bims-proarb 2022-09-25 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2022–09–25
ten papers selected by
Rich Giadone, Harvard University

Proteostasis unbalance in prion diseases: Mechanisms of neurodegeneration and therapeutic targets.
Elevated homocysteine activates unfolded protein responses and causes aberrant trophoblast differentiation and mouse blastocyst development.
A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production.
The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines.
Small soluble α-synuclein aggregates are the toxic species in Parkinson's disease.
Ageing Impairs Adaptive Unfolded Protein Response and Drives Beta Cell Dedifferentiation in Human.
Age-related pathological impairments in directly reprogrammed dopaminergic neurons derived from patients with idiopathic Parkinson's disease.
Proteomics Identifies Substrates and a Novel Component in hSnd2-Dependent ER Protein Targeting.
Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium.
Delineation of proteome changes driven by cell size and growth rate.

Front Neurosci. 2022 ;16 966019

Proteostasis unbalance in prion diseases: Mechanisms of neurodegeneration and therapeutic targets.

Stefano Thellung, Alessandro Corsaro, Irene Dellacasagrande, Mario Nizzari, Martina Zambito, Tullio Florio.

  Transmissible spongiform encephalopathies (TSEs), or prion diseases, are progressive neurodegenerative disorders of the central nervous system that affect humans and animals as sporadic, inherited, and infectious forms. Similarly to Alzheimer's disease and other neurodegenerative disorders, any attempt to reduce TSEs' lethality or increase the life expectancy of affected individuals has been unsuccessful. Typically, the onset of symptoms anticipates the fatal outcome of less than 1 year, although it is believed to be the consequence of a decades-long process of neuronal death. The duration of the symptoms-free period represents by itself a major obstacle to carry out effective neuroprotective therapies. Prions, the infectious entities of TSEs, are composed of a protease-resistant protein named prion protein scrapie (PrPSc) from the prototypical TSE form that afflicts ovines. PrPSc misfolding from its physiological counterpart, cellular prion protein (PrPC), is the unifying pathogenic trait of all TSEs. PrPSc is resistant to intracellular turnover and undergoes amyloid-like fibrillation passing through the formation of soluble dimers and oligomers, which are likely the effective neurotoxic entities. The failure of PrPSc removal is a key pathogenic event that defines TSEs as proteopathies, likewise other neurodegenerative disorders, including Alzheimer's, Parkinson's, and Huntington's disease, characterized by alteration of proteostasis. Under physiological conditions, protein quality control, led by the ubiquitin-proteasome system, and macroautophagy clears cytoplasm from improperly folded, redundant, or aggregation-prone proteins. There is evidence that both of these crucial homeostatic pathways are impaired during the development of TSEs, although it is still unclear whether proteostasis alteration facilitates prion protein misfolding or, rather, PrPSc protease resistance hampers cytoplasmic protein quality control. This review is aimed to critically analyze the most recent advancements in the cause-effect correlation between PrPC misfolding and proteostasis alterations and to discuss the possibility that pharmacological restoring of ubiquitin-proteasomal competence and stimulation of autophagy could reduce the intracellular burden of PrPSc and ameliorate the severity of prion-associated neurodegeneration.

Keywords:  autophagy; neurodegeneration; prion protein; proteasome; protein misfolding

DOI:  https://doi.org/10.3389/fnins.2022.966019
Physiol Rep. 2022 Sep;10(18): e15467

Elevated homocysteine activates unfolded protein responses and causes aberrant trophoblast differentiation and mouse blastocyst development.

Nadejda Capatina, Graham J Burton, Hong Wa Yung.

  Hyperhomocysteinemia may arise from folate/vitamin B12 deficiency, genetic polymorphisms, kidney disease, or hypothyroidism. It is associated with an increased risk of early pregnancy loss and placenta-related complications of pregnancy, including pre-eclampsia and fetal growth restriction. While the majority of studies of hyperhomocysteinemia focus on epigenetic changes secondary to metabolic disruption, the effects of homocysteine toxicity on placental development remain unexplored. Here, we investigated the influence of hyperhomocysteinemia on early blastocyst development and trophoblast differentiation. Exposure of cultured blastocysts to high homocysteine levels reduces cell number in the trophectoderm layer, most likely through increased apoptosis. Homocysteine also promotes differentiation of a trophoblast stem cell line. Both effects diminish the stem cell pool, and are mediated in an endoplasmic reticulum (ER) unfolded protein response (UPRER )-dependent manner. Targeted alleviation of UPRER may therefore provide a new therapeutic intervention to improve pregnancy outcome in women with hyperhomocysteinemia.

Keywords:  endoplasmic reticulum stress; hyperhomocysteinemia; placenta; pregnancy; trophoblast stem cells; unfolded protein response

DOI:  https://doi.org/10.14814/phy2.15467
Nat Commun. 2022 Sep 19. 13(1): 5491

A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production.

Naomi R Genuth, Zhen Shi, Koshi Kunimoto, Victoria Hung, Adele F Xu, Craig H Kerr, Gerald C Tiu, Juan A Oses-Prieto, Rachel E A Salomon-Shulman, Jeffrey D Axelrod, Alma L Burlingame, Kyle M Loh, Maria Barna.

Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control cell fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem cell differentiation, we identify dozens of ribosome composition changes underlying cell fate specification. We observe upregulation of RPL10A/uL1-containing ribosomes in the primitive streak followed by progressive decreases during mesoderm differentiation. An Rpl10a loss-of-function allele in mice causes striking early mesodermal phenotypes, including posterior trunk truncations, and inhibits paraxial mesoderm production in culture. Ribosome profiling in Rpl10a loss-of-function mice reveals decreased translation of mesoderm regulators, including Wnt pathway mRNAs, which are also enriched on RPL10A/uL1-containing ribosomes. We further show that RPL10A/uL1 regulates canonical and non-canonical Wnt signaling during stem cell differentiation and in the developing embryo. These findings reveal unexpected ribosome composition modularity that controls differentiation and development through the specialized translation of key signaling networks.

DOI: https://doi.org/10.1038/s41467-022-33263-3
Hum Mol Genet. 2022 Sep 20. pii: ddac233. [Epub ahead of print]

The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines.

Laura J Smith, Magdalena M Bolsinger, Kai-Yin Chau, Matthew E Gegg, Anthony H V Schapira.

Sequence variants or mutations in the GBA gene are numerically the most important risk factor for Parkinson disease (PD). The GBA gene encodes for the lysosomal hydrolase enzyme, glucocerebrosidase (GCase). GBA mutations often reduce GCase activity and lead to impairment of the autophagy-lysosomal pathway, which is important in the turnover of alpha-synuclein, accumulation of which is a key pathological hallmark of PD. Although the E326K variant is one of the most common GBA variants associated with PD, there is limited understanding of its biochemical effects. We have characterised homozygous and heterozygous E326K variants in human fibroblasts. We found that E326K variants did not cause significant loss of GCase protein or activity, endoplasmic reticulum (ER) retention or ER stress, in contrast to the L444P GBA mutation. This was confirmed in human dopaminergic SH-SY5Y neuroblastoma cell lines over-expressing GCase with either E326K or L444P protein. Despite no loss of GCase activity, a significant increase of insoluble alpha-synuclein aggregates in E326K and L444P mutants was observed. Notably, SH-SY5Y over-expressing E326K demonstrated a significant increase in lipid droplet number under basal conditions, which was exacerbated following treatment with the fatty acid oleic acid. Similarly, a significant increase in lipid droplet formation following lipid loading was observed in heterozygous and homozygous E326K fibroblasts. In conclusion, the work presented here demonstrates that the E326K mutation behaves differently to common loss of function GBA mutations, however lipid dyshomeostasis and alpha-synuclein pathology is still evident.

DOI: https://doi.org/10.1093/hmg/ddac233
Nat Commun. 2022 Sep 20. 13(1): 5512

Small soluble α-synuclein aggregates are the toxic species in Parkinson's disease.

Derya Emin, Yu P Zhang, Evgeniia Lobanova, Alyssa Miller, Xuecong Li, Zengjie Xia, Helen Dakin, Dimitrios I Sideris, Jeff Y L Lam, Rohan T Ranasinghe, Antonina Kouli, Yanyan Zhao, Suman De, Tuomas P J Knowles, Michele Vendruscolo, Francesco S Ruggeri, Franklin I Aigbirhio, Caroline H Williams-Gray, David Klenerman.

Soluble α-synuclein aggregates varying in size, structure, and morphology have been closely linked to neuronal death in Parkinson's disease. However, the heterogeneity of different co-existing aggregate species makes it hard to isolate and study their individual toxic properties. Here, we show a reliable non-perturbative method to separate a heterogeneous mixture of protein aggregates by size. We find that aggregates of wild-type α-synuclein smaller than 200 nm in length, formed during an in vitro aggregation reaction, cause inflammation and permeabilization of single-liposome membranes and that larger aggregates are less toxic. Studying soluble aggregates extracted from post-mortem human brains also reveals that these aggregates are similar in size and structure to the smaller aggregates formed in aggregation reactions in the test tube. Furthermore, we find that the soluble aggregates present in Parkinson's disease brains are smaller, largely less than 100 nm, and more inflammatory compared to the larger aggregates present in control brains. This study suggests that the small non-fibrillar α-synuclein aggregates are the critical species driving neuroinflammation and disease progression.

DOI: https://doi.org/10.1038/s41467-022-33252-6
J Clin Endocrinol Metab. 2022 Sep 19. pii: dgac535. [Epub ahead of print]

Ageing Impairs Adaptive Unfolded Protein Response and Drives Beta Cell Dedifferentiation in Human.

Jiaxi Song, Qicheng Ni, Jiajun Sun, Jing Xie, Jianmin Liu, Guang Ning, Weiqing Wang, Qidi Wang.

   CONTEXT: Diabetes is an age-related disease; however, the mechanism underlies senescent beta cell failure is still unknown. The present study was designed to investigate whether and how differentiated state was altered in senescent human beta cells by excluding the effects of impaired glucose tolerance.
METHODS: We calculated the percentage of hormones-negative/Chromogranin A-positive endocrine cells and evaluated the expressions of Forkhead box O1(FoxO1) and Urocortin 3 (UCN3) in islets from 31 non-diabetic individuals, divided into young (<40y), middle-aged (40-60y) and elderly (>60y) groups. We also assessed adaptive unfolded protein response markers Glucose-regulated protein 94 (GRP94) and spliced X-box binding protein 1(XBP1s) in senescent beta cells and their possible contributions to maintaining beta cell identity and differentiation state.
RESULTS: We found an almost two-fold increase in the proportion of dedifferentiated cells in elderly and middle-aged groups, compared with the young group (3.1 ± 1.0% and 3.0 ± 0.9% vs 1.7 ± 0.5%, p < 0.001). This was accompanied by inactivation of FoxO1 and loss of UCN3 expression in senescent human beta cells. In addition, we demonstrated that the expression levels of adaptive unfolded protein response (UPR) components GRP94 and XBP1s were declined with age. In vitro data showed knockdown GRP94 in Min6 cells triggered cells to dedifferentiate and acquired progenitor features, while restored GRP94 levels in H2O2-induced senescent Min6 cells rescued beta cell identity.
CONCLUSIONS: Our finding highlights that the failure to establish proper adaptive unfolded protein response in senescent human beta cells shifts their differentiated states, possibly representing a crucial step in the pathogenesis of age-related beta cell failure.

Keywords:  Ageing; Beta cell dedifferentiation; Type 2 diabetes; Unfolded protein response

DOI:  https://doi.org/10.1210/clinem/dgac535
Stem Cell Reports. 2022 Sep 09. pii: S2213-6711(22)00419-2. [Epub ahead of print]

Age-related pathological impairments in directly reprogrammed dopaminergic neurons derived from patients with idiopathic Parkinson's disease.

Janelle Drouin-Ouellet, Emilie M Legault, Fredrik Nilsson, Karolina Pircs, Julie Bouquety, Florence Petit, Shelby Shrigley, Marcella Birtele, Maria Pereira, Petter Storm, Yogita Sharma, Andreas Bruzelius, Romina Vuono, Malin Kele, Thomas B Stoker, Daniella Rylander Ottosson, Anna Falk, Johan Jakobsson, Roger A Barker, Malin Parmar.

  We have developed an efficient approach to generate functional induced dopaminergic (DA) neurons from adult human dermal fibroblasts. When performing DA neuronal conversion of patient fibroblasts with idiopathic Parkinson's disease (PD), we could specifically detect disease-relevant pathology in these cells. We show that the patient-derived neurons maintain age-related properties of the donor and exhibit lower basal chaperone-mediated autophagy compared with healthy donors. Furthermore, stress-induced autophagy resulted in an age-dependent accumulation of macroautophagic structures. Finally, we show that these impairments in patient-derived DA neurons leads to an accumulation of phosphorylated alpha-synuclein, the classical hallmark of PD pathology. This pathological phenotype is absent in neurons generated from induced pluripotent stem cells from the same patients. Taken together, our results show that direct neural reprogramming can be used for obtaining patient-derived DA neurons, which uniquely function as a cellular model to study age-related pathology relevant to idiopathic PD.

Keywords:  Parkinson's disease; alpha-synuclein; autophagy; direct neural reprogramming; dopaminergic neurons; induced neurons; induced pluripotent stem cells

DOI:  https://doi.org/10.1016/j.stemcr.2022.08.010
Cells. 2022 Sep 19. pii: 2925. [Epub ahead of print]11(18):

Proteomics Identifies Substrates and a Novel Component in hSnd2-Dependent ER Protein Targeting.

Andrea Tirincsi, Sarah O'Keefe, Duy Nguyen, Mark Sicking, Johanna Dudek, Friedrich Förster, Martin Jung, Drazena Hadzibeganovic, Volkhard Helms, Stephen High, Richard Zimmermann, Sven Lang.

  Importing proteins into the endoplasmic reticulum (ER) is essential for about 30% of the human proteome. It involves the targeting of precursor proteins to the ER and their insertion into or translocation across the ER membrane. Furthermore, it relies on signals in the precursor polypeptides and components, which read the signals and facilitate their targeting to a protein-conducting channel in the ER membrane, the Sec61 complex. Compared to the SRP- and TRC-dependent pathways, little is known about the SRP-independent/SND pathway. Our aim was to identify additional components and characterize the client spectrum of the human SND pathway. The established strategy of combining the depletion of the central hSnd2 component from HeLa cells with proteomic and differential protein abundance analysis was used. The SRP and TRC targeting pathways were analyzed in comparison. TMEM109 was characterized as hSnd3. Unlike SRP but similar to TRC, the SND clients are predominantly membrane proteins with N-terminal, central, or C-terminal targeting signals.

Keywords:  SRP-independent targeting; Sec61 complex; differential protein abundance analysis; endoplasmic reticulum; guided entry of tail-anchored proteins; membrane proteins; protein targeting; protein translocation; signal recognition particle

DOI:  https://doi.org/10.3390/cells11182925
EMBO Rep. 2022 Sep 19. e55209

Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium.

Nicolette M Johnson, Louis R Parham, Jeeyoon Na, Keara E Monaghan, Hannah M Kolev, Alena Klochkova, Melissa S Kim, Charles H Danan, Zvi Cramer, Lauren A Simon, Kaitlyn E Naughton, Stephanie Adams-Tzivelekidis, Yuhua Tian, Patrick A Williams, N Adrian Leu, Simone Sidoli, Kelly A Whelan, Ning Li, Christopher J Lengner, Kathryn E Hamilton.

  The intestinal epithelium exhibits a rapid and efficient regenerative response to injury. Emerging evidence supports a model where plasticity of differentiated cells, particularly those in the secretory lineages, contributes to epithelial regeneration upon ablation of injury-sensitive stem cells. However, such facultative stem cell activity is rare within secretory populations. Here, we ask whether specific functional properties predict facultative stem cell activity. We utilize in vivo labeling combined with ex vivo organoid formation assays to evaluate how cell age and autophagic state contribute to facultative stem cell activity within secretory lineages. Strikingly, we find that cell age (time elapsed since cell cycle exit) does not correlate with secretory cell plasticity. Instead, high autophagic vesicle content predicts plasticity and resistance to DNA damaging injury independently of cell lineage. Our findings indicate that autophagic status prior to injury serves as a lineage-agnostic marker for the prospective identification of facultative stem cells.

Keywords:  autophagy; facultative stem cell; organoid formation; paligenosis; regeneration

DOI:  https://doi.org/10.15252/embr.202255209
Front Cell Dev Biol. 2022 ;10 980721

Delineation of proteome changes driven by cell size and growth rate.

Evgeny Zatulovskiy, Michael C Lanz, Shuyuan Zhang, Frank McCarthy, Joshua E Elias, Jan M Skotheim.

  Increasing cell size drives changes to the proteome, which affects cell physiology. As cell size increases, some proteins become more concentrated while others are diluted. As a result, the state of the cell changes continuously with increasing size. In addition to these proteomic changes, large cells have a lower growth rate (protein synthesis rate per unit volume). That both the cell's proteome and growth rate change with cell size suggests they may be interdependent. To test this, we used quantitative mass spectrometry to measure how the proteome changes in response to the mTOR inhibitor rapamycin, which decreases the cellular growth rate and has only a minimal effect on cell size. We found that large cell size and mTOR inhibition, both of which lower the growth rate of a cell, remodel the proteome in similar ways. This suggests that many of the effects of cell size are mediated by the size-dependent slowdown of the cellular growth rate. For example, the previously reported size-dependent expression of some senescence markers could reflect a cell's declining growth rate rather than its size per se. In contrast, histones and other chromatin components are diluted in large cells independently of the growth rate, likely so that they remain in proportion with the genome. Finally, size-dependent changes to the cell's growth rate and proteome composition are still apparent in cells continually exposed to a saturating dose of rapamycin, which indicates that cell size can affect the proteome independently of mTORC1 signaling. Taken together, our results clarify the dependencies between cell size, growth, mTOR activity, and the proteome remodeling that ultimately controls many aspects of cell physiology.

Keywords:  cell size; growth rate; mTOR; protein synthesis rate; quantitative proteomics; rapamycin; senescence

DOI:  https://doi.org/10.3389/fcell.2022.980721