bims-proarb 2023-06-18 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2023‒06‒18
ten papers selected by
Rich Giadone
Harvard University

Editorial: The regulation of proteostasis in aging.
The Hsp90 molecular chaperone governs client proteins by targeting intrinsically disordered regions.
PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid.
Extracellular protein homeostasis: The dawning of a new age for human disease therapies?
Assays of Monitoring and Measuring Autophagic Flux for iPSC-Derived Human Neurons and Other Brain Cell Types.
Astrocytic deletion of protein kinase R-like ER kinase (PERK) does not affect learning and memory in aged mice but worsens outcome from experimental stroke.
Tau mutation S356T in the three repeat isoform leads to microtubule dysfunction and promotes prion-like seeded aggregation.
Proteomics of the astrocyte secretome reveals changes in their response to soluble oligomeric Aβ.
Aging disrupts gene expression timing during muscle regeneration.
The temporal balance between self-renewal and differentiation of human neural stem cells requires the amyloid precursor protein.

Front Cell Dev Biol. 2023 ;11 1221510

Editorial: The regulation of proteostasis in aging.

Ji-Xin Tang, Fu-Hui Xiao.



Keywords:  aging; autophagic flux; non-canonical autophagy; proteasome; protein translation; proteostasis

DOI:  https://doi.org/10.3389/fcell.2023.1221510
Mol Cell. 2023 Jun 15. pii: S1097-2765(23)00377-5. [Epub ahead of print]83(12): 2035-2044.e7

The Hsp90 molecular chaperone governs client proteins by targeting intrinsically disordered regions.

Janhavi A Kolhe, Neethu L Babu, Brian C Freeman.

  Molecular chaperones govern proteome health to support cell homeostasis. An essential eukaryotic component of the chaperone system is Hsp90. Using a chemical-biology approach, we characterized the features driving the Hsp90 physical interactome. We found that Hsp90 associated with ∼20% of the yeast proteome using its three domains to preferentially target intrinsically disordered regions (IDRs) of client proteins. Hsp90 selectively utilized an IDR to regulate client activity as well as maintained IDR-protein health by preventing the transition to stress granules or P-bodies at physiological temperatures. We also discovered that Hsp90 controls the fidelity of ribosome initiation that triggers a heat shock response when disrupted. Our study provides insights into how this abundant molecular chaperone supports a dynamic and healthy native protein landscape.

Keywords:  Hsp90; fidelity of translation initiation; intrinsically disordered regions; molecular chaperone; proteostasis

DOI:  https://doi.org/10.1016/j.molcel.2023.05.021
EMBO J. 2023 Jun 12. e113908

PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid.

Valerie Perea, Christian Cole, Justine Lebeau, Vivian Dolina, Kelsey R Baron, Aparajita Madhavan, Jeffery W Kelly, Danielle A Grotjahn, R Luke Wiseman.

  Endoplasmic reticulum (ER) stress and mitochondrial dysfunction are linked in the onset and pathogenesis of numerous diseases. This has led to considerable interest in defining the mechanisms responsible for regulating mitochondria during ER stress. The PERK signaling arm of the unfolded protein response (UPR) has emerged as a prominent ER stress-responsive signaling pathway that regulates diverse aspects of mitochondrial biology. Here, we show that PERK activity promotes adaptive remodeling of mitochondrial membrane phosphatidic acid (PA) to induce protective mitochondrial elongation during acute ER stress. We find that PERK activity is required for ER stress-dependent increases in both cellular PA and YME1L-dependent degradation of the intramitochondrial PA transporter PRELID1. These two processes lead to the accumulation of PA on the outer mitochondrial membrane where it can induce mitochondrial elongation by inhibiting mitochondrial fission. Our results establish a new role for PERK in the adaptive remodeling of mitochondrial phospholipids and demonstrate that PERK-dependent PA regulation adapts organellar shape in response to ER stress.

Keywords:  endoplasmic reticulum (ER) stress; mitochondrial morphology; phosphatidic acid; unfolded protein response (UPR)

DOI:  https://doi.org/10.15252/embj.2023113908
Clin Transl Med. 2023 Jun;13(6): e1305

Extracellular protein homeostasis: The dawning of a new age for human disease therapies?

Mark R Wilson, Sandeep Satapathy, Michele Vendruscolo.

DOI: https://doi.org/10.1002/ctm2.1305
Methods Mol Biol. 2023 ;2683 221-233

Assays of Monitoring and Measuring Autophagic Flux for iPSC-Derived Human Neurons and Other Brain Cell Types.

Ryan O'Rourke, Guzide Ayse Erdemir, Yu-Wen Alvin Huang.

  Autophagy is a highly conserved, cytoprotective, catabolic process induced in response to conditions of cellular stress and nutrient deprivation. It is responsible for the degradation of large intracellular substrates such as misfolded or aggregated proteins and organelles. This self-degradative mechanism is crucial for proteostasis in post-mitotic neurons, requiring its careful regulation. Due to its homeostatic role and the implications, it has for certain disease pathologies, autophagy has become a growing area of research. We describe here two assays that can be used as part of a tool kit for measuring autophagy-lysosomal flux in human iPSC-derived neurons.One way to measure autophagic flux is through a western blotting assay, which can be used to analyze two important autophagy proteins: microtubule-associated protein 1 light chain 3 (LC3) and p62. In this chapter, we describe a western blotting assay for use in human iPSC neurons that can be used to quantify these two proteins of interest to measure autophagic flux.In addition to conventional western blotting techniques, more sophisticated tools have come available to readout autophagic flux in a sensitive and high-throughput manner. In the latter portion of this chapter, we describe a flow cytometry assay which utilizes a pH-sensitive fluorescent reporter which can also be used to measure autophagic flux.

Keywords:  Aitophagic flux; Autophagy; Immunoblotting flow cytometry; Induced pluripotent stem cells (iPS cells); Microtubule associated protein 1 light chain 3 (LC3); Neurons; p62

DOI:  https://doi.org/10.1007/978-1-0716-3287-1_18
J Neurosci Res. 2023 Jun 14.

Astrocytic deletion of protein kinase R-like ER kinase (PERK) does not affect learning and memory in aged mice but worsens outcome from experimental stroke.

Anirudhya Lahiri, James C Walton, Ning Zhang, Neil Billington, A Courtney DeVries, Gordon P Meares.

  Aging is associated with cognitive decline and is the main risk factor for a myriad of conditions including neurodegeneration and stroke. Concomitant with aging is the progressive accumulation of misfolded proteins and loss of proteostasis. Accumulation of misfolded proteins in the endoplasmic reticulum (ER) leads to ER stress and activation of the unfolded protein response (UPR). The UPR is mediated, in part, by the eukaryotic initiation factor 2α (eIF2α) kinase protein kinase R-like ER kinase (PERK). Phosphorylation of eIF2α reduces protein translation as an adaptive mechanism but this also opposes synaptic plasticity. PERK, and other eIF2α kinases, have been widely studied in neurons where they modulate both cognitive function and response to injury. The impact of astrocytic PERK signaling in cognitive processes was previously unknown. To examine this, we deleted PERK from astrocytes (AstroPERKKO ) and examined the impact on cognitive functions in middle-aged and old mice of both sexes. Additionally, we tested the outcome following experimental stroke using the transient middle cerebral artery occlusion (MCAO) model. Tests of short-term and long-term learning and memory as well as of cognitive flexibility in middle-aged and old mice revealed that astrocytic PERK does not regulate these processes. Following MCAO, AstroPERKKO had increased morbidity and mortality. Collectively, our data demonstrate that astrocytic PERK has limited impact on cognitive function and has a more prominent role in the response to neural injury.

Keywords:  MCAO; RRID:AB_10692650; RRID:AB_2095847; RRID:AB_2096481; RRID:AB_2107445; RRID:AB_2631098; RRID:AB_304334; RRID:Addgene_28306; RRID:IMSR_JAX:023066; RRID:IMSR_JAX:024098; RRID:SCR_002798; RRID:SCR_014210; RRID:SCR_014289; RRID:nif-0000-00280; aging; astrocytes; glia; learning and memory; protein kinase R-like ER kinase (PERK); stroke; unfolded protein response

DOI:  https://doi.org/10.1002/jnr.25224
Front Neurosci. 2023 ;17 1181804

Tau mutation S356T in the three repeat isoform leads to microtubule dysfunction and promotes prion-like seeded aggregation.

Yuxing Xia, Brach M Bell, Justin D Kim, Benoit I Giasson.

  Tauopathies are a group of neurodegenerative diseases, which include frontotemporal dementia (FTD) and Alzheimer's disease (AD), broadly defined by the development of tau brain aggregates. Both missense and splicing tau mutations can directly cause early onset FTD. Tau protein is a microtubule-associated protein that stabilizes and regulates microtubules, but this function can be disrupted in disease states. One contributing factor is the balance of different tau isoforms, which can be categorized into either three repeat (3R) or four repeat (4R) isoforms based on the number of microtubule-binding repeats that are expressed. Imbalance of 3R and 4R isoforms in either direction can cause FTD and neurodegeneration. There is also increasing evidence that 3R tauopathies such as Pick's disease form tau aggregates predominantly comprised of 3R isoforms and these can present differently from 4R and mixed 3R/4R tauopathies. In this study, multiple mutations in 3R tau were assessed for MT binding properties and prion-like aggregation propensity. Different missense tau mutations showed varying effects on MT binding depending on molecular location and properties. Of the mutations that were surveyed, S356T tau is uniquely capable of prion-like seeded aggregation and forms extensive Thioflavin positive aggregates. This unique prion-like tau strain will be useful to model 3R tau aggregation and will contribute to the understanding of diverse presentations of different tauopathies.

Keywords:  Alzheimer’s disease; aggregation; frontotemporal dementia; microtubule; tau protein

DOI:  https://doi.org/10.3389/fnins.2023.1181804
J Neurochem. 2023 Jun 11.

Proteomics of the astrocyte secretome reveals changes in their response to soluble oligomeric Aβ.

Vittoria Matafora, Alena Gorb, Fangjia Yang, Wendy Noble, Angela Bachi, Beatriz Gomez Perez-Nievas, Maria Jimenez-Sanchez.

Astrocytes associate with amyloid plaques in Alzheimer's disease (AD). Astrocytes react to changes in the brain environment, including increasing concentrations of amyloid-β (Aβ). However, the precise response of astrocytes to soluble small Aβ oligomers at concentrations similar to those present in the human brain has not been addressed. In this study, we exposed astrocytes to media from neurons that express the human amyloid precursor protein (APP) transgene with the double Swedish mutation (APPSwe), and which contains APP-derived fragments, including soluble human Aβ oligomers. We then used proteomics to investigate changes in the astrocyte secretome. Our data show dysregulated secretion of astrocytic proteins involved in the extracellular matrix and cytoskeletal organization and increase secretion of proteins involved in oxidative stress responses and those with chaperone activity. Several of these proteins have been identified in previous transcriptomic and proteomic studies using brain tissue from human AD and cerebrospinal fluid (CSF). Our work highlights the relevance of studying astrocyte secretion to understand the brain response to AD pathology and the potential use of these proteins as biomarkers for the disease.

DOI: https://doi.org/10.1111/jnc.15875
Stem Cell Reports. 2023 Jun 13. pii: S2213-6711(23)00183-2. [Epub ahead of print]18(6): 1325-1339

Aging disrupts gene expression timing during muscle regeneration.

Jesse V Kurland, Alicia A Cutler, Jacob T Stanley, Nicole Dalla Betta, Ashleigh Van Deusen, Brad Pawlikowski, Monica Hall, Tiffany Antwine, Alan Russell, Mary Ann Allen, Robin Dowell, Bradley Olwin.

  Skeletal muscle function and regenerative capacity decline during aging, yet factors driving these changes are incompletely understood. Muscle regeneration requires temporally coordinated transcriptional programs to drive myogenic stem cells to activate, proliferate, fuse to form myofibers, and to mature as myonuclei, restoring muscle function after injury. We assessed global changes in myogenic transcription programs distinguishing muscle regeneration in aged mice from young mice by comparing pseudotime trajectories from single-nucleus RNA sequencing of myogenic nuclei. Aging-specific differences in coordinating myogenic transcription programs necessary for restoring muscle function occur following muscle injury, likely contributing to compromised regeneration in aged mice. Differences in pseudotime alignment of myogenic nuclei when comparing aged with young mice via dynamic time warping revealed pseudotemporal differences becoming progressively more severe as regeneration proceeds. Disruptions in timing of myogenic gene expression programs may contribute to incomplete skeletal muscle regeneration and declines in muscle function as organisms age.

Keywords:  MuSC; aging; cell fate; differentiation; myonuclei; pseudotime; regeneration; single-nucleus RNA sequencing; skeletal muscle regeneration

DOI:  https://doi.org/10.1016/j.stemcr.2023.05.005
Sci Adv. 2023 Jun 16. 9(24): eadd5002

The temporal balance between self-renewal and differentiation of human neural stem cells requires the amyloid precursor protein.

Khadijeh Shabani, Julien Pigeon, Marwan Benaissa Touil Zariouh, Tengyuan Liu, Azadeh Saffarian, Jun Komatsu, Elise Liu, Natasha Danda, Mathilde Becmeur-Lefebvre, Ridha Limame, Delphine Bohl, Carlos Parras, Bassem A Hassan.

Neurogenesis in the developing human cerebral cortex occurs at a particularly slow rate owing in part to cortical neural progenitors preserving their progenitor state for a relatively long time, while generating neurons. How this balance between the progenitor and neurogenic state is regulated, and whether it contributes to species-specific brain temporal patterning, is poorly understood. Here, we show that the characteristic potential of human neural progenitor cells (NPCs) to remain in a progenitor state as they generate neurons for a prolonged amount of time requires the amyloid precursor protein (APP). In contrast, APP is dispensable in mouse NPCs, which undergo neurogenesis at a much faster rate. Mechanistically, APP cell-autonomously contributes to protracted neurogenesis through suppression of the proneurogenic activator protein-1 transcription factor and facilitation of canonical WNT signaling. We propose that the fine balance between self-renewal and differentiation is homeostatically regulated by APP, which may contribute to human-specific temporal patterns of neurogenesis.

DOI: https://doi.org/10.1126/sciadv.add5002