bims-proarb 2022-10-16 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2022–10–16
twenty-six papers selected by
Rich Giadone, Harvard University

The Role of Small Heat Shock Proteins in Protein Misfolding Associated Motoneuron Diseases.
Editorial: Unfolded protein response (UPR): An impending target for multiple neurological disorders.
Inhibition of High-Temperature Requirement Protein A2 Protease Activity Represses Myogenic Differentiation via UPRmt.
Neuronal induction of BNIP3-mediated mitophagy slows systemic aging in Drosophila.
Defective Human SRP Induces Protein Quality Control and Triggers Stress Response.
Synthesis of O-GlcNAcylated small heat shock proteins.
Overexpression of mouse prion protein in transgenic mice causes a non-transmissible spongiform encephalopathy.
In situ cell-type-specific cell-surface proteomic profiling in mice.
Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta.
Scleral PERK and ATF6 as targets of myopic axial elongation of mouse eyes.
A possible connection between reactive oxygen species and the unfolded protein response in lens development: From insight to foresight.
Dynamic proteomic and phosphoproteomic atlas of corticostriatal axons in neurodevelopment.
Heat shock factor HSF1 regulates BDNF gene promoters upon acute stress in the hippocampus, together with pCREB.
Evolutionarily conserved proline residues impede the misfolding of the mouse prion protein by destabilizing an aggregation-competent partially unfolded form.
Cerebrospinal fluid biomarker panel of synaptic dysfunction in Alzheimer's disease and other neurodegenerative disorders.
Different phenotypes of microglia in animal models of Alzheimer disease.
AR12 increases BAG3 expression which is essential for Tau and APP degradation via LC3-associated phagocytosis and macroautophagy.
Consequences of Autophagy Deletion on the Age-Related Changes in the Epidermal Lipidome of Mice.
Genetic deletion of hspa8 leads to selective tissue malformations in zebrafish embryonic development.
Astroglial and microglial pathology in Down syndrome: Focus on Alzheimer's disease.
Diseased, differentiated and difficult: Strategies for improved engineering of in vitro neurological systems.
Inhibition of mitochondrial respiration has fundamentally different effects on proliferation, cell survival and stress response in immature versus differentiated cardiomyocyte cell lines.
Single Nucleus Transcriptome Data from Alzheimer's Disease Mouse Models Yield New Insight into Pathophysiology.
Profiling epigenetic age in single cells.
Defective UPR linked to β-cell dedifferentiation.
Variation in ubiquitin system genes creates substrate-specific effects on proteasomal protein degradation.

Int J Mol Sci. 2022 Oct 04. pii: 11759. [Epub ahead of print]23(19):

The Role of Small Heat Shock Proteins in Protein Misfolding Associated Motoneuron Diseases.

Barbara Tedesco, Veronica Ferrari, Marta Cozzi, Marta Chierichetti, Elena Casarotto, Paola Pramaggiore, Francesco Mina, Mariarita Galbiati, Paola Rusmini, Valeria Crippa, Riccardo Cristofani, Angelo Poletti.

  Motoneuron diseases (MNDs) are neurodegenerative conditions associated with death of upper and/or lower motoneurons (MNs). Proteostasis alteration is a pathogenic mechanism involved in many MNDs and is due to the excessive presence of misfolded and aggregated proteins. Protein misfolding may be the product of gene mutations, or due to defects in the translation process, or to stress agents; all these conditions may alter the native conformation of proteins making them prone to aggregate. Alternatively, mutations in members of the protein quality control (PQC) system may determine a loss of function of the proteostasis network. This causes an impairment in the capability to handle and remove aberrant or damaged proteins. The PQC system consists of the degradative pathways, which are the autophagy and the proteasome, and a network of chaperones and co-chaperones. Among these components, Heat Shock Protein 70 represents the main factor in substrate triage to folding, refolding, or degradation, and it is assisted in this task by a subclass of the chaperone network, the small heat shock protein (sHSPs/HSPBs) family. HSPBs take part in proteostasis by bridging misfolded and aggregated proteins to the HSP70 machinery and to the degradative pathways, facilitating refolding or clearance of the potentially toxic proteins. Because of its activity against proteostasis alteration, the chaperone system plays a relevant role in the protection against proteotoxicity in MNDs. Here, we discuss the role of HSPBs in MNDs and which HSPBs may represent a valid target for therapeutic purposes.

Keywords:  HSPBs; MNDs; chaperones; protein quality control; proteostasis

DOI:  https://doi.org/10.3390/ijms231911759
Front Aging Neurosci. 2022 ;14 1014450

Editorial: Unfolded protein response (UPR): An impending target for multiple neurological disorders.

Arif Tasleem Jan, Safikur Rahman, Khurshid Ahmad, Rinki Minakshi.



Keywords:  aggregation; endoplasmic reticulum stress; neurological disorders; protein folding; proteinopathies; unfolded protein response

DOI:  https://doi.org/10.3389/fnagi.2022.1014450
Int J Mol Sci. 2022 Oct 04. pii: 11761. [Epub ahead of print]23(19):

Inhibition of High-Temperature Requirement Protein A2 Protease Activity Represses Myogenic Differentiation via UPRmt.

Hongyu Sun, Luyan Shen, Ping Zhang, Fu Lin, Jiaoyan Ma, Ying Wu, Huimei Yu, Liankun Sun.

  Skeletal muscles require muscle satellite cell (MuSC) differentiation to facilitate the replenishment and repair of muscle fibers. A key step in this process is called myogenic differentiation. The differentiation ability of MuSCs decreases with age and can result in sarcopenia. Although mitochondria have been reported to be involved in myogenic differentiation by promoting a bioenergetic remodeling, little is known about the interplay of mitochondrial proteostasis and myogenic differentiation. High-temperature-requirement protein A2 (HtrA2/Omi) is a protease that regulates proteostasis in the mitochondrial intermembrane space (IMS). Mice deficient in HtrA2 protease activity show a distinct phenotype of sarcopenia. To investigate the role of IMS proteostasis during myogenic differentiation, we treated C2C12 myoblasts with UCF101, a specific inhibitor of HtrA2 during differentiation process. A key step in this process is called myogenic differentiation. The differentiation ability of MuSCs decreases with age and can result in sarcopenia. Further, CHOP, p-eIF2α, and other mitochondrial unfolded protein response (UPRmt)-related proteins are upregulated. Therefore, we suggest that imbalance of mitochondrial IMS proteostasis acts via a retrograde signaling pathway to inhibit myogenic differentiation via the UPRmt pathway. These novel mechanistic insights may have implications for the development of new strategies for the treatment of sarcopenia.

Keywords:  HtrA2/Omi; UPRmt; mitonuclear imbalance; sarcopenia; skeletal muscle

DOI:  https://doi.org/10.3390/ijms231911761
Nat Aging. 2022 Jun;2(6): 494-507

Neuronal induction of BNIP3-mediated mitophagy slows systemic aging in Drosophila.

Edward T Schmid, Jung-Hoon Pyo, David W Walker.

  The effects of aging on the brain are widespread and can have dramatic implications on the overall health of an organism. Mitochondrial dysfunction is a hallmark of brain aging, but, the interplay between mitochondrial quality control, neuronal aging, and organismal health is not well understood. Here, we show that aging leads to a decline in mitochondrial autophagy (mitophagy) in the Drosophila brain with a concomitant increase in mitochondrial content. We find that induction of BCL2-interacting protein 3 (BNIP3), a mitochondrial outer membrane protein, in the adult nervous system induces mitophagy and prevents the accumulation of dysfunctional mitochondria in the aged brain. Importantly, neuronal induction of BNIP3-mediated mitophagy increases organismal longevity and healthspan. Furthermore, BNIP3-mediated mitophagy in the nervous system improves muscle and intestinal homeostasis in aged flies, indicating cell non-autonomous effects. Our findings identify BNIP3 as a therapeutic target to counteract brain aging and prolong overall organismal health with age.

Keywords:  Autophagy; Intestinal barrier dysfunction; Intestinal stem cell; Mito-QC; Mitophagy; Muscle aging; Neuronal aging

DOI:  https://doi.org/10.1038/s43587-022-00214-y
J Mol Biol. 2022 Sep 19. pii: S0022-2836(22)00452-1. [Epub ahead of print]434(22): 167832

Defective Human SRP Induces Protein Quality Control and Triggers Stress Response.

Elena B Tikhonova, Sneider Alexander Gutierrez Guarnizo, Morgana K Kellogg, Alexander Karamyshev, Igor M Dozmorov, Zemfira N Karamysheva, Andrey L Karamyshev.

  Regulation of Aberrant Protein Production (RAPP) is a protein quality control in mammalian cells. RAPP degrades mRNAs of nascent proteins not able to associate with their natural interacting partners during synthesis at the ribosome. However, little is known about the molecular mechanism of the pathway, its substrates, or its specificity. The Signal Recognition Particle (SRP) is the first interacting partner for secretory proteins. It recognizes signal sequences of the nascent polypeptides when they are exposed from the ribosomal exit tunnel. Here, we reveal the generality of the RAPP pathway on the whole transcriptome level through depletion of human SRP54, an SRP subunit. This depletion triggers RAPP and leads to decreased expression of the mRNAs encoding a number of secretory and membrane proteins. The loss of SRP54 also leads to the dramatic upregulation of a specific network of HSP70/40/90 chaperones (HSPA1A, DNAJB1, HSP90AA1, and others), increased ribosome associated ubiquitination, and change in expression of RPS27 and RPS27L suggesting ribosome rearrangement. These results demonstrate the complex nature of defects in protein trafficking, mRNA and protein quality control, and provide better understanding of their mechanisms at the ribosome.

Keywords:  protein synthesis and transport; secretory proteins; signal Recognition particle; signal sequence; translational control

DOI:  https://doi.org/10.1016/j.jmb.2022.167832
Methods Enzymol. 2022 ;pii: S0076-6879(22)00242-7. [Epub ahead of print]675 63-82

Synthesis of O-GlcNAcylated small heat shock proteins.

Stuart P Moon, Matthew R Pratt.

  A protein's structure and function often depend not only on its primary sequence, but also the presence or absence of any number of non-coded posttranslational modifications. Complicating their study is the fact that the physiological consequences of these modifications are context-, protein-, and site-dependent, and there exist no purely biological techniques to unambiguously study their effects. To this end, protein semisynthesis has become an invaluable chemical biology tool to specifically install non-coded or non-native moieties onto proteins in vitro using synthetic and/or recombinant polypeptides. Here, we describe two facets of protein semisynthesis (solid-phase peptide synthesis and expressed protein ligation) and their use in generating site-specifically glycosylated small heat shock proteins for functional studies. The procedures herein require limited specialized equipment, employ mild reaction conditions, and can be extended to myriad other proteins, modifications, and contexts.

Keywords:  Chaperone; Chemical ligation; Heat shock protein; O-GlcNAc; Posttranslational modification

DOI:  https://doi.org/10.1016/bs.mie.2022.07.004
Sci Rep. 2022 Oct 13. 12(1): 17198

Overexpression of mouse prion protein in transgenic mice causes a non-transmissible spongiform encephalopathy.

Graham S Jackson, Jacqueline Linehan, Sebastian Brandner, Emmanuel A Asante, Jonathan D F Wadsworth, John Collinge.

Transgenic mice over-expressing human PRNP or murine Prnp transgenes on a mouse prion protein knockout background have made key contributions to the understanding of human prion diseases and have provided the basis for many of the fundamental advances in prion biology, including the first report of synthetic mammalian prions. In this regard, the prion paradigm is increasingly guiding the exploration of seeded protein misfolding in the pathogenesis of other neurodegenerative diseases. Here we report that a well-established and widely used line of such mice (Tg20 or tga20), which overexpress wild-type mouse prion protein, exhibit spontaneous aggregation and accumulation of misfolded prion protein in a strongly age-dependent manner, which is accompanied by focal spongiosis and occasional neuronal loss. In some cases a clinical syndrome developed with phenotypic features that closely resemble those seen in prion disease. However, passage of brain homogenate from affected, aged mice failed to transmit this syndrome when inoculated intracerebrally into further recipient animals. We conclude that overexpression of the wild-type mouse prion protein can cause an age-dependent protein misfolding disorder or proteinopathy that is not associated with the production of an infectious agent but can produce a phenotype closely similar to authentic prion disease.

DOI: https://doi.org/10.1038/s41598-022-21608-3
Neuron. 2022 Oct 06. pii: S0896-6273(22)00864-9. [Epub ahead of print]

In situ cell-type-specific cell-surface proteomic profiling in mice.

S Andrew Shuster, Jiefu Li, URee Chon, Miley C Sinantha-Hu, David J Luginbuhl, Namrata D Udeshi, Dominique Kiki Carey, Yukari H Takeo, Qijing Xie, Chuanyun Xu, D R Mani, Shuo Han, Alice Y Ting, Steven A Carr, Liqun Luo.

  Cell-surface proteins (CSPs) mediate intercellular communication throughout the lives of multicellular organisms. However, there are no generalizable methods for quantitative CSP profiling in specific cell types in vertebrate tissues. Here, we present in situ cell-surface proteome extraction by extracellular labeling (iPEEL), a proximity labeling method in mice that enables spatiotemporally precise labeling of cell-surface proteomes in a cell-type-specific environment in native tissues for discovery proteomics. Applying iPEEL to developing and mature cerebellar Purkinje cells revealed differential enrichment in CSPs with post-translational protein processing and synaptic functions in the developing and mature cell-surface proteomes, respectively. A proteome-instructed in vivo loss-of-function screen identified a critical, multifaceted role for Armh4 in Purkinje cell dendrite morphogenesis. Armh4 overexpression also disrupts dendrite morphogenesis; this effect requires its conserved cytoplasmic domain and is augmented by disrupting its endocytosis. Our results highlight the utility of CSP profiling in native mammalian tissues for identifying regulators of cell-surface signaling.

Keywords:  Purkinje cell; cell-surface protein; cell-surface proteome; cell-surface signaling; dendrite morphogenesis; discovery proteomics; proximity labeling

DOI:  https://doi.org/10.1016/j.neuron.2022.09.025
Mass Spectrom Rev. 2022 Oct 12.

Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta.

Wesley J Wagner, Michael L Gross.

Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.

DOI: https://doi.org/10.1002/mas.21814
Nat Commun. 2022 Oct 10. 13(1): 5859

Scleral PERK and ATF6 as targets of myopic axial elongation of mouse eyes.

Shin-Ichi Ikeda, Toshihide Kurihara, Xiaoyan Jiang, Yukihiro Miwa, Deokho Lee, Naho Serizawa, Heonuk Jeong, Kiwako Mori, Yusaku Katada, Hiromitsu Kunimi, Nobuhiro Ozawa, Chiho Shoda, Mari Ibuki, Kazuno Negishi, Hidemasa Torii, Kazuo Tsubota.

Axial length is the primary determinant of eye size, and it is elongated in myopia. However, the underlying mechanism of the onset and progression of axial elongation remain unclear. Here, we show that endoplasmic reticulum (ER) stress in sclera is an essential regulator of axial elongation in myopia development through activation of both PERK and ATF6 axis followed by scleral collagen remodeling. Mice with lens-induced myopia (LIM) showed ER stress in sclera. Pharmacological interventions for ER stress could induce or inhibit myopia progression. LIM activated all IRE1, PERK and ATF6 axis, and pharmacological inhibition of both PERK and ATF6 suppressed myopia progression, which was confirmed by knocking down above two genes via CRISPR/Cas9 system. LIM dramatically changed the expression of scleral collagen genes responsible for ER stress. Furthermore, collagen fiber thinning and expression of dysregulated collagens in LIM were ameliorated by 4-PBA administration. We demonstrate that scleral ER stress and PERK/ATF6 pathway controls axial elongation during the myopia development in vivo model and 4-PBA eye drop is promising drug for myopia suppression/treatment.

DOI: https://doi.org/10.1038/s41467-022-33605-1
Front Cell Dev Biol. 2022 ;10 820949

A possible connection between reactive oxygen species and the unfolded protein response in lens development: From insight to foresight.

Lixiong Gao, Ni Jin, Zi Ye, Tianju Ma, Yang Huang, Hongyu Li, Jinlin Du, Zhaohui Li.

  The lens is a relatively special and simple organ. It has become an ideal model to study the common developmental characteristics among different organic systems. Lens development is a complex process influenced by numerous factors, including signals from the intracellular and extracellular environment. Reactive oxygen species (ROS) are a group of highly reactive and oxygen-containing molecules that can cause endoplasmic reticulum stress in lens cells. As an adaptive response to ER stress, lens cells initiate the unfolded protein response (UPR) to maintain normal protein synthesis by selectively increasing/decreasing protein synthesis and increasing the degradation of misfolded proteins. Generally, the UPR signaling pathways have been well characterized in the context of many pathological conditions. However, recent studies have also confirmed that all three UPR signaling pathways participate in a variety of developmental processes, including those of the lens. In this review, we first briefly summarize the three stages of lens development and present the basic profiles of ROS and the UPR. We then discuss the interconnections between lens development and these two mechanisms. Additionally, the potential adoption of human pluripotent stem-cell-based lentoids in lens development research is proposed to provide a novel perspective on future developmental studies.

Keywords:  PSCs; ROS; UPR; lens development; lentoid body

DOI:  https://doi.org/10.3389/fcell.2022.820949
Elife. 2022 Oct 14. pii: e78847. [Epub ahead of print]11

Dynamic proteomic and phosphoproteomic atlas of corticostriatal axons in neurodevelopment.

Vasin Dumrongprechachan, Ryan B Salisbury, Lindsey Butler, Matthew L MacDonald, Yevgenia Kozorovitskiy.

  Mammalian axonal development begins in embryonic stages and continues postnatally. After birth, axonal proteomic landscape changes rapidly, coordinated by transcription, protein turnover, and post-translational modifications. Comprehensive profiling of axonal proteomes across neurodevelopment is limited, with most studies lacking cell-type and neural circuit specificity, resulting in substantial information loss. We create a Cre-dependent APEX2 reporter mouse line and map cell-type specific proteome of corticostriatal projections across postnatal development. We synthesize analysis frameworks to define temporal patterns of axonal proteome and phosphoproteome, identifying co-regulated proteins and phosphorylations associated with genetic risk for human brain disorders. We discover proline-directed kinases as major developmental regulators. APEX2 transgenic reporter proximity labeling offers flexible strategies for subcellular proteomics with cell type specificity in early neurodevelopment, a critical period for neuropsychiatric disease.

Keywords:  mouse; neuroscience

DOI:  https://doi.org/10.7554/eLife.78847
J Neurochem. 2022 Oct 13.

Heat shock factor HSF1 regulates BDNF gene promoters upon acute stress in the hippocampus, together with pCREB.

Hunter Franks, Ruishan Wang, Mingqi Li, Bin Wang, Ashton Wildmann, Tyler Ortyl, Shannon O'Brien, Deborah Young, Francesca-Fang Liao, Kazuko Sakata.

  Heat shock factor (HSF1) is a master stress-responsive transcriptional factor, protecting cells from death. However, its gene regulation in vivo in the brain in response to neuronal stimuli remains elusive. Here, we investigated its direct regulation of the brain-derived neurotrophic factor (BDNF) gene (Bdnf) in response to acute neuronal stress stimuli in the brain. The results of immunohistochemistry and chromatin immunoprecipitation quantitative PCR (ChIP-qPCR) showed that administration of kainic acid (a glutamate receptor agonist inducing excitotoxity) to young adult mice induced HSF1 nuclear translocation and its binding to multiple Bdnf promoters in the hippocampus. Footshock, a physical stressor used for learning, also induced HSF1 binding to selected Bdnf promoters I and IV. This is, to our knowledge, the first demonstration of HSF1 gene regulation in response to neuronal stimuli in the hippocampus in vivo. HSF1 binding sites (HSEs) in Bdnf promoters I and IV were also detected when immunoprecipitated by an antibody of phosphorylated (p)CREB (cAMP-responsive element-binding protein), suggesting their possible interplay in acute stress-induced Bdnf transcription. Interestingly, their promoter binding patterns differed by KA and footshock, suggesting that HSF1 and pCREB orchestrate to render fine-tuned promoter control depending on the types of stress. Further, HSF1 overexpression increased Bdnf promoter activity in a luciferase assay, while virus infection of constitutively active-form HSF1 increased levels of BDNF mRNA and protein in vitro in primary cultured neurons. These results indicated that HSF1 activation of Bdnf promoter was sufficient to induce BDNF expression. Taken together, these results suggest that HSF1 promoter-specific control of Bdnf gene regulation plays an important role in neuronal protection and plasticity in the hippocampus in response to acute stress, possibly interplaying with pCREB.

Keywords:  BDNF; HSF1; acute stress; hippocampus; pCREB; promoter regulation

DOI:  https://doi.org/10.1111/jnc.15707
J Mol Biol. 2022 Oct 10. pii: S0022-2836(22)00474-0. [Epub ahead of print] 167854

Evolutionarily conserved proline residues impede the misfolding of the mouse prion protein by destabilizing an aggregation-competent partially unfolded form.

Suman Pal, Jayant B Udgaonkar.

  The misfolding of the prion protein has been linked to several neurodegenerative diseases. Despite extensive studies, the mechanism of the misfolding process remains poorly understood. The present study structurally delineates the role of the conserved proline residues present in the structured C-terminal domain of the mouse prion protein (moPrP) in the misfolding process. It is shown that mutation of these Pro residues to Ala leads to destabilization of the native (N) state, and also to rapid misfolding. Using hydrogen-deuterium exchange (HDX) studies coupled with mass spectrometry (MS), it has been shown that the N state of moPrP is in rapid equilibrium with a partially unfolded form (PUF2*) at pH 4. It has been shown that the Pro to Ala mutations make PUF2* energetically more accessible from the N state by stabilizing it relative to the unfolded (U) state. The apparent rate constant of misfolding is found to be linearly proportional to the extent to which PUF2* is populated in equilibrium with the N state, strongly indicating that misfolding commences from PUF2*. It has also been shown that the Pro residues restrict the boundary of the structural core of the misfolded oligomers. Overall, this study highlights how the conserved proline residues control misfolding of the prion protein by modulating the stability of the partially unfolded form from which misfolding commences.

Keywords:  hydrogen-deuterium exchange; mass-spectrometry; partially unfolded form; prion misfolding; proline

DOI:  https://doi.org/10.1016/j.jmb.2022.167854
Alzheimers Dement. 2022 Oct 14.

Cerebrospinal fluid biomarker panel of synaptic dysfunction in Alzheimer's disease and other neurodegenerative disorders.

Johanna Nilsson, Katheryn A Q Cousins, Johan Gobom, Erik Portelius, Alice Chen-Plotkin, Leslie M Shaw, Murray Grossman, David J Irwin, John Q Trojanowski, Henrik Zetterberg, Kaj Blennow, Ann Brinkmalm.

   INTRODUCTION: Synaptic degeneration is a key part of the pathophysiology of neurodegenerative diseases, and biomarkers reflecting the pathological alterations are greatly needed.
METHOD: Seventeen synaptic proteins were quantified in a pathology-confirmed cerebrospinal fluid cohort of patients with Alzheimer's disease (AD; n = 63), frontotemporal lobar degeneration (FTLD; n = 53), and Lewy body spectrum of disorders (LBD; n = 21), as well as healthy controls (HC; n = 48).
RESULTS: Comparisons revealed four distinct patterns: markers decreased across all neurodegenerative conditions compared to HC (the neuronal pentraxins), markers increased across all neurodegenerative conditions (14-3-3 zeta/delta), markers selectively increased in AD compared to other neurodegenerative conditions (neurogranin and beta-synuclein), and markers selectively decreased in LBD and FTLD compared to HC and AD (AP2B1 and syntaxin-1B).
DISCUSSION: Several of the synaptic proteins may serve as biomarkers for synaptic dysfunction in AD, LBD, and FTLD. Additionally, differential patterns of synaptic protein alterations seem to be present across neurodegenerative diseases.
HIGHLIGHTS: A panel of synaptic proteins were quantified in the cerebrospinal fluid using mass spectrometry. We compared Alzheimer's disease, frontotemporal degeneration, and Lewy body spectrum of disorders. Pathology was confirmed by autopsy or familial mutations. We discovered synaptic biomarkers for synaptic degeneration and cognitive decline. We found differential patterns of synaptic proteins across neurodegenerative diseases.

Keywords:  Alzheimer's disease; Lewy body spectrum of disorders; biomarkers; frontotemporal lobar degeneration; mass spectrometry; synaptic pathology

DOI:  https://doi.org/10.1002/alz.12809
Immun Ageing. 2022 Oct 08. 19(1): 44

Different phenotypes of microglia in animal models of Alzheimer disease.

Yun Wei, Xianxiao Li.

  Microglia are immune-competent cells that are critically involved in maintaining normal brain function. A prominent characteristic of Alzheimer disease (AD) is microglial proliferation and activation concentrated around amyloid plaques in the brain. Recent research has revealed numerous microglial phenotypes related to aging and AD, apart from the traditional M1 and M2 types. Redox signalling modulates the acquisition of the classical or alternative microglia activation phenotypes. The numerous microglial functions can be achieved through these multiple phenotypes, which are associated with distinct molecular signatures.

Keywords:  Alzheimer disease; Microglia; Microglia phenotype; Neurodegeneration

DOI:  https://doi.org/10.1186/s12979-022-00300-0
Aging (Albany NY). 2022 Oct 13. 14(undefined):

AR12 increases BAG3 expression which is essential for Tau and APP degradation via LC3-associated phagocytosis and macroautophagy.

Paul Dent, Laurence Booth, Jane L Roberts, Andrew Poklepovic, Jennifer Martinez, Derek Cridebring, Eric M Reiman.

  We defined the mechanisms by which the chaperone ATPase inhibitor AR12 and the multi-kinase inhibitor neratinib interacted to reduce expression of Tau and amyloid-precursor protein (APP) in microglia and neuronal cells. AR12 and neratinib interacted to increase the phosphorylation of eIF2A S51 and the expression of BAG3, Beclin1 and ATG5, and in parallel, enhanced autophagosome formation and autophagic flux. Knock down of BAG3, Beclin1 or ATG5 abolished autophagosome formation and significantly reduced degradation of p62, LAMP2, Tau, APP, and GRP78 (total and plasma membrane). Knock down of Rubicon, a key component of LC3-associated phagocytosis (LAP), significantly reduced autophagosome formation but not autophagic flux and prevented degradation of Tau, APP, and cell surface GRP78, but not ER-localized GRP78. Knock down of Beclin1, ATG5 or Rubicon or over-expression of GRP78 prevented the significant increase in eIF2A phosphorylation. Knock down of eIF2A prevented the increase in BAG3 expression and significantly reduced autophagosome formation, autophagic flux, and it prevented Tau and APP degradation. We conclude that AR12 has the potential to reduce Tau and APP levels in neurons and microglia via the actions of LAP, endoplasmic reticulum stress signaling and macroautophagy. We hypothesize that the initial inactivation of GRP78 catalytic function by AR12 facilitates an initial increase in eIF2A phosphorylation which in turn is essential for greater levels of eIF2A phosphorylation, greater levels of BAG3 and macroautophagy and eventually leading to significant amounts of APP/Tau degradation.

Keywords:  AR12; Alzheimer’s disease; GRP78; LAP / LANDO; macroautophagy

DOI:  https://doi.org/10.18632/aging.204337
Int J Mol Sci. 2022 Sep 21. pii: 11110. [Epub ahead of print]23(19):

Consequences of Autophagy Deletion on the Age-Related Changes in the Epidermal Lipidome of Mice.

Yiwen Yang, Christopher Kremslehner, Sophia Derdak, Christina Bauer, Sarah Jelleschitz, Ionela-Mariana Nagelreiter, Heidemarie Rossiter, Marie Sophie Narzt, Florian Gruber, Michaela Sochorová.

  Autophagy is a controlled mechanism of intracellular self-digestion with functions in metabolic adaptation to stress, in development, in proteostasis and in maintaining cellular homeostasis in ageing. Deletion of autophagy in epidermal keratinocytes does not prevent the formation of a functional epidermis and the permeability barrier but causes increased susceptibility to damage stress and metabolic alterations and accelerated ageing phenotypes. We here investigated how epidermal autophagy deficiency using Keratin 14 driven Atg7 deletion would affect the lipid composition of the epidermis of young and old mice. Using mass spectrometric lipidomics we found a reduction of age-related accumulation of storage lipids in the epidermis of autophagy-deficient mice, and specific changes in chain length and saturation of fatty acids in several lipid classes. Transcriptomics and immunostaining suggest that these changes are accompanied by changes in expression and localisation of lipid and fatty acid transporter proteins, most notably fatty acid binding protein 5 (FABP5) in autophagy knockouts. Thus, maintaining autophagic activity at an advanced age may be necessary to maintain epidermal lipid homeostasis in mammals.

Keywords:  ageing; autophagy; cholesterol ester; epidermis; lipidome; sphingomyelin; transcriptome; triglyceride

DOI:  https://doi.org/10.3390/ijms231911110
J Cell Sci. 2022 Oct 13. pii: jcs.259734. [Epub ahead of print]

Genetic deletion of hspa8 leads to selective tissue malformations in zebrafish embryonic development.

Caixia Wang, Xin Zhang, Xinyu Wang, Yanpeng Zhai, Mengjiao Li, Jun Pan, Yan Bai, Xiaozhi Rong, Jianfeng Zhou.

  The heat shock cognate 71 kDa protein HSPA8/HSC70, a constitutively expressed cognate member of the heat shock protein 70 family, plays an essential role in protein quality control and cell homeostasis maintenance. HSPA8 has been implicated in many diseases, including cancers and neurodegenerative diseases. Due to massive cell death after knockdown of HSPA8 and nonviable Hspa8 knockout mice, the physiological role of HSPA8 in vertebrates and its underlying mechanism have not yet been elucidated. To address this issue, we used CRISPR/Cas9 technology and genetically deleted hspa8 in zebrafish embryos. Genetic deletion of hspa8 resulted in malformations of the pharyngeal arches, pectoral fins, head, and eyes at the later stages. We next focused on pharyngeal arch deficiency and found that pharyngeal arches in hspa8 mutant embryos exhibited induction of endoplasmic reticulum stress and activation of the unfolded protein response via the Perk/p-eIF2α/Atf4 signaling cascade. Inhibition of Perk/p-eIF2α/Atf4 signaling rescued developmental deficiency of pharyngeal arches due to depletion of Hspa8. Taken together, our results provide novel insights into the tissue-specific roles of Hspa8 in the regulation of vertebrate embryonic development.

Keywords:  ATF4; Hspa8/Hsc70; Pharyngeal arch cartilages; Unfolded protein response; Zebrafish; eIF2α

DOI:  https://doi.org/10.1242/jcs.259734
Front Cell Neurosci. 2022 ;16 987212

Astroglial and microglial pathology in Down syndrome: Focus on Alzheimer's disease.

Octavio García, Lisi Flores-Aguilar.

  Down syndrome (DS) arises from the triplication of human chromosome 21 and is considered the most common genetic cause of intellectual disability. Glial cells, specifically astroglia and microglia, display pathological alterations that might contribute to DS neuropathological alterations. Further, in middle adulthood, people with DS develop clinical symptoms associated with premature aging and Alzheimer's disease (AD). Overexpression of the amyloid precursor protein (APP) gene, encoded on chromosome 21, leads to increased amyloid-β (Aβ) levels and subsequent formation of Aβ plaques in the brains of individuals with DS. Amyloid-β deposition might contribute to astroglial and microglial reactivity, leading to neurotoxic effects and elevated secretion of inflammatory mediators. This review discusses evidence of astroglial and microglial alterations that might be associated with the AD continuum in DS.

Keywords:  Alzheimer's disease; Down syndrome; aging; astrocytes; cytokines; microglia; neuroinflammation; β-amyloid

DOI:  https://doi.org/10.3389/fncel.2022.987212
Front Cell Neurosci. 2022 ;16 962103

Diseased, differentiated and difficult: Strategies for improved engineering of in vitro neurological systems.

Nicholas Elder, Faranak Fattahi, Todd C McDevitt, Lyandysha V Zholudeva.

  The rapidly growing field of cellular engineering is enabling scientists to more effectively create in vitro models of disease and develop specific cell types that can be used to repair damaged tissue. In particular, the engineering of neurons and other components of the nervous system is at the forefront of this field. The methods used to engineer neural cells can be largely divided into systems that undergo directed differentiation through exogenous stimulation (i.e., via small molecules, arguably following developmental pathways) and those that undergo induced differentiation via protein overexpression (i.e., genetically induced and activated; arguably bypassing developmental pathways). Here, we highlight the differences between directed differentiation and induced differentiation strategies, how they can complement one another to generate specific cell phenotypes, and impacts of each strategy on downstream applications. Continued research in this nascent field will lead to the development of improved models of neurological circuits and novel treatments for those living with neurological injury and disease.

Keywords:  cellular engineering; directed neurons; induced neurons; micro RNA; stem cells; transcription factor complexes

DOI:  https://doi.org/10.3389/fncel.2022.962103
Front Cell Dev Biol. 2022 ;10 1011639

Inhibition of mitochondrial respiration has fundamentally different effects on proliferation, cell survival and stress response in immature versus differentiated cardiomyocyte cell lines.

Bent Grün, Michaela Tirre, Simon Pyschny, Vijay Singh, Hans-Gerd Kehl, Christian Jux, Jörg-Detlef Drenckhahn.

  Myocardial tissue homeostasis is critically important for heart development, growth and function throughout the life course. The loss of cardiomyocytes under pathological conditions ultimately leads to cardiovascular disease due to the limited regenerative capacity of the postnatal mammalian heart. Inhibition of electron transport along the mitochondrial respiratory chain causes cellular stress characterized by ATP depletion as well as excessive generation of reactive oxygen species. Adult cardiomyocytes are highly susceptible to mitochondrial dysfunction whereas embryonic cardiomyocytes in the mouse heart have been shown to be resistant towards mitochondrial complex III inhibition. To functionally characterize the molecular mechanisms mediating this stress tolerance, we used H9c2 cells as an in vitro model for immature cardiomyoblasts and treated them with various inhibitors of mitochondrial respiration. The complex I inhibitor rotenone rapidly induced cell cycle arrest and apoptosis whereas the complex III inhibitor antimycin A (AMA) had no effect on proliferation and only mildly increased cell death. HL-1 cells, a differentiated and contractile cardiomyocyte cell line from mouse atrium, were highly susceptible to AMA treatment evident by cell cycle arrest and death. AMA induced various stress response mechanisms in H9c2 cells, such as the mitochondrial unfolded protein response (UPRmt), integrated stress response (ISR), heat shock response (HSR) and antioxidative defense. Inhibition of the UPR, ISR and HSR by siRNA mediated knock down of key components does not impair growth of H9c2 cells upon AMA treatment. In contrast, knock down of NRF2, an important transcriptional regulator of genes involved in detoxification of reactive oxygen species, reduces growth of H9c2 cells upon AMA treatment. Various approaches to activate cell protective mechanisms and alleviate oxidative stress in HL-1 cells failed to rescue them from AMA induced growth arrest and death. In summary, these data show that the site of electron transport interruption along the mitochondrial respiratory chain determines cell fate in immature cardiomyoblasts. The study furthermore points to fundamental differences in stress tolerance and cell survival between immature and differentiated cardiomyocytes which may underlie the growth plasticity of embryonic cardiomyocytes during heart development but also highlight the obstacles of cardioprotective therapies in the adult heart.

Keywords:  cardiomyocyte differentiation; cardiomyocyte proliferation; cardiomyocyte survival; cellular stress response; mitochondrial dysfunction; oxidative stress

DOI:  https://doi.org/10.3389/fcell.2022.1011639
J Alzheimers Dis. 2022 Oct 01.

Single Nucleus Transcriptome Data from Alzheimer's Disease Mouse Models Yield New Insight into Pathophysiology.

Andrew E Weller, Thomas N Ferraro, Glenn A Doyle, Benjamin C Reiner, Richard C Crist, Wade H Berrettini.

   BACKGROUND: 5XFAD humanized mutant mice and Trem2 knockout (T2KO) mice are two mouse models relevant to the study of Alzheimer's disease (AD)-related pathology.
OBJECTIVE: To determine hippocampal transcriptomic and polyadenylation site usage alterations caused by genetic mutations engineered in 5XFAD and T2KO mice.
METHODS: Employing a publicly available single-nucleus RNA sequencing dataset, we used Seurat and Sierra analytic programs to identify differentially expressed genes (DEGs) and differential transcript usage (DTU), respectively, in hippocampal cell types from each of the two mouse models. We analyzed cell type-specific DEGs further using Ingenuity Pathway Analysis (IPA).
RESULTS: We identified several DEGs in both neuronal and glial cell subtypes in comparisons of wild type (WT) versus 5XFAD and WT versus T2KO mice, including Ttr, Fth1, Pcsk1n, Malat1, Rpl37, Rtn1, Sepw1, Uba52, Mbp, Arl6ip5, Gm26917, Vwa1, and Pgrmc1. We also observed DTU in common between the two comparisons in neuronal and glial subtypes, specifically in the genes Prnp, Rbm4b, Pnisr, Opcml, Cpne7, Adgrb1, Gabarapl2, Ubb, Ndfip1, Car11, and Stmn4. IPA identified 3 statistically significant canonical pathways that appeared in multiple cell types and that overlapped between 5XFAD and T2KO comparisons to WT, including 'FXR/RXR Activation', 'LXR/RXR Activation', and 'Acute Phase Response Signaling'.
CONCLUSION: DEG, DTU, and IPA findings, derived from two different mouse models of AD, highlight the importance of energy imbalance and inflammatory processes in specific hippocampal cell types, including subtypes of neurons and glial cells, in the development of AD-related pathology. Additional studies are needed to further characterize these findings.

Keywords:  Alzheimer’s disease; RNA-seq; animal disease models; gene expression profiling; knockout mice; mice; polyadenylation

DOI:  https://doi.org/10.3233/JAD-220391
Nat Aging. 2021 Dec;1(12): 1189-1201

Profiling epigenetic age in single cells.

Alexandre Trapp, Csaba Kerepesi, Vadim N Gladyshev.

DNA methylation dynamics emerged as a promising biomarker of mammalian aging, with multivariate machine learning models ('epigenetic clocks') enabling measurement of biological age in bulk tissue samples. However, intrinsically sparse and binarized methylation profiles of individual cells have so far precluded the assessment of aging in single-cell data. Here, we introduce scAge, a statistical framework for epigenetic age profiling at single-cell resolution, and validate our approach in mice. Our method recapitulates the chronological age of tissues, while uncovering heterogeneity among cells. We show accurate tracking of the aging process in hepatocytes, demonstrate attenuated epigenetic aging in muscle stem cells, and track age dynamics in embryonic stem cells. We also use scAge to reveal, at the single-cell level, a natural and stratified rejuvenation event occurring during early embryogenesis. We provide our framework as a resource to enable exploration of epigenetic aging trajectories at single-cell resolution.

DOI: https://doi.org/10.1038/s43587-021-00134-3
Nat Rev Endocrinol. 2022 Oct 13.

Defective UPR linked to β-cell dedifferentiation.

Katrin Legg.

DOI: https://doi.org/10.1038/s41574-022-00766-4
Elife. 2022 Oct 11. pii: e79570. [Epub ahead of print]11

Variation in ubiquitin system genes creates substrate-specific effects on proteasomal protein degradation.

Mahlon A Collins, Gemechu Mekonnen, Frank Wolfgang Albert.

  Precise control of protein degradation is critical for life, yet how natural genetic variation affects this essential process is largely unknown. Here, we developed a statistically powerful mapping approach to characterize how genetic variation affects protein degradation by the ubiquitin-proteasome system (UPS). Using the yeast Saccharomyces cerevisiae, we systematically mapped genetic influences on the N-end rule, a UPS pathway in which protein N-terminal amino acids function as degradation-promoting signals. Across all 20 possible N-terminal amino acids, we identified 149 genomic loci that influence UPS activity, many of which had pathway- or substrate-specific effects. Fine-mapping of four loci identified multiple causal variants in each of four ubiquitin system genes whose products process (NTA1), recognize (UBR1 and DOA10), and ubiquitinate (UBC6) cellular proteins. A cis-acting promoter variant that modulates UPS activity by altering UBR1 expression alters the abundance of 36 proteins without affecting levels of the corresponding mRNAs. Our results reveal a complex genetic basis of variation in UPS activity.

Keywords:  S. cerevisiae; genetics; genomics

DOI:  https://doi.org/10.7554/eLife.79570