kinase, and TBK1-phosphosites on LC3C. These findings identify LEAP as an unexpected LC3C-dependent pathway, providing new understanding of selective coupling of PM signalling with autophagic degradation.

DOI: https://doi.org/10.1038/s41467-022-31465-3