bims-proarb 2023-02-12 papers

bims-proarb

Biomed News

on Proteostasis in aging and regenerative biology

Issue of 2023–02–12
twenty-one papers selected by
Rich Giadone, Harvard University

A journey in UPR modeling.
A selective type of autophagy to maintain glioma stem cell activity.
To Kill or to Be Killed: How Does the Battle between the UPS and Autophagy Maintain the Intracellular Homeostasis in Eukaryotes?
Limited Proteolysis-Mass Spectrometry Reveals Aging-Associated Changes in Cerebrospinal Fluid Protein Abundances and Structures.
DNAJB12 and Hsp70 Mediate Triage of Misfolded Membrane Proteins for Proteasomal versus Lysosomal Degradation.
Immortalized hippocampal astrocytes from 3xTg-AD mice, a new model to study disease-related astrocytic dysfunction: a comparative review.
Excessive Protein Accumulation and Impaired Autophagy in the Hippocampus of Angelman Syndrome Modeled in Mice.
Autophagy Meets Aging: An Overview.
Structural Proteomic Profiling of Cerebrospinal Fluids to Reveal Novel Conformational Biomarkers for Alzheimer's Disease.
Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms.
Stabilization of Monomeric Tau Protein by All D-Enantiomeric Peptide Ligands as Therapeutic Strategy for Alzheimer's Disease and Other Tauopathies.
How a tiny genetic change inflicts old age on young kids.
The Ubiquitin Proteasome System as a Therapeutic Area in Parkinson's Disease.
BMP4-SMAD1/5/9-RUNX2 pathway activation inhibits neurogenesis and oligodendrogenesis in Alzheimer's patients' iPSCs in senescence-related conditions.
Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD.
Neural atrophy produced by AAV tau injections into hippocampus and anterior cortex of middle-aged mice.
Longevity, Centenarians and Modified Cellular Proteodynamics.
Aging Effects on Optic Nerve Neurodegeneration.
Selective Translation of Maternal mRNA by eIF4E1B Controls Oocyte to Embryo Transition.
The Pursuit of the "Inside" of the Amyloid Hypothesis-Is C99 a Promising Therapeutic Target for Alzheimer's Disease?
MANF regulates neuronal survival and UPR through its ER-located receptor IRE1α.

Biol Cell. 2023 Feb 07.

A journey in UPR modeling.

Ilaria Pontisso, Roberto Ornelas Guevara, Laurent Combettes, Geneviève Dupont.

  Protein folding and protein maturation largely occur in the controlled environment of the Endoplasmic Reticulum (ER). Perturbation to the correct functioning of this organelle leads to altered proteostasis and accumulation of misfolded proteins in the ER lumen. This condition is commonly known as ER stress and is appearing as an important contributor in the pathogenesis of several human diseases. Monitoring of the quality control processes is mediated by the Unfolded Protein Response (UPR). This response consists in a complex network of signaling pathways that aim to restore protein folding and ER homeostasis. Conditions in which UPR is not able to overcome ER stress lead to a switch of the UPR signaling program from an adaptive to a pro-apoptotic one, revealing a key role of UPR in modulating cell fate decisions. Because of its high complexity and its involvement in the regulation of different cellular outcomes, UPR has been the center of the development of computational models, which tried to better dissect the role of UPR or of its specific components in several contexts. In this review, we go through the existing mathematical models of UPR. We emphasize how their study contributed to an improved characterization of the role of this intricate response in the modulation of cellular functions. This article is protected by copyright. All rights reserved.

Keywords:  ATF6; ER stress; IRE1; PERK; Unfolded Protein Response; computational model; mathematical model; signaling

DOI:  https://doi.org/10.1111/boc.202200111
Stem Cell Investig. 2023 ;10 1

A selective type of autophagy to maintain glioma stem cell activity.

Khushbu Patel, Esperanza Arias.



Keywords:  Chaperone-mediated autophagy (CMA); glioblastoma; proteostasis; stem cell

DOI:  https://doi.org/10.21037/sci-2022-047
Int J Mol Sci. 2023 Jan 22. pii: 2221. [Epub ahead of print]24(3):

To Kill or to Be Killed: How Does the Battle between the UPS and Autophagy Maintain the Intracellular Homeostasis in Eukaryotes?

Peifeng Yu, Zhihua Hua.

  The ubiquitin-26S proteasome system and autophagy are two major protein degradation machineries encoded in all eukaryotic organisms. While the UPS is responsible for the turnover of short-lived and/or soluble misfolded proteins under normal growth conditions, the autophagy-lysosomal/vacuolar protein degradation machinery is activated under stress conditions to remove long-lived proteins in the forms of aggregates, either soluble or insoluble, in the cytoplasm and damaged organelles. Recent discoveries suggested an integrative function of these two seemly independent systems for maintaining the proteome homeostasis. One such integration is represented by their reciprocal degradation, in which the small 76-amino acid peptide, ubiquitin, plays an important role as the central signaling hub. In this review, we summarized the current knowledge about the activity control of proteasome and autophagosome at their structural organization, biophysical states, and turnover levels from yeast and mammals to plants. Through comprehensive literature studies, we presented puzzling questions that are awaiting to be solved and proposed exciting new research directions that may shed light on the molecular mechanisms underlying the biological function of protein degradation.

Keywords:  autophagy; biophysical state; development; liquid–liquid phase separation; proteasome; protein degradation; stress; ubiquitin; ubiquitylation

DOI:  https://doi.org/10.3390/ijms24032221
Nat Aging. 2022 May;2(5): 379-388

Limited Proteolysis-Mass Spectrometry Reveals Aging-Associated Changes in Cerebrospinal Fluid Protein Abundances and Structures.

Steven R Shuken, Jarod Rutledge, Tal Iram, Patricia Moran Losada, Edward N Wilson, Katrin I Andreasson, Ryan D Leib, Tony Wyss-Coray.

Cerebrospinal fluid (CSF) proteins and their structures have been implicated repeatedly in aging and neurodegenerative diseases. Limited proteolysis-mass spectrometry (LiP-MS) is a method that enables proteome-wide screening for changes in both protein abundance and structure. To screen for novel aging-associated changes in the CSF proteome, we performed LiP-MS on CSF from young and old mice with a modified analysis pipeline. We found 38 protein groups change in abundance with aging, most dominantly immunoglobulins of the IgM subclass. We discovered six high-confidence candidates that appeared to change in structure with aging, of which Kng1, Itih2, Lp-PLA2, and 14-3-3 proteins have binding partners or proteoforms known previously to change in the brain with Alzheimer's disease. Intriguingly, using orthogonal validation by Western blot we found the LiP-MS hit Cd5l forms a covalent complex with IgM in mouse and human CSF whose abundance increases with aging. SOMAmer probe signals for all six LiP-MS hits in human CSF, especially 14-3-3 proteins, significantly associate with several clinical features relevant to cognitive function and neurodegeneration. Together, our findings show that LiP-MS can uncover age-related structural changes in CSF with relevance to neurodegeneration.

DOI: https://doi.org/10.1038/s43587-022-00196-x
Autophagy Rep. 2022 ;1(1): 559-562

DNAJB12 and Hsp70 Mediate Triage of Misfolded Membrane Proteins for Proteasomal versus Lysosomal Degradation.

Andrew Kennedy, Douglas M Cyr.

The endoplasmic reticulum (ER) fills the cell with a continuous network of sealed membrane tubules and sheets. The ER is subdivided into microdomains mediating one-third of total protein biosynthesis, oxidative protein folding, secretion, protein quality control, calcium signaling, marcoautophagy/autophagy, stress sensing, and apoptosis. Defects in ER-calcium homeostasis underlie several diseases. Damage to the ER by misfolded membrane proteins is suppressed by specific HSPA/Hsp70 and DNAJ/Hsp40 chaperone pairs that select intermediates for ubiquitination and ER-associated degradation (ERAD) via the proteasome. The ER-transmembrane Hsp40 chaperone DNAJB12 and HSPA/Hsp70 also target toxic intermediates of misfolded membrane proteins for ER-associated autophagy (ERAA). DNAJB12-HSPA/Hsp70 maintain membrane protein degradation intermediates in detergent-soluble and degradation-competent states. DNAJB12-HSPA/Hsp70 also interact with the autophagy initiation kinase ULK1 on ER tubules containing ERAD-resistant misfolded membrane proteins (ERAD-RMPs). Omegasomes are ER microdomains where the autophagosome precursor or phagophore (PG) forms. ER tubules loaded with ERAD-RMPs enter omegasomes where they are converted into ER-connected PG (ER-PG). The Atg8 (autophagy related 8)-family member GABARAP (GABA type A receptor-associated protein) facilitates transfer of ERAD-RMPs from ER-PGs to autolysosomes (AL) that dock transiently with omegasomes. This article describes a model for DNAJB12-HSPA/Hsp70 action during the conformation-dependent triage in the ER of misfolded membrane proteins for folding versus proteasomal or AL degradation.

DOI: https://doi.org/10.1080/27694127.2022.2139335
Neural Regen Res. 2023 Aug;18(8): 1672-1678

Immortalized hippocampal astrocytes from 3xTg-AD mice, a new model to study disease-related astrocytic dysfunction: a comparative review.

Laura Tapella, Giulia Dematteis, Armando A Genazzani, Massimiliano De Paola, Dmitry Lim.

  Alzheimer's disease (AD) is characterized by complex etiology, long-lasting pathogenesis, and cell-type-specific alterations. Currently, there is no cure for AD, emphasizing the urgent need for a comprehensive understanding of cell-specific pathology. Astrocytes, principal homeostatic cells of the central nervous system, are key players in the pathogenesis of neurodegenerative diseases, including AD. Cellular models greatly facilitate the investigation of cell-specific pathological alterations and the dissection of molecular mechanisms and pathways. Tumor-derived and immortalized astrocytic cell lines, alongside the emerging technology of adult induced pluripotent stem cells, are widely used to study cellular dysfunction in AD. Surprisingly, no stable cell lines were available from genetic mouse AD models. Recently, we established immortalized hippocampal astroglial cell lines from amyloid-β precursor protein/presenilin-1/Tau triple-transgenic (3xTg)-AD mice (denominated as wild type (WT)- and 3Tg-iAstro cells) using retrovirus-mediated transduction of simian virus 40 large T-antigen and propagation without clonal selection, thereby maintaining natural heterogeneity of primary cultures. Several groups have successfully used 3Tg-iAstro cells for single-cell and omics approaches to study astrocytic AD-related alterations of calcium signaling, mitochondrial dysfunctions, disproteostasis, altered homeostatic and signaling support to neurons, and blood-brain barrier models. Here we provide a comparative overview of the most used models to study astrocytes in vitro, such as primary culture, tumor-derived cell lines, immortalized astroglial cell lines, and induced pluripotent stem cell-derived astrocytes. We conclude that immortalized WT- and 3Tg-iAstro cells provide a non-competitive but complementary, low-cost, easy-to-handle, and versatile cellular model for dissection of astrocyte-specific AD-related alterations and preclinical drug discovery.

Keywords:  Alzheimer’s disease; astrocytes immortalization; astroglial Alzheimers’s disease model; blood-brain barrier; calcium signaling; central nervous system homeostasis; disproteostasis; endoplasmic reticulum-mitochondria contacts; induced pluripotent stem cell-derived astrocytes; protein synthesis

DOI:  https://doi.org/10.4103/1673-5374.363192
Biol Psychiatry. 2022 Dec 05. pii: S0006-3223(22)01796-6. [Epub ahead of print]

Excessive Protein Accumulation and Impaired Autophagy in the Hippocampus of Angelman Syndrome Modeled in Mice.

Francesca Aria, Kiran Pandey, Cristina M Alberini.

   BACKGROUND: Angelman syndrome (AS), a neurodevelopmental disorder caused by abnormalities of the 15q11.2-q13.1 chromosome region, is characterized by impairment of cognitive and motor functions, sleep problems, and seizures. How the genetic defects of AS produce these neurological symptoms is unclear. Mice modeling AS (AS mice) accumulate activity-regulated cytoskeleton-associated protein (ARC/ARG3.1), a neuronal immediate early gene (IEG) critical for synaptic plasticity. This accumulation suggests an altered protein metabolism.
METHODS: Focusing on the dorsal hippocampus (dHC), a brain region critical for memory formation and cognitive functions, we assessed levels and tissue distribution of IEGs, de novo protein synthesis, and markers of protein synthesis, endosomes, autophagy, and synaptic functions in AS mice at baseline and following learning. We also tested autophagic flux and memory retention following autophagy-promoting treatment.
RESULTS: AS dHC exhibited accumulation of IEGs ARC, FOS, and EGR1; autophagy proteins MLP3B, SQSTM1, and LAMP1; and reduction of the endosomal protein RAB5A. AS dHC also had increased levels of de novo protein synthesis, impaired autophagic flux with accumulation of autophagosome, and altered synaptic protein levels. Contextual fear conditioning significantly increased levels of IEGs and autophagy proteins, de novo protein synthesis, and autophagic flux in the dHC of normal mice, but not in AS mice. Enhancing autophagy in the dHC alleviated AS-related memory and autophagic flux impairments.
CONCLUSIONS: A major biological deficit of AS brain is a defective protein metabolism, particularly that dynamically regulated by learning, resulting in stalled autophagy and accumulation of neuronal proteins. Activating autophagy ameliorates AS cognitive impairments and dHC protein accumulation.

Keywords:  Angelman syndrome; Autophagy; Hippocampus; Immediate early genes; Mouse; Protein synthesis

DOI:  https://doi.org/10.1016/j.biopsych.2022.11.016
Cells. 2023 Feb 02. pii: 489. [Epub ahead of print]12(3):

Autophagy Meets Aging: An Overview.

Anna Picca, Emanuele Marzetti, Christiaan Leeuwenburgh.

Aging is characterized by biological disarrangements that increase vulnerability to stressors, the development of chronic diseases (e [...].

DOI: https://doi.org/10.3390/cells12030489
J Am Soc Mass Spectrom. 2023 Feb 06.

Structural Proteomic Profiling of Cerebrospinal Fluids to Reveal Novel Conformational Biomarkers for Alzheimer's Disease.

Bin Wang, Xiaofang Zhong, Lauren Fields, Haiyan Lu, Zexin Zhu, Lingjun Li.

  Alzheimer's disease (AD) is the most common representation of dementia, with brain pathological hallmarks of protein abnormal aggregation, such as with amyloid beta and tau protein. It is well established that posttranslational modifications on tau protein, particularly phosphorylation, increase the likelihood of its aggregation and subsequent formation of neurofibrillary tangles, another hallmark of AD. As additional misfolded proteins presumably exist distinctly in AD disease states, which would serve as potential source of AD biomarkers, we used limited proteolysis-coupled with mass spectrometry (LiP-MS) to probe protein structural changes. After optimizing the LiP-MS conditions, we further applied this method to human cerebrospinal fluid specimens collected from healthy control, mild cognitive impairment (MCI), and AD subject groups to characterize proteome-wide misfolding tendencies as a result of disease progression. The fully tryptic peptides embedding LiP sites were compared with the half-tryptic peptides generated from internal cleavage of the same region to determine any structural unfolding or misfolding. We discovered hundreds of significantly up- and down-regulated peptides associated with MCI and AD indicating their potential structural changes in AD progression. Moreover, we detected 53 structurally changed regions in 12 proteins with high confidence between the healthy control and disease groups, illustrating the functional relevance of these proteins with AD progression. These newly discovered conformational biomarker candidates establish valuable future directions for exploring the molecular mechanism of designing therapeutic targets for AD.

Keywords:  Alzheimer’s disease; LiP-MS; conformational biomarker; limited proteolysis; proteomics; structural mass spectrometry

DOI:  https://doi.org/10.1021/jasms.2c00332
Proc Natl Acad Sci U S A. 2023 Feb 14. 120(7): e2215371120

Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms.

Melissa D Stuchell-Brereton, Maxwell I Zimmerman, Justin J Miller, Upasana L Mallimadugula, J Jeremías Incicco, Debjit Roy, Louis G Smith, Jasmine Cubuk, Berevan Baban, Gregory T DeKoster, Carl Frieden, Gregory R Bowman, Andrea Soranno.

  The ε4-allele variant of apolipoprotein E (ApoE4) is the strongest genetic risk factor for Alzheimer's disease, although it only differs from its neutral counterpart ApoE3 by a single amino acid substitution. While ApoE4 influences the formation of plaques and neurofibrillary tangles, the structural determinants of pathogenicity remain undetermined due to limited structural information. Previous studies have led to conflicting models of the C-terminal region positioning with respect to the N-terminal domain across isoforms largely because the data are potentially confounded by the presence of heterogeneous oligomers. Here, we apply a combination of single-molecule spectroscopy and molecular dynamics simulations to construct an atomically detailed model of monomeric ApoE4 and probe the effect of lipid association. Importantly, our approach overcomes previous limitations by allowing us to work at picomolar concentrations where only the monomer is present. Our data reveal that ApoE4 is far more disordered and extended than previously thought and retains significant conformational heterogeneity after binding lipids. Comparing the proximity of the N- and C-terminal domains across the three major isoforms (ApoE4, ApoE3, and ApoE2) suggests that all maintain heterogeneous conformations in their monomeric form, with ApoE2 adopting a slightly more compact ensemble. Overall, these data provide a foundation for understanding how ApoE4 differs from nonpathogenic and protective variants of the protein.

Keywords:  Alzheimer’s disease; apolipoprotein E; protein folding; single-molecule FRET

DOI:  https://doi.org/10.1073/pnas.2215371120
Int J Mol Sci. 2023 Jan 21. pii: 2161. [Epub ahead of print]24(3):

Stabilization of Monomeric Tau Protein by All D-Enantiomeric Peptide Ligands as Therapeutic Strategy for Alzheimer's Disease and Other Tauopathies.

Tim Altendorf, Ian Gering, Beatrix Santiago-Schübel, Selma Aghabashlou Saisan, Gültekin Tamgüney, Markus Tusche, Dominik Honold, Sarah Schemmert, Wolfgang Hoyer, Jeannine Mohrlüder, Dieter Willbold.

  Alzheimer's disease and other tauopathies are the world's leading causes of dementia and memory loss. These diseases are thought to be caused by the misfolding and aggregation of the intracellular tau protein, ultimately leading to neurodegeneration. The tau protein is involved in a multitude of different neurodegenerative diseases. During the onset of tauopathies, tau undergoes structural changes and posttranslational modifications and aggregates into amyloid fibrils that are able to spread with a prion-like behavior. Up to now, there is no therapeutic agent which effectively controls or reverses the disease. Most of the therapeutics that were developed and underwent clinical trials targeted misfolded or aggregated forms of tau. In the current manuscript, we present the selection and characterization of two all D-enantiomeric peptides that bind monomeric tau protein with a low nanomolar KD, stabilize tau in its monomeric intrinsically disordered conformation, and stop the conversion of monomers into aggregates. We show that the effect of the two all D-enantiomeric peptides is strong enough to stop ongoing tau aggregation in vitro and is able to significantly reduce tau fibril assembly in cell culture. Both compounds may serve as new lead components for the development of therapeutic agents against Alzheimer's disease and other tauopathies.

Keywords:  Alzheimer’s disease; all D-enantiomeric peptides; mirror-image phage display; tau aggregation; tauopathies

DOI:  https://doi.org/10.3390/ijms24032161
Nature. 2023 Feb 09.

How a tiny genetic change inflicts old age on young kids.



Keywords:  Medical research

DOI:  https://doi.org/10.1038/d41586-023-00355-z
Neuromolecular Med. 2023 Feb 05.

The Ubiquitin Proteasome System as a Therapeutic Area in Parkinson's Disease.

Kumar Suresh, Michael Mattern, Matthew S Goldberg, Tauseef R Butt.

  Parkinson's disease (PD) is the most common neurodegenerative movement disorder. There are no available therapeutics that slow or halt the progressive loss of dopamine-producing neurons, which underlies the primary clinical symptoms. Currently approved PD drugs can provide symptomatic relief by increasing brain dopamine content or activity; however, the alleviation is temporary, and the effectiveness diminishes with the inevitable progression of neurodegeneration. Discovery and development of disease-modifying neuroprotective therapies has been hampered by insufficient understanding of the root cause of PD-related neurodegeneration. The etiology of PD involves a combination of genetic and environmental factors. Although a single cause has yet to emerge, genetic, cell biological and neuropathological evidence implicates mitochondrial dysfunction and protein aggregation. Postmortem PD brains show pathognomonic Lewy body intraneuronal inclusions composed of aggregated α-synuclein, indicative of failure to degrade misfolded protein. Mutations in the genes that code for α-synuclein, as well as the E3 ubiquitin ligase Parkin, cause rare inherited forms of PD. While many ubiquitin ligases label proteins with ubiquitin chains to mark proteins for degradation by the proteasome, Parkin has been shown to mark dysfunctional mitochondria for degradation by mitophagy. The ubiquitin proteasome system participates in several aspects of the cell's response to mitochondrial damage, affording numerous therapeutic opportunities to augment mitophagy and potentially stop PD progression. This review examines the role and therapeutic potential of such UPS modulators, exemplified by both ubiquitinating and deubiquitinating enzymes.

Keywords:  Mitochondria; Mitophagy; Neurodegeneration; Parkin; Parkinson’s disease; Ubiquitin

DOI:  https://doi.org/10.1007/s12017-023-08738-1
Stem Cell Reports. 2023 Jan 30. pii: S2213-6711(23)00007-3. [Epub ahead of print]

BMP4-SMAD1/5/9-RUNX2 pathway activation inhibits neurogenesis and oligodendrogenesis in Alzheimer's patients' iPSCs in senescence-related conditions.

Daiki Nakatsu, Rina Kunishige, Yuki Taguchi, Naeko Shinozaki-Narikawa, Kishiko Osaka, Kayo Yokomizo, Mami Ishida, Shunsuke Takei, Shoko Yamasaki, Keita Hagiya, Kotaro Hattori, Tadashi Tsukamoto, Masayuki Murata, Fumi Kano.

  In addition to increasing β-amyloid plaque deposition and tau tangle formation, inhibition of neurogenesis has recently been observed in Alzheimer's disease (AD). This study generated a cellular model that recapitulated neurogenesis defects observed in patients with AD, using induced pluripotent stem cell lines derived from sporadic and familial AD (AD iPSCs). AD iPSCs exhibited impaired neuron and oligodendrocyte generation when expression of several senescence markers was induced. Compound screening using these cellular models identified three drugs able to restore neurogenesis, and extensive morphological quantification revealed cell-line- and drug-type-dependent neuronal generation. We also found involvement of elevated Sma- and Mad-related protein 1/5/9 (SMAD1/5/9) phosphorylation and greater Runt-related transcription factor 2 (RUNX2) expression in neurogenesis defects in AD. Moreover, BMP4 was elevated in AD iPSC medium during neural differentiation and cerebrospinal fluid of patients with AD, suggesting a BMP4-SMAD1/5/9-RUNX2 signaling pathway contribution to neurogenesis defects in AD under senescence-related conditions.

Keywords:  Alzheimer’s disease; BMP4; RUNX2; SMAD1/5/9; compound screening; induced pluripotent stem cell (iPSC); morphological analysis; neurogenesis

DOI:  https://doi.org/10.1016/j.stemcr.2023.01.004
bioRxiv. 2023 Jan 23. pii: 2023.01.23.525149. [Epub ahead of print]

Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD.

Sahba Seddighi, Yue A Qi, Anna-Leigh Brown, Oscar G Wilkins, Colleen Bereda, Cedric Belair, Yongjie Zhang, Mercedes Prudencio, Matthew J Keuss, Aditya Khandeshi, Sarah Pickles, Sarah E Hill, James Hawrot, Daniel M Ramos, Hebao Yuan, Jessica Roberts, Erika Kelmer Sacramento, Syed I Shah, Mike A Nalls, Jenn Colon-Mercado, Joel F Reyes, Veronica H Ryan, Matthew P Nelson, Casey Cook, Ziyi Li, Laurel Screven, Justin Y Kwan, Anantharaman Shantaraman, Lingyan Ping, Yuka Koike, Bj Rn Oskarsson, Nathan Staff, Duc M Duong, Aisha Ahmed, Maria Secrier, Jerneg Ule, Steven Jacobson, Jonathan Rohrer, Andrea Malaspina, Jonathan D Glass, Alessandro Ori, Nicholas T Seyfried, Manolis Maragkakis, Leonard Petrucelli, Pietro Fratta, Michael E Ward.

Functional loss of TDP-43, an RNA-binding protein genetically and pathologically linked to ALS and FTD, leads to inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. However, the possibility of de novo protein synthesis from cryptic exon transcripts has not been explored. Here, we show that mRNA transcripts harboring cryptic exons generate de novo proteins both in TDP-43 deficient cellular models and in disease. Using coordinated transcriptomic and proteomic studies of TDP-43 depleted iPSC-derived neurons, we identified numerous peptides that mapped to cryptic exons. Cryptic exons identified in iPSC models were highly predictive of cryptic exons expressed in brains of patients with TDP-43 proteinopathy, including cryptic transcripts that generated de novo proteins. We discovered that inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Finally, we showed that these de novo peptides were present in CSF from patients with ALS. The demonstration of cryptic exon translation suggests new mechanisms for ALS pathophysiology downstream of TDP-43 dysfunction and may provide a strategy for novel biomarker development.
One Sentence Summary: Loss of TDP-43 function results in the expression of de novo proteins from mis-spliced mRNA transcripts.

DOI: https://doi.org/10.1101/2023.01.23.525149
Neurobiol Aging. 2022 Dec 21. pii: S0197-4580(22)00262-7. [Epub ahead of print]124 39-50

Neural atrophy produced by AAV tau injections into hippocampus and anterior cortex of middle-aged mice.

Amber M Tetlow, Brianna M Jackman, Mohammed M Alhadidy, Patricia Muskus, David G Morgan, Marcia N Gordon.

  Animal models of tauopathy help in understanding the role of mutations in tau pathobiology. Here, we used adeno-associated viral (AAV) vectors to administer three tau genetic variants (tauwild-type, tauP301L, and tauR406W) intracranially into 12-month-old C57BL/6Nia mice and collected tissue at 16 months. Vectors designed to express green fluorescent protein controlled for surgical procedures and exogenous protein expression by AAV. The tau genetic variants produced considerably different phenotypes. Tauwild-type and tauP301L caused memory impairments. The tauP301L caused increased amounts of aggregated tau, measured both neurochemically and histologically. Tauwild-type produced elevated levels of soluble tau and phosphorylated tau by ELISA and increased staining for phosphorylated forms of tau histologically. However, only the tauwild-type caused localized atrophy of brain tissue at the sites near the injection. The tauR406W had low protein expression and produced no atrophy or memory impairments. This supports the potential use of AAV expressing tauwild-type in aged mice to examine events leading to neurodegeneration in Alzheimer's disease pathology.

Keywords:  Aging; Mouse models; Neurodegeneration; Tau; Viral models

DOI:  https://doi.org/10.1016/j.neurobiolaging.2022.06.014
Int J Mol Sci. 2023 Feb 02. pii: 2888. [Epub ahead of print]24(3):

Longevity, Centenarians and Modified Cellular Proteodynamics.

Natalia Frankowska, Ewa Bryl, Tamas Fulop, Jacek M Witkowski.

  We have shown before that at least one intracellular proteolytic system seems to be at least as abundant in the peripheral blood lymphocytes of centenarians as in the same cells of young individuals (with the cells of the elderly population showing a significant dip compared to both young and centenarian cohorts). Despite scarce published data, in this review, we tried to answer the question how do different types of cells of longevous people-nonagenarians to (semi)supercentenarians-maintain the quality and quantity of their structural and functional proteins? Specifically, we asked if more robust proteodynamics participate in longevity. We hypothesized that at least some factors controlling the maintenance of cellular proteomes in centenarians will remain at the "young" level (just performing better than in the average elderly). In our quest, we considered multiple aspects of cellular protein maintenance (proteodynamics), including the quality of transcribed DNA, its epigenetic changes, fidelity and quantitative features of transcription of both mRNA and noncoding RNAs, the process of translation, posttranslational modifications leading to maturation and functionalization of nascent proteins, and, finally, multiple facets of the process of elimination of misfolded, aggregated, and otherwise dysfunctional proteins (autophagy). We also included the status of mitochondria, especially production of ATP necessary for protein synthesis and maintenance. We found that with the exception of the latter and of chaperone function, practically all of the considered aspects did show better performance in centenarians than in the average elderly, and most of them approached the levels/activities seen in the cells of young individuals.

Keywords:  autophagy; centenarians; geroproteome; longevity; proteodynamics; proteostasis

DOI:  https://doi.org/10.3390/ijms24032888
Int J Mol Sci. 2023 Jan 29. pii: 2573. [Epub ahead of print]24(3):

Aging Effects on Optic Nerve Neurodegeneration.

Janet Coleman-Belin, Alon Harris, Bo Chen, Jing Zhou, Thomas Ciulla, Alice Verticchio, Gal Antman, Michael Chang, Brent Siesky.

  Common risk factors for many ocular pathologies involve non-pathologic, age-related damage to the optic nerve. Understanding the mechanisms of age-related changes can facilitate targeted treatments for ocular pathologies that arise at any point in life. In this review, we examine these age-related, neurodegenerative changes in the optic nerve, contextualize these changes from the anatomic to the molecular level, and appreciate their relationship with ocular pathophysiology. From simple structural and mechanical changes at the optic nerve head (ONH), to epigenetic and biochemical alterations of tissue and the environment, multiple age-dependent mechanisms drive extracellular matrix (ECM) remodeling, retinal ganglion cell (RGC) loss, and lowered regenerative ability of respective axons. In conjunction, aging decreases the ability of myelin to preserve maximal conductivity, even with "successfully" regenerated axons. Glial cells, however, regeneratively overcompensate and result in a microenvironment that promotes RGC axonal death. Better elucidating optic nerve neurodegeneration remains of interest, specifically investigating human ECM, RGCs, axons, oligodendrocytes, and astrocytes; clarifying the exact processes of aged ocular connective tissue alterations and their ultrastructural impacts; and developing novel technologies and pharmacotherapies that target known genetic, biochemical, matrisome, and neuroinflammatory markers. Management models should account for age-related changes when addressing glaucoma, diabetic retinopathy, and other blinding diseases.

Keywords:  active aging; diabetic retinopathy; embryology; glaucoma; inflammation; neurodegeneration; neuroregeneration; optic nerve; oxidative stress; senescence

DOI:  https://doi.org/10.3390/ijms24032573
Adv Sci (Weinh). 2023 Feb 08. e2205500

Selective Translation of Maternal mRNA by eIF4E1B Controls Oocyte to Embryo Transition.

Jing Guo, Hailian Zhao, Jue Zhang, Xiangjiang Lv, Shen Zhang, Ruibao Su, Wei Zheng, Jing Dai, Fei Meng, Fei Gong, Guangxiu Lu, Yuanchao Xue, Ge Lin.

  Maternal messenger ribonucleic acids (mRNAs) are driven by a highly orchestrated scheme of recruitment to polysomes and translational activation. However, selecting and regulating individual mRNAs for the translation from a competitive pool of mRNAs are little-known processes. This research shows that the maternal eukaryotic translation initiation factor 4e1b (Eif4e1b) expresses during the oocyte-to-embryo transition (OET), and maternal deletion of Eif4e1b leads to multiple defects concerning oogenesis and embryonic developmental competence during OET. The linear amplification of complementary deoxyribonucleic acid (cDNA) ends, and sequencing (LACE-seq) is used to identify the distinct subset of mRNA and its CG-rich binding sites within the 5' untranslated region (UTR) targeted by eIF4E1B. The proteomics analyses indicate that eIF4E1B-specific bound genes show stronger downregulation at the protein level, which further verify a group of proteins that plays a crucial role in oocyte maturation and embryonic developmental competence is insufficiently synthesized in Eif4e1b-cKO oocytes during OET. Moreover, the biochemical results in vitro are combined to further confirm the maternal-specific translation activation model assembled by eIF4E1B and 3'UTR-associated mRNA binding proteins. The findings demonstrate the indispensability of eIF4E1B for selective translation activation in mammalian oocytes and provide a potential network regulated by eIF4E1B in OET.

Keywords:  RNA-binding protein; eIF4E1B; infertility; oocyte to embryo transition; translation

DOI:  https://doi.org/10.1002/advs.202205500
Cells. 2023 Jan 31. pii: 454. [Epub ahead of print]12(3):

The Pursuit of the "Inside" of the Amyloid Hypothesis-Is C99 a Promising Therapeutic Target for Alzheimer's Disease?

Nobumasa Takasugi, Masato Komai, Nanaka Kaneshiro, Atsuya Ikeda, Yuji Kamikubo, Takashi Uehara.

  Aducanumab, co-developed by Eisai (Japan) and Biogen (U.S.), has received Food and Drug Administration approval for treating Alzheimer's disease (AD). In addition, its successor antibody, lecanemab, has been approved. These antibodies target the aggregated form of the small peptide, amyloid-β (Aβ), which accumulates in the patient brain. The "amyloid hypothesis" based therapy that places the aggregation and toxicity of Aβ at the center of the etiology is about to be realized. However, the effects of immunotherapy are still limited, suggesting the need to reconsider this hypothesis. Aβ is produced from a type-I transmembrane protein, Aβ precursor protein (APP). One of the APP metabolites, the 99-amino acids C-terminal fragment (C99, also called βCTF), is a direct precursor of Aβ and accumulates in the AD patient's brain to demonstrate toxicity independent of Aβ. Conventional drug discovery strategies have focused on Aβ toxicity on the "outside" of the neuron, but C99 accumulation might explain the toxicity on the "inside" of the neuron, which was overlooked in the hypothesis. Furthermore, the common region of C99 and Aβ is a promising target for multifunctional AD drugs. This review aimed to outline the nature, metabolism, and impact of C99 on AD pathogenesis and discuss whether it could be a therapeutic target complementing the amyloid hypothesis.

Keywords:  Alzheimer’s disease; BACE1; C99; amyloid beta precursor protein; amyloid-β; autolysosome; endolysosome; vesicular trafficking

DOI:  https://doi.org/10.3390/cells12030454
Cell Rep. 2023 Feb 03. pii: S2211-1247(23)00077-3. [Epub ahead of print]42(2): 112066

MANF regulates neuronal survival and UPR through its ER-located receptor IRE1α.

Vera Kovaleva, Li-Ying Yu, Larisa Ivanova, Olesya Shpironok, Jinhan Nam, Ave Eesmaa, Esa-Pekka Kumpula, Sven Sakson, Urve Toots, Mart Ustav, Juha T Huiskonen, Merja H Voutilainen, Päivi Lindholm, Mati Karelson, Mart Saarma.

  Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-located protein with cytoprotective effects in neurons and pancreatic β cells in vitro and in models of neurodegeneration and diabetes in vivo. However, the exact mode of MANF action has remained elusive. Here, we show that MANF directly interacts with the ER transmembrane unfolded protein response (UPR) sensor IRE1α, and we identify the binding interface between MANF and IRE1α. The expression of wild-type MANF, but not its IRE1α binding-deficient mutant, attenuates UPR signaling by decreasing IRE1α oligomerization; phosphorylation; splicing of Xbp1, Atf6, and Txnip levels; and protecting neurons from ER stress-induced death. MANF-IRE1α interaction and not MANF-BiP interaction is crucial for MANF pro-survival activity in neurons in vitro and is required to protect dopamine neurons in an animal model of Parkinson's disease. Our data show IRE1α as an intracellular receptor for MANF and regulator of neuronal survival.

Keywords:  BiP; CP: Molecular biology; CP: Neuroscience; ER stress; IRE1α; MANF; PD; Parkinson’s disease; UPR; mesencephalic astrocyte-derived neurotrophic factor; neuronal survival; unfolded protein response

DOI:  https://doi.org/10.1016/j.celrep.2023.112066