bims-proarb 2021-10-10 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2021–10–10
twelve papers selected by
Rich Giadone, Harvard University

Sevoflurane post-conditioning alleviated hypoxic-ischemic brain injury in neonatal rats by inhibiting endoplasmic reticulum stress-mediated autophagy via IRE1 signalings.
The interactions of molecular chaperones with client proteins: why are they so weak?
Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells.
Sirt1 promotes tissue regeneration in zebrafish through regulating the mitochondrial unfolded protein response.
Humanin-induced autophagy plays important roles in skeletal muscle function and lifespan extension.
Cortical alpha-synuclein preformed fibrils do not affect interval timing in mice.
A dipeptidyl peptidase IV inhibitory peptide relieves palmitic acid-induced endoplasmic reticulum stress in HepG2 cells independent of inhibiting dipeptidyl peptidase IV activity.
Isolation and Characterization of Heparan Sulfate Containing Amyloid Precursor Protein Degradation Products.
GPX7 Facilitates BMSCs Osteoblastogenesis via ER Stress and mTOR Pathway.
Analysis of Brain Protein Stability Changes in Mouse Models of Normal Aging and α-Synucleinopathy Reveals Age- and Disease-Related Differences.
Autophagy is involved in neurofibromatosis type I gene-modulated osteogenic differentiation in human bone mesenchymal stem cells.
LGALS3 (galectin 3) mediates an unconventional secretion of SNCA/α-synuclein in response to lysosomal membrane damage by the autophagic-lysosomal pathway in human midbrain dopamine neurons.

Neurochem Int. 2021 Sep 30. pii: S0197-0186(21)00244-8. [Epub ahead of print]150 105198

Sevoflurane post-conditioning alleviated hypoxic-ischemic brain injury in neonatal rats by inhibiting endoplasmic reticulum stress-mediated autophagy via IRE1 signalings.

Jiayuan Niu, Ziyi Wu, Hang Xue, Yahan Zhang, Qiushi Gao, Chang Li, Ping Zhao.

  Post-conditioning with sevoflurane, a volatile anesthetic, has been proved to be neuroprotective against hypoxic-ischemic brain injury (HIBI). Our previous research showed that autophagy is over-activated in a neonatal HIBI rat model, and inhibition of autophagy confers neuroprotection. There is increasing recognition that autophagy can be stimulated by activating endoplasmic reticulum (ER) stress. Herein, we purposed to explore: i) the association of ER stress with autophagy in the setting of neonatal HIBI; and ii) the possible roles of ER stress-triggered autophagy, as well as IRE1 signaling in the neuroprotection of sevoflurane post-conditioning against neonatal HIBI. Seven-day-old rats underwent ligation of the left common artery, and a subsequent 2 h hypoxia (8% O2/92% N2). The association of ER stress with autophagy was examined by ER stress inducer (tunicamycin), 4-PBA (ER stress inhibitor), or 3-MA (autophagy inhibitor). Rats in the sevoflurane post-conditioning groups were treated with 2.4% sevoflurane for 30 min after HIBI stimulation. The roles of ER stress-mediated autophagy, as well as the IRE1-JNK-beclin1 signaling cascade in the neuroprotection afforded by sevoflurane were explored by ER stress inducer (tunicamycin) and the IRE1 inhibitor (STF-083010). HIBI over-activated ER stress and autophagy in neonatal rats. HIBI-induced autophagy was significantly aggravated by tunicamycin but blocked by 4-PBA; however, HIBI-induced ER stress was not affected by 3-MA. Sevoflurane post-conditioning significantly alleviated ER stress, autophagy, cell apoptosis, and cognitive impairments, which were remarkably abolished by tunicamycin. Also, tunicamycin blocked sevoflurane-induced downregulation of IRE1-JNK-beclin1 signaling pathway. Whereas, IRE1 inhibitor could reverse the effects of tunicamycin. ER stress contributes to autophagy induced by HIBI. Furthermore, sevoflurane post-conditioning significantly protects against HIBI in neonatal rats by inhibiting ER stress-mediated autophagy via IRE1-JNK-beclin1 signaling cascade.

Keywords:  Autophagy; Endoplasmic reticulum stress; Hypoxic-ischemic brain injury; IRE1; Sevoflurane post-conditioning

DOI:  https://doi.org/10.1016/j.neuint.2021.105198
J Biol Chem. 2021 Oct 05. pii: S0021-9258(21)01085-1. [Epub ahead of print] 101282

The interactions of molecular chaperones with client proteins: why are they so weak?

Taylor Arhar, Arielle Shkedi, Cory M Nadel, Jason E Gestwicki.

  The major classes of molecular chaperones have highly variable sequences, sizes and shapes, yet they all bind to unfolded proteins, limit their aggregation and assist in their folding. Despite the central importance of this process to protein homeostasis, it has not been clear exactly how chaperones guide this process or whether the diverse families of chaperones use similar mechanisms. For the first time, recent advances in NMR spectroscopy have enabled detailed studies of how unfolded, "client" proteins interact with both ATP-dependent and ATP-independent classes of chaperones. Here, we review examples from four distinct chaperones, Spy, Trigger Factor, DnaK and HscA-HscB, highlighting the similarities and differences between their mechanisms. One striking similarity is that the chaperones all bind weakly to their clients, such that the chaperone-client interactions are readily outcompeted by stronger, intra- and inter-molecular contacts in the folded state. Thus, the relatively weak affinity of these interactions seems to provide directionality to the folding process. However, there are also key differences, especially in the details of how the chaperones release clients and how ATP cycling impacts that process. For example, Spy releases clients in a largely folded state, while clients seem to be unfolded upon release from Trigger Factor or DnaK. Together, these studies are beginning to uncover the similarities and differences in how chaperones use weak interactions to guide protein folding.

Keywords:  Chaperone; nuclear magnetic resonance (NMR); protein aggregation; protein folding; protein-protein interactions (PPIs)

DOI:  https://doi.org/10.1016/j.jbc.2021.101282
Chembiochem. 2021 Oct 06.

Chemical Biology Toolbox to Visualize Protein Aggregation in Live Cells.

Di Shen, Yulong Bai, Yu Liu.

  Protein misfolding and aggregation is a complex biochemical process and has been associated with numerous human degenerative diseases. Developing novel tools and methods to visualize aggregated proteins in live cells is in high demand for mechanistic studies, diagnosis, and therapeutics. In this review, we summarized the recent progress on the chemical biology toolbox applied to protein aggregation studies in live cells. These methods exploited fluorescent protein tags, chemical protein tags, and small molecule probes to visualize protein aggregation process, detect proteome stresses, and quantify protein homeostasis network capacity. Inspired by these seminal works, we generalized design principles to develop new detection methods and probes that illuminate this important biological process in the future.

Keywords:  protein aggregation, fluorescent protein, AggTag, proteostasis capacity sensor, small molecule probe

DOI:  https://doi.org/10.1002/cbic.202100443
iScience. 2021 Oct 22. 24(10): 103118

Sirt1 promotes tissue regeneration in zebrafish through regulating the mitochondrial unfolded protein response.

Yi-Fan Lin, Jessica Sam, Todd Evans.

  The mitochondrial unfolded protein response (UPRmt) is an organellar stress signaling pathway that functions to detect and restore disruption of mitochondrial proteostasis. The UPRmt is involved in a wide range of physiological and disease conditions, including aging, stem cell maintenance, innate immunity, neurodegeneration, and cancer. Here we report that the UPRmt is integral to zebrafish fin regeneration. Taking advantage of a novel zebrafish UPRmt reporter, we observed that UPRmt activation occurs in regenerating fin tissue shortly after injury. Through chemical and genetic approaches, we discovered that the Sirt1-UPRmt pathway, best known for its role in promoting lifespan extension, is crucial for fin regeneration. The metabolism of NAD+ is an important contributor to Sirt1 activity in this context. We propose that Sirt1 activation induces mitochondrial biogenesis in injured fin tissue, which leads to UPRmt activation and promotes tissue regeneration.

Keywords:  Cell biology; Developmental biology; Molecular biology

DOI:  https://doi.org/10.1016/j.isci.2021.103118
Biochim Biophys Acta Gen Subj. 2021 Oct 05. pii: S0304-4165(21)00176-8. [Epub ahead of print] 130017

Humanin-induced autophagy plays important roles in skeletal muscle function and lifespan extension.

Su-Jeong Kim, Anjali Devgan, Brendan Miller, Sam Mool Lee, Hiroshi Kumagai, Kenneth A Wilson, Gabriella Wassef, Richard Wong, Hemal H Mehta, Pinchas Cohen, Kelvin Yen.

   BACKGROUND: Autophagy, a highly conserved homeostatic mechanism, is essential for cell survival. The decline of autophagy function has been implicated in various diseases as well as aging. Although mitochondria play a key role in the autophagy process, whether mitochondrial-derived peptides are involved in this process has not been explored.
METHODS: We developed a high through put screening method to identify potential autophagy inducers among mitochondrial-derived peptides. We used three different cell lines, mice, c.elegans, and a human cohort to validate the observation.
RESULTS: Humanin, a mitochondrial-derived peptide, increases autophagy and maintains autophagy flux in several cell types. Humanin administration increases the expression of autophagy-related genes and lowers accumulation of harmful misfolded proteins in mice skeletal muscle, suggesting that humanin-induced autophagy potentially contributes to the improved skeletal function. Moreover, autophagy is a critical role in humanin-induced lifespan extension in C. elegans.
CONCLUSIONS: Humanin is an autophagy inducer.
GENERAL SIGNIFICANCE: This paper presents a significant, novel discovery regarding the role of the mitochondrial derived peptide humanin in autophagy regulation and as a possible therapeutic target for autophagy in various age-related diseases.

Keywords:  Autophagy; Humanin; Lifespan; Mitochondrial-derived peptides

DOI:  https://doi.org/10.1016/j.bbagen.2021.130017
Neurosci Lett. 2021 Sep 30. pii: S0304-3940(21)00652-2. [Epub ahead of print] 136273

Cortical alpha-synuclein preformed fibrils do not affect interval timing in mice.

Qiang Zhang, Hisham Abdelmotilib, Travis Larson, Cameron Keomanivong, Mackenzie Conlon, Georgina M Aldridge, Nandakumar S Narayanan.

  One hallmark feature of Parkinson's disease (PD) is Lewy body pathology associated with misfolded alpha-synuclein. Previous studies have shown that striatal injection of alpha-synuclein preformed fibrils (PFF) can induce misfolding and aggregation of native alpha-synuclein in a prion-like manner, leading to cell death and motor dysfunction in mouse models. Here, we tested whether alpha-synuclein PFFs injected into the medial prefrontal cortex results in deficits in interval timing, a cognitive task which is disrupted in human PD patients and in rodent models of PD. We injected PFF or monomers of human alpha-synuclein into the medial prefrontal cortex of mice pre-injected with adeno-associated virus (AAV) coding for overexpression of human alpha-synuclein or control protein. Despite notable medial prefrontal cortical synucleinopathy, we did not observe consistent deficits in fixed-interval timing. These results suggest that cortical alpha-synuclein does not reliably disrupt fixed-interval timing.

Keywords:  alpha-synuclein; interval timing; preformed fibrils; prion

DOI:  https://doi.org/10.1016/j.neulet.2021.136273
Food Funct. 2021 Oct 05.

A dipeptidyl peptidase IV inhibitory peptide relieves palmitic acid-induced endoplasmic reticulum stress in HepG2 cells independent of inhibiting dipeptidyl peptidase IV activity.

Ritian Jin, Haowei Ren, Minhe Liao, Jiaqi Shang, Dangfeng Wang, Meng Li, Ning Liu.

The peptide VLATSGPG (VLA) is known to inhibit dipeptidyl peptidase IV (DPP-IV), although its mechanism in relieving endoplasmic reticulum (ER) stress is unclear. In this study, we found that treating HepG2 cells with 1.0 mM VLA reduced DPP-IV activity by 73.7 ± 4.8% without changing the DPP-IV mRNA expression level. In addition, 1.0 and 0.5 mM VLA alleviated palmitic acid (PA)-induced cell death and intracellular calcium imbalances. The levels of apoptosis-related proteins (caspase-3, caspase-9, and CHOP) were reduced by VLA treatment, which was presumed to be related to ER stress. Further studies confirmed that VLA alleviated PA-induced morphological damage to the ER and reduced the levels of the ER stress marker proteins (BIP, p-PERK, and p-IRE1α). VLA alleviated PA-induced ER stress in HepG2 cells independent of DPP-IV enzymatic activity inhibition. These findings have implications for developing novel treatment approaches for liver diseases caused by ER stress.

DOI: https://doi.org/10.1039/d1fo02283k
Methods Mol Biol. 2022 ;2303 279-288

Isolation and Characterization of Heparan Sulfate Containing Amyloid Precursor Protein Degradation Products.

Katrin Mani.

  Numerous studies indicate that heparan sulfate proteoglycans (HSPGs) participate in a network of complex molecular events involving amyloid precursor protein (APP) processing and formation, oligomerization, intracellular targeting, clearance, and propagation of amyloid β in Alzheimer's disease (AD). A mutual functional interplay between recycling glypican-1 and APP processing has been demonstrated where the HS released from glypican-1 by a Cu/NO-ascorbate-dependent reaction forms a conjugate with APP degradation products and undergoes an endosome-nucleus-autophagosome co-trafficking. HS has been shown to display contradictory and dual effects in AD involving both prevention and promotion of amyloid β formation. It is therefore important to identify the source, detailed structural features as well as factors that favor formation of the neuroprotective forms of HS. Here, a method for isolation and identification of HS-containing APP degradation products has been described. The method is based on isolation of radiolabeled HS followed by identification of accompanying APP degradation products by SDS-PAGE and Western blotting.

Keywords:  Alzheimer’s disease; Amyloid β, Glypican-1; Heparan sulfate

DOI:  https://doi.org/10.1007/978-1-0716-1398-6_22
J Cell Mol Med. 2021 Oct 09.

GPX7 Facilitates BMSCs Osteoblastogenesis via ER Stress and mTOR Pathway.

Xuchen Hu, Boer Li, Fanzi Wu, Xiaoyu Liu, Mengyu Liu, Chenglin Wang, Yu Shi, Ling Ye.

  Emerging evidence indicates extensive oxidative stress is a consequence of obesity which impairs bone formation. Glutathione peroxidase 7 (GPX7) is a conserved endoplasmic reticulum (ER) retention protein, lacking of which causes accumulation of reactive oxygen species (ROS) and promotes adipogenesis. Since the imbalance between osteogenic and adipogenic differentiation of bone marrow mesenchymal stem cell (BMSC) leads to severe bone diseases such as osteoporosis, it is critical to investigate the potential protective role of Gpx7 in osteogenesis. Here, we provide evidence that deficiency of Gpx7 reduces osteogenesis, but increases adipogenesis in both human BMSCs (hBMSCs) and mouse mesenchymal stem cell line. Interestingly, further studies indicate this defect can be alleviated by the ER stress antagonist, but not the ROS inhibitor, unveiling an unexpected finding that, unlike adipogenesis, lacking of Gpx7 inhibits osteogenesis mediating by induced ER stress instead of enhanced ROS. Furthermore, the mTOR signalling pathway is found down-regulation during osteogenic differentiation in Gpx7-deficient condition, which can be rescued by relief of ER stress. Taken together, for the first time we identify a novel function of Gpx7 in BMSCs' osteogenic differentiation and indicate that Gpx7 may protect against osteoporotic deficits in humans through ER stress and mTOR pathway interplay.

Keywords:  BMSCs; ER stress; GPX7; osteogenic differentiation

DOI:  https://doi.org/10.1111/jcmm.16974
J Proteome Res. 2021 Oct 04.

Analysis of Brain Protein Stability Changes in Mouse Models of Normal Aging and α-Synucleinopathy Reveals Age- and Disease-Related Differences.

Renze Ma, Julia H R Johnson, Yun Tang, Michael C Fitzgerald.

  Here, we utilize the stability of proteins from rates of oxidation (SPROX) technique, to profile the thermodynamic stabilities of proteins in brain tissue cell lysates from Huα-Syn(A53T) transgenic mice at three time points including at 1 month (n = 9), at 6 months (n = 7), and at the time (between 9 and 16 months) a mouse became symptomatic (n = 8). The thermodynamic stability profiles generated here on 332 proteins were compared to thermodynamic stability profiles generated on the same proteins from similarly aged wild-type mice using a two-way unbalanced analysis of variance (ANOVA) analysis. This analysis identified a group of 22 proteins with age-related protein stability changes and a group of 11 proteins that were differentially stabilized in the Huα-Syn(A53T) transgenic mouse model. A total of 9 of the 11 proteins identified here with disease-related stability changes have been previously detected in human cerebral spinal fluid and thus have potential utility as biomarkers of Parkinson's disease (PD). The differential stability observed for one protein, glutamate decarboxylase 2 (Gad2), with an age-related change in stability, was consistent with the differential presence of a known, age-related truncation product of this protein, which is shown here to have a higher folding stability than full-length Gad2. Mass spectrometry data were deposited at ProteomeXchange (PXD016985).

Keywords:  SPROX; chemical denaturation; mass spectrometry; protein folding

DOI:  https://doi.org/10.1021/acs.jproteome.1c00653
Exp Ther Med. 2021 Nov;22(5): 1262

Autophagy is involved in neurofibromatosis type I gene-modulated osteogenic differentiation in human bone mesenchymal stem cells.

Yiqiang Li, Mingwei Zhu, Xuemei Lin, Jingchun Li, Zhe Yuan, Yanhan Liu, Hongwen Xu.

  Neurofibromatosis type I (NF1) is an autosomal dominant genetic disease that is caused by mutations in the NF1 gene. Various studies have previously demonstrated that the mTOR complex 1 signaling pathway is essential for the NF1-modulated osteogenic differentiation of bone mesenchymal stem cells (BMSCs). Additionally, the mTOR signaling pathway plays a notable role in autophagy. The present study hypothesized that NF1 could modulate the osteogenic differentiation of BMSCs by regulating the autophagic activities of BMSCs. In the present study, human BMSCs were cultured in an osteogenic induction medium. The expression of the NF1 gene was either knocked down or overexpressed by transfection with a specific small interfering RNA (siRNA) targeting NF1 or the pcDNA3.0 NF1-overexpression plasmid, respectively. Autophagic activities of BMSCs (Beclin-1, P62, LC3B I, and LC3B II) were determined using western blotting, electron microscopy, acridine orange (AO) staining and autophagic flux/lysosomal detection by fluorescence microscopy. In addition, the autophagy activator rapamycin (RAPA) and inhibitor 3-methyladenine (3-MA) were used to investigate the effects of autophagy on NF1-modulated osteogenic differentiation in BMSCs. Inhibiting NF1 with siRNA significantly decreased the expression levels of autophagy markers Beclin-1 and LC3B-II, in addition to osteogenic differentiation markers osterix, runt-related transcription factor 2 and alkaline phosphatase. By contrast, overexpressing NF1 with pcDNA3.0 significantly increased their levels. Transmission electron microscopy, AO staining and autophagic flux/lysosomal detection assays revealed that the extent of autophagosome formation was significantly decreased in the NF1-siRNA group but significantly increased in the NF1-pcDNA3.0 group when compared with the NC-siRNA and pcDNA3.0 groups, respectively. In addition, the activity of the PI3K/AKT/mTOR pathway [phosphorylated (p)-PI3K, p-AKT, p-mTOR and p-p70S6 kinase] was significantly upregulated in the NF1-siRNA group compared with the NC-siRNA group, and significantly inhibited in the NF1-pcDNA3.0 group, compared with the pcDNA3.0 group. The knockdown effects of NF1-siRNA on the autophagy and osteogenic differentiation of BMSCs were reversed by the autophagy activator RAPA, while the overexpression effects of NF1-pcDNA3.0 on the autophagy and osteogenic differentiation of BMSCs were reversed by the autophagy inhibitor 3-MA. In conclusion, results from the present study suggest at the involvement of autophagy in the NF1-modulated osteogenic differentiation of BMSCs. Furthermore, NF1 may partially regulate the autophagic activity of BMSCs through the PI3K/AKT/mTOR signaling pathway.

Keywords:  PI3K/AKT/mTOR pathway; autophagy; bone marrow stem cells; neurofibromatosis type I; osteogenic differentiation

DOI:  https://doi.org/10.3892/etm.2021.10697
Autophagy. 2021 Oct 06. 1-29

LGALS3 (galectin 3) mediates an unconventional secretion of SNCA/α-synuclein in response to lysosomal membrane damage by the autophagic-lysosomal pathway in human midbrain dopamine neurons.

Kevin Burbidge, David J Rademacher, Jessica Mattick, Stephanie Zack, Andrea Grillini, Luc Bousset, Ochan Kwon, Konrad Kubicki, Alexander Simon, Ronald Melki, Edward M Campbell.

  Numerous lines of evidence support the premise that the misfolding and subsequent accumulation of SNCA/α-synuclein (synuclein alpha) is responsible for the underlying neuronal pathology observed in Parkinson disease (PD) and other synucleinopathies. Moreover, the cell-to-cell transfer of these misfolded SNCA species is thought to be responsible for disease progression and the spread of cellular pathology throughout the brain. Previous work has shown that when exogenous, misfolded SNCA fibrils enter cells through endocytosis, they can damage and rupture the membranes of their endocytotic vesicles in which they are trafficked. Rupture of these vesicular membranes exposes intralumenal glycans leading to galectin protein binding, subsequent autophagic protein recruitment, and, ultimately, their introduction into the autophagic-lysosomal pathway. Increasing evidence indicates that both pathological and non-pathological SNCA species undergo autophagy-dependent unconventional secretion. While other proteins have also been shown to be secreted from cells by autophagy, what triggers this release process and how these specific proteins are recruited to a secretory autophagic pathway is largely unknown. Here, we use a human midbrain dopamine (mDA) neuronal culture model to provide evidence in support of a cellular mechanism that explains the cell-to-cell transfer of pathological forms of SNCA that are observed in PD. We demonstrate that LGALS3 (galectin 3) mediates the release of SNCA following vesicular damage. SNCA release is also dependent on TRIM16 (tripartite motif containing 16) and ATG16L1 (autophagy related 16 like 1), providing evidence that secretion of SNCA is mediated by an autophagic secretory pathway.

Keywords:  Autophagy; Parkinson disease; alpha-synuclein (synuclein alpha); extracellular vesicles; galectins; induced pluripotent stem cells; lysosomes; tripartite motif proteins; unconventional secretion

DOI:  https://doi.org/10.1080/15548627.2021.1967615