bims-axbals 2024-01-21 papers

bims-axbals

Biomed News

on Axonal Biology and ALS

Issue of 2024‒01‒21
thirty-one papers selected by
TJ Krzystek, ALS Therapy Development Institute

Mutations in FUS lead to synaptic dysregulation in ALS-iPSC derived neurons.
Icariin prevents methylmercury-induced experimental neurotoxicity: Evidence from cerebrospinal fluid, blood plasma, brain samples, and in-silico investigations.
Intracellular delivery of Parkin-RING0-based fragments corrects Parkin-induced mitochondrial dysfunction through interaction with SLP-2.
Metformin ameliorates mitochondrial damage induced by C9orf72 poly(GR) via upregulating AKT phosphorylation.
USP30 inhibition induces mitophagy and reduces oxidative stress in parkin-deficient human neurons.
An optogenetic cell therapy to restore control of target muscles in an aggressive mouse model of amyotrophic lateral sclerosis.
The shared ancestry between the C9orf72 hexanucleotide repeat expansion and intermediate-length alleles using haplotype sharing trees and HAPTK.
TMEM106B core deposition associates with TDP-43 pathology and is increased in risk SNP carriers for frontotemporal dementia.
EphrinB2 knockdown in cervical spinal cord preserves diaphragm innervation in a mutant SOD1 mouse model of ALS.
Analysis of α-syn and parkin interaction in mediating neuronal death in Drosophila model of Parkinson's disease.
Towards a Machine Learning Empowered Prognostic Model for Predicting Disease Progression for Amyotrophic Lateral Sclerosis.
Computer simulations predict the impact of neuronal atrophy on the calcium dynamics in Huntington's disease.
SARS-CoV-2 infection causes dopaminergic neuron senescence.
Balancing act of small GTPases downstream of plexin-A4 signaling motifs promotes dendrite elaboration in mammalian cortical neurons.
CD73 contributes to the pathogenesis of fusion-negative rhabdomyosarcoma through the purinergic signaling pathway.
SERCA1 Overexpression in Skeletal Muscle Attenuates Muscle Atrophy and Improves Motor Function in a Mouse Model of ALS.
Multi-level profiling unravels mitochondrial dysfunction in myotonic dystrophy type 2.
Hypomorphic human SEL1L and HRD1 variants uncouple multilayered ER-associated degradation machinery.
Notch receptor-ligand binding facilitates extracellular vesicle-mediated neuron-to-neuron communication.
Manganese disrupts the maturation and degradation of axonal autophagosome leading to hippocampal synaptic toxicity in mice via the activation of LRRK2 on phosphorylation of Rab10.
The V-ATPase-ATG16L1 axis recruits LRRK2 to facilitate the lysosomal stress response.
Transmission-selective muscle pathology induced by the active propagation of mutant huntingtin across the human neuromuscular synapse.
Mitochondrial dysfunction in neurodegenerative disorders.
Static magnetic stimulation induces structural plasticity at the axon initial segment of inhibitory cortical neurons.
Telomere dynamics in human pluripotent stem cells.
Proteomics provides insights into the theranostic potential of extracellular vesicles.
TDP-43 was Involved in Radiation-induced Neuronal Damage and May Not Through the BDNF/TrkB Pathway.
Mo' m1A, mo' problems.
Phase separation as a possible mechanism for dosage sensitivity.
Characterising the Protein-Protein Interaction Between MDM2 and 14-3-3σ; Proof of Concept for Small Molecule Stabilisation.
Microinstrumentation for Brain Organoids.

Stem Cell Reports. 2024 Jan 01. pii: S2213-6711(23)00500-3. [Epub ahead of print]

Mutations in FUS lead to synaptic dysregulation in ALS-iPSC derived neurons.

Carole Shum, Erin C Hedges, Joseph Allison, Youn-Bok Lee, Natalia Arias, Graham Cocks, Siddharthan Chandran, Marc-David Ruepp, Christopher E Shaw, Agnes L Nishimura.

  Amyotrophic lateral sclerosis (ALS) is a fatal, adult-onset neurodegenerative disorder characterized by progressive muscular weakness due to the selective loss of motor neurons. Mutations in the gene Fused in Sarcoma (FUS) were identified as one cause of ALS. Here, we report that mutations in FUS lead to upregulation of synaptic proteins, increasing synaptic activity and abnormal release of vesicles at the synaptic cleft. Consequently, FUS-ALS neurons showed greater vulnerability to glutamate excitotoxicity, which raised neuronal swellings (varicose neurites) and led to neuronal death. Fragile X mental retardation protein (FMRP) is an RNA-binding protein known to regulate synaptic protein translation, and its expression is reduced in the FUS-ALS lines. Collectively, our data suggest that a reduction of FMRP levels alters the synaptic protein dynamics, leading to synaptic dysfunction and glutamate excitotoxicity. Here, we present a mechanistic hypothesis linking dysregulation of peripheral translation with synaptic vulnerability in the pathogenesis of FUS-ALS.

Keywords:  ALS; FMRP; FUS; amyotrophic lateral sclerosis; disease modelling; fragile X mental retardation protein; fused in sarcoma; iPSCs; induced pluripotent stem cells; neuronal degeneration; synaptic dysfunction

DOI:  https://doi.org/10.1016/j.stemcr.2023.12.007
Heliyon. 2024 Jan 15. 10(1): e24050

Icariin prevents methylmercury-induced experimental neurotoxicity: Evidence from cerebrospinal fluid, blood plasma, brain samples, and in-silico investigations.

Sarthak Sharma, Sidharth Mehan, Zuber Khan, Ghanshyam Das Gupta, Acharan S Narula.

  Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that causes significant neurodegeneration. Methylmercury (MeHg+) is a neurotoxin that induces axonal neurodegeneration and motor nerve degeneration by destroying oligodendrocytes, degenerating white matter, inducing apoptosis, excitotoxicity, and reducing myelin basic protein (MBP). This study examines the inhibition of SIRT-1 (silence information regulator 1), Nrf-2 (nuclear factor E2-related factor 2), HO-1 (heme oxygenase 1), and TDP-43 (TAR-DNA-binding protein 43) accumulation in the context of ALS, as well as the modulation of these proteins by icariin (15 and 30 mg/kg, orally), a glycoside flavonoid with neuroprotective properties. Neuroprotective icariin activates SIRT-1, Nrf-2, and HO-1, mitigating inflammation and neuronal injury in neurodegenerative disorders. In-vivo and in-silico testing of experimental ALS models confirmed icariin efficacy in modulating these cellular targets. The addition of sirtinol 10 mg/kg, an inhibitor of SIRT-1, helps determine the effectiveness of icariin. In this study, we also examined neurobehavioral, neurochemical, histopathological, and LFB (Luxol fast blue) markers in various biological samples, including Cerebrospinal fluid (CSF), blood plasma, and brain homogenates (Cerebral Cortex, Hippocampus, Striatum, mid-brain, and Cerebellum). These results demonstrate that the administration of icariin ameliorates experimental ALS and that the mechanism underlying these benefits is likely related to regulating the SIRT-1, Nrf-2, and HO-1 signaling pathways.

Keywords:  ALS; Demyelination; Icariin; Methylmercury; Neuroinflammation; Neuroprotection; Oligodendrocytes

DOI:  https://doi.org/10.1016/j.heliyon.2024.e24050
J Transl Med. 2024 Jan 16. 22(1): 59

Intracellular delivery of Parkin-RING0-based fragments corrects Parkin-induced mitochondrial dysfunction through interaction with SLP-2.

Alessandra Zanon, Marianna Guida, Alexandros A Lavdas, Corrado Corti, Maria Paulina Castelo Rueda, Alessandro Negro, Peter P Pramstaller, Francisco S Domingues, Andrew A Hicks, Irene Pichler.

  BACKGROUND: Loss-of-function mutations in the PRKN gene, encoding Parkin, are the most common cause of autosomal recessive Parkinson's disease (PD). We have previously identified mitoch ondrial Stomatin-like protein 2 (SLP-2), which functions in the assembly of respiratory chain proteins, as a Parkin-binding protein. Selective knockdown of either Parkin or SLP-2 led to reduced mitochondrial and neuronal function in neuronal cells and Drosophila, where a double knockdown led to a further worsening of Parkin-deficiency phenotypes. Here, we investigated the minimal Parkin region involved in the Parkin-SLP-2 interaction and explored the ability of Parkin-fragments and peptides from this minimal region to restore mitochondrial function.METHODS: In fibroblasts, human induced pluripotent stem cell (hiPSC)-derived neurons, and neuroblastoma cells the interaction between Parkin and SLP-2 was investigated, and the Parkin domain responsible for the binding to SLP-2 was mapped. High resolution respirometry, immunofluorescence analysis and live imaging were used to analyze mitochondrial function.
RESULTS: Using a proximity ligation assay, we quantitatively assessed the Parkin-SLP-2 interaction in skin fibroblasts and hiPSC-derived neurons. When PD-associated PRKN mutations were present, we detected a significantly reduced interaction between the two proteins. We found a preferential binding of SLP-2 to the N-terminal part of Parkin, with a highest affinity for the RING0 domain. Computational modeling based on the crystal structure of Parkin protein predicted several potential binding sites for SLP-2 within the Parkin RING0 domain. Amongst these, three binding sites were observed to overlap with natural PD-causing missense mutations, which we demonstrated interfere substantially with the binding of Parkin to SLP-2. Finally, delivery of the isolated Parkin RING0 domain and a Parkin mini-peptide, conjugated to cell-permeant and mitochondrial transporters, rescued compromised mitochondrial function in Parkin-deficient neuroblastoma cells and hiPSC-derived neurons with endogenous, disease causing PRKN mutations.
CONCLUSIONS: These findings place further emphasis on the importance of the protein-protein interaction between Parkin and SLP-2 for the maintenance of optimal mitochondrial function. The possibility of restoring an abolished binding to SLP-2 by delivering the Parkin RING0 domain or the Parkin mini-peptide involved in this specific protein-protein interaction into cells might represent a novel organelle-specific therapeutic approach for correcting mitochondrial dysfunction in Parkin-linked PD.

Keywords:  Mitochondria; Parkin; Parkin mini-peptide; Parkinson′s disease; SLP-2

DOI:  https://doi.org/10.1186/s12967-024-04850-3
J Cell Biochem. 2024 Jan 17.

Metformin ameliorates mitochondrial damage induced by C9orf72 poly(GR) via upregulating AKT phosphorylation.

Yiyuan Feng, Zhongyun Xu, Hongfu Jin, Yuanyuan Chen, Chenglai Fu, Yu Zhang, Yafu Yin, Hui Wang, Weiwei Cheng.

  Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are devastating neurodegenerative diseases with no effective cure. GGGGCC repeat expansion in C9orf72 is the most common genetic cause of both ALS and FTD. A key pathological feature of C9orf72 related ALS/FTD is the presence of abnormal dipeptide repeat proteins translated from GGGGCC repeat expansion, including poly Glycine-Arginine (GR). In this study, we observed that (GR)50 conferred significant mitochondria damage and cytotoxicity. Metformin, the most widely used clinical drug, successfully relieved (GR)50 induced mitochondrial damage and inhibited (GR)50 related cytotoxicity. Further research revealed metformin effectively restored mitochondrial function by upregulating AKT phosphorylation in (GR)50 expressed cells. Taken together, our results indicated restoring mitochondrial function with metformin may be a rational therapeutic strategy to reduce poly(GR) toxicity in C9orf72 ALS/FTD patients.

Keywords:  AKT; C9ALS/FTD; metformin; mitochondria; poly GR

DOI:  https://doi.org/10.1002/jcb.30526
Cell Death Dis. 2024 Jan 15. 15(1): 52

USP30 inhibition induces mitophagy and reduces oxidative stress in parkin-deficient human neurons.

Justyna Okarmus, Jette Bach Agergaard, Tina C Stummann, Henriette Haukedal, Malene Ambjørn, Kristine K Freude, Karina Fog, Morten Meyer.

Ubiquitination of mitochondrial proteins plays an important role in the cellular regulation of mitophagy. The E3 ubiquitin ligase parkin (encoded by PARK2) and the ubiquitin-specific protease 30 (USP30) have both been reported to regulate the ubiquitination of outer mitochondrial proteins and thereby mitophagy. Loss of E3 ligase activity is thought to be pathogenic in both sporadic and inherited Parkinson's disease (PD), with loss-of-function mutations in PARK2 being the most frequent cause of autosomal recessive PD. The aim of the present study was to evaluate whether mitophagy induced by USP30 inhibition provides a functional rescue in isogenic human induced pluripotent stem cell-derived dopaminergic neurons with and without PARK2 knockout (KO). Our data show that healthy neurons responded to CCCP-induced mitochondrial damage by clearing the impaired mitochondria and that this process was accelerated by USP30 inhibition. Parkin-deficient neurons showed an impaired mitophagic response to the CCCP challenge, although mitochondrial ubiquitination was enhanced. USP30 inhibition promoted mitophagy in PARK2 KO neurons, independently of whether left in basal conditions or treated with CCCP. In PARK2 KO, as in control neurons, USP30 inhibition balanced oxidative stress levels by reducing excessive production of reactive oxygen species. Interestingly, non-dopaminergic neurons were the main driver of the beneficial effects of USP30 inhibition. Our findings demonstrate that USP30 inhibition is a promising approach to boost mitophagy and improve cellular health, also in parkin-deficient cells, and support the potential relevance of USP30 inhibitors as a novel therapeutic approach in diseases with a need to combat neuronal stress mediated by impaired mitochondria.

DOI: https://doi.org/10.1038/s41419-024-06439-6
Elife. 2024 Jan 18. pii: RP88250. [Epub ahead of print]12

An optogenetic cell therapy to restore control of target muscles in an aggressive mouse model of amyotrophic lateral sclerosis.

J Barney Bryson, Alexandra Kourgiantaki, Dai Jiang, Andreas Demosthenous, Linda Greensmith.

  Breakdown of neuromuscular junctions (NMJs) is an early pathological hallmark of amyotrophic lateral sclerosis (ALS) that blocks neuromuscular transmission, leading to muscle weakness, paralysis and, ultimately, premature death. Currently, no therapies exist that can prevent progressive motor neuron degeneration, muscle denervation, or paralysis in ALS. Here, we report important advances in the development of an optogenetic, neural replacement strategy that can effectively restore innervation of severely affected skeletal muscles in the aggressive SOD1G93A mouse model of ALS, thus providing an interface to selectively control the function of targeted muscles using optical stimulation. We also identify a specific approach to confer complete survival of allogeneic replacement motor neurons. Furthermore, we demonstrate that an optical stimulation training paradigm can prevent atrophy of reinnervated muscle fibers and results in a tenfold increase in optically evoked contractile force. Together, these advances pave the way for an assistive therapy that could benefit all ALS patients.

Keywords:  ALS; Amyotrophic Lateral Sclerosis; cell transplant; motor neurons; mouse; optogenetics; paralysis; regenerative medicine; stem cells

DOI:  https://doi.org/10.7554/eLife.88250
Am J Hum Genet. 2024 Jan 09. pii: S0002-9297(23)00451-2. [Epub ahead of print]

The shared ancestry between the C9orf72 hexanucleotide repeat expansion and intermediate-length alleles using haplotype sharing trees and HAPTK.

Osma S Rautila, Karri Kaivola, Harri Rautila, Laura Hokkanen, Jyrki Launes, Timo E Strandberg, Hannu Laaksovirta, Johanna Palmio, Pentti J Tienari.

  The C9orf72 hexanucleotide repeat expansion (HRE) is a common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The inheritance is autosomal dominant, but a high proportion of subjects with the mutation are simplex cases. One possible explanation is de novo expansions of unstable intermediate-length alleles (IAs). Using haplotype sharing trees (HSTs) with the haplotype analysis tool kit (HAPTK), we derived majority-based ancestral haplotypes of HRE samples and discovered that IAs containing ≥18-20 repeats share large haplotypes in common with the HRE. Using HSTs of HRE and IA samples, we demonstrate that the longer IA haplotypes are largely indistinguishable from HRE haplotypes and that several ≥18-20 IA haplotypes share over 5 Mb (>600 markers) haplotypes in common with the HRE haplotypes. These analysis tools allow physical understanding of the haplotype blocks shared with the majority-based ancestral haplotype. Our results demonstrate that the haplotypes with longer IAs belong to the same pool of haplotypes as the HRE and suggest that longer IAs represent potential premutation alleles.

Keywords:  ALS; C9orf72; FTD; GGGGCC; HAPTK; HST; haplotype sharing tree; repeat disorders; repeat expansion

DOI:  https://doi.org/10.1016/j.ajhg.2023.12.019
Sci Transl Med. 2024 Jan 17. 16(730): eadf9735

TMEM106B core deposition associates with TDP-43 pathology and is increased in risk SNP carriers for frontotemporal dementia.

Jordan D Marks, Virginia Estades Ayuso, Yari Carlomagno, Mei Yue, Tiffany W Todd, Ying Hao, Ziyi Li, Zachary T McEachin, Anantharaman Shantaraman, Duc M Duong, Lillian M Daughrity, Karen Jansen-West, Wei Shao, Anna Calliari, Jesus Gonzalez Bejarano, Michael DeTure, Bailey Rawlinson, Monica Castanedes Casey, Meredith T Lilley, Megan H Donahue, Vidhya Maheswari Jawahar, Bradley F Boeve, Ronald C Petersen, David S Knopman, Björn Oskarsson, Neill R Graff-Radford, Zbigniew K Wszolek, Dennis W Dickson, Keith A Josephs, Yue A Qi, Nicholas T Seyfried, Michael E Ward, Yong-Jie Zhang, Mercedes Prudencio, Leonard Petrucelli, Casey N Cook.

Genetic variation at the transmembrane protein 106B gene (TMEM106B) has been linked to risk of frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) through an unknown mechanism. We found that presence of the TMEM106B rs3173615 protective genotype was associated with longer survival after symptom onset in a postmortem FTLD-TDP cohort, suggesting a slower disease course. The seminal discovery that filaments derived from TMEM106B is a common feature in aging and, across a range of neurodegenerative disorders, suggests that genetic variants in TMEM106B could modulate disease risk and progression through modulating TMEM106B aggregation. To explore this possibility and assess the pathological relevance of TMEM106B accumulation, we generated a new antibody targeting the TMEM106B filament core sequence. Analysis of postmortem samples revealed that the TMEM106B rs3173615 risk allele was associated with higher TMEM106B core accumulation in patients with FTLD-TDP. In contrast, minimal TMEM106B core deposition was detected in carriers of the protective allele. Although the abundance of monomeric full-length TMEM106B was unchanged, carriers of the protective genotype exhibited an increase in dimeric full-length TMEM106B. Increased TMEM106B core deposition was also associated with enhanced TDP-43 dysfunction, and interactome data suggested a role for TMEM106B core filaments in impaired RNA transport, local translation, and endolysosomal function in FTLD-TDP. Overall, these findings suggest that prevention of TMEM106B core accumulation is central to the mechanism by which the TMEM106B protective haplotype reduces disease risk and slows progression.

DOI: https://doi.org/10.1126/scitranslmed.adf9735
Elife. 2024 Jan 15. pii: RP89298. [Epub ahead of print]12

EphrinB2 knockdown in cervical spinal cord preserves diaphragm innervation in a mutant SOD1 mouse model of ALS.

Mark W Urban, Brittany A Charsar, Nicolette M Heinsinger, Shashirekha S Markandaiah, Lindsay Sprimont, Wei Zhou, Eric V Brown, Nathan T Henderson, Samantha J Thomas, Biswarup Ghosh, Rachel E Cain, Davide Trotti, Piera Pasinelli, Megan C Wright, Matthew B Dalva, Angelo C Lepore.

  Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by motor neuron loss. Importantly, non-neuronal cell types such as astrocytes also play significant roles in disease pathogenesis. However, mechanisms of astrocyte contribution to ALS remain incompletely understood. Astrocyte involvement suggests that transcellular signaling may play a role in disease. We examined contribution of transmembrane signaling molecule ephrinB2 to ALS pathogenesis, in particular its role in driving motor neuron damage by spinal cord astrocytes. In symptomatic SOD1G93A mice (a well-established ALS model), ephrinB2 expression was dramatically increased in ventral horn astrocytes. Reducing ephrinB2 in the cervical spinal cord ventral horn via viral-mediated shRNA delivery reduced motor neuron loss and preserved respiratory function by maintaining phrenic motor neuron innervation of diaphragm. EphrinB2 expression was also elevated in human ALS spinal cord. These findings implicate ephrinB2 upregulation as both a transcellular signaling mechanism in mutant SOD1-associated ALS and a promising therapeutic target.

Keywords:  ALS; astrocyte; ephrin; human; motor neuron; mouse; neuroscience; respiratory

DOI:  https://doi.org/10.7554/eLife.89298
Front Cell Neurosci. 2023 ;17 1295805

Analysis of α-syn and parkin interaction in mediating neuronal death in Drosophila model of Parkinson's disease.

Sonia Narwal, Amit Singh, Meghana Tare.

  One of the hallmarks of Parkinson's Disease (PD) is aggregation of incorrectly folded α-synuclein (SNCA) protein resulting in selective death of dopaminergic neurons. Another form of PD is characterized by the loss-of-function of an E3-ubiquitin ligase, parkin. Mutations in SNCA and parkin result in impaired mitochondrial morphology, causing loss of dopaminergic neurons. Despite extensive research on the individual effects of SNCA and parkin, their interactions in dopaminergic neurons remain understudied. Here we employ Drosophila model to study the effect of collective overexpression of SNCA along with the downregulation of parkin in the dopaminergic neurons of the posterior brain. We found that overexpression of SNCA along with downregulation of parkin causes a reduction in the number of dopaminergic neuronal clusters in the posterior region of the adult brain, which is manifested as progressive locomotor dysfunction. Overexpression of SNCA and downregulation of parkin collectively results in altered mitochondrial morphology in a cluster-specific manner, only in a subset of dopaminergic neurons of the brain. Further, we found that SNCA overexpression causes transcriptional downregulation of parkin. However, this downregulation is not further enhanced upon collective SNCA overexpression and parkin downregulation. This suggests that the interactions of SNCA and parkin may not be additive. Our study thus provides insights into a potential link between α-synuclein and parkin interactions. These interactions result in altered mitochondrial morphology in a cluster-specific manner for dopaminergic neurons over a time, thus unraveling the molecular interactions involved in the etiology of Parkinson's Disease.

Keywords:  Drosophila melanogaster; Parkinson's disease; dopaminergic neurons; mitochondrial morphology; parkin; tyrosine hydroxylase; α-synuclein

DOI:  https://doi.org/10.3389/fncel.2023.1295805
AMIA Annu Symp Proc. 2023 ;2023 718-725

Towards a Machine Learning Empowered Prognostic Model for Predicting Disease Progression for Amyotrophic Lateral Sclerosis.

Pooled Resource Open-Access ALS Clinical Trials Consortium*

Amyotrophic lateral sclerosis (ALS) is a rare and devastating neurodegenerative disorder that is highly heterogeneous and invariably fatal. Due to the unpredictable nature of its progression, accurate tools and algorithms are needed to predict disease progression and improve patient care. To address this need, we developed and compared an extensive set of screener-learner machine learning models to accurately predict the ALS Function-Rating-Scale (ALSFRS) score reduction between 3 and 12 months, by paring 5 state-of-arts feature selection algorithms with 17 predictive models and 4 ensemble models using the publicly available Pooled Open Access Clinical Trials Database (PRO-ACT). Our experiment showed promising results with the blender-type ensemble model achieving the best prediction accuracy and highest prognostic potential.
PNAS Nexus. 2024 Jan;3(1): pgad443

Computer simulations predict the impact of neuronal atrophy on the calcium dynamics in Huntington's disease.

Sara Sameni, Thomas M Bartol, Jody Corey-Bloom, Terrence J Sejnowski.

  One of the early hallmarks of Huntington's disease (HD) is neuronal cell atrophy, especially in the striatum, underlying motor dysfunction in HD. Here using a computer model, we have predicted the impact of cell shrinkage on calcium dynamics at the cellular level. Our model indicates that as cytosolic volume decreases, the amplitude of calcium transients increases and the endoplasmic reticulum (ER) becomes more leaky due to calcium-induced calcium release and a "toxic" positive feedback mechanism mediated by ryanodine receptors that greatly increases calcium release into the cytosol. The excessive calcium release from ER saturates the calcium buffering capacity of calbindin and forces further accumulation of free calcium in the cytosol and cellular compartments including mitochondria. This leads to imbalance of calcium in both cytosol and ER regions. Excessive calcium accumulation in the cytosol can damage the mitochondria resulting in metabolic dysfunction in the cell consistent with the pathology of HD. Our computational model points toward potential drug targets and can accelerate and greatly help the experimental studies of HD paving the way for treatments of patients suffering from HD.

Keywords:  Huntington's disease; aging; biomarkers; calcium metabolism; computational model

DOI:  https://doi.org/10.1093/pnasnexus/pgad443
Cell Stem Cell. 2024 Jan 10. pii: S1934-5909(23)00442-3. [Epub ahead of print]

SARS-CoV-2 infection causes dopaminergic neuron senescence.

Liuliu Yang, Tae Wan Kim, Yuling Han, Manoj S Nair, Oliver Harschnitz, Jiajun Zhu, Pengfei Wang, So Yeon Koo, Lauretta A Lacko, Vasuretha Chandar, Yaron Bram, Tuo Zhang, Wei Zhang, Feng He, Chendong Pan, Junjie Wu, Yaoxing Huang, Todd Evans, Paul van der Valk, Maarten J Titulaer, Jochem K H Spoor, Robert L Furler O'Brien, Marianna Bugiani, Wilma D J Van de Berg, Robert E Schwartz, David D Ho, Lorenz Studer, Shuibing Chen.

  COVID-19 patients commonly present with signs of central nervous system and/or peripheral nervous system dysfunction. Here, we show that midbrain dopamine (DA) neurons derived from human pluripotent stem cells (hPSCs) are selectively susceptible and permissive to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. SARS-CoV-2 infection of DA neurons triggers an inflammatory and cellular senescence response. High-throughput screening in hPSC-derived DA neurons identified several FDA-approved drugs that can rescue the cellular senescence phenotype by preventing SARS-CoV-2 infection. We also identified the inflammatory and cellular senescence signature and low levels of SARS-CoV-2 transcripts in human substantia nigra tissue of COVID-19 patients. Furthermore, we observed reduced numbers of neuromelanin+ and tyrosine-hydroxylase (TH)+ DA neurons and fibers in a cohort of severe COVID-19 patients. Our findings demonstrate that hPSC-derived DA neurons are susceptible to SARS-CoV-2, identify candidate neuroprotective drugs for COVID-19 patients, and suggest the need for careful, long-term monitoring of neurological problems in COVID-19 patients.

Keywords:  SARS-CoV-2; dopaminergic neuron; human pluripotent stem cells; senescence

DOI:  https://doi.org/10.1016/j.stem.2023.12.012
Sci Signal. 2024 Jan 16. 17(819): eadh7673

Balancing act of small GTPases downstream of plexin-A4 signaling motifs promotes dendrite elaboration in mammalian cortical neurons.

Oday Abushalbaq, Jiyeon Baek, Avraham Yaron, Tracy S Tran.

The precise development of neuronal morphologies is crucial to the establishment of synaptic circuits and, ultimately, proper brain function. Signaling by the axon guidance cue semaphorin 3A (Sema3A) and its receptor complex of neuropilin-1 and plexin-A4 has multifunctional outcomes in neuronal morphogenesis. Downstream activation of the RhoGEF FARP2 through interaction with the lysine-arginine-lysine motif of plexin-A4 and consequent activation of the small GTPase Rac1 promotes dendrite arborization, but this pathway is dispensable for axon repulsion. Here, we investigated the interplay of small GTPase signaling mechanisms underlying Sema3A-mediated dendritic elaboration in mouse layer V cortical neurons in vitro and in vivo. Sema3A promoted the binding of the small GTPase Rnd1 to the amino acid motif lysine-valine-serine (LVS) in the cytoplasmic domain of plexin-A4. Rnd1 inhibited the activity of the small GTPase RhoA and the kinase ROCK, thus supporting the activity of the GTPase Rac1, which permitted the growth and branching of dendrites. Overexpression of a dominant-negative RhoA, a constitutively active Rac1, or the pharmacological inhibition of ROCK activity rescued defects in dendritic elaboration in neurons expressing a plexin-A4 mutant lacking the LVS motif. Our findings provide insights into the previously unappreciated balancing act between Rho and Rac signaling downstream of specific motifs in plexin-A4 to mediate Sema3A-dependent dendritic elaboration in mammalian cortical neuron development.

DOI: https://doi.org/10.1126/scisignal.adh7673
Proc Natl Acad Sci U S A. 2024 Jan 23. 121(4): e2315925121

CD73 contributes to the pathogenesis of fusion-negative rhabdomyosarcoma through the purinergic signaling pathway.

Karla Cano Hernandez, Akansha M Shah, Victor A Lopez, Vincent S Tagliabracci, Kenian Chen, Lin Xu, Rhonda Bassel-Duby, Eric N Olson, Ning Liu.

  Rhabdomyosarcoma (RMS) is the most common type of soft tissue sarcoma in children and adolescents. Fusion-negative RMS (FN-RMS) accounts for more than 80% of all RMS cases. The long-term event-free survival rate for patients with high-grade FN-RMS is below 30%, highlighting the need for improved therapeutic strategies. CD73 is a 5' ectonucleotidase that hydrolyzes AMP to adenosine and regulates the purinergic signaling pathway. We found that CD73 is elevated in FN-RMS tumors that express high levels of TWIST2. While high expression of CD73 contributes to the pathogenesis of multiple cancers, its role in FN-RMS has not been investigated. We found that CD73 knockdown decreased FN-RMS cell growth while up-regulating the myogenic differentiation program. Moreover, mutation of the catalytic residues of CD73 rendered the protein enzymatically inactive and abolished its ability to stimulate FN-RMS growth. Overexpression of wildtype CD73, but not the catalytically inactive mutant, in CD73 knockdown FN-RMS cells restored their growth capacity. Likewise, treatment with an adenosine receptor A2A-B agonist partially rescued FN-RMS cell proliferation and bypassed the CD73 knockdown defective growth phenotype. These results demonstrate that the catalytic activity of CD73 contributes to the pathogenic growth of FN-RMS through the activation of the purinergic signaling pathway. Therefore, targeting CD73 and the purinergic signaling pathway represents a potential therapeutic approach for FN-RMS patients.

Keywords:  Cell biology; cell signaling; pediatric cancer; sarcoma

DOI:  https://doi.org/10.1073/pnas.2315925121
J Neuromuscul Dis. 2024 Jan 10.

SERCA1 Overexpression in Skeletal Muscle Attenuates Muscle Atrophy and Improves Motor Function in a Mouse Model of ALS.

Davi A G Mázala, Dapeng Chen, Eva R Chin.

  BACKGROUND: Amyotrophic lateral sclerosis (ALS) is characterized by progressive loss of muscle mass and muscle function. Previous work from our lab demonstrated that skeletal muscles from a mouse model of ALS show elevated intracellular calcium (Ca2 +) levels and heightened endoplasmic reticulum (ER) stress.OBJECTIVE: To investigate whether overexpression of sarcoplasmic reticulum (SR) Ca2 + ATPase 1 (SERCA1) in skeletal muscle would improve intracellular Ca2 + handling, attenuate ER stress, and improve motor function ALS transgenic mice.
METHODS: B6SJL-Tg (SOD1*G93A)1Gur/J (ALS-Tg) mice were bred with skeletal muscle α-actinin SERCA1 overexpressing mice to generate wild type (WT), SERCA1 overexpression (WT/+SERCA1), ALS-Tg, and SERCA1 overexpressing ALS-Tg (ALS-Tg/+SERCA1) mice. Motor function (grip test) was assessed weekly and skeletal muscles were harvested at 16 weeks of age to evaluate muscle mass, SR-Ca2 + ATPase activity, levels of SERCA1 and ER stress proteins - protein disulfide isomerase (PDI), Grp78/BiP, and C/EBP homologous protein (CHOP). Single muscle fibers were also isolated from the flexor digitorum brevis muscle to assess changes in resting and peak Fura-2 ratios.
RESULTS: ALS-Tg/+SERCA1 mice showed improved motor function, delayed onset of disease, and improved muscle mass compared to ALS-Tg. Further, ALS-Tg/+SERCA1 mice returned levels of SERCA1 protein and SR-Ca2 + ATPase activity back to levels in WT mice. Unexpectedly, SERCA-1 overexpression increased levels of the ER stress maker Grp78/BiP in both WT and ALS-Tg mice, while not altering protein levels of PDI or CHOP. Lastly, single muscle fibers from ALS-Tg/+SERCA1 had similar resting but lower peak Fura-2 levels (at 30 Hz and 100 Hz) compared to ALS-Tg mice.
CONCLUSIONS: These data indicate that SERCA1 overexpression attenuates the progressive loss of muscle mass and maintains motor function in ALS-Tg mice while not lowering resting Ca2 + levels or ER stress.

Keywords:  Amyotrophic lateral sclerosis; ER stress; SERCA1; SOD1; calcium

DOI:  https://doi.org/10.3233/JND-230123
Acta Neuropathol. 2024 Jan 19. 147(1): 19

Multi-level profiling unravels mitochondrial dysfunction in myotonic dystrophy type 2.

Felix Kleefeld, Rita Horvath, Iago Pinal-Fernandez, Andrew L Mammen, Maria Casal-Dominguez, Denisa Hathazi, Sarah Melchert, Katrin Hahn, Albert Sickmann, Claudia Muselmann-Genschow, Andreas Hentschel, Corinna Preuße, Andreas Roos, Benedikt Schoser, Werner Stenzel.

  Myotonic dystrophy type 2 (DM2) is an autosomal-dominant multisystemic disease with a core manifestation of proximal muscle weakness, muscle atrophy, myotonia, and myalgia. The disease-causing CCTG tetranucleotide expansion within the CNBP gene on chromosome 3 leads to an RNA-dominated spliceopathy, which is currently untreatable. Research exploring the pathophysiological mechanisms in myotonic dystrophy type 1 has resulted in new insights into disease mechanisms and identified mitochondrial dysfunction as a promising therapeutic target. It remains unclear whether similar mechanisms underlie DM2 and, if so, whether these might also serve as potential therapeutic targets. In this cross-sectional study, we studied DM2 skeletal muscle biopsy specimens on proteomic, molecular, and morphological, including ultrastructural levels in two separate patient cohorts consisting of 8 (explorative cohort) and 40 (confirmatory cohort) patients. Seven muscle biopsy specimens from four female and three male DM2 patients underwent proteomic analysis and respiratory chain enzymology. We performed bulk RNA sequencing, immunoblotting of respiratory chain complexes, mitochondrial DNA copy number determination, and long-range PCR (LR-PCR) to study mitochondrial DNA deletions on six biopsies. Proteomic and transcriptomic analyses revealed a downregulation of essential mitochondrial proteins and their respective RNA transcripts, namely of subunits of respiratory chain complexes I, III, and IV (e.g., mt-CO1, mt-ND1, mt-CYB, NDUFB6) and associated translation factors (TACO1). Light microscopy showed mitochondrial abnormalities (e.g., an age-inappropriate amount of COX-deficient fibers, subsarcolemmal accumulation) in most biopsy specimens. Electron microscopy revealed widespread ultrastructural mitochondrial abnormalities, including dysmorphic mitochondria with paracrystalline inclusions. Immunofluorescence studies with co-localization of autophagy (p62, LC-3) and mitochondrial marker proteins (TOM20, COX-IV), as well as immunohistochemistry for mitophagy marker BNIP3 indicated impaired mitophagic flux. Immunoblotting and LR-PCR did not reveal significant differences between patients and controls. In contrast, mtDNA copy number measurement showed a reduction of mtDNA copy numbers in the patient group compared to controls. This first multi-level study of DM2 unravels thus far undescribed functional and structural mitochondrial abnormalities. However, the molecular link between the tetranucleotide expansion and mitochondrial dysfunction needs to be further elucidated.

Keywords:  Mitochondrial dysfunction; Myotonic dystrophy type 2; Proximal myotonic myopathy

DOI:  https://doi.org/10.1007/s00401-023-02673-y
J Clin Invest. 2024 Jan 16. pii: e175448. [Epub ahead of print]134(2):

Hypomorphic human SEL1L and HRD1 variants uncouple multilayered ER-associated degradation machinery.

Katharine Umphred-Wilson, Stanley Adoro.

The suppressor of lin-12-like-HMG-CoA reductase degradation 1 (SEL1L-HRD1) complex of the endoplasmic reticulum-associated degradation (ERAD) machinery is a key cellular proteostasis pathway. Although previous studies have shown ERAD as promoting the development and maintenance of many cell types in mice, its importance to human physiology remained undetermined. In two articles in this issue of the JCI, Qi and colleagues describe four biallelic hypomorphic SEL1L and HRD1 variants that were associated with neurodevelopment disorders, locomotor dysfunction, impaired immunity, and premature death in patients. These pathogenic SEL1L-HRD1 variants shine a light on the critical importance of ERAD in humans and pave the way for future studies dissecting ERAD mechanisms in specific cell types.

DOI: https://doi.org/10.1172/JCI175448
Cell Rep. 2024 Jan 17. pii: S2211-1247(24)00008-1. [Epub ahead of print]43(2): 113680

Notch receptor-ligand binding facilitates extracellular vesicle-mediated neuron-to-neuron communication.

Yi-Zhi Wang, Charlotte C M Castillon, Kamil K Gebis, Elizabeth T Bartom, Alessandra d'Azzo, Anis Contractor, Jeffrey N Savas.

  Extracellular vesicles (EVs) facilitate intercellular communication by transferring cargo between cells in a variety of tissues. However, how EVs achieve cell-type-specific intercellular communication is still largely unknown. We found that Notch1 and Notch2 proteins are expressed on the surface of neuronal EVs that have been generated in response to neuronal excitatory synaptic activity. Notch ligands bind these EVs on the neuronal plasma membrane, trigger their internalization, activate the Notch signaling pathway, and drive the expression of Notch target genes. The generation of these neuronal EVs requires the endosomal sorting complex required for transport-associated protein Alix. Adult Alix conditional knockout mice have reduced hippocampal Notch signaling activation and glutamatergic synaptic protein expression. Thus, EVs facilitate neuron-to-neuron communication via the Notch receptor-ligand system in the brain.

Keywords:  Alix; CP: Neuroscience; Notch; excitatory synaptic activity; extracellular vesicles; glutamatergic synapse; neuron communication

DOI:  https://doi.org/10.1016/j.celrep.2024.113680
Sci Total Environ. 2024 Jan 13. pii: S0048-9697(24)00155-4. [Epub ahead of print]915 170021

Manganese disrupts the maturation and degradation of axonal autophagosome leading to hippocampal synaptic toxicity in mice via the activation of LRRK2 on phosphorylation of Rab10.

Zhuo Ma, Kuan Liu, Rui-Feng Zhang, Zi-Xin Xie, Wei Liu, Bin Xu.

  Manganese (Mn) overexposure induces hippocampal synaptotoxicity by the accumulation of dysfunctional synaptic vesicles (SVs). Leucine-rich repeat kinase 2 (LRRK2) kinase activity is involved in regulating axonal transport (autophagosomal maturation) and lysosomal function. Nevertheless, it remains unclear whether Mn-induced synaptotoxicity is associated with the LRRK2-mediated disruption of autophagosomal maturation in axonal transport and the impairment of lysosomes in hippocampal neurons. Here, we established models of manganism in C57BL/6 mice and hippocampal neuronal HT22 cells to verify the role of LRRK2-mediated Rab10 phosphorylation in the Mn-induced dysfunction of autophagy- lysosomal fusion. Our results proved that Mn-induced the disorder of axonal transport and that lysosome impairments were associated with the increased recruitment of phospho-Rab10 at the axon and lysosomes. Next, we established Lrrk2-KD and LRRK2 kinase- specific inhibitor (GNE-0877, GNE) pre-treated HT22 cells to inhibit Lrrk2 gene expression and kinase activity, respectively. In Mn-treated Lrrk2-KD or GNE-pretreated normal neurons, our results indicated that lysosomal pH and integrity and autophagic flow were restored, indicating by decreased levels of phospho-Rab10 on lysosomes and JNK-interacting proteins (JIP4). In addition, GNE pretreatment could provide protection against Mn-induced synaptotoxicity in vivo, which was evidenced by the partial recovery in synaptic plasticity and synaptic damage. Thus, the Mn-induced abnormal activation of LRRK2 affected lysosomes and the recruitment of phospho-Rab10 by JIP4, which disrupted autophagosomal maturation in proximal axons and resulted in the hippocampal synaptic toxicity of mice.

Keywords:  Autophagy-lysosomal fusion; LRRK2; Manganese; Synaptotoxicity

DOI:  https://doi.org/10.1016/j.scitotenv.2024.170021
J Cell Biol. 2024 Mar 04. pii: e202302067. [Epub ahead of print]223(3):

The V-ATPase-ATG16L1 axis recruits LRRK2 to facilitate the lysosomal stress response.

Tomoya Eguchi, Maria Sakurai, Yingxue Wang, Chieko Saito, Gen Yoshii, Thomas Wileman, Noboru Mizushima, Tomoki Kuwahara, Takeshi Iwatsubo.

Leucine-rich repeat kinase 2 (LRRK2), a Rab kinase associated with Parkinson's disease and several inflammatory diseases, has been shown to localize to stressed lysosomes and get activated to regulate lysosomal homeostasis. However, the mechanisms of LRRK2 recruitment and activation have not been well understood. Here, we found that the ATG8 conjugation system regulates the recruitment of LRRK2 as well as LC3 onto single membranes of stressed lysosomes/phagosomes. This recruitment did not require FIP200-containing autophagy initiation complex, nor did it occur on double-membrane autophagosomes, suggesting independence from canonical autophagy. Consistently, LRRK2 recruitment was regulated by the V-ATPase-ATG16L1 axis, which requires the WD40 domain of ATG16L1 and specifically mediates ATG8 lipidation on single membranes. This mechanism was also responsible for the lysosomal stress-induced activation of LRRK2 and the resultant regulation of lysosomal secretion and enlargement. These results indicate that the V-ATPase-ATG16L1 axis serves a novel non-autophagic role in the maintenance of lysosomal homeostasis by recruiting LRRK2.

DOI: https://doi.org/10.1083/jcb.202302067
Front Mol Neurosci. 2023 ;16 1287510

Transmission-selective muscle pathology induced by the active propagation of mutant huntingtin across the human neuromuscular synapse.

Margarita C Dinamarca, Laura Colombo, Urszula Brykczynska, Amandine Grimm, Isabelle Fruh, Imtiaz Hossain, Daniela Gabriel, Anne Eckert, Matthias Müller, Eline Pecho-Vrieseling.

  Neuron-to-neuron transmission of aggregation-prone, misfolded proteins may potentially explain the spatiotemporal accumulation of pathological lesions in the brains of patients with neurodegenerative protein-misfolding diseases (PMDs). However, little is known about protein transmission from the central nervous system to the periphery, or how this propagation contributes to PMD pathology. To deepen our understanding of these processes, we established two functional neuromuscular systems derived from human iPSCs. One was suitable for long-term high-throughput live-cell imaging and the other was adapted to a microfluidic system assuring that connectivity between motor neurons and muscle cells was restricted to the neuromuscular junction. We show that the Huntington's disease (HD)-associated mutant HTT exon 1 protein (mHTTEx1) is transmitted from neurons to muscle cells across the human neuromuscular junction. We found that transmission is an active and dynamic process that starts before aggregate formation and is regulated by synaptic activity. We further found that transmitted mHTTEx1 causes HD-relevant pathology at both molecular and functional levels in human muscle cells, even in the presence of the ubiquitous expression of mHTTEx1. In conclusion, we have uncovered a causal link between mHTTEx1 synaptic transmission and HD pathology, highlighting the therapeutic potential of blocking toxic protein transmission in PMDs.

Keywords:  Huntington's disease; hiPSC; mutant huntingtin; neurodegeneration; neuromuscular system; protein transmission; synaptic

DOI:  https://doi.org/10.3389/fnmol.2023.1287510
Neurotherapeutics. 2023 Dec 19. pii: S1878-7479(23)01900-1. [Epub ahead of print]21(1): e00292

Mitochondrial dysfunction in neurodegenerative disorders.

Madelyn M Klemmensen, Seth H Borrowman, Colin Pearce, Benjamin Pyles, Bharatendu Chandra.

  Recent advances in understanding the role of mitochondrial dysfunction in neurodegenerative diseases have expanded the opportunities for neurotherapeutics targeting mitochondria to alleviate symptoms and slow disease progression. In this review, we offer a historical account of advances in mitochondrial biology and neurodegenerative disease. Additionally, we summarize current knowledge of the normal physiology of mitochondria and the pathogenesis of mitochondrial dysfunction, the role of mitochondrial dysfunction in neurodegenerative disease, current therapeutics and recent therapeutic advances, as well as future directions for neurotherapeutics targeting mitochondrial function. A focus is placed on reactive oxygen species and their role in the disruption of telomeres and their effects on the epigenome. The effects of mitochondrial dysfunction in the etiology and progression of Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, and Huntington's disease are discussed in depth. Current clinical trials for mitochondria-targeting neurotherapeutics are discussed.

Keywords:  Aging; Bioenergetics; Mitochondria; Neurodegeneration; Reactive oxygen species (ROS)

DOI:  https://doi.org/10.1016/j.neurot.2023.10.002
Sci Rep. 2024 01 17. 14(1): 1479

Static magnetic stimulation induces structural plasticity at the axon initial segment of inhibitory cortical neurons.

J L Beros, E S King, D Clarke, L Jaeschke-Angi, J Rodger, A D Tang.

Static magnetic stimulation (SMS) is a form of non-invasive brain stimulation that alters neural activity and induces neural plasticity that outlasts the period of stimulation. This can modify corticospinal excitability or motor behaviours, suggesting that SMS may alter the intrinsic excitability of neurons. In mammalian neurons, the axon initial segment (AIS) is the site of action potential initiation and undergoes structural plasticity (changes in length and position from the soma) as a homeostatic mechanism to counteract chronic changes in neuronal activity. We investigated whether the chronic application of SMS (6 and 48 h, 0.5 T) induces structural AIS plasticity in postnatally derived primary cortical neurons. Following 6 h of SMS, we observed a shortening in mean AIS length compared to control, that persisted 24 h post stimulation. In contrast, 48 h of SMS induced an immediate distal shift that persisted 24 h post-stimulation. Pharmacological blockade of voltage gated L/T-type calcium channels during stimulation did not prevent SMS-induced AIS structural plasticity. Our findings provide the foundation to expand the use of chronic SMS as a non-invasive method to promote AIS plasticity.

DOI: https://doi.org/10.1038/s41598-024-51845-7
Cell Cycle. 2024 Jan 14. 1-17

Telomere dynamics in human pluripotent stem cells.

Buyun Ma, Paula Martínez, Raúl Sánchez-Vázquez, Maria A Blasco.

  Pluripotent stem cells (PSCs) are a promising source of stem cells for regenerative therapies. Stem cell function depends on telomere maintenance mechanisms that provide them with the proliferative capacity and genome stability necessary to multiply and regenerate tissues. We show here that established human embryonic stem cells (hESCs) have stable telomere length that is dependent on telomerase but not on alternative mechanisms based on homologous recombination pathways. Here, we show that human-induced pluripotent stem cells (hiPSCs) reprogrammed from somatic cells show progressive telomere lengthening until reaching a length similar to ESCs. hiPSCs also acquire telomeric chromatin marks of ESCs including decreased abundance of tri-methylated histone H3K9 and H4K20 and HP1 heterochromatic marks, as well as of the shelterin component TRF2. These chromatin features are accompanied with increased abundance of telomere transcripts or TERRAs. We also found that telomeres of both hESCs and hiPSCs are well protected from DNA damage during telomere elongation and once full telomere length is achieved, and exhibit stable genomes. Collectively, this study highlights that hiPSCs acquire ESC features during reprogramming and reveals the telomere biology in human pluripotent stem cells (hPSCs).

Keywords:  Telomerase; Telomeres; hESCs; hiPSCs

DOI:  https://doi.org/10.1080/15384101.2023.2285551
Adv Protein Chem Struct Biol. 2024 ;pii: S1876-1623(23)00078-0. [Epub ahead of print]138 101-133

Proteomics provides insights into the theranostic potential of extracellular vesicles.

Morteza Abyadeh, Mehdi Alikhani, Mehdi Mirzaei, Vivek Gupta, Faezeh Shekari, Ghasem Hosseini Salekdeh.

  Extracellular vesicles (EVs) encompass a diverse range of membranous structures derived from cells, including exosomes and microvesicles. These vesicles are present in biological fluids and play vital roles in various physiological and pathological processes. They facilitate intercellular communication by enabling the exchange of proteins, lipids, and genetic material between cells. Understanding the cellular processes that govern EV biology is essential for unraveling their physiological and pathological functions and their potential clinical applications. Despite significant advancements in EV research in recent years, there is still much to learn about these vesicles. The advent of improved mass spectrometry (MS)-based techniques has allowed for a deeper characterization of EV protein composition, providing valuable insights into their roles in different physiological and pathological conditions. In this chapter, we provide an overview of proteomics studies conducted to identify the protein contents of EVs, which contribute to their therapeutic and pathological features. We also provided evidence on the potential of EV proteome contents as biomarkers for early disease diagnosis, progression, and treatment response, as well as factors that influence their composition. Additionally, we discuss the available databases containing information on EV proteome contents, and finally, we highlight the need for further research to pave the way toward their utilization in clinical settings.

Keywords:  Diagnostic; Exosome; Extracellular vesicles; Proteomics; Theranostic; Therapeutic

DOI:  https://doi.org/10.1016/bs.apcsb.2023.08.001
Radiat Res. 2024 Jan 18.

TDP-43 was Involved in Radiation-induced Neuronal Damage and May Not Through the BDNF/TrkB Pathway.

Rui Sun, Kedi Xi, Shengjun Ji, Xing Song, Dan Xi, Wenming Yin, Yingjie Shao, Wendong Gu, Jingting Jiang.

Cognitive dysfunction is the most common form of radiation-induced brain injury. TDP-43 is known to be associated with hippocampal degeneration and cognitive dysfunction, in this study we wanted to know if it also had an effect on radiation-induced hippocampus damage. At first, we found the expression of TDP-43 and p-TDP-43 was increased in the hippocampus of rats with radiation-induced cognitive dysfunction. Single-cell RNA-seq analysis of the rat hippocampus showed that TDP-43 was expressed in all cell types and was significantly upregulated in neuron cells after irradiation. Enrichment analysis of gene ontology (GO) functions and KEGG pathways showed that the differential expression genes in neuron after irradiation may be involved in synaptic plasticity. In vitro, the expression of TDP-43 was also increased in neuron cells after irradiation, while the expression of brain-derived neurotrophic factor (BDNF), TrkB, typical synaptic signature proteins (SYN, GAP43 and PSD95), β-tubulin and dendritic spines were decreased. In the irradiated neurons, the β-tubulin, dendritic and spines typical synaptic signature proteins had more severe damage in pcDNA3.1-TDP-43 plasmid transfections group, however, the damages were alleviated in the siRNA-TDP-43 plasmid transfections group. BDNF was highly expressed in the irradiated pcDNA3.1-TDP-43 plasmid transfections group, while its expression was decreased in the siRNA-TDP-43 group. The TrkB expression was significantly reduced in neurons after exposure to ionizing radiation, however, there was no significant correlation with TDP-43 expression. These data indicate that TDP-43 is involved in radiation-induced neuronal synaptic plasticity decline and developmental damage, furthermore, the BDNF/TrkB signaling pathway may not be involved in this process.

DOI: https://doi.org/10.1667/RADE-23-00168.1
Cell Chem Biol. 2024 Jan 18. pii: S2451-9456(23)00470-1. [Epub ahead of print]31(1): 14-16

Mo' m1A, mo' problems.

Linamarie Miller, James Shorter.

CAG-repeat expansions underlie fatal neurodegenerative disorders. In a lodestar study published in a recent issue of Nature, Sun et al.1 identify a writer and eraser of N1-methyladenosine (m1A) modifications of CAG-repeat RNA. They establish that m1A modifications in CAG-repeat expanded RNA promote neurodegeneration and aberrant phase transitions of TDP-43. These findings suggest therapeutic strategies for CAG-repeat expansion disorders.

DOI: https://doi.org/10.1016/j.chembiol.2023.12.013
Genome Biol. 2024 Jan 15. 25(1): 17

Phase separation as a possible mechanism for dosage sensitivity.

Liang Yang, Jiali Lyu, Xi Li, Gaigai Guo, Xueya Zhou, Taoyu Chen, Yi Lin, Tingting Li.

BACKGROUND: Deletion of haploinsufficient genes or duplication of triplosensitive ones results in phenotypic effects in a concentration-dependent manner, and the mechanisms underlying these dosage-sensitive effects remain elusive. Phase separation drives functional compartmentalization of biomolecules in a concentration-dependent manner as well, which suggests a potential link between these two processes, and warrants further systematic investigation.RESULTS: Here we provide bioinformatic and experimental evidence to show a close link between phase separation and dosage sensitivity. We first demonstrate that haploinsufficient or triplosensitive gene products exhibit a higher tendency to undergo phase separation. Assessing the well-established dosage-sensitive genes HNRNPK, PAX6, and PQBP1 with experiments, we show that these proteins undergo phase separation. Critically, pathogenic variations in dosage-sensitive genes disturb the phase separation process either through reduced protein levels, or loss of phase-separation-prone regions. Analysis of multi-omics data further demonstrates that loss-of-function genetic perturbations on phase-separating genes cause similar dysfunction phenotypes as dosage-sensitive gene perturbations. In addition, dosage-sensitive scores derived from population genetics data predict phase-separating proteins with much better performance than available sequence-based predictors, further illustrating close ties between these two parameters.
CONCLUSIONS: Together, our study shows that phase separation is functionally linked to dosage sensitivity and provides novel insights for phase-separating protein prediction from the perspective of population genetics data.

DOI: https://doi.org/10.1186/s13059-023-03128-z
J Biol Chem. 2024 Jan 16. pii: S0021-9258(24)00027-9. [Epub ahead of print] 105651

Characterising the Protein-Protein Interaction Between MDM2 and 14-3-3σ; Proof of Concept for Small Molecule Stabilisation.

Jake A Ward, Beatriz Romartinez-Alonso, Danielle F Kay, Jeddidiah Bellamy-Carter, Bethany Thurairajah, Jaswir Basran, Hanna Kwon, Aneika C Leney, Salvador Macip, Pietro Roversi, Frederick W Muskett, Richard G Doveston.

Mouse Double Minute 2 (MDM2) is a key negative regulator of the tumour suppressor protein p53. MDM2 overexpression occurs in many types of cancer and results in the suppression of wild type p53. The 14-3-3 family of adaptor proteins are known to bind MDM2 and the 14-3-3σ isoform controls MDM2 cellular localisation and stability to inhibit its activity. Therefore, small molecule stabilisation of the 14-3-3σ/MDM2 protein-protein interaction (PPI) is a potential therapeutic strategy for the treatment of cancer. Here, we provide a detailed biophysical and structural characterisation of the phosphorylation-dependent interaction between 14-3-3σ and peptides that mimic the 14-3-3 binding motifs within MDM2. The data show that di-phosphorylation of MDM2 at S166 and S186 is essential for high affinity 14-3-3 binding and that the binary complex formed involves one MDM2 di-phosphorylated peptide bound to a dimer of 14-3-3σ. However, the two phosphorylation sites do not simultaneously interact so as to bridge the 14-3-3 dimer in a 'multivalent' fashion. Instead, the two phosphorylated MDM2 motifs 'rock' between the two binding grooves of the dimer, which is unusual in the context of 14-3-3 proteins. In addition, we show that the 14-3-3σ/MDM2 interaction is amenable to small molecule stabilisation. The natural product fusicoccin A forms a ternary complex with a 14-3-3σ dimer and an MDM2 di-phosphorylated peptide resulting in stablisation of the 14-3-3σ/MDM2 PPI. This work serves as a proof-of-concept of the drugability of the 14-3-3/MDM2 PPI and paves the way toward the development of more selective and efficacious small molecule stabilisers.

DOI: https://doi.org/10.1016/j.jbc.2024.105651
Adv Healthc Mater. 2024 Jan 13. e2302456

Microinstrumentation for Brain Organoids.

Devan Patel, Saniya Shetty, Chris Acha, Itzy E Morales Pantoja, Alice Zhao, Derosh George, David H Gracias.

  Brain organoids are three-dimensional aggregates of self-organized differentiated stem cells that mimic the structure and function of human brain regions. Organoids bridge the gaps between conventional drug screening models such as planar mammalian cell culture, animal studies, and clinical trials. They can revolutionize the fields of developmental biology, neuroscience, toxicology, and computer engineering. Conventional microinstrumentation for conventional cellular engineering, such as planar microfluidic chips; microelectrode arrays (MEAs), and optical, magnetic, and acoustic techniques, have limitations when applied to 3D organoids, primarily due to their limits with inherently 2D geometry and interfacing. Hence, there is an urgent need to develop new instrumentation that is compatible with live cell culture techniques and with scalable 3D formats of relevance to organoids. This review discusses conventional planar approaches and emerging 3D microinstrumentation necessary for advanced organoid-machine interfaces. Specifically, the article surveys recently developed microinstrumentation, including 3D printed and curved microfluidics, 3D and fast-scan optical techniques, buckling and self-folding microelectrode arrays, 3D interfaces for electrochemical measurements, and 3D spatially controllable magnetic and acoustic technologies relevant to two-way information transfer with brain organoids. The article highlights key challenges that must be addressed for robust organoid culture and reliable 3D spatiotemporal information transfer. This article is protected by copyright. All rights reserved.

Keywords:  Microphysiological systems; microfluidics; neuromodulation; neuromorphic computing; organoid intelligence

DOI:  https://doi.org/10.1002/adhm.202302456