bims-proarb 2022-11-06 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2022–11–06
twelve papers selected by
Rich Giadone, Harvard University

Unfolded protein response IRE1/XBP1 signaling is required for healthy mammalian brain aging.
Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response.
The functions of IRE1α in neurodegenerative diseases: Beyond ER stress.
Beneficial effects of neuronal ATF6 activation in permanent ischemic stroke.
The emerging role of autophagy and mitophagy in tauopathies: From pathogenesis to translational implications in Alzheimer's disease.
Age-related SUMOylation of PLK1 is essential to meiosis progression in mouse oocytes.
A single-cell transcriptome atlas of glial diversity in the human hippocampus across the postnatal lifespan.
Metformin suppresses vascular smooth muscle cell senescence by promoting autophagic flux.
Single-cell spatial proteomic imaging for human neuropathology.
Increased autophagy leads to decreased apoptosis during β-thalassaemic mouse and patient erythropoiesis.
Translation regulatory factor BZW1 regulates preimplantation embryo development and compaction by restricting global non-AUG Initiation.
Cap-dependent translation initiation monitored in living cells.

EMBO J. 2022 Oct 31. e111952

Unfolded protein response IRE1/XBP1 signaling is required for healthy mammalian brain aging.

Felipe Cabral-Miranda, Giovanni Tamburini, Gabriela Martinez, Alvaro O Ardiles, Danilo B Medinas, Yannis Gerakis, Mei-Li Diaz Hung, René Vidal, Matias Fuentealba, Tim Miedema, Claudia Duran-Aniotz, Javier Diaz, Cristobal Ibaceta-Gonzalez, Carleen M Sabusap, Francisca Bermedo-Garcia, Paula Mujica, Stuart Adamson, Kaitlyn Vitangcol, Hernan Huerta, Xu Zhang, Tomohiro Nakamura, Sergio Pablo Sardi, Stuart A Lipton, Brian K Kennedy, Juan Pablo Henriquez, J Cesar Cárdenas, Lars Plate, Adrian G Palacios, Claudio Hetz.

  Aging is a major risk factor for neurodegenerative diseases and is associated with decreased buffering capacity of the proteostasis network. We investigated the significance of the unfolded protein response (UPR), a major signaling pathway activated to cope with endoplasmic reticulum (ER) stress, in the functional deterioration of the mammalian brain during aging. We report that genetic disruption of the ER stress sensor IRE1 accelerated age-related cognitive decline. In mouse models, overexpressing an active form of the UPR transcription factor XBP1 restored synaptic and cognitive function, in addition to reducing cell senescence. Proteomic profiling of hippocampal tissue showed that XBP1 expression significantly restore changes associated with aging, including factors associated with synaptic function and pathways linked to neurodegenerative diseases. Similar changes were observed in human brain aging. Collectively, our results demonstrate that strategies to manipulate the UPR in mammals may help sustain healthy brain aging.

Keywords:  ER stress; UPR; XBP1s; aging brain; proteostasis

DOI:  https://doi.org/10.15252/embj.2022111952
Mol Cell. 2022 Oct 26. pii: S1097-2765(22)00970-4. [Epub ahead of print]

Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response.

Surabhi Chowdhary, Amoldeep S Kainth, Sarah Paracha, David S Gross, David Pincus.

  Mammalian developmental and disease-associated genes concentrate large quantities of the transcriptional machinery by forming membrane-less compartments known as transcriptional condensates. However, it is unknown whether these structures are evolutionarily conserved or involved in 3D genome reorganization. Here, we identify inducible transcriptional condensates in the yeast heat shock response (HSR). HSR condensates are biophysically dynamic spatiotemporal clusters of the sequence-specific transcription factor heat shock factor 1 (Hsf1) with Mediator and RNA Pol II. Uniquely, HSR condensates drive the coalescence of multiple Hsf1 target genes, even those located on different chromosomes. Binding of the chaperone Hsp70 to a site on Hsf1 represses clustering, whereas an intrinsically disordered region on Hsf1 promotes condensate formation and intergenic interactions. Mutation of both Hsf1 determinants reprograms HSR condensates to become constitutively active without intergenic coalescence, which comes at a fitness cost. These results suggest that transcriptional condensates are ancient and flexible compartments of eukaryotic gene control.

Keywords:  3D genome; Hsf1; Mediator; RNA Pol II; biomolecular condensates; chaperone; gene transcription; heat shock response; inter-chromosomal interactions; phase separation

DOI:  https://doi.org/10.1016/j.molcel.2022.10.013
Ageing Res Rev. 2022 Nov 01. pii: S1568-1637(22)00216-1. [Epub ahead of print] 101774

The functions of IRE1α in neurodegenerative diseases: Beyond ER stress.

Ling Chen, Mingxia Bi, Zhen Zhang, Xixun Du, Xi Chen, Qian Jiao, Hong Jiang.

  Inositol-requiring enzyme 1 α (IRE1α) is a type I transmembrane protein that resides in the endoplasmic reticulum (ER). IRE1α, which is the primary sensor of ER stress, has been proven to maintain intracellular protein homeostasis by activating X-box binding protein 1 (XBP1). Further studies have revealed novel physiological functions of the IRE1α, such as its roles in mRNA and protein degradation, inflammation, immunity, cell proliferation and cell death. Therefore, the function of IRE1α is not limited to its role in ER stress; IRE1α is also important for regulating other processes related to cellular physiology. Furthermore, IRE1α is a significant factor in the regulation of neurodegenerative diseases that are caused by the phosphorylation of Tau protein, the accumulation of α-synuclein (α-syn) and the toxic effects of mutant Htt (mHtt). Therefore, targeting IRE1α is a valuable approach for treating neurodegenerative diseases and regulating cell function. This review discusses the role of IRE1α in different cellular processes, and emphasizes the importance of IRE1α in neurodegenerative diseases.

Keywords:  ER stress; IRE1α; XBP1; neurodegenerative diseases

DOI:  https://doi.org/10.1016/j.arr.2022.101774
Front Cell Neurosci. 2022 ;16 1016391

Beneficial effects of neuronal ATF6 activation in permanent ischemic stroke.

Xuan Li, Ran Li, Liping Lu, Ashis Dhar, Huaxin Sheng, Wei Yang.

  Objective: Brain ischemia leads to the accumulation of unfolded/misfolded proteins in the endoplasmic reticulum (ER) lumen and consequently, ER stress. To help cells restore ER function, a series of adaptive stress response pathways, collectively termed the unfolded protein response (UPR), are activated. We have previously demonstrated that the UPR pathway initiated by ATF6 is pro-survival in transient ischemic stroke. However, the effect of ATF6 activation on the outcome after permanent ischemic stroke remains unknown. Here, we addressed this knowledge gap. Method: sATF6-KI mice with functional short-form ATF6 (sATF6) predominantly expressed in forebrain neurons were subjected to two ischemic stroke models: photothrombotic stroke and permanent middle cerebral artery occlusion (pMCAO). Both short-term and long-term functional outcomes were evaluated. Changes in neuroinflammation and cerebrovascular density after pMCAO were also assessed. Results: Compared to littermate controls, sATF6-KI mice performed significantly better in open field, cylinder, and foot fault tests on day 1 or 3 after photothrombotic stroke. However, on days 7 and 14 after stroke, the performance of these functional tests was not significantly different between groups, which is likely related to mild brain damage associated with this stroke model. Thus, to evaluate the long-term effects of ATF6 activation in permanent stroke, we turned to our pMCAO model. We first found that on day 4 after pMCAO, functional outcome was better, and infarct volumes were smaller in sATF6-KI mice vs controls. Next, the 15-day stroke outcome study indicated that compared to control mice, sATF6-KI mice consistently exhibited improved performance in neurologic scoring, tight rope test, and tape removal test, after pMCAO. Moreover, sATF6-KI mice showed higher vascular density and lower activation of both astrocytes and microglia around stroke regions on day 16 after pMCAO. Conclusions: Here, we presented the first evidence that activation of the ATF6 UPR branch is protective in permanent ischemic stroke, which further supports the therapeutic potential of targeting the ATF6 pathway in stroke.

Keywords:  ER stress; MCAO; UPR; long-term; photothrombotic stroke; proteostasis; transgenic mice

DOI:  https://doi.org/10.3389/fncel.2022.1016391
Front Aging Neurosci. 2022 ;14 1022821

The emerging role of autophagy and mitophagy in tauopathies: From pathogenesis to translational implications in Alzheimer's disease.

Xiaolan Liu, Meng Ye, Liang Ma.

  Alzheimer's disease (AD) is the most prevalent neurodegenerative disease, affecting more than 55 million individuals worldwide in 2021. In addition to the "amyloid hypothesis," an increasing number of studies have demonstrated that phosphorylated tau plays an important role in AD pathogenesis. Both soluble tau oligomers and insoluble tau aggregates in the brain can induce structural and functional neuronal damage through multiple pathways, eventually leading to memory deficits and neurodegeneration. Autophagy is an important cellular response to various stress stimuli and can generally be categorized into non-selective and selective autophagy. Recent studies have indicated that both types of autophagy are involved in AD pathology. Among the several subtypes of selective autophagy, mitophagy, which mediates the selective removal of mitochondria, has attracted increasing attention because dysfunctional mitochondria have been suggested to contribute to tauopathies. In this review, we summarize the latest findings on the bidirectional association between abnormal tau proteins and defective autophagy, as well as mitophagy, which might constitute a vicious cycle in the induction of neurodegeneration. Neuroinflammation, another important feature in the pathogenesis and progression of AD, has been shown to crosstalk with autophagy and mitophagy. Additionally, we comprehensively discuss the relationship between neuroinflammation, autophagy, and mitophagy. By elucidating the underlying molecular mechanisms governing these pathologies, we highlight novel therapeutic strategies targeting autophagy, mitophagy and neuroinflammation, such as those using rapamycin, urolithin, spermidine, curcumin, nicotinamide, and actinonin, for the prevention and treatment of AD.

Keywords:  Alzheimer’s disease; autophagy; mitophagy; neuroinflammation; prevention and treatment; tau protein

DOI:  https://doi.org/10.3389/fnagi.2022.1022821
J Cell Physiol. 2022 Nov 01.

Age-related SUMOylation of PLK1 is essential to meiosis progression in mouse oocytes.

Xiao-Long Mo, Feng Liu, Chun-Hua Xing, Meng-Meng Shan, Bo Yao, Qi-Qi Sun, Yuan-Jing Zou, Kun-Huan Zhang, Jun Tan, Shao-Chen Sun, Yan-Ping Ren.

  Polo like kinase 1 (PLK1) is a protein kinase involved in regulating the spindle assembly and cell cycle control in mammalian oocytes. SUMOylation, one way of post-translational modification, regulates oocyte meiosis by controlling several substrates. However, the relation between PLK1 and SUMOylation in oocytes is still unknown. In this study, we investigated that whether PLK1 was modified by SUMOylation in oocytes and its potential relationship with age-related meiotic abnormalities. We showed that PLK1 had colocalization and protein interaction with Small Ubiquitin-Like Modifier (SUMO)-1 and SUMO-2/3 in mouse oocytes, indicating that PLK1 could be modified by SUMO-1 and SUMO-2/3. Overexpression of PLK1 SUMOylation site mutants PLK1K178R and PLK1K191R caused the increase of the abnormal spindle rate of oocytes and the decline of the first polar body extrusion rate with the abnormal localization of PLK1, suggesting that the SUMOylation modification of PLK1 is essential for normal meiosis in oocytes. Compared with young mice, the expression of PLK1 protein increased and the expression of SUMO-1 and SUMO-2/3 protein decreased in the oocytes of aged mice, indicating that the SUMOylation of PLK1 might be related to the mouse aging. Therefore, our data suggested that PLK1 could be SUMOylated by SUMO-1 and SUMO-2/3 in mouse oocytes and SUMOylation of PLK1 regulated the meiosis progression of oocytes which was related with aging.

Keywords:  Polo-like kinase 1; SUMOylation; aging; meiosis; oocyte

DOI:  https://doi.org/10.1002/jcp.30910
Cell Stem Cell. 2022 Nov 03. pii: S1934-5909(22)00418-0. [Epub ahead of print]29(11): 1594-1610.e8

A single-cell transcriptome atlas of glial diversity in the human hippocampus across the postnatal lifespan.

Yijing Su, Yi Zhou, Mariko L Bennett, Shiying Li, Marc Carceles-Cordon, Lu Lu, Sooyoung Huh, Dennisse Jimenez-Cyrus, Benjamin C Kennedy, Sudha K Kessler, Angela N Viaene, Ingo Helbig, Xiaosong Gu, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, David W Nauen, Hongjun Song, Guo-Li Ming.

  The molecular diversity of glia in the human hippocampus and their temporal dynamics over the lifespan remain largely unknown. Here, we performed single-nucleus RNA sequencing to generate a transcriptome atlas of the human hippocampus across the postnatal lifespan. Detailed analyses of astrocytes, oligodendrocyte lineages, and microglia identified subpopulations with distinct molecular signatures and revealed their association with specific physiological functions, age-dependent changes in abundance, and disease relevance. We further characterized spatiotemporal heterogeneity of GFAP-enriched astrocyte subpopulations in the hippocampal formation using immunohistology. Leveraging glial subpopulation classifications as a reference map, we revealed the diversity of glia differentiated from human pluripotent stem cells and identified dysregulated genes and pathological processes in specific glial subpopulations in Alzheimer's disease (AD). Together, our study significantly extends our understanding of human glial diversity, population dynamics across the postnatal lifespan, and dysregulation in AD and provides a reference atlas for stem-cell-based glial differentiation.

Keywords:  Alzheimer’s disease; astrocytes; brain disorders; brain organoids; glial cell diversity; glial differentiation; human hippocampus; microglia; oligodendrocytes; single-nucleus transcriptomics

DOI:  https://doi.org/10.1016/j.stem.2022.09.010
J Adv Res. 2022 Nov;pii: S2090-1232(21)00262-9. [Epub ahead of print]41 205-218

Metformin suppresses vascular smooth muscle cell senescence by promoting autophagic flux.

Shi Tai, Jiaxing Sun, Yuying Zhou, Zhaowei Zhu, Yuhu He, Mingxian Chen, Hui Yang, Yichao Xiao, Tao Tu, Liang Tang, Xuping Li, Jianping Zeng, Xilong Zheng, Shenghua Zhou.

   INTRODUCTION: Vascular smooth muscle cell (VSMC) senescence in the vasculature results in vascular aging as well as age-related diseases, while metformin improves the inflamm-aging profile by enhancing autophagy. However, metformin's impact on VSMC senescence is largely undefined.
OBJECTIVES: To test the hypothesis that metformin exerts an anti-senescence role by restoring autophagic activity in VSMCs and vascular tissues.
METHODS: Animal models established by angiotensin II (Ang II) induction and physiological aging and senescent primary VSMCs from the aortas of elderly patients were treated with metformin. Cellular and vascular senescence were assessed by measuring the amounts of senescence-associated β-galactosidase and senescence markers, including p21 and p53. Autophagy levels were assessed by autophagy-related protein expression, transmission electron microscope, and autolysosome staining. In order to explore the underlying mechanism of the anti-senescence effects of metformin, 4D label-free quantitative proteomics and bioinformatic analyses were conducted, with subsequent experiments validating these findings.
RESULTS: Ang II-dependent senescence was suppressed by metformin in VSMCs and vascular tissues. Metformin also significantly improved arterial stiffness and alleviated structural changes in aged arteries, reduced senescence-associated secretory phenotype (SASP), and improved proliferation and migration of senescent VSMCs. Mechanistically, the proteomic analysis indicated that autophagy might contribute to metformin's anti-senescence effects. Reduced autophagic flux was observed in Ang II-induced cellular and vascular senescence; this reduction was reversed by metformin. Specifically, metformin enhanced the autophagic flux at the autophagosome-lysosome fusion level, whereas blockade of autophagosome-lysosome fusion inhibited the anti-senescence effects of metformin.
CONCLUSIONS: Metformin prevents VSMC and vascular senescence by promoting autolysosome formation.

Keywords:  Aging; Autophagic flux; Lysosome; Senescence; VSMC

DOI:  https://doi.org/10.1016/j.jare.2021.12.009
Acta Neuropathol Commun. 2022 Nov 04. 10(1): 158

Single-cell spatial proteomic imaging for human neuropathology.

Kausalia Vijayaragavan, Bryan J Cannon, Dmitry Tebaykin, Marc Bossé, Alex Baranski, J P Oliveria, Syed A Bukhari, Dunja Mrdjen, M Ryan Corces, Erin F McCaffrey, Noah F Greenwald, Yari Sigal, Diana Marquez, Zumana Khair, Trevor Bruce, Mako Goldston, Anusha Bharadwaj, Kathleen S Montine, R Michael Angelo, Thomas J Montine, Sean C Bendall.

Neurodegenerative disorders are characterized by phenotypic changes and hallmark proteopathies. Quantifying these in archival human brain tissues remains indispensable for validating animal models and understanding disease mechanisms. We present a framework for nanometer-scale, spatial proteomics with multiplex ion beam imaging (MIBI) for capturing neuropathological features. MIBI facilitated simultaneous, quantitative imaging of 36 proteins on archival human hippocampus from individuals spanning cognitively normal to dementia. Customized analysis strategies identified cell types and proteopathies in the hippocampus across stages of Alzheimer's disease (AD) neuropathologic change. We show microglia-pathologic tau interactions in hippocampal CA1 subfield in AD dementia. Data driven, sample independent creation of spatial proteomic regions identified persistent neurons in pathologic tau neighborhoods expressing mitochondrial protein MFN2, regardless of cognitive status, suggesting a survival advantage. Our study revealed unique insights from multiplexed imaging and data-driven approaches for neuropathologic analysis and serves broadly as a methodology for spatial proteomic analysis of archival human neuropathology. TEASER: Multiplex Ion beam Imaging enables deep spatial phenotyping of human neuropathology-associated cellular and disease features.

DOI: https://doi.org/10.1186/s40478-022-01465-x
Sci Rep. 2022 Nov 03. 12(1): 18628

Increased autophagy leads to decreased apoptosis during β-thalassaemic mouse and patient erythropoiesis.

Pornthip Chaichompoo, Ramaneeya Nithipongvanitch, Wasinee Kheansaard, Alisa Tubsuwan, Kanitta Srinoun, Jim Vadolas, Suthat Fucharoen, Duncan R Smith, Pranee Winichagoon, Saovaros Svasti.

β-Thalassaemia results from defects in β-globin chain production, leading to ineffective erythropoiesis and subsequently to severe anaemia and other complications. Apoptosis and autophagy are the main pathways that regulate the balance between cell survival and cell death in response to diverse cellular stresses. Herein, the death of erythroid lineage cells in the bone marrow from both βIVS2-654-thalassaemic mice and β-thalassaemia/HbE patients was investigated. Phosphatidylserine (PS)-bearing basophilic erythroblasts and polychromatophilic erythroblasts were significantly increased in β-thalassaemia as compared to controls. However, the activation of caspase 8, caspase 9 and caspase 3 was minimal and not different from control in both murine and human thalassaemic erythroblasts. Interestingly, bone marrow erythroblasts from both β-thalassaemic mice and β-thalassaemia/HbE patients had significantly increased autophagy as shown by increased autophagosomes and increased co-localization between LC3 and LAMP-1. Inhibition of autophagy by chloroquine caused significantly increased erythroblast apoptosis. We have demonstrated increased autophagy which led to minimal apoptosis in β-thalassaemic erythroblasts. However, increased PS exposure occurring through other mechanisms in thalassaemic erythroblasts might cause rapid phagocytic removal by macrophages and consequently ineffective erythropoiesis in β-thalassaemia.

DOI: https://doi.org/10.1038/s41598-022-21249-6
Nat Commun. 2022 Nov 04. 13(1): 6621

Translation regulatory factor BZW1 regulates preimplantation embryo development and compaction by restricting global non-AUG Initiation.

Jue Zhang, Shuai-Bo Pi, Nan Zhang, Jing Guo, Wei Zheng, Lizhi Leng, Ge Lin, Heng-Yu Fan.

Protein synthesis is an essential step in gene expression during the development of mammalian preimplantation embryos. This is a complex and highly regulated process. The accuracy of the translation initiation codon is important in various gene expression programs. However, the mechanisms that regulate AUG and non-AUG codon initiation in early embryos remain poorly understood. BZW1 is a key factor in determining the mRNA translation start codon. Here, we show that BZW1 is essential for early embryonic development in mice. Bzw1-knockdown embryos fail to undergo compaction, and show decreased blastocyst formation rates. We also observe defects in the differentiation capacity and implantation potential after Bzw1 interference. Further investigation revealed that Bzw1 knockdown causes the levels of translation initiation with CUG as the start codon to increase. The decline in BZW1 levels result in a decrease in protein synthesis in preimplantation embryos, whereas the total mRNA levels are not altered. Therefore, we concluded that BZW1 contributes to protein synthesis during early embryonic development by restricting non-AUG translational initiation.

DOI: https://doi.org/10.1038/s41467-022-34427-x
Nat Commun. 2022 Nov 02. 13(1): 6558

Cap-dependent translation initiation monitored in living cells.

Valentina Gandin, Brian P English, Melanie Freeman, Louis-Philippe Leroux, Stephan Preibisch, Deepika Walpita, Maritza Jaramillo, Robert H Singer.

mRNA translation is tightly regulated to preserve cellular homeostasis. Despite extensive biochemical, genetic, and structural studies, a detailed understanding of mRNA translation regulation is lacking. Imaging methodologies able to resolve the binding dynamics of translation factors at single-cell and single-mRNA resolution were necessary to fully elucidate regulation of this paramount process. Here live-cell spectroscopy and single-particle tracking were combined to interrogate the binding dynamics of endogenous initiation factors to the 5'cap. The diffusion of initiation factors (IFs) changed markedly upon their association with mRNA. Quantifying their diffusion characteristics revealed the sequence of IFs assembly and disassembly in cell lines and the clustering of translation in neurons. This approach revealed translation regulation at high spatial and temporal resolution that can be applied to the formation of any endogenous complex that results in a measurable shift in diffusion.

DOI: https://doi.org/10.1038/s41467-022-34052-8