bims-proarb Biomed News
on Proteostasis in aging and regenerative biology
Issue of 2023–02–05
thirteen papers selected by
Rich Giadone, Harvard University
  1. Frontotemporal Dementia Patient Neurons With Progranulin Deficiency Display Protein Dyshomeostasis.
  2. Simultaneous proteome localization and turnover analysis reveals spatiotemporal dynamics of unfolded protein responses.
  3. Divergent Proteome Reactivity Influences Arm-Selective Activation of Pharmacological Endoplasmic Reticulum Proteostasis Regulators.
  4. Tardigrade small heat shock proteins can limit desiccation-induced protein aggregation.
  5. Immortalized Alzheimer's Disease Astrocytes: Characterization of Their Proteolytic Systems.
  6. Phosphorylation of EIF2S1 (eukaryotic translation initiation factor 2 subunit alpha) is indispensable for nuclear translocation of TFEB and TFE3 during ER stress.
  7. CCPG1 recognizes ER luminal proteins for selective ER-phagy.
  8. Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson's disease.
  9. What repeat expansion disorders can teach us about the Central Dogma.
  10. Protein translation paradox: Implications in translational regulation of aging.
  11. Single-cell aging clocks.
  12. An intrinsically disordered protein, osteopontin, driving neuropathology in Alzheimer's dementia.
  13. Contrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain.
  1. bioRxiv. 2023 Jan 20. pii: 2023.01.18.524611. [Epub ahead of print]
    Frontotemporal Dementia Patient Neurons With Progranulin Deficiency Display Protein Dyshomeostasis.
    Lisa Elia, Bianca Herting, Amela Alijagic, Christina Buselli, Leela Wong, Grace Morrison, Miguel A Prado, Joao A Paulo, Steven P Gygi, Daniel Finley, Steven Finkbeiner.
      Haploinsufficiency of progranulin (PGRN) causes frontotemporal dementia (FTD), a devastating neurodegenerative disease with no effective treatment. PGRN is required for efficient proteostasis, as loss of neuronal PGRN results in dysfunctional lysosomes and impaired clearance and cytoplasmic aggregation of TDP-43, a protein involved in neurodegeneration in FTD. These and other events lead to neurodegeneration and neuroinflammation. However, the detailed mechanisms leading to protein dyshomeostasis in PGRN-deficient cells remain unclear. We report here the development of human cell models of FTD with PGRN-deficiency to explore the molecular mechanisms underlying proteostasis breakdown and TDP-43 aggregation in FTD. Neurons differentiated from FTD patient induced pluripotent stem cells (iPSCs) have reduced PGRN levels, and the neurons recapitulate key disease features, including impaired lysosomal function, defective TDP-43 turnover and accumulation, neurodegeneration, and death. Proteomic analysis revealed altered levels of proteins linked to the autophagy-lysosome pathway (ALP) and the ubiquitin-proteasome system (UPS) in FTD patient neurons, providing new mechanistic insights into the link between PGRN-deficiency and disease pathobiology.
    DOI:  https://doi.org/10.1101/2023.01.18.524611
  2. bioRxiv. 2023 Jan 04. pii: 2023.01.04.521821. [Epub ahead of print]
    Simultaneous proteome localization and turnover analysis reveals spatiotemporal dynamics of unfolded protein responses.
    Jordan Currie, Vyshnavi Manda, Veronica Hidalgo, R W Ludwig, Maggie P Y Lam, Edward Lau.
      The functions of proteins depend on their spatial and temporal distributions, which are not directly measured by static protein abundance. Under protein misfolding stress, the unfolded protein response (UPR) pathway remediates proteostasis in part by altering the turnover kinetics and spatial distribution of proteins, yet a global view of these spatiotemporal changes has yet to emerge and it is unknown how they affect different cellular compartments and pathways. Here we describe a mass spectrometry-based proteomics strategy and data analysis pipeline, named Simultaneous Proteome Localization and Turnover (SPLAT), to measure concurrently the changes in protein turnover and subcellular distribution in the same experiment. Investigating two common UPR models of thapsigargin and tunicamycin challenge, we find that the global suppression of protein synthesis during UPR is dependent on subcellular localization, with more severe slowdown in lysosome vs. endoplasmic reticulum (ER) protein turnover. Most candidate translocation events affect pre-existing proteins and likely involve vesicular transport across endomembrane fractions including an expansion of an ER-derived vesicle (ERV) compartment containing RNA binding proteins and stress response proteins. In parallel, we observed specific translocations involving only newly synthesized protein pools that are indicative of endomembrane stalling. The translocation of a subclass of cell surface proteins to the endomembrane including EGFR and ITGAV upon UPR affects only heavy labeled proteins, which suggest their internalization is driven by nascent protein trafficking rather than ligand dependent endocytosis. The approach described here may be broadly useful for inferring the coordinations between spatial and temporal proteome regulations in normal and stressed cells.
    DOI:  https://doi.org/10.1101/2023.01.04.521821
  3. bioRxiv. 2023 Jan 17. pii: 2023.01.16.524237. [Epub ahead of print]
    Divergent Proteome Reactivity Influences Arm-Selective Activation of Pharmacological Endoplasmic Reticulum Proteostasis Regulators.
    Gabriel M Kline, Ryan J Paxman, Chung-Yon Lin, Nicole Madrazo, Julia M Grandjean, Kyunga Lee, Karina Nugroho, Evan T Powers, R Luke Wiseman, Jeffery W Kelly.
      Pharmacological activation of the activating transcription factor 6 (ATF6) arm of the Unfolded Protein Response (UPR) has proven useful for ameliorating proteostasis deficiencies in a variety of etiologically diverse diseases. Previous high-throughput screening efforts identified the small molecule AA147 as a potent and selective ATF6 activating compound that operates through a mechanism involving metabolic activation of its 2-amino- p -cresol substructure affording a quinone methide, which then covalently modifies a subset of ER protein disulfide isomerases (PDIs). Intriguingly, another compound identified in this screen, AA132, also contains a 2-amino- p -cresol moiety; however, this compound showed less transcriptional selectivity, instead globally activating all three arms of the UPR. Here, we show that AA132 activates global UPR signaling through a mechanism analogous to that of AA147, involving metabolic activation and covalent PDI modification. Chemoproteomic-enabled analyses show that AA132 covalently modifies PDIs to a greater extent than AA147. Paradoxically, activated AA132 reacts slower with PDIs, indicating it is less reactive than activated AA147. This suggests that the higher labeling of PDIs observed with activated AA132 can be attributed to its lower reactivity, which allows this activated compound to persist longer in the cellular environment prior to quenching by endogenous nucleophiles. Collectively, these results suggest that AA132 globally activates the UPR through increased engagement of ER PDIs. Consistent with this, reducing the cellular concentration of AA132 decreases PDI modifications and allows for selective ATF6 activation. Our results highlight the relationship between metabolically activatable-electrophile stability, ER proteome reactivity, and the transcriptional response observed with the enaminone chemotype of ER proteostasis regulators, enabling continued development of next-generation ATF6 activating compounds.
    DOI:  https://doi.org/10.1101/2023.01.16.524237
  4. Commun Biol. 2023 Jan 30. 6(1): 121
    Tardigrade small heat shock proteins can limit desiccation-induced protein aggregation.
    Jonathan D Hibshman, Serena Carra, Bob Goldstein.
      Small heat shock proteins (sHSPs) are chaperones with well-characterized roles in heat stress, but potential roles for sHSPs in desiccation tolerance have not been as thoroughly explored. We identified nine sHSPs from the tardigrade Hypsibius exemplaris, each containing a conserved alpha-crystallin domain flanked by disordered regions. Many of these sHSPs are highly expressed. Multiple tardigrade and human sHSPs could improve desiccation tolerance of E. coli, suggesting that the capacity to contribute to desicco-protection is a conserved property of some sHSPs. Purification and subsequent analysis of two tardigrade sHSPs, HSP21 and HSP24.6, revealed that these proteins can oligomerize in vitro. These proteins limited heat-induced aggregation of the model enzyme citrate synthase. Heterologous expression of HSP24.6 improved bacterial heat shock survival, and the protein significantly reduced heat-induced aggregation of soluble bacterial protein. Thus, HSP24.6 likely chaperones against protein aggregation to promote heat tolerance. Furthermore, HSP21 and HSP24.6 limited desiccation-induced aggregation and loss of function of citrate synthase. This suggests a mechanism by which tardigrade sHSPs promote desiccation tolerance, by limiting desiccation-induced protein aggregation, thereby maintaining proteostasis and supporting survival. These results suggest that sHSPs provide a mechanism of general stress resistance that can also be deployed to support survival during anhydrobiosis.
    DOI:  https://doi.org/10.1038/s42003-023-04512-y
  5. Mol Neurobiol. 2023 Feb 02.
    Immortalized Alzheimer's Disease Astrocytes: Characterization of Their Proteolytic Systems.
    Chunmei Gong, Laura Bonfili, Yadong Zheng, Valentina Cecarini, Massimiliano Cuccioloni, Mauro Angeletti, Giulia Dematteis, Laura Tapella, Armando A Genazzani, Dmitry Lim, Anna Maria Eleuteri.
      Alzheimer's disease (AD) is a progressive neurodegeneration with dysfunctions in both the ubiquitin-proteasome system (UPS) and autophagy. Astroglia participation in AD is an attractive topic of research, but molecular patterns are partially defined and available in vitro models have technical limitations. Immortalized astrocytes from the hippocampus of 3xTg-AD and wild-type mice (3Tg-iAstro and WT-iAstro, respectively) have been obtained as an attempt to overcome primary cell line limitations and this study aims at characterizing their proteolytic systems, focusing on UPS and autophagy. Both 26S and 20S proteasomal activities were downregulated in 3Tg-iAstro, in which a shift in catalytic subunits from constitutive 20S proteasome to immunoproteasome occurred, with consequences on immune functions. In fact, immunoproteasome is the specific complex in charge of clearing damaged proteins under inflammatory conditions. Parallelly, augmented expression and activity of the lysosomal cathepsin B, enhanced levels of lysosomal-associated membrane protein 1, beclin1, and LC3-II, together with an increased uptake of monodansylcadaverine in autophagic vacuoles, suggested autophagy activation in 3Tg-iAstro. The two proteolytic pathways were linked by p62 that accumulated in 3Tg-iAstro due to both increased synthesis and decreased degradation in the UPS defective astrocytes. Treatment with 4-phenylbutyric acid, a neuroprotective small chemical chaperone, partially restored proteasome and autophagy-mediated proteolysis in 3Tg-iAstro. Our data shed light on the impaired proteostasis in 3Tg-iAstro with proteasome inhibition and autophagic compensatory activation, providing additional validation of this AD in vitro model, and propose a new mechanism of action of 4-phenylbutyric acid in neurodegenerative disorders.
    Keywords:  4-Phenylbutyric acid; Alzheimer’s disease; Astrocytes; Autophagy; Ubiquitin–proteasome system
    DOI:  https://doi.org/10.1007/s12035-023-03231-z
  6. Autophagy. 2023 Jan 31.
    Phosphorylation of EIF2S1 (eukaryotic translation initiation factor 2 subunit alpha) is indispensable for nuclear translocation of TFEB and TFE3 during ER stress.
    Thao Thi Dang, Mi-Jeong Kim, Yoon Young Lee, Hien Thi Le, Kook Hwan Kim, Somi Nam, Seung Hwa Hyun, Hong Lim Kim, Su Wol Chung, Hun Taeg Chung, Eek-Hoon Jho, Hiderou Yoshida, Kyoungmi Kim, Chan Young Park, Myung-Shik Lee, Sung Hoon Back.
      There are diverse links between macroautophagy/autophagy pathways and unfolded protein response (UPR) pathways under endoplasmic reticulum (ER) stress conditions to restore ER homeostasis. Phosphorylation of EIF2S1/eIF2α is an important mechanism that can regulate all three UPR pathways through transcriptional and translational reprogramming to maintain cellular homeostasis and overcome cellular stresses. In this study, to investigate the roles of EIF2S1 phosphorylation in regulation of autophagy during ER stress, we used EIF2S1 phosphorylation-deficient (A/A) cells in which residue 51 was mutated from serine to alanine. A/A cells exhibited defects in several steps of autophagic processes (such as autophagosome and autolysosome formation) that are regulated by the transcriptional activities of the autophagy master transcription factors TFEB and TFE3 under ER stress conditions. EIF2S1 phosphorylation was required for nuclear translocation of TFEB and TFE3 during ER stress. In addition, EIF2AK3/PERK, PPP3/calcineurin-mediated dephosphorylation of TFEB and TFE3, and YWHA/14-3-3 dissociation were required for their nuclear translocation, but were insufficient to induce their nuclear retention during ER stress. Overexpression of the activated ATF6/ATF6α form, XBP1s, and ATF4 differentially rescued defects of TFEB and TFE3 nuclear translocation in A/A cells during ER stress. Consequently, overexpression of the activated ATF6 or TFEB form more efficiently rescued autophagic defects, although XBP1s and ATF4 also displayed an ability to restore autophagy in A/A cells during ER stress. Our results suggest that EIF2S1 phosphorylation is important for autophagy and UPR pathways, to restore ER homeostasis and reveal how EIF2S1 phosphorylation connects UPR pathways to autophagy.
    Keywords:  ATF6; EIF2S1 phosphorylation; ER stress; TFEB; autophagy; nuclear translocation; phosphorylation TFE3; transcription factor E3; transcription factor EB
    DOI:  https://doi.org/10.1080/15548627.2023.2173900
  7. Mol Biol Cell. 2023 Feb 03. mbcE22090432
    CCPG1 recognizes ER luminal proteins for selective ER-phagy.
    Shunsuke Ishii, Haruka Chino, Koji L Ode, Yoshitaka Kurikawa, Hiroki R Ueda, Akira Matsuura, Noboru Mizushima, Eisuke Itakura.
      The endoplasmic reticulum (ER) is a major cell compartment where protein synthesis, folding and post-translational modifications occur with assistance from a wide variety of chaperones and enzymes. Quality control systems selectively eliminate abnormal proteins that accumulate inside the ER due to cellular stresses. ER-phagy, i.e., selective autophagy of the ER, is a mechanism that maintains or re-establishes cellular and ER-specific homeostasis through removal of abnormal proteins. However, how ER luminal proteins are recognized by the ER-phagy machinery remains unclear. Here, we applied the aggregation-prone protein, six-repeated islet amyloid polypeptide (6xIAPP), as a model ER-phagy substrate, and found that cell cycle progression 1 (CCPG1), which is an ER-phagy receptor, efficiently mediates its degradation via ER-phagy. We also identified prolyl 3-hydroxylase family member 4 (P3H4) as an endogenous cargo of CCPG1-dependent ER-phagy. The ER luminal region of CCPG1 contains several highly conserved regions that we refer to as cargo interaction regions (CIRs); these directly interact with specific luminal cargos for ER-phagy. Notably, 6xIAPP and P3H4 directly interact with different CIRs. These findings indicate that CCPG1 is a bispecific ER-phagy receptor for ER luminal proteins and the autophagosomal membrane that contributes to the efficient removal of aberrant ER-resident proteins through ER-phagy.
    DOI:  https://doi.org/10.1091/mbc.E22-09-0432
  8. iScience. 2023 Feb 17. 26(2): 105925
    Altered transcriptome-proteome coupling indicates aberrant proteostasis in Parkinson's disease.
    Fiona Dick, Ole-Bjørn Tysnes, Guido W Alves, Gonzalo S Nido, Charalampos Tzoulis.
      Aberrant proteostasis is thought to be implicated in Parkinson's disease (PD), but patient-derived evidence is scant. We hypothesized that impaired proteostasis is reflected as altered transcriptome-proteome correlation in the PD brain. We integrated transcriptomic and proteomic data from prefrontal cortex of PD patients and young and aged controls to assess RNA-protein correlations across samples. The aged brain showed a genome-wide decrease in mRNA-protein correlation. Genes encoding synaptic vesicle proteins showed negative correlations, likely reflecting spatial separation of mRNA and protein into soma and synapses. PD showed a broader transcriptome-proteome decoupling, consistent with a proteome-wide decline in proteostasis. Genes showing negative correlation in PD were enriched for proteasome subunits, indicating accentuated spatial separation of transcript and protein in PD neurons. In addition, PD showed positive correlations for mitochondrial respiratory chain genes, suggesting a tighter regulation in the face of mitochondrial dysfunction. Our results support the hypothesis that aberrant proteasomal function is implicated in PD pathogenesis.
    Keywords:  Proteomics; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2023.105925
  9. Mol Cell. 2023 Feb 02. pii: S1097-2765(22)01174-1. [Epub ahead of print]83(3): 324-329
    What repeat expansion disorders can teach us about the Central Dogma.
    Eric T Wang, Catherine H Freudenreich, Natalia Gromak, Ankur Jain, Peter K Todd, Yoshitaka Nagai.
      Pathogenic repeat sequences underlie several human disorders, including amyotrophic lateral sclerosis, Huntington's disease, and myotonic dystrophy. Here, we speak to several researchers about how repeat sequences have been implicated in affecting all aspects of the Central Dogma of molecular biology through their effects on DNA, RNA, and protein.
    DOI:  https://doi.org/10.1016/j.molcel.2022.12.017
  10. Front Cell Dev Biol. 2023 ;11 1129281
    Protein translation paradox: Implications in translational regulation of aging.
    Harper S Kim, Andrew M Pickering.
      Protein translation is an essential cellular process playing key roles in growth and development. Protein translation declines over the course of age in multiple animal species, including nematodes, fruit flies, mice, rats, and even humans. In all these species, protein translation transiently peaks in early adulthood with a subsequent drop over the course of age. Conversely, lifelong reductions in protein translation have been found to extend lifespan and healthspan in multiple animal models. These findings raise the protein synthesis paradox: age-related declines in protein synthesis should be detrimental, but life-long reductions in protein translation paradoxically slow down aging and prolong lifespan. This article discusses the nature of this paradox and complies an extensive body of work demonstrating protein translation as a modulator of lifespan and healthspan.
    Keywords:  ageing; aging; eIF; hallmarks of aging; lifespan; protein translation; sk6; theories of aging
    DOI:  https://doi.org/10.3389/fcell.2023.1129281
  11. Lab Anim (NY). 2023 Feb;52(2): 33
    Single-cell aging clocks.
    Charlotte Harrison.
      
    DOI:  https://doi.org/10.1038/s41684-023-01118-z
  12. Proc Natl Acad Sci U S A. 2023 Feb 07. 120(6): e2221816120
    An intrinsically disordered protein, osteopontin, driving neuropathology in Alzheimer's dementia.
    Lawrence Steinman.
      
    DOI:  https://doi.org/10.1073/pnas.2221816120
  13. bioRxiv. 2023 Jan 14. pii: 2023.01.14.523958. [Epub ahead of print]
    Contrasting patterns of somatic mutations in neurons and glia reveal differential predisposition to disease in the aging human brain.
    Javier Ganz, Lovelace J Luquette, Sara Bizzotto, Craig L Bohrson, Hu Jin, Michael B Miller, Zinan Zhou, Alon Galor, Peter J Park, Christopher A Walsh.
      Characterizing the mechanisms of somatic mutations in the brain is important for understanding aging and disease, but little is known about the mutational patterns of different cell types. We performed whole-genome sequencing of 71 oligodendrocytes and 51 neurons from neurotypical individuals (0.4 to 104 years old) and identified >67,000 somatic single nucleotide variants (sSNVs) and small insertions and deletions (indels). While both cell types accumulate mutations with age, oligodendrocytes accumulate sSNVs 69% faster than neurons (27/year versus 16/year) whereas indels accumulate 42% slower (1.8/year versus 3.1/year). Correlation with single-cell RNA and chromatin accessibility from the same brains revealed that oligodendrocyte mutations are enriched in inactive genomic regions and are distributed similarly to mutations in brain cancers. In contrast, neuronal mutations are enriched in open, transcriptionally active chromatin. These patterns highlight differences in the mutagenic processes in glia and neurons and suggest cell type-specific, age-related contributions to neurodegeneration and oncogenesis.
    DOI:  https://doi.org/10.1101/2023.01.14.523958
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