bims-axbals Biomed News
on Axonal biology and ALS
Issue of 2024–04–28
83 papers selected by
TJ Krzystek, ALS Therapy Development Institute
  1. C9ORF72 deficiency results in neurodegeneration in the zebrafish retina.
  2. Increased Vulnerability to Ferroptosis in FUS-ALS.
  3. LINC complex alterations are a key feature of sporadic and familial ALS/FTD.
  4. Investigating Repeat Expansions in NIPA1, NOP56, and NOTCH2NLC Genes: A Closer Look at Amyotrophic Lateral Sclerosis Patients from Southern Italy.
  5. Precise editing of pathogenic nucleotide repeat expansions in iPSCs using paired prime editor.
  6. A Poem About ALS.
  7. Clinical and molecular outcomes from the 5-Year natural history study of SSADH Deficiency, a model metabolic neurodevelopmental disorder.
  8. Organoid intelligence: Integration of organoid technology and artificial intelligence in the new era of in vitro models.
  9. Micro-and mesoscale aspects of neurodegeneration in engineered human neural networks carrying the LRRK2 G2019S mutation.
  10. Unlocking mitochondrial drug targets: The importance of mitochondrial transport proteins.
  11. Human pluripotent stem cell (hPSC)-derived microglia for the study of brain disorders. A comprehensive review of existing protocols.
  12. Regulation of human microglial gene expression and function via RNAase-H active antisense oligonucleotides in vivo in Alzheimer's disease.
  13. Motor band sign is specific for amyotrophic lateral sclerosis and corresponds to motor symptoms.
  14. Pan-neuronal expression of human mutant SOD1 in Drosophila impairs survival and motor performance, induces early neuroinflammation and chromosome aberrations.
  15. Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications.
  16. An increase in ER stress and unfolded protein response in iPSCs-derived neuronal cells from neuronopathic Gaucher disease patients.
  17. Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis.
  18. Revisiting distinct nerve excitability patterns in patients with amyotrophic lateral sclerosis.
  19. Distinct transcriptomic profile of satellite cells contributes to preservation of neuromuscular junctions in extraocular muscles of ALS mice.
  20. Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue.
  21. Epigenetic modulation through BET bromodomain inhibitors as a novel therapeutic strategy for progranulin-deficient frontotemporal dementia.
  22. Analgesic effect of Botulinum toxin in neuropathic pain is sodium channel independent.
  23. Neuronal glycolysis: focus on developmental morphogenesis and localized subcellular functions.
  24. Slow kinesin-dependent microtubular transport facilitates ribbon synapse assembly in developing cochlear inner hair cells.
  25. Functional sensory circuits built from neurons of two species.
  26. Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.
  27. The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders.
  28. GABAergic interneuron diversity and organization are crucial for the generation of human-specific functional neural networks in cerebral organoids.
  29. Exploring the intricacies of calcium dysregulation in ischemic stroke: Insights into neuronal cell death and therapeutic strategies.
  30. Knockdown of tgfb1a partially improves ALS phenotype in a transient zebrafish model.
  31. Unveiling new horizons in heart research: the promise of multi-chamber cardiac organoids.
  32. Neurofilaments in Sporadic and Familial Amyotrophic Lateral Sclerosis: A Systematic Review and Meta-Analysis.
  33. Biomarkers for Managing Neurodegenerative Diseases.
  34. Protein painting for structural and binding site analysis via intracellular lysine reactivity profiling with o-phthalaldehyde.
  35. Identity and Maturity of iPSC-Derived Oligodendrocytes in 2D and Organoid Systems.
  36. The two C. elegans class VI myosins, SPE-15/HUM-3 and HUM-8, share similar motor properties, but have distinct developmental and tissue expression patterns.
  37. Copper enhances aggregational toxicity of mutant huntingtin in a Drosophila model of Huntington's Disease.
  38. The migration pattern of cells during the mesoderm and endoderm differentiation from human pluripotent stem cells.
  39. Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.
  40. STING promotes homeostatic maintenance of tissues and confers longevity with aging.
  41. Discovery of a novel homozygous SOD1 truncating variant bolsters infantile SOD1 deficiency syndrome.
  42. Transcriptional Variabilities in Human hiPSC-derived Cardiomyocytes: All Genes Are Not Equal and Their Robustness May Foretell Donor's Disease Susceptibility.
  43. Artificial Intelligence (AI) for Early Diagnosis of Retinal Diseases.
  44. Multimodal joint deconvolution and integrative signature selection in proteomics.
  45. Dopamine‑iron homeostasis interaction rescues mitochondrial fitness in Parkinson's disease.
  46. Stepwise combined cell transplantation using mesenchymal stem cells and induced pluripotent stem cell-derived motor neuron progenitor cells in spinal cord injury.
  47. Contribution of the Type III Secretion System (T3SS2) of Vibrio parahaemolyticus in Mitochondrial Stress in Human Intestinal Cells.
  48. Engineered platforms for mimicking cardiac development and drug screening.
  49. Inhibitory roles of Apolipoprotein E Christchurch astrocytes in curbing tau propagation using human pluripotent stem cell-derived models.
  50. A Comparative Study of Human Pluripotent Stem Cell-Derived Macrophages in Modeling Viral Infections.
  51. Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists.
  52. Baseline Unfolded Protein Response Signaling Adjusts the Timing of the Mammalian Cell Cycle.
  53. Inhibition of Metalloproteinases Extends Longevity and Function of In Vitro Human iPSC-Derived Skeletal Muscle.
  54. Correction: Current Strategies of Modeling Human Trophoblast Using Human Pluripotent Stem Cells in vitro.
  55. Essential Role of COPII Proteins in Maintaining the Contractile Ring Anchoring to the Plasma Membrane during Cytokinesis in Drosophila Male Meiosis.
  56. Symptom-based staging for logopenic variant primary progressive aphasia.
  57. Generation of a PPM1A-deficient human induced pluripotent stem cell line using CRISPR-Cas9 technology.
  58. Chaotic neural dynamics facilitate probabilistic computations through sampling.
  59. Neuronal cell cycle reentry events in the aging brain are more prevalent in neurodegeneration and lead to cellular senescence.
  60. Disentangling Knots of Misfolded Proteins: Do We Really Know the Prognostic Implications of the Pathogenic V122I TTR Variant?
  61. Lipidomic Analysis of Plasma Extracellular Vesicles Derived from Alzheimer's Disease Patients.
  62. Spaced training activates Miro/Milton-dependent mitochondrial dynamics in neuronal axons to sustain long-term memory.
  63. Structural Features and Physiological Associations of Human 14-3-3ζ Pseudogenes.
  64. Spatiotemporal expression of thyroid hormone transporter MCT8 and THRA mRNA in human cerebral organoids recapitulating first trimester cortex development.
  65. Low-dose BPA-induced neuronal energy metabolism dysfunction and apoptosis mediated by PINK1/parkin mitophagy pathway in juvenile rats.
  66. Fragile X Messenger Ribonucleoprotein Protein and Its Multifunctionality: From Cytosol to Nucleolus and Back.
  67. Mechanism of Decision Making between Autophagy and Apoptosis Induction upon Endoplasmic Reticulum Stress.
  68. A single ALS center experience with clinical use of sodium phenylbutyrate-taurursodiol.
  69. The Zn2+ transporter ZIP7 enhances endoplasmic-reticulum-associated protein degradation and prevents neurodegeneration in Drosophila.
  70. Editorial: Foretelling the future-Emerging role of magnetic resonance enterography as a prognostic tool in Crohn's disease.
  71. Reactivating Hippo by Drug Compounds to Suppress Gastric Cancer and Enhance Chemotherapy Sensitivity.
  72. DNA Damage and Parkinson's Disease.
  73. MEF2C contributes to axonal branching by regulating Kif2c transcription.
  74. Testosterone Reduces Myelin Abnormalities in the Wobbler Mouse Model of Amyotrophic Lateral Sclerosis.
  75. Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina.
  76. Targeting NRAS via miR-1304-5p or farnesyltransferase inhibition confers sensitivity to ALK inhibitors in ALK-mutant neuroblastoma.
  77. Loss of Midbrain Dopamine Neurons Does Not Alter GABAergic Inhibition Mediated by Parvalbumin-Expressing Interneurons in Mouse Primary Motor Cortex.
  78. An individualized protein-based prognostic model to stratify pediatric patients with papillary thyroid carcinoma.
  79. RAPID resistance to BET inhibitors is mediated by FGFR1 in glioblastoma.
  80. Missing WD40 Repeats in ATG16L1 Delays Canonical Autophagy and Inhibits Noncanonical Autophagy.
  81. Pragmatic or pristine surgical research.
  82. Beta: bursts of cognition.
  83. Closed-loop automated drug infusion regulator: A clinically translatable, closed-loop drug delivery system for personalized drug dosing.
  1. J Neurosci. 2024 Apr 24. pii: e2128232024. [Epub ahead of print]
    C9ORF72 deficiency results in neurodegeneration in the zebrafish retina.
    Natalia Jaroszynska, Andrea Salzinger, Themistoklis M Tsarouchas, Catherina G Becker, Thomas Becker, David A Lyons, Ryan B MacDonald, Marcus Keatinge.
      Hexanucleotide repeat expansions within the gene C9ORF72 are the most common cause of the neurodegenerative diseases Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal dementia (FTD). This disease-causing expansion leads to a reduction in C9ORF72 expression levels in patients, suggesting loss of C9ORF72 function could contribute to disease. To further understand the consequences of C9ORF72 deficiency in vivo, we generated a c9orf72 mutant zebrafish line. Analysis of the adult female spinal cords revealed no appreciable neurodegenerative pathology such as loss of motor neurons, or increased levels of neuroinflammation. However, detailed examination of adult female c9orf72-/- retinas showed prominent neurodegenerative features, including a decrease in retinal thickness, gliosis, and an overall reduction in neurons of all subtypes. Analysis of rod and cone cells within the photoreceptor layer showed a disturbance in their outer segment structure and rhodopsin mis-localisation from rod outer segments to their cell bodies and synaptic terminals. Thus, C9ORF72 may play a previously unappreciated role in retinal homeostasis and suggests C9ORF72 deficiency can induce tissue specific neuronal loss.Significance statement Hexanucleotide expansions in the gene C9ORF72 are the most common cause of the Amyotrophic lateral sclerosis (ALS)/ Frontotemporal dementia (FTD) disease spectrum. The expansion reduces expression of C9ORF72 and so may play a role in neuronal loss. However, C9ORF72 loss of function has been comparatively understudied in vivo. Using the zebrafish as a model of C9ORF72 deficiency, we demonstrate that loss of C9ORF72 results in marked inflammation and neuronal loss in the aged adult zebrafish retina. Development of the retina is unaffected regardless of C9ORF72 status. This demonstrates that C9ORF72 loss of function can cause spontaneous neurodegeneration in vivo and highlights a novel role of C9ORF72 in retinal homeostasis.
    DOI:  https://doi.org/10.1523/JNEUROSCI.2128-23.2024
  2. Biology (Basel). 2024 Mar 26. pii: 215. [Epub ahead of print]13(4):
    Increased Vulnerability to Ferroptosis in FUS-ALS.
    Muhammad Ismail, Dajana Großmann, Andreas Hermann.
      Ferroptosis, a regulated form of cell death characterized by iron-dependent lipid peroxide accumulation, plays a pivotal role in various pathological conditions, including neurodegenerative diseases. While reasonable evidence for ferroptosis exists, e.g., in Parkinson's disease or Alzheimer's disease, there are only a few reports on amyotrophic lateral sclerosis (ALS), a fast progressive and incurable neurodegenerative disease characterized by progressive motor neuron degeneration. Interestingly, initial studies have suggested that ferroptosis might be significantly involved in ALS. Key features of ferroptosis include oxidative stress, glutathione depletion, and alterations in mitochondrial morphology and function, mediated by proteins such as GPX4, xCT, ACSL4 FSP1, Nrf2, and TfR1. Induction of ferroptosis involves small molecule compounds like erastin and RSL3, which disrupt system Xc- and GPX4 activity, respectively, resulting in lipid peroxidation and cellular demise. Mutations in fused in sarcoma (FUS) are associated with familial ALS. Pathophysiological hallmarks of FUS-ALS involve mitochondrial dysfunction and oxidative damage, implicating ferroptosis as a putative cell-death pathway in motor neuron demise. However, a mechanistic understanding of ferroptosis in ALS, particularly FUS-ALS, remains limited. Here, we investigated the vulnerability to ferroptosis in FUS-ALS cell models, revealing mitochondrial disturbances and increased susceptibility to ferroptosis in cells harboring ALS-causing FUS mutations. This was accompanied by an altered expression of ferroptosis-associated proteins, particularly by a reduction in xCT expression, leading to cellular imbalance in the redox system and increased lipid peroxidation. Iron chelation with deferoxamine, as well as inhibition of the mitochondrial calcium uniporter (MCU), significantly alleviated ferroptotic cell death and lipid peroxidation. These findings suggest a link between ferroptosis and FUS-ALS, offering potential new therapeutic targets.
    Keywords:  amyotrophic lateral sclerosis; cell death; mitochondria; oxidative damage
    DOI:  https://doi.org/10.3390/biology13040215
  3. Acta Neuropathol Commun. 2024 Apr 25. 12(1): 69
    LINC complex alterations are a key feature of sporadic and familial ALS/FTD.
    Riccardo Sirtori, Michelle J Gregoire, Emily M Potts, Alicia Collins, Liviana Donatelli, Claudia Fallini.
      Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder that primarily affects motor neurons, leading to progressive muscle weakness and loss of voluntary muscle control. While the exact cause of ALS is not fully understood, emerging research suggests that dysfunction of the nuclear envelope (NE) may contribute to disease pathogenesis and progression. The NE plays a role in ALS through several mechanisms, including nuclear pore defects, nucleocytoplasmic transport impairment, accumulation of mislocalized proteins, and nuclear morphology abnormalities. The LINC complex is the second biggest multi-protein complex in the NE and consists of the SUN1/2 proteins spanning the inner nuclear membrane and Nesprin proteins embedded in the outer membrane. The LINC complex, by interacting with both the nuclear lamina and the cytoskeleton, transmits mechanical forces to the nucleus regulating its morphology and functional homeostasis. In this study we show extensive alterations to the LINC complex in motor and cortical iPSC-derived neurons and spinal cord organoids carrying the ALS causative mutation in the C9ORF72 gene (C9). Importantly, we show that such alterations are present in vivo in a cohort of sporadic ALS and C9-ALS postmortem spinal cord and motor cortex specimens. We also found that LINC complex disruption strongly correlated with nuclear morphological alterations occurring in ALS neurons, independently of TDP43 mislocalization. Altogether, our data establish morphological and functional alterations to the LINC complex as important events in ALS pathogenic cascade, making this pathway a possible target for both biomarker and therapy development.
    Keywords:  ALS; C9ORF72; FTD; LINC complex; Nesprin; SUN
    DOI:  https://doi.org/10.1186/s40478-024-01778-z
  4. Cells. 2024 Apr 14. pii: 677. [Epub ahead of print]13(8):
    Investigating Repeat Expansions in NIPA1, NOP56, and NOTCH2NLC Genes: A Closer Look at Amyotrophic Lateral Sclerosis Patients from Southern Italy.
    Paola Ruffo, Francesca De Amicis, Vincenzo La Bella, Francesca Luisa Conforti.
      The discovery of hexanucleotide repeats expansion (RE) in Chromosome 9 Open Reading frame 72 (C9orf72) as the major genetic cause of amyotrophic lateral sclerosis (ALS) and the association between intermediate repeats in Ataxin-2 (ATXN2) with the disorder suggest that repetitive sequences in the human genome play a significant role in ALS pathophysiology. Investigating the frequency of repeat expansions in ALS in different populations and ethnic groups is therefore of great importance. Based on these premises, this study aimed to define the frequency of REs in the NIPA1, NOP56, and NOTCH2NLC genes and the possible associations between phenotypes and the size of REs in the Italian population. Using repeat-primed-PCR and PCR-fragment analyses, we screened 302 El-Escorial-diagnosed ALS patients and compared the RE distribution to 167 age-, gender-, and ethnicity-matched healthy controls. While the REs distribution was similar between the ALS and control groups, a moderate association was observed between longer RE lengths and clinical features such as age at onset, gender, site of onset, and family history. In conclusion, this is the first study to screen ALS patients from southern Italy for REs in NIPA1, NOP56, and NOTCH2NLC genes, contributing to our understanding of ALS genetics. Our results highlighted that the extremely rare pathogenic REs in these genes do not allow an association with the disease.
    Keywords:  NIPA1; NOP56; NOTCH2NLC; amyotrophic lateral sclerosis; repeats expansion
    DOI:  https://doi.org/10.3390/cells13080677
  5. Nucleic Acids Res. 2024 Apr 25. pii: gkae310. [Epub ahead of print]
    Precise editing of pathogenic nucleotide repeat expansions in iPSCs using paired prime editor.
    Hye-Yeon Hwang, Dongmin Gim, Hwalin Yi, Hyewon Jung, Jaecheol Lee, Daesik Kim.
      Nucleotide repeat expansion disorders, a group of genetic diseases characterized by the expansion of specific DNA sequences, pose significant challenges to treatment and therapy development. Here, we present a precise and programmable method called prime editor-mediated correction of nucleotide repeat expansion (PE-CORE) for correcting pathogenic nucleotide repeat expansion. PE-CORE leverages a prime editor and paired pegRNAs to achieve targeted correction of repeat sequences. We demonstrate the effectiveness of PE-CORE in HEK293T cells and patient-derived induced pluripotent stem cells (iPSCs). Specifically, we focus on spinal and bulbar muscular atrophy and spinocerebellar ataxia type, two diseases associated with nucleotide repeat expansion. Our results demonstrate the successful correction of pathogenic expansions in iPSCs and subsequent differentiation into motor neurons. Specifically, we detect distinct downshifts in the size of both the mRNA and protein, confirming the functional correction of the iPSC-derived motor neurons. These findings highlight PE-CORE as a precision tool for addressing the intricate challenges of nucleotide repeat expansion disorders, paving the way for targeted therapies and potential clinical applications.
    DOI:  https://doi.org/10.1093/nar/gkae310
  6. Am J Nurs. 2024 May 01. 124(5): 10
    A Poem About ALS.
    Jane Rosenberg LaForge.
      
    DOI:  https://doi.org/10.1097/01.NAJ.0001016304.08449.3a
  7. J Neurodev Disord. 2024 Apr 24. 16(1): 21
    Clinical and molecular outcomes from the 5-Year natural history study of SSADH Deficiency, a model metabolic neurodevelopmental disorder.
    Itay Tokatly Latzer, Jean-Baptiste Roullet, Wardiya Afshar-Saber, Henry H C Lee, Mariarita Bertoldi, Gabrielle E McGinty, Melissa L DiBacco, Erland Arning, Melissa Tsuboyama, Alexander Rotenberg, Thomas Opladen, Kathrin Jeltsch, Àngels García-Cazorla, Natalia Juliá-Palacios, K Michael Gibson, Mustafa Sahin, Phillip L Pearl.
       BACKGROUND: Succinic semialdehyde dehydrogenase deficiency (SSADHD) represents a model neurometabolic disease at the fulcrum of translational research within the Boston Children's Hospital Intellectual and Developmental Disabilities Research Centers (IDDRC), including the NIH-sponsored natural history study of clinical, neurophysiological, neuroimaging, and molecular markers, patient-derived induced pluripotent stem cells (iPSC) characterization, and development of a murine model for tightly regulated, cell-specific gene therapy.
    METHODS: SSADHD subjects underwent clinical evaluations, neuropsychological assessments, biochemical quantification of γ-aminobutyrate (GABA) and related metabolites, electroencephalography (standard and high density), magnetoencephalography, transcranial magnetic stimulation, magnetic resonance imaging and spectroscopy, and genetic tests. This was parallel to laboratory molecular investigations of in vitro GABAergic neurons derived from induced human pluripotent stem cells (hiPSCs) of SSADHD subjects and biochemical analyses performed on a versatile murine model that uses an inducible and reversible rescue strategy allowing on-demand and cell-specific gene therapy.
    RESULTS: The 62 SSADHD subjects [53% females, median (IQR) age of 9.6 (5.4-14.5) years] included in the study had a reported symptom onset at ∼ 6 months and were diagnosed at a median age of 4 years. Language developmental delays were more prominent than motor. Autism, epilepsy, movement disorders, sleep disturbances, and various psychiatric behaviors constituted the core of the disorder's clinical phenotype. Lower clinical severity scores, indicating worst severity, coincided with older age (R= -0.302, p = 0.03), as well as age-adjusted lower values of plasma γ-aminobutyrate (GABA) (R = 0.337, p = 0.02) and γ-hydroxybutyrate (GHB) (R = 0.360, p = 0.05). While epilepsy and psychiatric behaviors increase in severity with age, communication abilities and motor function tend to improve. iPSCs, which were differentiated into GABAergic neurons, represent the first in vitro neuronal model of SSADHD and express the neuronal marker microtubule-associated protein 2 (MAP2), as well as GABA. GABA-metabolism in induced GABAergic neurons could be reversed using CRISPR correction of the pathogenic variants or mRNA transfection and SSADHD iPSCs were associated with excessive glutamatergic activity and related synaptic excitation.
    CONCLUSIONS: Findings from the SSADHD Natural History Study converge with iPSC and animal model work focused on a common disorder within our IDDRC, deepening our knowledge of the pathophysiology and longitudinal clinical course of a complex neurodevelopmental disorder. This further enables the identification of biomarkers and changes throughout development that will be essential for upcoming targeted trials of enzyme replacement and gene therapy.
    Keywords:  Development; GABA; Neurotransmitters; Succinic semialdehyde dehydrogenase
    DOI:  https://doi.org/10.1186/s11689-024-09538-9
  8. Med Nov Technol Devices. 2024 Mar;pii: 100276. [Epub ahead of print]21
    Organoid intelligence: Integration of organoid technology and artificial intelligence in the new era of in vitro models.
    Huaiyu Shi, Andrew Kowalczewski, Danny Vu, Xiyuan Liu, Asif Salekin, Huaxiao Yang, Zhen Ma.
      Organoid Intelligence ushers in a new era by seamlessly integrating cutting-edge organoid technology with the power of artificial intelligence. Organoids, three-dimensional miniature organ-like structures cultivated from stem cells, offer an unparalleled opportunity to simulate complex human organ systems in vitro. Through the convergence of organoid technology and AI, researchers gain the means to accelerate discoveries and insights across various disciplines. Artificial intelligence algorithms enable the comprehensive analysis of intricate organoid behaviors, intricate cellular interactions, and dynamic responses to stimuli. This synergy empowers the development of predictive models, precise disease simulations, and personalized medicine approaches, revolutionizing our understanding of human development, disease mechanisms, and therapeutic interventions. Organoid Intelligence holds the promise of reshaping how we perceive in vitro modeling, propelling us toward a future where these advanced systems play a pivotal role in biomedical research and drug development.
    Keywords:  Artificial intelligence; Deep learning; Machine learning; Organoids; Stem cells
    DOI:  https://doi.org/10.1016/j.medntd.2023.100276
  9. Front Cell Neurosci. 2024 ;18 1366098
    Micro-and mesoscale aspects of neurodegeneration in engineered human neural networks carrying the LRRK2 G2019S mutation.
    Vibeke Devold Valderhaug, Ola Huse Ramstad, Rosanne van de Wijdeven, Kristine Heiney, Stefano Nichele, Axel Sandvig, Ioanna Sandvig.
      Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene have been widely linked to Parkinson's disease, where the G2019S variant has been shown to contribute uniquely to both familial and sporadic forms of the disease. LRRK2-related mutations have been extensively studied, yet the wide variety of cellular and network events related to these mutations remain poorly understood. The advancement and availability of tools for neural engineering now enable modeling of selected pathological aspects of neurodegenerative disease in human neural networks in vitro. Our study revealed distinct pathology associated dynamics in engineered human cortical neural networks carrying the LRRK2 G2019S mutation compared to healthy isogenic control neural networks. The neurons carrying the LRRK2 G2019S mutation self-organized into networks with aberrant morphology and mitochondrial dynamics, affecting emerging structure-function relationships both at the micro-and mesoscale. Taken together, the findings of our study points toward an overall heightened metabolic demand in networks carrying the LRRK2 G2019S mutation, as well as a resilience to change in response to perturbation, compared to healthy isogenic controls.
    Keywords:  LRRK2 G2019S mutation; Parkinsons disease (PD); human neural networks; mitochondrial dynamics; neurodegenerative disease model; structure–function
    DOI:  https://doi.org/10.3389/fncel.2024.1366098
  10. Acta Physiol (Oxf). 2024 Apr 26. e14150
    Unlocking mitochondrial drug targets: The importance of mitochondrial transport proteins.
    Charlotte A Hoogstraten, Tom J J Schirris, Frans G M Russel.
      A disturbed mitochondrial function contributes to the pathology of many common diseases. These organelles are therefore important therapeutic targets. On the contrary, many adverse effects of drugs can be explained by a mitochondrial off-target effect, in particular, due to an interaction with carrier proteins in the inner membrane. Yet this class of transport proteins remains underappreciated and understudied. The aim of this review is to provide a deeper understanding of the role of mitochondrial carriers in health and disease and their significance as drug targets. We present literature-based evidence that mitochondrial carrier proteins are associated with prevalent diseases and emphasize their potential as drug (off-)target sites by summarizing known mitochondrial drug-transporter interactions. Studying these carriers will enhance our knowledge of mitochondrial drug on- and off-targets and provide opportunities to further improve the efficacy and safety of drugs.
    Keywords:  carrier proteins; drugs; efficacy and safety; inner mitochondrial membrane; mitochondria; on‐ and off‐target
    DOI:  https://doi.org/10.1111/apha.14150
  11. IBRO Neurosci Rep. 2024 Jun;16 497-508
    Human pluripotent stem cell (hPSC)-derived microglia for the study of brain disorders. A comprehensive review of existing protocols.
    Fionicca Teo, Catherine Yen Li Kok, Mao-Jia Tan, H Shawn Je.
      Microglia, resident immune cells of the brain that originate from the yolk sac, play a critical role in maintaining brain homeostasis by monitoring and phagocytosing pathogens and cellular debris in the central nervous system (CNS). While they share characteristics with myeloid cells, they are distinct from macrophages. In response to injury, microglia release pro-inflammatory factors and contribute to brain homeostasis through activities such as synapse pruning and neurogenesis. To better understand their role in neurological disorders, the generation of in vitro models of human microglia has become essential. These models, derived from patient-specific induced pluripotent stem cells (iPSCs), provide a controlled environment to study the molecular and cellular mechanisms underlying microglia-mediated neuroinflammation and neurodegeneration. The incorporation or generation of microglia into three-dimensional (3D) organoid cultures provides a more physiologically relevant environment that offers further opportunities to study microglial dynamics and disease modeling. This review describes several protocols that have been recently developed for the generation of human-induced microglia. Importantly, it highlights the promise of these in vitro models in advancing our understanding of brain disorders and facilitating personalized drug screening.
    Keywords:  Classical differentiation; Directed differentiation; Human pluripotent stem cells; Microglia; Neurodegenerative diseases; Organoid
    DOI:  https://doi.org/10.1016/j.ibneur.2024.03.005
  12. Mol Neurodegener. 2024 Apr 24. 19(1): 37
    Regulation of human microglial gene expression and function via RNAase-H active antisense oligonucleotides in vivo in Alzheimer's disease.
    Lina Vandermeulen, Ivana Geric, Laura Fumagalli, Mohamed Kreir, Ashley Lu, Annelies Nonneman, Jessie Premereur, Leen Wolfs, Rafaela Policarpo, Nicola Fattorelli, An De Bondt, Ilse Van Den Wyngaert, Bob Asselbergh, Mark Fiers, Bart De Strooper, Constantin d'Ydewalle, Renzo Mancuso.
       BACKGROUND: Microglia play important roles in maintaining brain homeostasis and neurodegeneration. The discovery of genetic variants in genes predominately or exclusively expressed in myeloid cells, such as Apolipoprotein E (APOE) and triggering receptor expressed on myeloid cells 2 (TREM2), as the strongest risk factors for Alzheimer's disease (AD) highlights the importance of microglial biology in the brain. The sequence, structure and function of several microglial proteins are poorly conserved across species, which has hampered the development of strategies aiming to modulate the expression of specific microglial genes. One way to target APOE and TREM2 is to modulate their expression using antisense oligonucleotides (ASOs).
    METHODS: In this study, we identified, produced, and tested novel, selective and potent ASOs for human APOE and TREM2. We used a combination of in vitro iPSC-microglia models, as well as microglial xenotransplanted mice to provide proof of activity in human microglial in vivo.
    RESULTS: We proved their efficacy in human iPSC microglia in vitro, as well as their pharmacological activity in vivo in a xenografted microglia model. We demonstrate ASOs targeting human microglia can modify their transcriptional profile and their response to amyloid-β plaques in vivo in a model of AD.
    CONCLUSIONS: This study is the first proof-of-concept that human microglial can be modulated using ASOs in a dose-dependent manner to manipulate microglia phenotypes and response to neurodegeneration in vivo.
    Keywords:  APOE; Alzheimer’s disease; Antisense oligonucleotide; Microglia; Neuroinflammation; TREM2
    DOI:  https://doi.org/10.1186/s13024-024-00725-9
  13. Ann Clin Transl Neurol. 2024 Apr 22.
    Motor band sign is specific for amyotrophic lateral sclerosis and corresponds to motor symptoms.
    Charlotte Zejlon, Stefan Sennfält, Johannes Finnsson, Bryan Connolly, Sven Petersson, Tobias Granberg, Caroline Ingre.
       OBJECTIVE: Magnetic resonance imaging can detect neurodegenerative iron accumulation in the motor cortex, called the motor band sign. This study aims to evaluate its sensitivity/specificity and correlations to symptomatology, biomarkers, and clinical outcome in amyotrophic lateral sclerosis.
    METHODS: This prospective study consecutively enrolled 114 persons with amyotrophic lateral sclerosis and 79 mimics referred to Karolinska University Hospital, and also 31 healthy controls. All underwent 3-Tesla brain susceptibility-weighted imaging. Three raters independently assessed motor cortex susceptibility with total and regional motor band scores. Survival was evaluated at a median of 34.2 months after the imaging.
    RESULTS: The motor band sign identified amyotrophic lateral sclerosis with a sensitivity of 59.6% and a specificity of 91.1% versus mimics and 96.8% versus controls. Higher motor band scores were more common with genetic risk factors (p = 0.032), especially with C9orf72 mutation, and were associated with higher neurofilament light levels (std. β 0.22, p = 0.019). Regional scores correlated strongly with focal symptoms (medial region vs. gross motor dysfunction, std. β -0.64, p = 0.001; intermediate region vs. fine motor dysfunction, std. β -0.51, p = 0.031; lateral region vs. bulbar symptoms std. β -0.71, p < 0.001). There were no associations with cognition, progression rate, or survival.
    INTERPRETATION: In a real-life clinical setting, the motor band sign has high specificity but relatively low sensitivity for identifying amyotrophic lateral sclerosis. Associations with genetic risk factors, neurofilament levels and somatotopic correspondence to focal motor weakness suggest that the motor band sign could be a suitable biomarker for diagnostics and clinical trials in amyotrophic lateral sclerosis.
    DOI:  https://doi.org/10.1002/acn3.52066
  14. Biochim Biophys Acta Mol Basis Dis. 2024 Apr 22. pii: S0925-4439(24)00181-9. [Epub ahead of print] 167192
    Pan-neuronal expression of human mutant SOD1 in Drosophila impairs survival and motor performance, induces early neuroinflammation and chromosome aberrations.
    Francesco Liguori, Francesca Alberti, Susanna Amadio, Daniela Francesca Angelini, Eleonora Pilesi, Giuseppe Vitale, Giulia Tesoriere, Giovanna Borsellino, Fiammetta Vernì, Cinzia Volonté.
      Several mutations in the SOD1 gene encoding for the antioxidant enzyme Superoxide Dismutase 1, are associated with amyotrophic lateral sclerosis, a rare and devastating disease characterized by motor neuron degeneration and patients' death within 2-5 years from diagnosis. Motor neuron loss and related symptomatology manifest mostly in adult life and, to date, there is still a gap of knowledge on the precise cellular and molecular events preceding neurodegeneration. To deepen our awareness of the early phases of the disease, we leveraged two Drosophila melanogaster models pan-neuronally expressing either the mutation A4V or G85R of the human gene SOD1 (hSOD1A4V or hSOD1G85R). We demonstrate that pan-neuronal expression of the hSOD1A4V or hSOD1G85R pathogenic construct impairs survival and motor performance in transgenic flies. Moreover, protein and transcript analysis on fly heads indicates that mutant hSOD1 induction stimulates the glial marker Repo, up-regulates the IMD/Toll immune pathways through antimicrobial peptides and interferes with oxidative metabolism. Finally, cytological analysis of larval brains demonstrates hSOD1-induced chromosome aberrations. Of note, these parameters are found modulated in a timeframe when neurodegeneration is not detected. The novelty of our work is twofold: we have expressed for the first time hSOD1 mutations in all neurons of Drosophila and confirmed some ALS-related pathological phenotypes in these flies, confirming the power of SOD1 mutations in generating ALS-like phenotypes. Moreover, we have related SOD1 pathogenesis to chromosome aberrations and antimicrobial peptides up-regulation. These findings were unexplored in the SOD1-ALS field.
    Keywords:  Amyotrophic lateral sclerosis; Antimicrobial peptides; Chromosome aberrations; Drosophila; Neuroinflammation
    DOI:  https://doi.org/10.1016/j.bbadis.2024.167192
  15. Signal Transduct Target Ther. 2024 Apr 26. 9(1): 112
    Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications.
    Jonas Cerneckis, Hongxia Cai, Yanhong Shi.
      The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and holds great promise to advance regenerative medicine. iPSCs have the capacity for an almost unlimited expansion, are amenable to genetic engineering, and can be differentiated into most somatic cell types. iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies. In this review, we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications. We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs. We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency. Subsequently, we discuss various iPSC-based cellular models, from mono-cultures of a single cell type to complex three-dimensional organoids, and how these models can be applied to elucidate the mechanisms of human development and diseases. We use examples of neurological disorders, coronavirus disease 2019 (COVID-19), and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells. We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies. Finally, we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.
    DOI:  https://doi.org/10.1038/s41392-024-01809-0
  16. Sci Rep. 2024 04 22. 14(1): 9177
    An increase in ER stress and unfolded protein response in iPSCs-derived neuronal cells from neuronopathic Gaucher disease patients.
    Tanapat Pornsukjantra, Nongluk Saikachain, Nareerat Sutjarit, Arthaporn Khongkrapan, Alisa Tubsuwan, Kanit Bhukhai, Thipwimol Tim-Aroon, Usanarat Anurathapan, Suradej Hongeng, Nithi Asavapanumas.
      Gaucher disease (GD) is a lysosomal storage disorder caused by a mutation in the GBA1 gene, responsible for encoding the enzyme Glucocerebrosidase (GCase). Although neuronal death and neuroinflammation have been observed in the brains of individuals with neuronopathic Gaucher disease (nGD), the exact mechanism underlying neurodegeneration in nGD remains unclear. In this study, we used two induced pluripotent stem cells (iPSCs)-derived neuronal cell lines acquired from two type-3 GD patients (GD3-1 and GD3-2) to investigate the mechanisms underlying nGD by biochemical analyses. These iPSCs-derived neuronal cells from GD3-1 and GD3-2 exhibit an impairment in endoplasmic reticulum (ER) calcium homeostasis and an increase in unfolded protein response markers (BiP and CHOP), indicating the presence of ER stress in nGD. A significant increase in the BAX/BCL-2 ratio and an increase in Annexin V-positive cells demonstrate a notable increase in apoptotic cell death in GD iPSCs-derived neurons, suggesting downstream signaling after an increase in the unfolded protein response. Our study involves the establishment of iPSCs-derived neuronal models for GD and proposes a possible mechanism underlying nGD. This mechanism involves the activation of ER stress and the unfolded protein response, ultimately leading to apoptotic cell death in neurons.
    Keywords:  ER stress; Gaucher disease; LSDs; UPR; iPSCs-derived neurons
    DOI:  https://doi.org/10.1038/s41598-024-59834-6
  17. medRxiv. 2024 Apr 10. pii: 2024.04.08.24305503. [Epub ahead of print]
    Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis.
    C Caggiano, M Morselli, X Qian, B Celona, M Thompson, S Wani, A Tosevska, K Taraszka, G Heuer, S Ngo, F Steyn, P Nestor, L Wallace, P McCombe, S Heggie, K Thorpe, C McElligott, G English, A Henders, R Henderson, C Lomen-Hoerth, N Wray, A McRae, M Pellegrini, F Garton, N Zaitlen.
      Cell-free DNA (cfDNA) is increasingly recognized as a promising biomarker candidate for disease monitoring. However, its utility in neurodegenerative diseases, like amyotrophic lateral sclerosis (ALS), remains underexplored. Existing biomarker discovery approaches are tailored to a specific disease context or are too expensive to be clinically practical. Here, we address these challenges through a new approach combining advances in molecular and computational technologies. First, we develop statistical tools to select tissue-informative DNA methylation sites relevant to a disease process of interest. We then employ a capture protocol to select these sites and perform targeted methylation sequencing. Multi-modal information about the DNA methylation patterns are then utilized in machine learning algorithms trained to predict disease status and disease progression. We applied our method to two independent cohorts of ALS patients and controls (n=192). Overall, we found that the targeted sites accurately predicted ALS status and replicated between cohorts. Additionally, we identified epigenetic features associated with ALS phenotypes, including disease severity. These findings highlight the potential of cfDNA as a non-invasive biomarker for ALS.
    DOI:  https://doi.org/10.1101/2024.04.08.24305503
  18. Brain. 2024 Apr 25. pii: awae131. [Epub ahead of print]
    Revisiting distinct nerve excitability patterns in patients with amyotrophic lateral sclerosis.
    Diederik J L Stikvoort García, H Stephan Goedee, Ruben P A van Eijk, Leonard J van Schelven, Leonard H van den Berg, Boudewijn T H M Sleutjes.
      Amyotrophic lateral sclerosis is a devastating neurodegenerative disease, characterized by loss of central and peripheral motor neurones. Although the disease is clinically and genetically heterogeneous, axonal hyperexcitability is a commonly observed feature that has been suggested to reflect an early pathophysiological step linked to the neurodegenerative cascade. Therefore, it is important to clarify the mechanisms causing axonal hyperexcitability and how these relate to the clinical characteristics of patients. Measures derived directly from a nerve excitability recording are frequently used as study endpoints, even though their biophysical basis is difficult to deduce. Mathematical models can aid in the interpretation, but are only reliable when applied to group-averaged recordings. Consequently, model estimates of membrane properties cannot be compared to clinical characteristics or treatment effects in individual patients, posing a considerable limitation in heterogeneous diseases such as amyotrophic lateral sclerosis. To address these challenges, we revisited nerve excitability using a novel pattern-analysis-based approach (principal component analysis). We evaluated disease-specific patterns of excitability changes and established their biophysical origins. Based on the observed patterns, we developed novel compound measures of excitability that facilitate the implementation of this approach in clinical settings We found that excitability changes in amyotrophic lateral sclerosis patients (n = 161, median disease duration = 11 months) were characterized by four unique patterns compared to controls (n = 50, age-gender matched). These four patterns were best explained by changes in resting membrane potential (modulated by Na+/K + -currents), slow potassium- and sodium-currents (modulated by their gating kinetics) and refractory properties of the nerve. Consequently, we were able to show that altered gating of slow potassium-channels was associated with, and predictive of, the disease's progression rate on the amyotrophic lateral sclerosis functional rating scale. Based on these findings, we designed four composite measures that capture these properties to facilitate implementation outside of this study. Our findings demonstrate that nerve excitability changes in patients with amyotrophic lateral sclerosis are dominated by four distinct patterns, each with a distinct biophysical origin. Based on this new approach, we provide evidence that altered slow potassium-channel function may play a role in the rate of disease progression. The magnitudes of these patterns, quantified using either a similar approach or our novel composite measures, have potential as efficient measures to study membrane properties directly in amyotrophic lateral sclerosis patients, and thus aid prognostic stratification and trial design.
    Keywords:  EMG; amyotrophic lateral sclerosis; composite measures; ion-channels; nerve excitability; progression rate
    DOI:  https://doi.org/10.1093/brain/awae131
  19. Elife. 2024 Apr 25. pii: RP92644. [Epub ahead of print]12
    Distinct transcriptomic profile of satellite cells contributes to preservation of neuromuscular junctions in extraocular muscles of ALS mice.
    Ang Li, Jianxun Yi, Xuejun Li, Li Dong, Lyle W Ostrow, Jianjie Ma, Jingsong Zhou.
      Amyotrophic lateral sclerosis (ALS) is a fatal neuromuscular disorder characterized by progressive weakness of almost all skeletal muscles, whereas extraocular muscles (EOMs) are comparatively spared. While hindlimb and diaphragm muscles of end-stage SOD1G93A (G93A) mice (a familial ALS mouse model) exhibit severe denervation and depletion of Pax7+satellite cells (SCs), we found that the pool of SCs and the integrity of neuromuscular junctions (NMJs) are maintained in EOMs. In cell sorting profiles, SCs derived from hindlimb and diaphragm muscles of G93A mice exhibit denervation-related activation, whereas SCs from EOMs of G93A mice display spontaneous (non-denervation-related) activation, similar to SCs from wild-type mice. Specifically, cultured EOM SCs contain more abundant transcripts of axon guidance molecules, including Cxcl12, along with more sustainable renewability than the diaphragm and hindlimb counterparts under differentiation pressure. In neuromuscular co-culture assays, AAV-delivery of Cxcl12 to G93A-hindlimb SC-derived myotubes enhances motor neuron axon extension and innervation, recapitulating the innervation capacity of EOM SC-derived myotubes. G93A mice fed with sodium butyrate (NaBu) supplementation exhibited less NMJ loss in hindlimb and diaphragm muscles. Additionally, SCs derived from G93A hindlimb and diaphragm muscles displayed elevated expression of Cxcl12 and improved renewability following NaBu treatment in vitro. Thus, the NaBu-induced transcriptomic changes resembling the patterns of EOM SCs may contribute to the beneficial effects observed in G93A mice. More broadly, the distinct transcriptomic profile of EOM SCs may offer novel therapeutic targets to slow progressive neuromuscular functional decay in ALS and provide possible 'response biomarkers' in pre-clinical and clinical studies.
    Keywords:  amyotrophic lateral sclerosis; cell biology; chemokine; mouse; neuromuscular junction; satellite cell
    DOI:  https://doi.org/10.7554/eLife.92644
  20. Biomolecules. 2024 Mar 28. pii: 411. [Epub ahead of print]14(4):
    Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue.
    Sharon Natasha Cox, Claudio Lo Giudice, Anna Lavecchia, Maria Luana Poeta, Matteo Chiara, Ernesto Picardi, Graziano Pesole.
      Amyotrophic Lateral Sclerosis (ALS) is a progressive disease with prevalent mitochondrial dysfunctions affecting both upper and lower motor neurons in the motor cortex, brainstem, and spinal cord. Despite mitochondria having their own genome (mtDNA), in humans, most mitochondrial genes are encoded by the nuclear genome (nDNA). Our study aimed to simultaneously screen for nDNA and mtDNA genomes to assess for specific variant enrichment in ALS compared to control tissues. Here, we analysed whole exome (WES) and whole genome (WGS) sequencing data from spinal cord tissues, respectively, of 6 and 12 human donors. A total of 31,257 and 301,241 variants in nuclear-encoded mitochondrial genes were identified from WES and WGS, respectively, while mtDNA reads accounted for 73 and 332 variants. Despite technical differences, both datasets consistently revealed a specific enrichment of variants in the mitochondrial Control Region (CR) and in several of these genes directly associated with mitochondrial dynamics or with Sirtuin pathway genes within ALS tissues. Overall, our data support the hypothesis of a variant burden in specific genes, highlighting potential actionable targets for therapeutic interventions in ALS.
    Keywords:  Amyotrophic Lateral Sclerosis; WES; WGS; bioinformatic pipeline; heteroplasmy; mtDNA; nDNA; variants
    DOI:  https://doi.org/10.3390/biom14040411
  21. Sci Rep. 2024 04 20. 14(1): 9064
    Epigenetic modulation through BET bromodomain inhibitors as a novel therapeutic strategy for progranulin-deficient frontotemporal dementia.
    Zachary C Rosenthal, Daniel M Fass, N Connor Payne, Angela She, Debasis Patnaik, Krista M Hennig, Rachel Tesla, Gordon C Werthmann, Charlotte Guhl, Surya A Reis, Xiaoyu Wang, Yueting Chen, Michael Placzek, Noelle S Williams, Jacob Hooker, Joachim Herz, Ralph Mazitschek, Stephen J Haggarty.
      Frontotemporal dementia (FTD) is a debilitating neurodegenerative disorder with currently no disease-modifying treatment options available. Mutations in GRN are one of the most common genetic causes of FTD, near ubiquitously resulting in progranulin (PGRN) haploinsufficiency. Small molecules that can restore PGRN protein to healthy levels in individuals bearing a heterozygous GRN mutation may thus have therapeutic value. Here, we show that epigenetic modulation through bromodomain and extra-terminal domain (BET) inhibitors (BETi) potently enhance PGRN protein levels, both intracellularly and secreted forms, in human central nervous system (CNS)-relevant cell types, including in microglia-like cells. In terms of potential for disease modification, we show BETi treatment effectively restores PGRN levels in neural cells with a GRN mutation known to cause PGRN haploinsufficiency and FTD. We demonstrate that BETi can rapidly and durably enhance PGRN in neural progenitor cells (NPCs) in a manner dependent upon BET protein expression, suggesting a gain-of-function mechanism. We further describe a CNS-optimized BETi chemotype that potently engages endogenous BRD4 and enhances PGRN expression in neuronal cells. Our results reveal a new epigenetic target for treating PGRN-deficient forms of FTD and provide mechanistic insight to aid in translating this discovery into therapeutics.
    DOI:  https://doi.org/10.1038/s41598-024-59110-7
  22. Neuropharmacology. 2024 Apr 22. pii: S0028-3908(24)00136-9. [Epub ahead of print] 109967
    Analgesic effect of Botulinum toxin in neuropathic pain is sodium channel independent.
    Aylin B Kesdoğan, Anika Neureiter, Arnim J Gaebler, Anil K Kalia, Jannis Körner, Angelika Lampert.
      Botulinum neurotoxin type A BoNT/A is used off-label as a third line therapy for neuropathic pain. However, the mechanism of action remains unclear. In recent years, the role of voltage-gated sodium channels (Nav) in neuropathic pain became evident and it was suggested that block of sodium channels by BoNT/A would contribute to its analgesic effect. We assessed sodium channel function in the presence of BoNT/A in heterologously expressed Nav1.7, Nav1.3, and the neuronal cell line ND7/23 by high throughput automated and manual patch-clamp. We used both the full protein and the isolated catalytic light chain LC/A for acute or long-term extracellular or intracellular exposure. To assess the toxin's effect in a human cellular system, we differentiated induced pluripotent stem cells (iPSC) into sensory neurons from a healthy control and a patient suffering from a hereditary neuropathic pain syndrome (inherited erythromelalgia) carrying the Nav1.7/p.Q875E-mutation and carried out multi electrode array measurements. Both BoNT/A and the isolated catalytic light chain LC/A showed limited effects in heterologous expression systems and the neuronal cell line ND7/23. Spontaneous activity in iPSC derived sensory neurons remained unaltered upon BoNT/A exposure both in neurons from the healthy control and the mutation carrying patient. BoNT/A may not specifically be beneficial in pain syndromes linked to sodium channel variants. The favorable effects of BoNT/A in neuropathic pain are likely based on mechanisms other than sodium channel blockage and new approaches to understand BoNT/A's therapeutic effects are necessary.
    DOI:  https://doi.org/10.1016/j.neuropharm.2024.109967
  23. Commun Integr Biol. 2024 ;17(1): 2343532
    Neuronal glycolysis: focus on developmental morphogenesis and localized subcellular functions.
    Gianluca Gallo.
      Glycolysis is a metabolic pathway that directly generates adenosine triphosphate (ATP), provides metabolic intermediates for anabolism, and supports mitochondrial oxidative phosphorylation. This review addresses recent advances in our understanding of the functions of neuronal glycolysis during the development of neuronal morphogenesis, focusing on the emergent concept that neuronal glycolysis serves local subcellular bioenergetic roles in maintaining neuronal function. The current evidence indicates that glycolysis is subcellularly targeted to specific organelles and molecular machinery to locally supply bioenergetic support for defined subcellular mechanisms underlying neuronal morphogenesis (i.e. axon extension, axon retraction and axonal transport). Thus, the concept of glycolysis as a "housekeeping" mechanism in neurons would benefit revision and future work aim to further define its subcellular functions at varied developmental stages.
    Keywords:  Bioenergetics; actin; axon; glycolysis; mitochondria
    DOI:  https://doi.org/10.1080/19420889.2024.2343532
  24. bioRxiv. 2024 Apr 15. pii: 2024.04.12.589153. [Epub ahead of print]
    Slow kinesin-dependent microtubular transport facilitates ribbon synapse assembly in developing cochlear inner hair cells.
    Roos Anouk Voorn, Michael Sternbach, Amandine Jarysta, Vladan Rankovic, Basile Tarchini, Fred Wolf, Christian Vogl.
      Sensory synapses are characterized by electron-dense presynaptic specializations, so-called synaptic ribbons. In cochlear inner hair cells (IHCs), ribbons play an essential role as core active zone (AZ) organizers, where they tether synaptic vesicles, cluster calcium channels and facilitate the temporally-precise release of primed vesicles. While a multitude of studies aimed to elucidate the molecular composition and function of IHC ribbon synapses, the developmental formation of these signalling complexes remains largely elusive to date. To address this shortcoming, we performed long-term live-cell imaging of fluorescently-labelled ribbon precursors in young postnatal IHCs to track ribbon precursor motion. We show that ribbon precursors utilize the apico-basal microtubular (MT) cytoskeleton for targeted trafficking to the presynapse, in a process reminiscent of slow axonal transport in neurons. During translocation, precursor volume regulation is achieved by highly dynamic structural plasticity - characterized by regularly-occurring fusion and fission events. Pharmacological MT destabilization negatively impacted on precursor translocation and attenuated structural plasticity, whereas genetic disruption of the anterograde molecular motor Kif1a impaired ribbon volume accumulation during developmental maturation. Combined, our data thus indicate an essential role of the MT cytoskeleton and Kif1a in adequate ribbon synapse formation and structural maintenance.
    DOI:  https://doi.org/10.1101/2024.04.12.589153
  25. Cell. 2024 Apr 25. pii: S0092-8674(24)00358-1. [Epub ahead of print]187(9): 2143-2157.e15
    Functional sensory circuits built from neurons of two species.
    Benjamin T Throesch, Muhammad Khadeesh Bin Imtiaz, Rodrigo Muñoz-Castañeda, Masahiro Sakurai, Andrea L Hartzell, Kiely N James, Alberto R Rodriguez, Greg Martin, Giordano Lippi, Sergey Kupriyanov, Zhuhao Wu, Pavel Osten, Juan Carlos Izpisua Belmonte, Jun Wu, Kristin K Baldwin.
      A central question for regenerative neuroscience is whether synthetic neural circuits, such as those built from two species, can function in an intact brain. Here, we apply blastocyst complementation to selectively build and test interspecies neural circuits. Despite approximately 10-20 million years of evolution, and prominent species differences in brain size, rat pluripotent stem cells injected into mouse blastocysts develop and persist throughout the mouse brain. Unexpectedly, the mouse niche reprograms the birth dates of rat neurons in the cortex and hippocampus, supporting rat-mouse synaptic activity. When mouse olfactory neurons are genetically silenced or killed, rat neurons restore information flow to odor processing circuits. Moreover, they rescue the primal behavior of food seeking, although less well than mouse neurons. By revealing that a mouse can sense the world using neurons from another species, we establish neural blastocyst complementation as a powerful tool to identify conserved mechanisms of brain development, plasticity, and repair.
    Keywords:  blastocyst complementation; brain evolution; brain regeneration; development; disease models; interspecies chimeras; neural circuits; neurons; olfaction; pluripotent stem cells
    DOI:  https://doi.org/10.1016/j.cell.2024.03.042
  26. Methods Mol Biol. 2024 ;2757 239-257
    Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.
    Viraj Muthye, Dennis V Lavrov.
      Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.
    Keywords:  Ctenophora; Machine learning; MitoPredictor; Mitochondria; Mnemiopsis; Proteome; Random Forest
    DOI:  https://doi.org/10.1007/978-1-0716-3642-8_10
  27. Annu Rev Neurosci. 2024 Apr 25.
    The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders.
    Bess Frost, Josh Dubnau.
      Over 40% of the human genome is composed of retrotransposons, DNA species that hold the potential to replicate via an RNA intermediate and are evolutionarily related to retroviruses. Retrotransposons are most studied for their ability to jump within a genome, which can cause DNA damage and novel insertional mutations. Retrotransposon-encoded products, including viral-like proteins, double-stranded RNAs, and extrachromosomal cytoplasmic DNAs, can also be potent activators of the innate immune system. A growing body of evidence suggests that retrotransposons are activated in age-related neurodegenerative disorders and that such activation causally contributes to neurotoxicity. Here we provide an overview of retrotransposon biology and outline evidence of retrotransposon activation in age-related neurodegenerative disorders, with an emphasis on those involving TAR-DNA binding protein-43 (TDP-43) and tau. Studies to date provide the basis for ongoing clinical trials and hold promise for innovative strategies to ameliorate the adverse effects of retrotransposon dysregulation in neurodegenerative disorders.
    DOI:  https://doi.org/10.1146/annurev-neuro-082823-020615
  28. Front Cell Neurosci. 2024 ;18 1389335
    GABAergic interneuron diversity and organization are crucial for the generation of human-specific functional neural networks in cerebral organoids.
    Sebastian H Heesen, Georg Köhr.
      This mini review investigates the importance of GABAergic interneurons for the network function of human-induced pluripotent stem cells (hiPSC)-derived brain organoids. The presented evidence suggests that the abundance, diversity and three-dimensional cortical organization of GABAergic interneurons are the primary elements responsible for the creation of synchronous neuronal firing patterns. Without intricate inhibition, coupled oscillatory patterns cannot reach a sufficient complexity to transfer spatiotemporal information constituting physiological network function. Furthermore, human-specific brain network function seems to be mediated by a more complex and interconnected inhibitory structure that remains developmentally flexible for a longer period when compared to rodents. This suggests that several characteristics of human brain networks cannot be captured by rodent models, emphasizing the need for model systems like organoids that adequately mimic physiological human brain function in vitro.
    Keywords:  2D/3D neuronal cell culture; E-I balance; GABAergic interneurons; cerebral organoids; functional neural networks; human-specific inhibition; phase-amplitude-coupling
    DOI:  https://doi.org/10.3389/fncel.2024.1389335
  29. Life Sci. 2024 Apr 18. pii: S0024-3205(24)00241-8. [Epub ahead of print] 122651
    Exploring the intricacies of calcium dysregulation in ischemic stroke: Insights into neuronal cell death and therapeutic strategies.
    Vikrant Rahi, Ravinder K Kaundal.
      Calcium ion (Ca2+) dysregulation is one of the main causes of neuronal cell death and brain damage after cerebral ischemia. During ischemic stroke, the ability of neurons to maintain Ca2+ homeostasis is compromised. Ca2+ regulates various functions of the nervous system, including neuronal activity and adenosine triphosphate (ATP) production. Disruptions in Ca2+ homeostasis can trigger a cascade of events, including activation of the unfolded protein response (UPR) pathway, which is associated with endoplasmic reticulum (ER) stress and mitochondrial dysfunction. This response occurs when the cell is unable to manage protein folding within the ER due to various stressors, such as a high influx of Ca2+. Consequently, the UPR is initiated to restore ER function and alleviate stress, but prolonged activation can lead to mitochondrial dysfunction and, ultimately, cell death. Hence, precise regulation of Ca2+ within the cell is mandatory. The ER and mitochondria are two such organelles that maintain intracellular Ca2+ homeostasis through various calcium-operating channels, including ryanodine receptors (RyRs), inositol trisphosphate receptors (IP3Rs), sarco/endoplasmic reticulum calcium ATPases (SERCAs), the mitochondrial Na+/Ca2+ exchanger (NCLX), the mitochondrial calcium uniporter (MCU) and voltage-dependent anion channels (VDACs). These channels utilize Ca2+ sequestering and release mechanisms to maintain intracellular Ca2+ homeostasis and ensure proper cellular function and survival. The present review critically evaluates the significance of Ca2+ and its physiological role in cerebral ischemia. We have compiled recent findings on calcium's role and emerging treatment strategies, particularly targeting mitochondria and the endoplasmic reticulum, to address Ca2+ overload in cerebral ischemia.
    Keywords:  Calcium dysregulation; Cerebral ischemia; ER stress; Mitochondrial dysfunction; Unfolded protein response
    DOI:  https://doi.org/10.1016/j.lfs.2024.122651
  30. Front Cell Neurosci. 2024 ;18 1384085
    Knockdown of tgfb1a partially improves ALS phenotype in a transient zebrafish model.
    David Gonzalez, Xiomara Cuenca, Miguel L Allende.
      Amyotrophic lateral sclerosis (ALS) corresponds to a neurodegenerative disorder marked by the progressive degeneration of both upper and lower motor neurons located in the brain, brainstem, and spinal cord. ALS can be broadly categorized into two main types: sporadic ALS (sALS), which constitutes approximately 90% of all cases, and familial ALS (fALS), which represents the remaining 10% of cases. Transforming growth factor type-β (TGF-β) is a cytokine involved in various cellular processes and pathological contexts, including inflammation and fibrosis. Elevated levels of TGF-β have been observed in the plasma and cerebrospinal fluid (CSF) of both ALS patients and mouse models. In this perspective, we explore the impact of the TGF-β signaling pathway using a transient zebrafish model for ALS. Our findings reveal that the knockdown of tgfb1a lead to a partial prevention of motor axon abnormalities and locomotor deficits in a transient ALS zebrafish model at 48 h post-fertilization (hpf). In this context, we delve into the proposed distinct roles of TGF-β in the progression of ALS. Indeed, some evidence suggests a dual role for TGF-β in ALS progression. Initially, it seems to exert a neuroprotective effect in the early stages, but paradoxically, it may contribute to disease progression in later stages. Consequently, we suggest that the TGF-β signaling pathway emerges as an attractive therapeutic target for treating ALS. Nevertheless, further research is crucial to comprehensively understand the nuanced role of TGF-β in the pathological context.
    Keywords:  amyotrophic lateral sclerosis; danio rerio; motor neuron; neurodegenerative disease; transforming growth factor type β; zebrafish
    DOI:  https://doi.org/10.3389/fncel.2024.1384085
  31. Cell Regen. 2024 Apr 23. 13(1): 10
    Unveiling new horizons in heart research: the promise of multi-chamber cardiac organoids.
    Junjie Hou, Ye-Guang Chen, Jing-Wei Xiong.
      Human cardiac and other organoids have recently emerged as a groundbreaking tool for advancing our understanding the developmental biology of human organs. A recent paper from Sasha Mendjan's laboratory published in the journal Cell on December 7, 2023, reported the generation of multi-chamber cardioids from human pluripotent stem cells, a transformative technology in the field of cardiology. In this short highlight paper, we summarize their findings. Their cardioids remarkably recapitulate the complexity of the human embryonic heart, including tissue architecture, cellular diversity, and functionality providing an excellent in vitro model for investigation of human heart development, disease modeling, precision medicine, and regenerative medicine. Thus, generating cardioids is an important step forward for understanding human heart development and developing potential therapies for heart diseases.
    Keywords:  Cardiac organoid; Heart development; Organ development
    DOI:  https://doi.org/10.1186/s13619-024-00193-y
  32. Genes (Basel). 2024 Apr 16. pii: 496. [Epub ahead of print]15(4):
    Neurofilaments in Sporadic and Familial Amyotrophic Lateral Sclerosis: A Systematic Review and Meta-Analysis.
    Pashtun Shahim, Gina Norato, Ninet Sinaii, Henrik Zetterberg, Kaj Blennow, Leighton Chan, Christopher Grunseich.
       BACKGROUND: Neurofilament proteins have been implicated to be altered in amyotrophic lateral sclerosis (ALS). The objectives of this study were to assess the diagnostic and prognostic utility of neurofilaments in ALS.
    METHODS: Studies were conducted in electronic databases (PubMed/MEDLINE, Embase, Web of Science, and Cochrane CENTRAL) from inception to 17 August 2023, and investigated neurofilament light (NfL) or phosphorylated neurofilament heavy chain (pNfH) in ALS. The study design, enrolment criteria, neurofilament concentrations, test accuracy, relationship between neurofilaments in cerebrospinal fluid (CSF) and blood, and clinical outcome were recorded. The protocol was registered with PROSPERO, CRD42022376939.
    RESULTS: Sixty studies with 8801 participants were included. Both NfL and pNfH measured in CSF showed high sensitivity and specificity in distinguishing ALS from disease mimics. Both NfL and pNfH measured in CSF correlated with their corresponding levels in blood (plasma or serum); however, there were stronger correlations between CSF NfL and blood NfL. NfL measured in blood exhibited high sensitivity and specificity in distinguishing ALS from controls. Both higher levels of NfL and pNfH either measured in blood or CSF were correlated with more severe symptoms as assessed by the ALS Functional Rating Scale Revised score and with a faster disease progression rate; however, only blood NfL levels were associated with shorter survival.
    DISCUSSION: Both NfL and pNfH measured in CSF or blood show high diagnostic utility and association with ALS functional scores and disease progression, while CSF NfL correlates strongly with blood (either plasma or serum) and is also associated with survival, supporting its use in clinical diagnostics and prognosis. Future work must be conducted in a prospective manner with standardized bio-specimen collection methods and analytical platforms, further improvement in immunoassays for quantification of pNfH in blood, and the identification of cut-offs across the ALS spectrum and controls.
    Keywords:  CSF; amyotrophic lateral sclerosis; blood; neurofilament light; phosphorylated neurofilament heavy chain
    DOI:  https://doi.org/10.3390/genes15040496
  33. Biomolecules. 2024 Mar 26. pii: 398. [Epub ahead of print]14(4):
    Biomarkers for Managing Neurodegenerative Diseases.
    Lara Cheslow, Adam E Snook, Scott A Waldman.
      Neurological disorders are the leading cause of cognitive and physical disability worldwide, affecting 15% of the global population. Due to the demographics of aging, the prevalence of neurological disorders, including neurodegenerative diseases, will double over the next two decades. Unfortunately, while available therapies provide symptomatic relief for cognitive and motor impairment, there is an urgent unmet need to develop disease-modifying therapies that slow the rate of pathological progression. In that context, biomarkers could identify at-risk and prodromal patients, monitor disease progression, track responses to therapy, and parse the causality of molecular events to identify novel targets for further clinical investigation. Thus, identifying biomarkers that discriminate between diseases and reflect specific stages of pathology would catalyze the discovery and development of therapeutic targets. This review will describe the prevalence, known mechanisms, ongoing or recently concluded therapeutic clinical trials, and biomarkers of three of the most prevalent neurodegenerative diseases, including Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD).
    Keywords:  Alzheimer’s disease; Parkinson’s disease; amyotrophic lateral sclerosis; biomarkers
    DOI:  https://doi.org/10.3390/biom14040398
  34. Chem Sci. 2024 Apr 24. 15(16): 6064-6075
    Protein painting for structural and binding site analysis via intracellular lysine reactivity profiling with o-phthalaldehyde.
    Zhenxiang Zheng, Ya Zeng, Kunjia Lai, Bin Liao, Pengfei Li, Chris Soon Heng Tan.
      The three-dimensional structure and the molecular interaction of proteins determine their roles in many cellular processes. Chemical protein painting with protein mass spectrometry can identify changes in structural conformations and molecular interactions of proteins including their binding sites. Nevertheless, most current protein painting techniques identify protein targets and binding sites of drugs in vitro using a cell lysate or purified protein. Here, we tested 11 membrane-permeable lysine-reactive chemical probes for intracellular covalent labeling of endogenous proteins, which reveals ortho-phthalaldehyde (OPA) as the most reactive probe in the intracellular environment. An MS workflow and a new data analysis strategy termed RAPID (Reactive Amino acid Profiling by Inverse Detection) was developed to enhance detection sensitivity. RAPID with OPA successfully identified structural changes induced by the allosteric drug TEPP-46 on its target protein PKM2 and was applied to profile the conformation change of the proteome occurring in cells during thermal denaturation. The application of RAPID-OPA on cells treated with geldanamycin, selumetinib, and staurosporine successfully revealed their binding sites on target proteins. Thus, RAPID-OPA for cellular protein painting enables the identification of ligand-binding sites and detection of protein structural changes occurring in cells.
    DOI:  https://doi.org/10.1039/d4sc00032c
  35. Cells. 2024 Apr 13. pii: 674. [Epub ahead of print]13(8):
    Identity and Maturity of iPSC-Derived Oligodendrocytes in 2D and Organoid Systems.
    Ella Zeldich, Sandeep Rajkumar.
      Oligodendrocytes originating in the brain and spinal cord as well as in the ventral and dorsal domains of the neural tube are transcriptomically and functionally distinct. These distinctions are also reflected in the ultrastructure of the produced myelin, and the susceptibility to myelin-related disorders, which highlights the significance of the choice of patterning protocols in the differentiation of induced pluripotent stem cells (iPSCs) into oligodendrocytes. Thus, our first goal was to survey the different approaches applied to the generation of iPSC-derived oligodendrocytes in 2D culture and in organoids, as well as reflect on how these approaches pertain to the regional and spatial fate of the generated oligodendrocyte progenitors and myelinating oligodendrocytes. This knowledge is increasingly important to disease modeling and future therapeutic strategies. Our second goal was to recap the recent advances in the development of oligodendrocyte-enriched organoids, as we explore their relevance to a regional specification alongside their duration, complexity, and maturation stages of oligodendrocytes and myelin biology. Finally, we discuss the shortcomings of the existing protocols and potential future explorations.
    Keywords:  brain organoids; iPSCs; myelin; oligodendrocytes; regional patterning
    DOI:  https://doi.org/10.3390/cells13080674
  36. Front Physiol. 2024 ;15 1368054
    The two C. elegans class VI myosins, SPE-15/HUM-3 and HUM-8, share similar motor properties, but have distinct developmental and tissue expression patterns.
    Ranya Behbehani, Chloe Johnson, Alexander J Holmes, Matthew J Gratian, Daniel P Mulvihill, Folma Buss.
      Myosins of class VI move toward the minus-end of actin filaments and play vital roles in cellular processes such as endocytosis, autophagy, protein secretion, and the regulation of actin filament dynamics. In contrast to the majority of metazoan organisms examined to date which contain a single MYO6 gene, C. elegans, possesses two MYO6 homologues, SPE-15/HUM-3 and HUM-8. Through a combination of in vitro biochemical/biophysical analysis and cellular assays, we confirmed that both SPE-15/HUM-3 and HUM-8 exhibit reverse directionality, velocities, and ATPase activity similar to human MYO6. Our characterization also revealed that unlike SPE-15/HUM-3, HUM-8 is expressed as two distinct splice isoforms, one with an additional unique 14 amino acid insert in the cargo-binding domain. While lipid and adaptor binding sites are conserved in SPE-15/HUM-3 and HUM-8, this conservation does not enable recruitment to endosomes in mammalian cells. Finally, we performed super-resolution confocal imaging on transgenic worms expressing either mNeonGreen SPE-15/HUM-3 or wrmScarlet HUM-8. Our results show a clear distinction in tissue distribution between SPE-15/HUM-3 and HUM-8. While SPE-15/HUM-3 exhibited specific expression in the gonads and neuronal tissue in the head, HUM-8 was exclusively localized in the intestinal epithelium. Overall, these findings align with the established tissue distributions and localizations of human MYO6.
    Keywords:  C. elegans; HUM-8; MYO6; SPE-15/HUM-3; actin
    DOI:  https://doi.org/10.3389/fphys.2024.1368054
  37. Biochim Biophys Acta Mol Basis Dis. 2024 Jan;pii: S0925-4439(23)00294-6. [Epub ahead of print]1870(1): 166928
    Copper enhances aggregational toxicity of mutant huntingtin in a Drosophila model of Huntington's Disease.
    Amanda G Lobato, Natalie Ortiz-Vega, Yi Zhu, Deepa Neupane, Katlyn K Meier, R Grace Zhai.
      Huntington's disease (HD) is a progressive neurodegenerative disorder with clinical presentations of moderate to severe cognitive, motor, and psychiatric disturbances. HD is caused by the trinucleotide repeat expansion of CAG of the huntingtin (HTT) gene. The mutant HTT protein containing pathological polyglutamine (polyQ) extension is prone to misfolding and aggregation in the brain. It has previously been observed that copper and iron concentrations are increased in the striata of post-mortem human HD brains. Although it has been shown that the accumulation of mutant HTT protein can interact with copper, the underlying HD progressive phenotypes due to copper overload remains elusive. Here, in a Drosophila model of HD, we showed that copper induces dose-dependent aggregational toxicity and enhancement of Htt-induced neurodegeneration. Specifically, we found that copper increases mutant Htt aggregation, enhances the accumulation of Thioflavin S positive β-amyloid structures within Htt aggregates, and consequently alters autophagy in the brain. Administration of copper chelator D-penicillamine (DPA) through feeding significantly decreases β-amyloid aggregates in the HD pathological model. These findings reveal a direct role of copper in potentiating mutant Htt protein-induced aggregational toxicity, and further indicate the potential impact of environmental copper exposure in the disease onset and progression of HD.
    Keywords:  Aggregates; Chelation; Copper; Huntingtin; Huntington's disease
    DOI:  https://doi.org/10.1016/j.bbadis.2023.166928
  38. In Vitro Cell Dev Biol Anim. 2024 Apr 24.
    The migration pattern of cells during the mesoderm and endoderm differentiation from human pluripotent stem cells.
    Kenshiro Maruyama, Shota Miyazaki, Ryo Kobayashi, Haru Hikita, Tadashi Tsubone, Kiyoshi Ohnuma.
      Gastrulation is the first major differentiation process in animal embryos. However, the dynamics of human gastrulation remain mostly unknown owing to the ethical limitations. We studied the dynamics of the mesoderm and endoderm cell differentiation from human pluripotent stem cells for insight into the cellular dynamics of human gastrulation. Human pluripotent stem cells have properties similar to those of the epiblast, which gives rise to the three germ layers. The mesoderm and endoderm were induced with more than 75% purity from human induced pluripotent stem cells. Single-cell dynamics of pluripotent stem cell-derived mesoderm and endoderm cells were traced using time-lapse imaging. Both mesoderm and endoderm cells migrate randomly, accompanied by short-term directional persistence. No substantial differences were detected between mesoderm and endoderm migration. Computer simulations created using the measured parameters revealed that random movement and external force, such as the spread out of cells from the primitive streak area, mimicked the homogeneous discoidal germ layer formation. These results were consistent with the development of amniotes, which suggests the effectiveness of human pluripotent stem cells as a good model for studying human embryogenesis.
    Keywords:  Cell migration; Endoderm; Gastrulation; Mesoderm; Random walk
    DOI:  https://doi.org/10.1007/s11626-024-00904-4
  39. STAR Protoc. 2024 Apr 25. pii: S2666-1667(24)00205-3. [Epub ahead of print]5(2): 103040
    Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.
    Shuhao Xu, Grady G Nguyen, Jack T Naritomi, Hema M Kopalle, Brian A Yee, Katherine L Rothamel, Evan A Boyle, Gene W Yeo.
      Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We describe steps for partitioning annotated transcript regions and fitting data to a beta-binomial model to call windows of enriched binding. From raw CLIP data, we detail how users can map reproducible RNA-binding sites to call enriched windows and perform downstream analysis. This protocol supports optional customizations for different use cases. For complete details on the use and execution of this protocol, please refer to Boyle et al.1.
    Keywords:  Bioinformatics; Gene Expression; Genomics; RNA-seq; Sequence analysis
    DOI:  https://doi.org/10.1016/j.xpro.2024.103040
  40. bioRxiv. 2024 Apr 08. pii: 2024.04.04.588107. [Epub ahead of print]
    STING promotes homeostatic maintenance of tissues and confers longevity with aging.
    Jacob W Hopkins, Katherine B Sulka, Machlan Sawden, Kimberly A Carroll, Ronald D Brown, Stephen C Bunnell, Alexander Poltorak, Albert Tai, Eric R Reed, Shruti Sharma.
      Local immune processes within aging tissues are a significant driver of aging associated dysfunction, but tissue-autonomous pathways and cell types that modulate these responses remain poorly characterized. The cytosolic DNA sensing pathway, acting through cyclic GMP-AMP synthase (cGAS) and Stimulator of Interferon Genes (STING), is broadly expressed in tissues, and is poised to regulate local type I interferon (IFN-I)-dependent and independent inflammatory processes within tissues. Recent studies suggest that the cGAS/STING pathway may drive pathology in various in vitro and in vivo models of accelerated aging. To date, however, the role of the cGAS/STING pathway in physiological aging processes, in the absence of genetic drivers, has remained unexplored. This remains a relevant gap, as STING is ubiquitously expressed, implicated in multitudinous disorders, and loss of function polymorphisms of STING are highly prevalent in the human population (>50%). Here we reveal that, during physiological aging, STING-deficiency leads to a significant shortening of murine lifespan, increased pro-inflammatory serum cytokines and tissue infiltrates, as well as salient changes in histological composition and organization. We note that aging hearts, livers, and kidneys express distinct subsets of inflammatory, interferon-stimulated gene (ISG), and senescence genes, collectively comprising an immune fingerprint for each tissue. These distinctive patterns are largely imprinted by tissue-specific stromal and myeloid cells. Using cellular interaction network analyses, immunofluorescence, and histopathology data, we show that these immune fingerprints shape the tissue architecture and the landscape of cell-cell interactions in aging tissues. These age-associated immune fingerprints are grossly dysregulated with STING-deficiency, with key genes that define aging STING- sufficient tissues greatly diminished in the absence of STING. Changes in immune signatures are concomitant with a restructuring of the stromal and myeloid fractions, whereby cell:cell interactions are grossly altered and resulting in disorganization of tissue architecture in STING-deficient organs. This altered homeostasis in aging STING-deficient tissues is associated with a cross-tissue loss of homeostatic tissue-resident macrophage (TRM) populations in these tissues. Ex vivo analyses reveal that basal STING- signaling limits the susceptibility of TRMs to death-inducing stimuli and determines their in situ localization in tissue niches, thereby promoting tissue homeostasis. Collectively, these data upend the paradigm that cGAS/STING signaling is primarily pathological in aging and instead indicate that basal STING signaling sustains tissue function and supports organismal longevity. Critically, our study urges caution in the indiscriminate targeting of these pathways, which may result in unpredictable and pathological consequences for health during aging.
    HIGHLIGHTS: Aging tissues are associated with tissue-autonomous immune fingerprints, primarily driven by interactions of tissue stromal and myeloid populations. STING shapes these immune fingerprints of aging tissues in unexpected ways.Loss of STING alters the location, numbers, and viability of tissue resident macrophages.STING signaling is critical for longer lifespans and maintenance of tissue architecture.
    DOI:  https://doi.org/10.1101/2024.04.04.588107
  41. Mol Biol Rep. 2024 Apr 26. 51(1): 580
    Discovery of a novel homozygous SOD1 truncating variant bolsters infantile SOD1 deficiency syndrome.
    Mustafa Dogan, Kerem Teralı, Recep Eroz, Hüseyin Kılıç, Alper Gezdirici, Burçin Gönüllü.
       OBJECTIVE: Superoxide dismutase 1 (SOD1) is an important antioxidant enzyme whose main function is to neutralise superoxide free radicals in the cytoplasm. Heterozygous variants in SOD1 are responsible for a substantial percentage of familial amyotrophic lateral sclerosis (ALS) cases. Recently, several reports have shown that biallelic loss of SOD1 function results in a novel phenotype called infantile SOD1 deficiency syndrome, which is consistent with a recessive pattern of inheritance and can be distinguished from typical (adult-onset) ALS.
    METHODS: We documented detailed family histories and clinical data, followed by whole-exome sequencing and family co-segregation analysis through Sanger sequencing. To facilitate comparisons, relevant data from fifteen previously reported patients with SOD1-related neurodevelopmental disorders were included.
    RESULTS: This study presents a new Turkish family with two affected children exhibiting severe delayed motor development, infancy-onset loss of motor skills, axial hypotonia, tetraspasticity, and impaired cognitive functions. Genetic analysis revealed a novel homozygous frameshift variant in SOD1 (c.248dupG [p.Asp84Argfs*8]), with computational biochemical studies shedding light on the mechanistic aspects of SOD1 dysfunction.
    CONCLUSIONS: Our findings contribute an affirmative report of a fourth biallelic variant resulting in a severe clinical phenotype, reminiscent of those induced by previously identified homozygous loss-of-function SOD1 variants. This research not only advances our understanding of the pathogenesis of this debilitating neurological syndrome but also aligns with ongoing intensive efforts to comprehend and address SOD1-linked ALS.
    Keywords:  Axial hypotonia; Loss of motor skills; Non-amyotrophic lateral sclerosis; SOD1 deficiency; Tetraspasticity
    DOI:  https://doi.org/10.1007/s11033-024-09513-6
  42. bioRxiv. 2024 Apr 21. pii: 2024.04.18.584138. [Epub ahead of print]
    Transcriptional Variabilities in Human hiPSC-derived Cardiomyocytes: All Genes Are Not Equal and Their Robustness May Foretell Donor's Disease Susceptibility.
    C Charles Gu, Andrea Matter, Amy Turner, Praful Aggarwal, Wei Yang, Xiao Sun, Steven C Hunt, Cora E Lewis, Donna K Arnett, Blake Anson, Steve Kattman, Ulrich Broeckel.
      Human induced pluripotent stem cells (hiPSCs) are frequently used to study disease-associated variations. We characterized transcriptional variability from a hiPSC-derived cardiomyocyte (hiPSC-CM) study of left ventricular hypertrophy (LVH) using donor samples from the HyperGEN study. Multiple hiPSC-CM differentiations over reprogramming events (iPSC generation) across 7 donors were used to assess variabilities from reprogramming, differentiation, and donor LVH status. Variability arising from pathological alterations was assessed using a cardiac stimulant applied to the hiPSC-CMs to trigger hypertrophic responses. We found that for most genes (73.3%~85.5%), technical variability was smaller than biological variability. Further, we identified and characterized lists of "noise" genes showing greater technical variability and "signal" genes showing greater biological variability. Together, they support a "genetic robustness" hypothesis of disease-modeling whereby cellular response to relevant stimuli in hiPSC-derived somatic cells from diseased donors tends to show more transcriptional variability. Our findings suggest that hiPSC-CMs can provide a valid model for cardiac hypertrophy and distinguish between technical and disease-relevant transcriptional changes.
    DOI:  https://doi.org/10.1101/2024.04.18.584138
  43. Medicina (Kaunas). 2024 Mar 23. pii: 527. [Epub ahead of print]60(4):
    Artificial Intelligence (AI) for Early Diagnosis of Retinal Diseases.
    Uday Pratap Singh Parmar, Pier Luigi Surico, Rohan Bir Singh, Francesco Romano, Carlo Salati, Leopoldo Spadea, Mutali Musa, Caterina Gagliano, Tommaso Mori, Marco Zeppieri.
      Artificial intelligence (AI) has emerged as a transformative tool in the field of ophthalmology, revolutionizing disease diagnosis and management. This paper provides a comprehensive overview of AI applications in various retinal diseases, highlighting its potential to enhance screening efficiency, facilitate early diagnosis, and improve patient outcomes. Herein, we elucidate the fundamental concepts of AI, including machine learning (ML) and deep learning (DL), and their application in ophthalmology, underscoring the significance of AI-driven solutions in addressing the complexity and variability of retinal diseases. Furthermore, we delve into the specific applications of AI in retinal diseases such as diabetic retinopathy (DR), age-related macular degeneration (AMD), Macular Neovascularization, retinopathy of prematurity (ROP), retinal vein occlusion (RVO), hypertensive retinopathy (HR), Retinitis Pigmentosa, Stargardt disease, best vitelliform macular dystrophy, and sickle cell retinopathy. We focus on the current landscape of AI technologies, including various AI models, their performance metrics, and clinical implications. Furthermore, we aim to address challenges and pitfalls associated with the integration of AI in clinical practice, including the "black box phenomenon", biases in data representation, and limitations in comprehensive patient assessment. In conclusion, this review emphasizes the collaborative role of AI alongside healthcare professionals, advocating for a synergistic approach to healthcare delivery. It highlights the importance of leveraging AI to augment, rather than replace, human expertise, thereby maximizing its potential to revolutionize healthcare delivery, mitigate healthcare disparities, and improve patient outcomes in the evolving landscape of medicine.
    Keywords:  AI; artificial intelligence; early diagnosis; retinal diseases
    DOI:  https://doi.org/10.3390/medicina60040527
  44. Commun Biol. 2024 Apr 24. 7(1): 493
    Multimodal joint deconvolution and integrative signature selection in proteomics.
    Yue Pan, Xusheng Wang, Jiao Sun, Chunyu Liu, Junmin Peng, Qian Li.
      Deconvolution is an efficient approach for detecting cell-type-specific (cs) transcriptomic signals without cellular segmentation. However, this type of methods may require a reference profile from the same molecular source and tissue type. Here, we present a method to dissect bulk proteome by leveraging tissue-matched transcriptome and proteome without using a proteomics reference panel. Our method also selects the proteins contributing to the cellular heterogeneity shared between bulk transcriptome and proteome. The deconvoluted result enables downstream analyses such as cs-protein Quantitative Trait Loci (cspQTL) mapping. We benchmarked the performance of this multimodal deconvolution approach through CITE-seq pseudo bulk data, a simulation study, and the bulk multi-omics data from human brain normal tissues and breast cancer tumors, individually, showing robust and accurate cell abundance quantification across different datasets. This algorithm is implemented in a tool MICSQTL that also provides cspQTL and multi-omics integrative visualization, available at https://bioconductor.org/packages/MICSQTL .
    DOI:  https://doi.org/10.1038/s42003-024-06155-z
  45. Neurobiol Dis. 2024 Apr 20. pii: S0969-9961(24)00105-0. [Epub ahead of print] 106506
    Dopamine‑iron homeostasis interaction rescues mitochondrial fitness in Parkinson's disease.
    Chiara Buoso, Markus Seifert, Martin Lang, Corey M Griffith, Begoña Talavera Andújar, Maria Paulina Castelo Rueda, Christine Fischer, Carolina Doerrier, Heribert Talasz, Alessandra Zanon, Peter P Pramstaller, Emma L Schymanski, Irene Pichler, Guenter Weiss.
      Imbalances of iron and dopamine metabolism along with mitochondrial dysfunction have been linked to the pathogenesis of Parkinson's disease (PD). We have previously suggested a direct link between iron homeostasis and dopamine metabolism, as dopamine can increase cellular uptake of iron into macrophages thereby promoting oxidative stress responses. In this study, we investigated the interplay between iron, dopamine, and mitochondrial activity in neuroblastoma SH-SY5Y cells and human induced pluripotent stem cell (hiPSC)-derived dopaminergic neurons differentiated from a healthy control and a PD patient with a mutation in the α-synuclein (SNCA) gene. In SH-SY5Y cells, dopamine treatment resulted in increased expression of the transmembrane iron transporters transferrin receptor 1 (TFR1), ferroportin (FPN), and mitoferrin2 (MFRN2) and intracellular iron accumulation, suggesting that dopamine may promote iron uptake. Furthermore, dopamine supplementation led to reduced mitochondrial fitness including decreased mitochondrial respiration, increased cytochrome c control efficiency, reduced mtDNA copy number and citrate synthase activity, increased oxidative stress and impaired aconitase activity. In dopaminergic neurons derived from a healthy control individual, dopamine showed comparable effects as observed in SH-SY5Y cells. The hiPSC-derived PD neurons harboring an endogenous SNCA mutation demonstrated altered mitochondrial iron homeostasis, reduced mitochondrial capacity along with increased oxidative stress and alterations of tricarboxylic acid cycle linked metabolic pathways compared with control neurons. Importantly, dopamine treatment of PD neurons promoted a rescue effect by increasing mitochondrial respiration, activating antioxidant stress response, and normalizing altered metabolite levels linked to mitochondrial function. These observations provide evidence that dopamine affects iron homeostasis, intracellular stress responses and mitochondrial function in healthy cells, while dopamine supplementation can restore the disturbed regulatory network in PD cells.
    Keywords:  Dopamine; Iron; Mitochondrial function; Parkinson's disease; hiPSC-derived neurons
    DOI:  https://doi.org/10.1016/j.nbd.2024.106506
  46. Stem Cell Res Ther. 2024 Apr 23. 15(1): 114
    Stepwise combined cell transplantation using mesenchymal stem cells and induced pluripotent stem cell-derived motor neuron progenitor cells in spinal cord injury.
    Jang-Woon Kim, Juryun Kim, Hyunkyung Mo, Heeju Han, Yeri Alice Rim, Ji Hyeon Ju.
       BACKGROUND: Spinal cord injury (SCI) is an intractable neurological disease in which functions cannot be permanently restored due to nerve damage. Stem cell therapy is a promising strategy for neuroregeneration after SCI. However, experimental evidence of its therapeutic effect in SCI is lacking. This study aimed to investigate the efficacy of transplanted cells using stepwise combined cell therapy with human mesenchymal stem cells (hMSC) and induced pluripotent stem cell (iPSC)-derived motor neuron progenitor cells (iMNP) in a rat model of SCI.
    METHODS: A contusive SCI model was developed in Sprague-Dawley rats using multicenter animal spinal cord injury study (MASCIS) impactor. Three protocols were designed and conducted as follows: (Subtopic 1) chronic SCI + iMNP, (Subtopic 2) acute SCI + multiple hMSC injections, and (Main topic) chronic SCI + stepwise combined cell therapy using multiple preemptive hMSC and iMNP. Neurite outgrowth was induced by coculturing hMSC and iPSC-derived motor neuron (iMN) on both two-dimensional (2D) and three-dimensional (3D) spheroid platforms during mature iMN differentiation in vitro.
    RESULTS: Stepwise combined cell therapy promoted mature motor neuron differentiation and axonal regeneration at the lesional site. In addition, stepwise combined cell therapy improved behavioral recovery and was more effective than single cell therapy alone. In vitro results showed that hMSC and iMN act synergistically and play a critical role in the induction of neurite outgrowth during iMN differentiation and maturation.
    CONCLUSIONS: Our findings show that stepwise combined cell therapy can induce alterations in the microenvironment for effective cell therapy in SCI. The in vitro results suggest that co-culturing hMSC and iMN can synergistically promote induction of MN neurite outgrowth.
    Keywords:  Cell transplantation; Induced pluripotent stem cells; Mesenchymal stem cells; Motor neuron progenitor cells; Spinal cord injury
    DOI:  https://doi.org/10.1186/s13287-024-03714-3
  47. Microorganisms. 2024 Apr 17. pii: 813. [Epub ahead of print]12(4):
    Contribution of the Type III Secretion System (T3SS2) of Vibrio parahaemolyticus in Mitochondrial Stress in Human Intestinal Cells.
    Nicolás Plaza, Diliana Pérez-Reytor, Gino Corsini, Katherine García, Ítalo M Urrutia.
      Vibrio parahaemolyticus is an important human pathogen that is currently the leading cause of shellfish-borne gastroenteritis in the world. Particularly, the pandemic strain has the capacity to induce cytotoxicity and enterotoxicity through its Type 3 Secretion System (T3SS2) that leads to massive cell death. However, the specific mechanism by which the T3SS2 induces cell death remains unclear and its contribution to mitochondrial stress is not fully understood. In this work, we evaluated the contribution of the T3SS2 of V. parahaemolyticus in generating mitochondrial stress during infection in human intestinal HT-29 cells. To evaluate the contribution of the T3SS2 of V. parahaemolyticus in mitochondrial stress, infection assays were carried out to evaluate mitochondrial transition pore opening, mitochondrial fragmentation, ATP quantification, and cell viability during infection. Our results showed that the Δvscn1 (T3SS2+) mutant strain contributes to generating the sustained opening of the mitochondrial transition pore. Furthermore, it generates perturbations in the ATP production in infected cells, leading to a significant decrease in cell viability and loss of membrane integrity. Our results suggest that the T3SS2 from V. parahaemolyticus plays a role in generating mitochondrial stress that leads to cell death in human intestinal HT-29 cells. It is important to highlight that this study represents the first report indicating the possible role of the V. parahaemolyticus T3SS2 and its effector proteins involvement in generating mitochondrial stress, its impact on the mitochondrial pore, and its effect on ATP production in human cells.
    Keywords:  T3SS2; Vibrio parahaemolyticus; cell death; foodborne illness; mitochondria
    DOI:  https://doi.org/10.3390/microorganisms12040813
  48. Cell Mol Life Sci. 2024 Apr 25. 81(1): 197
    Engineered platforms for mimicking cardiac development and drug screening.
    Madison Stiefbold, Haokang Zhang, Leo Q Wan.
      Congenital heart defects are associated with significant health challenges, demanding a deep understanding of the underlying biological mechanisms and, thus, better devices or platforms that can recapitulate human cardiac development. The discovery of human pluripotent stem cells has substantially reduced the dependence on animal models. Recent advances in stem cell biology, genetic editing, omics, microfluidics, and sensor technologies have further enabled remarkable progress in the development of in vitro platforms with increased fidelity and efficiency. In this review, we provide an overview of advancements in in vitro cardiac development platforms, with a particular focus on technological innovation. We categorize these platforms into four areas: two-dimensional solid substrate cultures, engineered substrate architectures that enhance cellular functions, cardiac organoids, and embryos/explants-on-chip models. We conclude by addressing current limitations and presenting future perspectives.
    Keywords:  Cardiac development; Cardiac morphogenesis; Cardiac tissue engineering; Congenital heart diseases; Embryo-on-chip; In vitro platforms; Organ-on-chip
    DOI:  https://doi.org/10.1007/s00018-024-05231-1
  49. J Neurosci. 2024 Apr 22. pii: e1709232024. [Epub ahead of print]
    Inhibitory roles of Apolipoprotein E Christchurch astrocytes in curbing tau propagation using human pluripotent stem cell-derived models.
    Dominantly Inherited Alzheimer Network (DIAN)
      Genetic variants in the apolipoprotein E (APOE) gene affect the onset and progression of Alzheimer's disease (AD). The APOE Christchurch (APOE Ch) variant has been identified as the most prominent candidate for preventing the onset and progression of AD. In this study, we generated isogenic APOE3Ch/3Ch human induced pluripotent stem cells (iPSCs) from APOE3/3 healthy control female iPSCs and induced them into astrocytes. RNA expression analysis revealed the inherent resilience of APOE3Ch/3Ch astrocytes to induce a reactive state in response to inflammatory cytokines. Moreover, cytokine treatment changed astrocytic morphology with more complexity in APOE3/3 astrocytes, but not in APOE3Ch/3Ch astrocytes, indicating resilience of the rare variant to a reactive state. Interestingly, we observed robust morphological alterations containing more intricate processes when cocultured with iPSC-derived cortical neurons, in which APOE3Ch/3Ch astrocytes reduced complexity compared with APOE3/3 astrocytes. To assess the impacts of tau propagation effects, we next developed a sophisticated and sensitive assay utilizing cortical neurons derived from human iPSCs, previously generated from donors of both sexes. We showed that APOE3Ch/3Ch astrocytes effectively mitigated tau propagation within iPSC-derived neurons. This study provides important experimental evidence of the characteristic functions exhibited by APOE3Ch/3Ch astrocytes, thereby offering valuable insights for the advancement of novel clinical interventions in AD research.Significance Statement Alzheimer's disease (AD) is a degenerative disease that causes cognitive decline. Familial AD is a severe form caused by mutations in the PSEN1, PSEN2, or APP genes. One carrier of the PSEN1 mutation did not develop dementia. This carrier also had a rare variant of the APOE gene, the Christchurch variant. The APOE Christchurch variant may protect against familial AD. The mechanism of this protection is not fully understood. In the present study, we have successfully demonstrated that the APOE Christchurch variant suppresses the propagation of tau and exhibits a diminished capacity to convert native astrocytes into reactive astrocytes. These significant findings contribute novel insights to the field of the APOE gene and AD research.
    DOI:  https://doi.org/10.1523/JNEUROSCI.1709-23.2024
  50. Viruses. 2024 Apr 01. pii: 552. [Epub ahead of print]16(4):
    A Comparative Study of Human Pluripotent Stem Cell-Derived Macrophages in Modeling Viral Infections.
    Yaxuan Zhang, Hui Qiu, Fuyu Duan, Haoran An, Huimin Qiao, Xingwu Zhang, Jing-Ren Zhang, Qiang Ding, Jie Na.
      Macrophages play multiple roles in innate immunity including phagocytosing pathogens, modulating the inflammatory response, presenting antigens, and recruiting other immune cells. Tissue-resident macrophages (TRMs) adapt to the local microenvironment and can exhibit different immune responses upon encountering distinct pathogens. In this study, we generated induced macrophages (iMACs) derived from human pluripotent stem cells (hPSCs) to investigate the interactions between the macrophages and various human pathogens, including the hepatitis C virus (HCV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Streptococcus pneumoniae. iMACs can engulf all three pathogens. A comparison of the RNA-seq data of the iMACs encountering these pathogens revealed that the pathogens activated distinct gene networks related to viral response and inflammation in iMACs. Interestingly, in the presence of both HCV and host cells, iMACs upregulated different sets of genes involved in immune cell migration and chemotaxis. Finally, we constructed an image-based high-content analysis system consisting of iMACs, recombinant GFP-HCV, and hepatic cells to evaluate the effect of a chemical inhibitor on HCV infection. In summary, we developed a human cell-based in vitro model to study the macrophage response to human viral and bacterial infections; the results of the transcriptome analysis indicated that the iMACs were a useful resource for modeling pathogen-macrophage-tissue microenvironment interactions.
    Keywords:  SARS-CoV-2; hepatitis C virus; human pluripotent stem cell; infection; macrophage
    DOI:  https://doi.org/10.3390/v16040552
  51. bioRxiv. 2024 Apr 20. pii: 2024.04.19.590338. [Epub ahead of print]
    Spatiotemporal proteomic profiling of cellular responses to NLRP3 agonists.
    L Robert Hollingsworth, Priya Veeraraghavan, Joao A Paulo, J Wade Harper, Isabella Rauch.
      Nucleotide-binding domain and leucine-rich repeat pyrin-domain containing protein 3 (NLRP3) is an innate immune sensor that forms an inflammasome in response to various cellular stressors. Gain-of-function mutations in NLRP3 cause autoinflammatory diseases and NLRP3 signalling itself exacerbates the pathogenesis of many other human diseases. Despite considerable therapeutic interest, the primary drivers of NLRP3 activation remain controversial due to the diverse array of signals that are integrated through NLRP3. Here, we mapped subcellular proteome changes to lysosomes, mitochondrion, EEA1-positive endosomes, and Golgi caused by the NLRP3 inflammasome agonists nigericin and CL097. We identified several common disruptions to retrograde trafficking pathways, including COPI and Shiga toxin-related transport, in line with recent studies. We further characterized mouse NLRP3 trafficking throughout its activation using temporal proximity proteomics, which supports a recent model of NLRP3 recruitment to endosomes during inflammasome activation. Collectively, these findings provide additional granularity to our understanding of the molecular events driving NLRP3 activation and serve as a valuable resource for cell biological research. We have made our proteomics data accessible through an open-access Shiny browser to facilitate future research within the community, available at: https://harperlab.connect.hms.harvard.edu/inflame/ . We will display anonymous peer review for this manuscript on pubpub.org ( https://harperlab.pubpub.org/pub/nlrp3/ ) rather than a traditional journal. Moreover, we invite community feedback on the pubpub version of this manuscript, and we will address criticisms accordingly.
    DOI:  https://doi.org/10.1101/2024.04.19.590338
  52. Mol Biol Cell. 2024 Apr 24. mbcE23110419
    Baseline Unfolded Protein Response Signaling Adjusts the Timing of the Mammalian Cell Cycle.
    Soham P Chowdhury, Sabrina C Solley, Elena Polishchuk, Julien Bacal, Julia E Conrad, Brooke M Gardner, Diego Acosta-Alvear, Francesca Zappa.
      The endoplasmic reticulum (ER) is a single-copy organelle that cannot be generated de novo, suggesting coordination between the mechanisms overseeing ER integrity and those controlling the cell cycle to maintain organelle inheritance. The Unfolded Protein Response (UPR) is a conserved signaling network that regulates ER homeostasis. Here, we show that pharmacological and genetic inhibition of the UPR sensors IRE1, ATF6, and PERK in unstressed cells delays the cell cycle, with PERK inhibition showing the most penetrant effect, which was associated with a slowdown of the G1-to-S/G2 transition. Treatment with the small molecule ISRIB to bypass the effects of PERK-dependent phosphorylation of the translation initiation factor eIF2⍺ had no such effect, suggesting that cell cycle timing depends on PERK's kinase activity but is independent of eIF2⍺ phosphorylation. Using complementary light and electron microscopy and flow cytometry-based analyses, we also demonstrate that the ER enlarges before mitosis. Together, our results suggest coordination between UPR signaling and the cell cycle to maintain ER physiology during cell division.
    DOI:  https://doi.org/10.1091/mbc.E23-11-0419
  53. Biomedicines. 2024 Apr 12. pii: 856. [Epub ahead of print]12(4):
    Inhibition of Metalloproteinases Extends Longevity and Function of In Vitro Human iPSC-Derived Skeletal Muscle.
    Natali Barakat, Himanshi Jangir, Leandro Gallo, Marcella Grillo, Xiufang Guo, James Hickman.
      In vitro culture longevity has long been a concern for disease modeling and drug testing when using contractable cells. The dynamic nature of certain cells, such as skeletal muscle, contributes to cell surface release, which limits the system's ability to conduct long-term studies. This study hypothesized that regulating the extracellular matrix (ECM) dynamics should be able to prolong cell attachment on a culture surface. Human induced pluripotent stem cell (iPSC)-derived skeletal muscle (SKM) culture was utilized to test this hypothesis due to its forceful contractions in mature muscle culture, which can cause cell detachment. By specifically inhibiting matrix metalloproteinases (MMPs) that work to digest components of the ECM, it was shown that the SKM culture remained adhered for longer periods of time, up to 80 days. Functional testing of myofibers indicated that cells treated with the MMP inhibitors, tempol, and doxycycline, displayed a significantly reduced fatigue index, although the fidelity was not affected, while those treated with the MMP inducer, PMA, indicated a premature detachment and increased fatigue index. The MMP-modulating activity by the inhibitors and inducer was further validated by gel zymography analysis, where the MMP inhibitor showed minimally active MMPs, while the inducer-treated cells indicated high MMP activity. These data support the hypotheses that regulating the ECM dynamics can help maximize in vitro myotube longevity. This proof-of-principle strategy would benefit the modeling of diseases that require a long time to develop and the evaluation of chronic effects of potential therapeutics.
    Keywords:  cell adhesion; extracellular matrix; human iPSC-derived skeletal muscle; metalloproteinases
    DOI:  https://doi.org/10.3390/biomedicines12040856
  54. Curr Protoc. 2024 Apr;4(4): e1049
    Correction: Current Strategies of Modeling Human Trophoblast Using Human Pluripotent Stem Cells in vitro.
    Virginia Chu Cheung, Tony Bui, Francesca Soncin, Tao Bai, John A Kessler, Mana M Parast, Mariko Horii.
      
    DOI:  https://doi.org/10.1002/cpz1.1049
  55. Int J Mol Sci. 2024 Apr 20. pii: 4526. [Epub ahead of print]25(8):
    Essential Role of COPII Proteins in Maintaining the Contractile Ring Anchoring to the Plasma Membrane during Cytokinesis in Drosophila Male Meiosis.
    Yoshiki Matsuura, Kana Kaizuka, Yoshihiro H Inoue.
      Coatomer Protein Complex-II (COPII) mediates anterograde vesicle transport from the endoplasmic reticulum (ER) to the Golgi apparatus. Here, we report that the COPII coatomer complex is constructed dependent on a small GTPase, Sar1, in spermatocytes before and during Drosophila male meiosis. COPII-containing foci co-localized with transitional endoplasmic reticulum (tER)-Golgi units. They showed dynamic distribution along astral microtubules and accumulated around the spindle pole, but they were not localized on the cleavage furrow (CF) sites. The depletion of the four COPII coatomer subunits, Sec16, or Sar1 that regulate COPII assembly resulted in multinucleated cell production after meiosis, suggesting that cytokinesis failed in both or either of the meiotic divisions. Although contractile actomyosin and anilloseptin rings were formed once plasma membrane ingression was initiated, they were frequently removed from the plasma membrane during furrowing. We explored the factors conveyed toward the CF sites in the membrane via COPII-mediated vesicles. DE-cadherin-containing vesicles were formed depending on Sar1 and were accumulated in the cleavage sites. Furthermore, COPII depletion inhibited de novo plasma membrane insertion. These findings suggest that COPII vesicles supply the factors essential for the anchoring and/or constriction of the contractile rings at cleavage sites during male meiosis in Drosophila.
    Keywords:  COPII; Drosophila; contractile ring; cytokinesis; male meiosis
    DOI:  https://doi.org/10.3390/ijms25084526
  56. Eur J Neurol. 2024 Apr 26. e16304
    Symptom-based staging for logopenic variant primary progressive aphasia.
    Chris J D Hardy, Cathleen Taylor-Rubin, Beatrice Taylor, Emma Harding, Aida Suarez Gonzalez, Jessica Jiang, Laura Thompson, Rachel Kingma, Anthipa Chokesuwattanaskul, Ffion Walker, Suzie Barker, Emilie Brotherhood, Claire Waddington, Olivia Wood, Nikki Zimmermann, Nuriye Kupeli, Keir X X Yong, Paul M Camic, Joshua Stott, Charles R Marshall, Neil P Oxtoby, Jonathan D Rohrer, Frankie O'Shea, Anna Volkmer, Sebastian J Crutch, Jason D Warren.
       BACKGROUND AND PURPOSE: Logopenic variant primary progressive aphasia (lvPPA) is a major variant presentation of Alzheimer's disease (AD) that signals the importance of communication dysfunction across AD phenotypes. A clinical staging system is lacking for the evolution of AD-associated communication difficulties that could guide diagnosis and care planning. Our aim was to create a symptom-based staging scheme for lvPPA, identifying functional milestones relevant to the broader AD spectrum.
    METHODS: An international lvPPA caregiver cohort was surveyed on symptom development under an 'exploratory' survey (34 UK caregivers). Feedback from this survey informed the development of a 'consolidation' survey (27 UK, 10 Australian caregivers) in which caregivers were presented with six provisional clinical stages and feedback was analysed using a mixed-methods approach.
    RESULTS: Six clinical stages were endorsed. Early symptoms included word-finding difficulty, with loss of message comprehension and speech intelligibility signalling later-stage progression. Additionally, problems with hearing in noise, memory and route-finding were prominent early non-verbal symptoms. 'Milestone' symptoms were identified that anticipate daily-life functional transitions and care needs.
    CONCLUSIONS: This work introduces a new symptom-based staging scheme for lvPPA, and highlights milestone symptoms that could inform future clinical scales for anticipating and managing communication dysfunction across the AD spectrum.
    Keywords:  Alzheimer's disease; logopenic; primary progressive aphasia; staging
    DOI:  https://doi.org/10.1111/ene.16304
  57. Stem Cell Res. 2024 Apr 12. pii: S1873-5061(24)00118-1. [Epub ahead of print]77 103420
    Generation of a PPM1A-deficient human induced pluripotent stem cell line using CRISPR-Cas9 technology.
    Xinrui Guo, Kui Zhao, Yanqi Zhang, Tiancheng Zhou, Guangjin Pan.
      PPM1A is a member of the serine/threonine protein phosphatase family. It can bind to a variety of proteins to dephosphorylate them, and extensively regulates many life activities such as cell growth, cell stress, immune response, and tumor formation. Here we constructed a human induced pluripotent stem cell (hiPSC) line with knockout of PPM1A using CRISPR/Cas9-mediated gene targeting. This cell line exhibits normal karyotype, pluripotency, and trilineage differentiation potential, which could provide a useful cellular resource for exploring the mechanism of PPM1A in regulating downstream signaling pathways and explore the application of PPM1A in anti-tumor and anti-infection.
    DOI:  https://doi.org/10.1016/j.scr.2024.103420
  58. Proc Natl Acad Sci U S A. 2024 Apr 30. 121(18): e2312992121
    Chaotic neural dynamics facilitate probabilistic computations through sampling.
    Yu Terada, Taro Toyoizumi.
      Cortical neurons exhibit highly variable responses over trials and time. Theoretical works posit that this variability arises potentially from chaotic network dynamics of recurrently connected neurons. Here, we demonstrate that chaotic neural dynamics, formed through synaptic learning, allow networks to perform sensory cue integration in a sampling-based implementation. We show that the emergent chaotic dynamics provide neural substrates for generating samples not only of a static variable but also of a dynamical trajectory, where generic recurrent networks acquire these abilities with a biologically plausible learning rule through trial and error. Furthermore, the networks generalize their experience in the stimulus-evoked samples to the inference without partial or all sensory information, which suggests a computational role of spontaneous activity as a representation of the priors as well as a tractable biological computation for marginal distributions. These findings suggest that chaotic neural dynamics may serve for the brain function as a Bayesian generative model.
    Keywords:  Bayesian computation; chaos; computational neuroscience; cue integration; recurrent neural networks
    DOI:  https://doi.org/10.1073/pnas.2312992121
  59. PLoS Biol. 2024 Apr;22(4): e3002559
    Neuronal cell cycle reentry events in the aging brain are more prevalent in neurodegeneration and lead to cellular senescence.
    Deng Wu, Jacquelyne Ka-Li Sun, Kim Hei-Man Chow.
      Increasing evidence indicates that terminally differentiated neurons in the brain may recommit to a cell cycle-like process during neuronal aging and under disease conditions. Because of the rare existence and random localization of these cells in the brain, their molecular profiles and disease-specific heterogeneities remain unclear. Through a bioinformatics approach that allows integrated analyses of multiple single-nucleus transcriptome datasets from human brain samples, these rare cell populations were identified and selected for further characterization. Our analyses indicated that these cell cycle-related events occur predominantly in excitatory neurons and that cellular senescence is likely their immediate terminal fate. Quantitatively, the number of cell cycle re-engaging and senescent neurons decreased during the normal brain aging process, but in the context of late-onset Alzheimer's disease (AD), these cells accumulate instead. Transcriptomic profiling of these cells suggested that disease-specific differences were predominantly tied to the early stage of the senescence process, revealing that these cells presented more proinflammatory, metabolically deregulated, and pathology-associated signatures in disease-affected brains. Similarly, these general features of cell cycle re-engaging neurons were also observed in a subpopulation of dopaminergic neurons identified in the Parkinson's disease (PD)-Lewy body dementia (LBD) model. An extended analysis conducted in a mouse model of brain aging further validated the ability of this bioinformatics approach to determine the robust relationship between the cell cycle and senescence processes in neurons in this cross-species setting.
    DOI:  https://doi.org/10.1371/journal.pbio.3002559
  60. Am J Cardiol. 2024 Apr 22. pii: S0002-9149(24)00310-2. [Epub ahead of print]
    Disentangling Knots of Misfolded Proteins: Do We Really Know the Prognostic Implications of the Pathogenic V122I TTR Variant?
    Anas Jawaid, Isabel Wees, Justin L Grodin.
      
    DOI:  https://doi.org/10.1016/j.amjcard.2024.04.028
  61. Cells. 2024 Apr 18. pii: 702. [Epub ahead of print]13(8):
    Lipidomic Analysis of Plasma Extracellular Vesicles Derived from Alzheimer's Disease Patients.
    Marios G Krokidis, Krishna A Pucha, Maja Mustapic, Themis P Exarchos, Panagiotis Vlamos, Dimitrios Kapogiannis.
      Analysis of blood-based indicators of brain health could provide an understanding of early disease mechanisms and pinpoint possible intervention strategies. By examining lipid profiles in extracellular vesicles (EVs), secreted particles from all cells, including astrocytes and neurons, and circulating in clinical samples, important insights regarding the brain's composition can be gained. Herein, a targeted lipidomic analysis was carried out in EVs derived from plasma samples after removal of lipoproteins from individuals with Alzheimer's disease (AD) and healthy controls. Differences were observed for selected lipid species of glycerolipids (GLs), glycerophospholipids (GPLs), lysophospholipids (LPLs) and sphingolipids (SLs) across three distinct EV subpopulations (all-cell origin, derived by immunocapture of CD9, CD81 and CD63; neuronal origin, derived by immunocapture of L1CAM; and astrocytic origin, derived by immunocapture of GLAST). The findings provide new insights into the lipid composition of EVs isolated from plasma samples regarding specific lipid families (MG, DG, Cer, PA, PC, PE, PI, LPI, LPE, LPC), as well as differences between AD and control individuals. This study emphasizes the crucial role of plasma EV lipidomics analysis as a comprehensive approach for identifying biomarkers and biological targets in AD and related disorders, facilitating early diagnosis and potentially informing novel interventions.
    Keywords:  Alzheimer’s disease; biomarkers; exosomes; extracellular vesicles; lipid profile; neurodegenerative diseases
    DOI:  https://doi.org/10.3390/cells13080702
  62. Curr Biol. 2024 Apr 17. pii: S0960-9822(24)00390-7. [Epub ahead of print]
    Spaced training activates Miro/Milton-dependent mitochondrial dynamics in neuronal axons to sustain long-term memory.
    Alice Pavlowsky, Typhaine Comyn, Julia Minatchy, David Geny, Philippe Bun, Lydia Danglot, Thomas Preat, Pierre-Yves Plaçais.
      Neurons have differential and fluctuating energy needs across distinct cellular compartments, shaped by brain electrochemical activity associated with cognition. In vitro studies show that mitochondria transport from soma to axons is key to maintaining neuronal energy homeostasis. Nevertheless, whether the spatial distribution of neuronal mitochondria is dynamically adjusted in vivo in an experience-dependent manner remains unknown. In Drosophila, associative long-term memory (LTM) formation is initiated by an early and persistent upregulation of mitochondrial pyruvate flux in the axonal compartment of neurons in the mushroom body (MB). Through behavior experiments, super-resolution analysis of mitochondria morphology in the neuronal soma and in vivo mitochondrial fluorescence recovery after photobleaching (FRAP) measurements in the axons, we show that LTM induction, contrary to shorter-lived memories, is sustained by the departure of some mitochondria from MB neuronal soma and increased mitochondrial dynamics in the axonal compartment. Accordingly, impairing mitochondrial dynamics abolished the increased pyruvate consumption, specifically after spaced training and in the MB axonal compartment, thereby preventing LTM formation. Our results thus promote reorganization of the mitochondrial network in neurons as an integral step in elaborating high-order cognitive processes.
    Keywords:  3D-STED microscopy; Drosophila; brain energy metabolism; long-term memory; mitochondria motility; mushroom body
    DOI:  https://doi.org/10.1016/j.cub.2024.03.050
  63. Genes (Basel). 2024 Mar 24. pii: 399. [Epub ahead of print]15(4):
    Structural Features and Physiological Associations of Human 14-3-3ζ Pseudogenes.
    Haroon Lughmani, Hrushil Patel, Ritu Chakravarti.
      There are about 14,000 pseudogenes that are mutated or truncated sequences resembling functional parent genes. About two-thirds of pseudogenes are processed, while others are duplicated. Although initially thought dead, emerging studies indicate they have functional and regulatory roles. We study 14-3-3ζ, an adaptor protein that regulates cytokine signaling and inflammatory diseases, including rheumatoid arthritis, cancer, and neurological disorders. To understand how 14-3-3ζ (gene symbol YWHAZ) performs diverse functions, we examined the human genome and identified nine YWHAZ pseudogenes spread across many chromosomes. Unlike the 32 kb exon-to-exon sequence in YWHAZ, all pseudogenes are much shorter and lack introns. Out of six, four YWHAZ exons are highly conserved, but the untranslated region (UTR) shows significant diversity. The putative amino acid sequence of pseudogenes is 78-97% homologous, resulting in striking structural similarities with the parent protein. The OMIM and Decipher database searches revealed chromosomal loci containing pseudogenes are associated with human diseases that overlap with the parent gene. To the best of our knowledge, this is the first report on pseudogenes of the 14-3-3 family protein and their implications for human health. This bioinformatics-based study introduces a new insight into the complexity of 14-3-3ζ's functions in biology.
    Keywords:  14-3-3; 14-3-3ζ; Alphafold; YWHAZ; autoimmune diseases; behavioral disorders; immune disorders; inflammatory arthritis; pseudogenes
    DOI:  https://doi.org/10.3390/genes15040399
  64. Sci Rep. 2024 04 23. 14(1): 9355
    Spatiotemporal expression of thyroid hormone transporter MCT8 and THRA mRNA in human cerebral organoids recapitulating first trimester cortex development.
    Adina Sophie Graffunder, Audrey Amber Julie Bresser, Valeria Fernandez Vallone, Matthias Megges, Harald Stachelscheid, Peter Kühnen, Robert Opitz.
      Thyroid hormones (TH) play critical roles during nervous system development and patients carrying coding variants of MCT8 (monocarboxylate transporter 8) or THRA (thyroid hormone receptor alpha) present a spectrum of neurological phenotypes resulting from perturbed local TH action during early brain development. Recently, human cerebral organoids (hCOs) emerged as powerful in vitro tools for disease modelling recapitulating key aspects of early human cortex development. To begin exploring prospects of this model for thyroid research, we performed a detailed characterization of the spatiotemporal expression of MCT8 and THRA in developing hCOs. Immunostaining showed MCT8 membrane expression in neuronal progenitor cell types including early neuroepithelial cells, radial glia cells (RGCs), intermediate progenitors and outer RGCs. In addition, we detected robust MCT8 protein expression in deep layer and upper layer neurons. Spatiotemporal SLC16A2 mRNA expression, detected by fluorescent in situ hybridization (FISH), was highly concordant with MCT8 protein expression across cortical cell layers. FISH detected THRA mRNA expression already in neuroepithelium before the onset of neurogenesis. THRA mRNA expression remained low in the ventricular zone, increased in the subventricular zone whereas strong THRA expression was observed in excitatory neurons. In combination with a robust up-regulation of known T3 response genes following T3 treatment, these observations show that hCOs provide a promising and experimentally tractable model to probe local TH action during human cortical neurogenesis and eventually to model the consequences of impaired TH function for early cortex development.
    Keywords:  Cerebral organoids; Human cortex; Human induced pluripotent stem cell; Neurogenesis; Thyroid hormone; Thyroid hormone receptor; Thyroid hormone transporter
    DOI:  https://doi.org/10.1038/s41598-024-59533-2
  65. Sci Total Environ. 2024 Apr 21. pii: S0048-9697(24)02802-X. [Epub ahead of print] 172655
    Low-dose BPA-induced neuronal energy metabolism dysfunction and apoptosis mediated by PINK1/parkin mitophagy pathway in juvenile rats.
    Lingxue Meng, Zedong Ouyang, Yuxin Chen, Chengmeng Huang, Yunjiang Yu, Ruifang Fan.
      Bisphenol A (BPA) is related to neurological disorders involving mitochondrial dysfunction, while the mechanism remains elusive. Therefore, we explored it through in vitro and in vivo experiments. In vitro, hippocampal neurons derived from neonatal rats of different genders were exposed to 1-100 nM and 100 μM BPA, autophagy activator Rapa and inhibitor 3-MA for 7 d. The results suggested that even nanomolar BPA (1-100 nM) disturbed Ca2+ homeostasis and damaged the integrity of mitochondrial cristae in neurons (p < 0.05). Furthermore, BPA increased the number of autophagic lysosomes, LC3II/LC3I ratio, and p62 expression, and decreased parkin expression (p < 0.05), suggesting that the entry of damaged mitochondria into autophagic pathway was prompted, while the autophagic degradation pathway was blocked. This further disrupts neuronal energy metabolism and promotes neuronal apoptosis. However, Rapa attenuated the adverse effects caused by BPA, while 3-MA exacerbated these reactions. In vivo, exposure of juvenile rats to 0.5, 50, 5000 μg/kg‧bw/day BPA during PND 7-21 markedly impaired the structure of hippocampal mitochondria, increased the number of autophagosomes, the rate of neuronal apoptosis, and the expression levels of pro-apoptotic proteins Cyt C, Bax, Bak1, and Caspase3, and decreased the expression of anti-apoptotic protein Bcl2 (p < 0.05). Particularly, male rats are more sensitive to low-dose BPA than females. Overall, environmental-doses BPA can induce the imbalance of energy metabolism in hippocampal neurons via PINK1/parkin mitophagy, thereby inducing their apoptosis. Importantly, this study provides a theoretical basis for attenuating BPA-related neurological diseases.
    Keywords:  Apoptosis; Bisphenol A; Energy metabolism; Mitochondria; Mitophagy
    DOI:  https://doi.org/10.1016/j.scitotenv.2024.172655
  66. Biomolecules. 2024 Mar 26. pii: 399. [Epub ahead of print]14(4):
    Fragile X Messenger Ribonucleoprotein Protein and Its Multifunctionality: From Cytosol to Nucleolus and Back.
    Mohamed S Taha, Mohammad Reza Ahmadian.
      Silencing of the fragile X messenger ribonucleoprotein 1 (FMR1) gene and a consequent lack of FMR protein (FMRP) synthesis are associated with fragile X syndrome, one of the most common inherited intellectual disabilities. FMRP is a multifunctional protein that is involved in many cellular functions in almost all subcellular compartments under both normal and cellular stress conditions in neuronal and non-neuronal cell types. This is achieved through its trafficking signals, nuclear localization signal (NLS), nuclear export signal (NES), and nucleolar localization signal (NoLS), as well as its RNA and protein binding domains, and it is modulated by various post-translational modifications such as phosphorylation, ubiquitination, sumoylation, and methylation. This review summarizes the recent advances in understanding the interaction networks of FMRP with a special focus on FMRP stress-related functions, including stress granule formation, mitochondrion and endoplasmic reticulum plasticity, ribosome biogenesis, cell cycle control, and DNA damage response.
    Keywords:  FMRP; RNA binding; fragile X messenger ribonucleoprotein protein; protein interaction network; stress granule
    DOI:  https://doi.org/10.3390/biom14040399
  67. Int J Mol Sci. 2024 Apr 15. pii: 4368. [Epub ahead of print]25(8):
    Mechanism of Decision Making between Autophagy and Apoptosis Induction upon Endoplasmic Reticulum Stress.
    Orsolya Kapuy.
      Dynamic regulation of the cellular proteome is mainly controlled in the endoplasmic reticulum (ER). Accumulation of misfolded proteins due to ER stress leads to the activation of unfolded protein response (UPR). The primary role of UPR is to reduce the bulk of damages and try to drive back the system to the former or a new homeostatic state by autophagy, while an excessive level of stress results in apoptosis. It has already been proven that the proper order and characteristic features of both surviving and self-killing mechanisms are controlled by negative and positive feedback loops, respectively. The new results suggest that these feedback loops are found not only within but also between branches of the UPR, fine-tuning the response to ER stress. In this review, we summarize the recent knowledge of the dynamical characteristic of endoplasmic reticulum stress response mechanism by using both theoretical and molecular biological techniques. In addition, this review pays special attention to describing the mechanism of action of the dynamical features of the feedback loops controlling cellular life-and-death decision upon ER stress. Since ER stress appears in diseases that are common worldwide, a more detailed understanding of the behaviour of the stress response is of medical importance.
    Keywords:  apoptosis; autophagy; bistability; endoplasmic reticulum stress; systems biology; unfolded protein response
    DOI:  https://doi.org/10.3390/ijms25084368
  68. Muscle Nerve. 2024 Apr 26.
    A single ALS center experience with clinical use of sodium phenylbutyrate-taurursodiol.
    Colin Quinn, Michael Baer, Defne A Amado, Mary Kelley, Lauren Elman.
       INTRODUCTION/AIMS: The aim of this study was to examine clinical utilization and discontinuation rates of sodium phenylbutyrate-taurursodiol (PB-TURSO) in a single Amyotrophic Lateral Sclerosis (ALS) center. PB-TURSO was approved by the United States Food and Drug Administration (FDA) in September 2022. Prior experience has been limited to clinical trials or expanded access protocols. In this manuscript, we discuss insurance approval rates, patient uptake, and discontinuation of PB-TURSO in a large academic center.
    METHODS: Records of patients seen for clinical visits between January 2022 and May 2023 were reviewed. Demographic and clinical characteristics of our clinic population and those initiating PB-TURSO were obtained from our clinical database.
    RESULTS: A total of 228 patients were seen during the observation period and 122 requested PB-TURSO prescriptions. 77% (94) were approved by insurance. 66% (65) of those who were approved or received free drug chose to start medication. 51% (34) of those who initiated PB-TURSO continued to take it through the end of the observation period. Four patients discontinued due to death during the observation period. Of the 29 patients who survived and discontinued, the main reasons for discontinuation were GI symptoms (17, 58.6%) and taste (8, 29.6%).
    DISCUSSION: PB-TURSO was approved by insurance for most patients. The discontinuation rate was high and was driven largely by GI side effects and taste. Future considerations would include deeper examination of demographic trends, patient costs, side effects, and potential benefits in clinical practice.
    Keywords:  ALS; clinical trials; neuromuscular therapeutics
    DOI:  https://doi.org/10.1002/mus.28096
  69. Dev Cell. 2024 Apr 22. pii: S1534-5807(24)00228-4. [Epub ahead of print]
    The Zn2+ transporter ZIP7 enhances endoplasmic-reticulum-associated protein degradation and prevents neurodegeneration in Drosophila.
    Xiaoran Guo, Morgan Mutch, Alba Yurani Torres, Maddalena Nano, Nishi Rauth, Jacob Harwood, Drew McDonald, Zijing Chen, Craig Montell, Wei Dai, Denise J Montell.
      Proteotoxic stress drives numerous degenerative diseases. Cells initially adapt to misfolded proteins by activating the unfolded protein response (UPR), including endoplasmic-reticulum-associated protein degradation (ERAD). However, persistent stress triggers apoptosis. Enhancing ERAD is a promising therapeutic approach for protein misfolding diseases. The ER-localized Zn2+ transporter ZIP7 is conserved from plants to humans and required for intestinal self-renewal, Notch signaling, cell motility, and survival. However, a unifying mechanism underlying these diverse phenotypes was unknown. In studying Drosophila border cell migration, we discovered that ZIP7-mediated Zn2+ transport enhances the obligatory deubiquitination of proteins by the Rpn11 Zn2+ metalloproteinase in the proteasome lid. In human cells, ZIP7 and Zn2+ are limiting for deubiquitination. In a Drosophila model of neurodegeneration caused by misfolded rhodopsin (Rh1), ZIP7 overexpression degrades misfolded Rh1 and rescues photoreceptor viability and fly vision. Thus, ZIP7-mediated Zn2+ transport is a previously unknown, rate-limiting step for ERAD in vivo with therapeutic potential in protein misfolding diseases.
    Keywords:  Drosophila; ER stress; ERAD; apoptosis; border cell migration; integrated stress response; neurodegeneration; proteasome; retinitis pigmentosa; zinc transport
    DOI:  https://doi.org/10.1016/j.devcel.2024.04.003
  70. Aliment Pharmacol Ther. 2024 Apr 21.
    Editorial: Foretelling the future-Emerging role of magnetic resonance enterography as a prognostic tool in Crohn's disease.
    Siri A Urquhart, Joel G Fletcher, David H Bruining.
      
    DOI:  https://doi.org/10.1111/apt.17991
  71. J Biol Chem. 2024 Apr 22. pii: S0021-9258(24)01812-X. [Epub ahead of print] 107311
    Reactivating Hippo by Drug Compounds to Suppress Gastric Cancer and Enhance Chemotherapy Sensitivity.
    Zhifa Cao, Yu Hou, Zhangting Zhao, Hui Zhang, Luyang Tian, Yiming Zhang, Chao Dong, Fenghua Guo, Lijie Tan, Yi Han, Wenjia Wang, Shi Jiao, Yang Tang, Liwei An, Zhaocai Zhou.
      The Hippo signaling pathway plays an essential role in organ size control and tumorigenesis. Loss of Hippo signal and hyper-activation of the downstream oncogenic YAP signaling are commonly observed in various types of cancers. We previously identified STRN3-containing PP2A phosphatase as a negative regulator of MST1/2 kinases (i.e. Hippo) in gastric cancer (GC), opening the possibility of selectively targeting the PP2Aa-STRN3-MST1/2 axis to recover Hippo signaling against cancer. Here, we further discovered 1) disulfiram (DSF), an FDA-approved drug, which can similarly block the binding of STRN3 to PP2A core enzyme, and 2) CX-6258 (CX), a chemical inhibitor, that can disrupt the interaction between STRN3 and MST1/2, both allowing reactivation of Hippo activity to inhibit GC. More importantly, we found these two compounds, via a MST1/2 kinase-dependent manner, inhibit DNA repair to sensitize GC towards chemotherapy. In addition, we identified thiram (TH), a structural analog of DSF, can function similarly to inhibit cancer cell proliferation or enhance chemotherapy sensitivity. Interestingly, inclusion of copper ion enhanced such effects of DSF and TH on GC treatment. Overall, this work demonstrated that pharmacological targeting of the PP2Aa-STRN3-MST1/2 axis by drug compounds can potently recover Hippo signal for tumor treatment.
    Keywords:  Chemotherapy; Drug compound; Gastric cancer; Hippo signaling; STRIPAK
    DOI:  https://doi.org/10.1016/j.jbc.2024.107311
  72. Int J Mol Sci. 2024 Apr 10. pii: 4187. [Epub ahead of print]25(8):
    DNA Damage and Parkinson's Disease.
    Gerd P Pfeifer.
      The etiology underlying most sporadic Parkinson's' disease (PD) cases is unknown. Environmental exposures have been suggested as putative causes of the disease. In cell models and in animal studies, certain chemicals can destroy dopaminergic neurons. However, the mechanisms of how these chemicals cause the death of neurons is not understood. Several of these agents are mitochondrial toxins that inhibit the mitochondrial complex I of the electron transport chain. Familial PD genes also encode proteins with important functions in mitochondria. Mitochondrial dysfunction of the respiratory chain, in combination with the presence of redox active dopamine molecules in these cells, will lead to the accumulation of reactive oxygen species (ROS) in dopaminergic neurons. Here, I propose a mechanism regarding how ROS may lead to cell killing with a specificity for neurons. One rarely considered hypothesis is that ROS produced by defective mitochondria will lead to the formation of oxidative DNA damage in nuclear DNA. Many genes that encode proteins with neuron-specific functions are extraordinary long, ranging in size from several hundred kilobases to well over a megabase. It is predictable that such long genes will contain large numbers of damaged DNA bases, for example in the form of 8-oxoguanine (8-oxoG), which is a major DNA damage type produced by ROS. These DNA lesions will slow down or stall the progression of RNA polymerase II, which is a term referred to as transcription stress. Furthermore, ROS-induced DNA damage may cause mutations, even in postmitotic cells such as neurons. I propose that the impaired transcription and mutagenesis of long, neuron-specific genes will lead to a loss of neuronal integrity, eventually leading to the death of these cells during a human lifetime.
    Keywords:  DNA damage; DNA repair; Parkinson’s disease; mitochondria; mutations; transcription
    DOI:  https://doi.org/10.3390/ijms25084187
  73. Eur J Neurosci. 2024 Apr 25.
    MEF2C contributes to axonal branching by regulating Kif2c transcription.
    Ronghua Wu, Ying Sun, Zhihao Zhou, Zhangji Dong, Yan Liu, Mei Liu, Huasong Gao.
      Neurons are post-mitotic cells, with microtubules playing crucial roles in axonal transport and growth. Kinesin family member 2c (KIF2C), a member of the Kinesin-13 family, possesses the ability to depolymerize microtubules and is involved in remodelling the microtubule lattice. Myocyte enhancer factor 2c (MEF2C) was initially identified as a regulator of muscle differentiation but has recently been associated with neurological abnormalities such as severe cognitive impairment, stereotyping, epilepsy and brain malformations when mutated or deleted. However, further investigation is required to determine which target genes MEF2C acts upon to influence neuronal function as a transcription regulator. Our data demonstrate that knockdown of both Mef2c and Kif2c significantly impacts spinal motor neuron development and behaviour in zebrafish. Luciferase reporter assays and chromosome immunoprecipitation assays, along with down/upregulated expression analysis, revealed that MFE2C functions as a novel transcription regulator for the Kif2c gene. Additionally, the knockdown of either Mef2c or Kif2c expression in E18 cortical neurons substantially reduces the number of primary neurites and axonal branches during neuronal development in vitro without affecting neurite length. Finally, depletion of Kif2c eliminated the effects of overexpression of Mef2c on the neurite branching. Based on these findings, we provided novel evidence demonstrating that MEF2C regulates the transcription of the Kif2c gene thereby influencing the axonal branching.
    Keywords:  KIF2C; MEF2C; axonal branching; neurons; zebrafish
    DOI:  https://doi.org/10.1111/ejn.16344
  74. Biomolecules. 2024 Apr 01. pii: 428. [Epub ahead of print]14(4):
    Testosterone Reduces Myelin Abnormalities in the Wobbler Mouse Model of Amyotrophic Lateral Sclerosis.
    Ivan J Esperante, Maria Meyer, Carolina Banzan, Maria Sol Kruse, Analia Lima, Paulina Roig, Rachida Guennoun, Michael Schumacher, Alejandro F De Nicola, Maria Claudia Gonzalez Deniselle.
      Amyotrophic lateral sclerosis (ALS) is a fatal motoneuron degenerative disease that is associated with demyelination. The Wobbler (WR) mouse exhibits motoneuron degeneration, gliosis and myelin deterioration in the cervical spinal cord. Since male WRs display low testosterone (T) levels in the nervous system, we investigated if T modified myelin-relative parameters in WRs in the absence or presence of the aromatase inhibitor, anastrozole (A). We studied myelin by using luxol-fast-blue (LFB) staining, semithin sections, electron microscopy and myelin protein expression, density of IBA1+ microglia and mRNA expression of inflammatory factors, and the glutamatergic parameters glutamine synthetase (GS) and the transporter GLT1. Controls and WR + T showed higher LFB, MBP and PLP staining, lower g-ratios and compact myelin than WRs and WR + T + A, and groups showing the rupture of myelin lamellae. WRs showed increased IBA1+ cells and mRNA for CD11b and inflammatory factors (IL-18, TLR4, TNFαR1 and P2Y12R) vs. controls or WR + T. IBA1+ cells, and CD11b were not reduced in WR + T + A, but inflammatory factors' mRNA remained low. A reduction of GS+ cells and GLT-1 immunoreactivity was observed in WRs and WR + T + A vs. controls and WR + T. Clinically, WR + T but not WR + T + A showed enhanced muscle mass, grip strength and reduced paw abnormalities. Therefore, T effects involve myelin protection, a finding of potential clinical translation.
    Keywords:  ALS; Wobbler mouse; anastrozole; androgens; aromatase; myelin; testosterone
    DOI:  https://doi.org/10.3390/biom14040428
  75. Nat Commun. 2024 Apr 26. 15(1): 3567
    Single-cell analyses reveal transient retinal progenitor cells in the ciliary margin of developing human retina.
    Birthe Dorgau, Joseph Collin, Agata Rozanska, Darin Zerti, Adrienne Unsworth, Moira Crosier, Rafiqul Hussain, Jonathan Coxhead, Tamil Dhanaseelan, Aara Patel, Jane C Sowden, David R FitzPatrick, Rachel Queen, Majlinda Lako.
      The emergence of retinal progenitor cells and differentiation to various retinal cell types represent fundamental processes during retinal development. Herein, we provide a comprehensive single cell characterisation of transcriptional and chromatin accessibility changes that underline retinal progenitor cell specification and differentiation over the course of human retinal development up to midgestation. Our lineage trajectory data demonstrate the presence of early retinal progenitors, which transit to late, and further to transient neurogenic progenitors, that give rise to all the retinal neurons. Combining single cell RNA-Seq with spatial transcriptomics of early eye samples, we demonstrate the transient presence of early retinal progenitors in the ciliary margin zone with decreasing occurrence from 8 post-conception week of human development. In retinal progenitor cells, we identified a significant enrichment for transcriptional enhanced associate domain transcription factor binding motifs, which when inhibited led to loss of cycling progenitors and retinal identity in pluripotent stem cell derived organoids.
    DOI:  https://doi.org/10.1038/s41467-024-47933-x
  76. Nat Commun. 2024 Apr 23. 15(1): 3422
    Targeting NRAS via miR-1304-5p or farnesyltransferase inhibition confers sensitivity to ALK inhibitors in ALK-mutant neuroblastoma.
    Perla Pucci, Liam C Lee, Miaojun Han, Jamie D Matthews, Leila Jahangiri, Michaela Schlederer, Eleanor Manners, Annabel Sorby-Adams, Joshua Kaggie, Ricky M Trigg, Christopher Steel, Lucy Hare, Emily R James, Nina Prokoph, Stephen P Ducray, Olaf Merkel, Firkret Rifatbegovic, Ji Luo, Sabine Taschner-Mandl, Lukas Kenner, G A Amos Burke, Suzanne D Turner.
      Targeting Anaplastic lymphoma kinase (ALK) is a promising therapeutic strategy for aberrant ALK-expressing malignancies including neuroblastoma, but resistance to ALK tyrosine kinase inhibitors (ALK TKI) is a distinct possibility necessitating drug combination therapeutic approaches. Using high-throughput, genome-wide CRISPR-Cas9 knockout screens, we identify miR-1304-5p loss as a desensitizer to ALK TKIs in aberrant ALK-expressing neuroblastoma; inhibition of miR-1304-5p decreases, while mimics of this miRNA increase the sensitivity of neuroblastoma cells to ALK TKIs. We show that miR-1304-5p targets NRAS, decreasing cell viability via induction of apoptosis. It follows that the farnesyltransferase inhibitor (FTI) lonafarnib in addition to ALK TKIs act synergistically in neuroblastoma, inducing apoptosis in vitro. In particular, on combined treatment of neuroblastoma patient derived xenografts with an FTI and an ALK TKI complete regression of tumour growth is observed although tumours rapidly regrow on cessation of therapy. Overall, our data suggests that combined use of ALK TKIs and FTIs, constitutes a therapeutic approach to treat high risk neuroblastoma although prolonged therapy is likely required to prevent relapse.
    DOI:  https://doi.org/10.1038/s41467-024-47771-x
  77. eNeuro. 2024 Apr 24. pii: ENEURO.0010-24.2024. [Epub ahead of print]
    Loss of Midbrain Dopamine Neurons Does Not Alter GABAergic Inhibition Mediated by Parvalbumin-Expressing Interneurons in Mouse Primary Motor Cortex.
    Suraj Cherian, Gabriel Simms, Liqiang Chen, Hong-Yuan Chu.
      The primary motor cortex (M1) integrates sensory and cognitive inputs to generate voluntary movement. Its functional impairments have been implicated in the pathophysiology of motor symptoms in Parkinson's disease (PD). Specifically, dopaminergic degeneration and basal ganglia dysfunction entrain M1 neurons into the abnormally synchronized bursting pattern of activity throughout the cortico-basal ganglia-thalamocortical network. However, how degeneration of the midbrain dopaminergic neurons affects the anatomy, microcircuit connectivity, and function of the M1 network remains poorly understood. The present study examined whether and how loss of dopamine (DA) affects the morphology, cellular excitability, and synaptic physiology of layer 5 parvalbumin-expressing (PV+) cells in the M1 of mice of both sexes. Here we reported that loss of midbrain dopaminergic neurons does not alter the number, morphology, and physiology of layer 5 PV+ cells in M1. Moreover, we demonstrated that the number of perisomatic PV+ puncta of M1 pyramidal neurons as well as their functional innervation of cortical pyramidal neurons were not altered following the loss of DA. Together, the present study documents an intact GABAergic inhibitory network formed by PV+ cells following the loss of midbrain dopaminergic neurons.Significance statement The pyramidal neurons in the motor cortex manifests highly synchronized bursting pattern of activity in parkinsonian state, but the underlying circuit mechanisms are poorly understood. One can easily consider PV interneurons-mediated inhibitory network as a potential microcircuitry mechanism. However, whether loss of DA affects cortical PV+ network remains unknown. The present work documented that loss of DA in parkinsonian state does not alter the number, morphology, cellular excitability, and synaptic physiology of PV+ cells in M1. An intact robust PV+ perisomatic inhibition of pyramidal neurons provides a microcircuit substrate for thalamic afferents to entrain cortical neurons to pathological oscillations throughout the cortico-basal ganglia-thalamocortical network in parkinsonian state.
    DOI:  https://doi.org/10.1523/ENEURO.0010-24.2024
  78. Nat Commun. 2024 Apr 26. 15(1): 3560
    An individualized protein-based prognostic model to stratify pediatric patients with papillary thyroid carcinoma.
    Zhihong Wang, He Wang, Yan Zhou, Lu Li, Mengge Lyu, Chunlong Wu, Tianen He, Lingling Tan, Yi Zhu, Tiannan Guo, Hongkun Wu, Hao Zhang, Yaoting Sun.
      Pediatric papillary thyroid carcinomas (PPTCs) exhibit high inter-tumor heterogeneity and currently lack widely adopted recurrence risk stratification criteria. Hence, we propose a machine learning-based objective method to individually predict their recurrence risk. We retrospectively collect and evaluate the clinical factors and proteomes of 83 pediatric benign (PB), 85 pediatric malignant (PM) and 66 adult malignant (AM) nodules, and quantify 10,426 proteins by mass spectrometry. We find 243 and 121 significantly dysregulated proteins from PM vs. PB and PM vs. AM, respectively. Function and pathway analyses show the enhanced activation of the inflammatory and immune system in PM patients compared with the others. Nineteen proteins are selected to predict recurrence using a machine learning model with an accuracy of 88.24%. Our study generates a protein-based personalized prognostic prediction model that can stratify PPTC patients into high- or low-recurrence risk groups, providing a reference for clinical decision-making and individualized treatment.
    DOI:  https://doi.org/10.1038/s41467-024-47926-w
  79. Sci Rep. 2024 04 23. 14(1): 9284
    RAPID resistance to BET inhibitors is mediated by FGFR1 in glioblastoma.
    Anna M Jermakowicz, Alison M Kurimchak, Katherine J Johnson, Florence Bourgain-Guglielmetti, Simon Kaeppeli, Maurizio Affer, Hari Pradhyumnan, Robert K Suter, Winston Walters, Maria Cepero, James S Duncan, Nagi G Ayad.
      Bromodomain and extra-terminal domain (BET) proteins are therapeutic targets in several cancers including the most common malignant adult brain tumor glioblastoma (GBM). Multiple small molecule inhibitors of BET proteins have been utilized in preclinical and clinical studies. Unfortunately, BET inhibitors have not shown efficacy in clinical trials enrolling GBM patients. One possible reason for this may stem from resistance mechanisms that arise after prolonged treatment within a clinical setting. However, the mechanisms and timeframe of resistance to BET inhibitors in GBM is not known. To identify the temporal order of resistance mechanisms in GBM we performed quantitative proteomics using multiplex-inhibitor bead mass spectrometry and demonstrated that intrinsic resistance to BET inhibitors in GBM treatment occurs rapidly within hours and involves the fibroblast growth factor receptor 1 (FGFR1) protein. Additionally, small molecule inhibition of BET proteins and FGFR1 simultaneously induces synergy in reducing GBM tumor growth in vitro and in vivo. Further, FGFR1 knockdown synergizes with BET inhibitor mediated reduction of GBM cell proliferation. Collectively, our studies suggest that co-targeting BET and FGFR1 may dampen resistance mechanisms to yield a clinical response in GBM.
    DOI:  https://doi.org/10.1038/s41598-024-60031-8
  80. Int J Mol Sci. 2024 Apr 19. pii: 4493. [Epub ahead of print]25(8):
    Missing WD40 Repeats in ATG16L1 Delays Canonical Autophagy and Inhibits Noncanonical Autophagy.
    Jiuge Tang, Dongmei Fang, Jialing Zhong, Min Li.
      Canonical autophagy is an evolutionarily conserved process that forms double-membrane structures and mediates the degradation of long-lived proteins (LLPs). Noncanonical autophagy (NCA) is an important alternative pathway involving the formation of microtubule-associated protein 1 light chain 3 (LC3)-positive structures that are independent of partial core autophagy proteins. NCA has been defined by the conjugation of ATG8s to single membranes (CASM). During canonical autophagy and NCA/CASM, LC3 undergoes a lipidation modification, and ATG16L1 is a crucial protein in this process. Previous studies have reported that the WDR domain of ATG16L1 is not necessary for canonical autophagy. However, our study found that WDR domain deficiency significantly impaired LLP degradation in basal conditions and slowed down LC3-II accumulation in canonical autophagy. We further demonstrated that the observed effect was due to a reduced interaction between ATG16L1 and FIP200/WIPI2, without affecting lysosome function or fusion. Furthermore, we also found that the WDR domain of ATG16L1 is crucial for chemical-induced NCA/CASM. The results showed that removing the WDR domain or introducing the K490A mutation in ATG16L1 significantly inhibited the NCA/CASM, which interrupted the V-ATPase-ATG16L1 axis. In conclusion, this study highlights the significance of the WDR domain of ATG16L1 for both canonical autophagy and NCA functions, improving our understanding of its role in autophagy.
    Keywords:  ATG16L1; WDR domain; canonical autophagy; noncanonical autophagy
    DOI:  https://doi.org/10.3390/ijms25084493
  81. Colorectal Dis. 2024 Apr 23.
    Pragmatic or pristine surgical research.
    Mina Sarofim, Alexander Engel.
      
    DOI:  https://doi.org/10.1111/codi.17008
  82. Trends Cogn Sci. 2024 Apr 18. pii: S1364-6613(24)00077-9. [Epub ahead of print]
    Beta: bursts of cognition.
    Mikael Lundqvist, Earl K Miller, Jonatan Nordmark, Johan Liljefors, Pawel Herman.
      Beta oscillations are linked to the control of goal-directed processing of sensory information and the timing of motor output. Recent evidence demonstrates they are not sustained but organized into intermittent high-power bursts mediating timely functional inhibition. This implies there is a considerable moment-to-moment variation in the neural dynamics supporting cognition. Beta bursts thus offer new opportunities for studying how sensory inputs are selectively processed, reshaped by inhibitory cognitive operations and ultimately result in motor actions. Recent method advances reveal diversity in beta bursts that provide deeper insights into their function and the underlying neural circuit activity motifs. We propose that brain-wide, spatiotemporal patterns of beta bursting reflect various cognitive operations and that their dynamics reveal nonlinear aspects of cortical processing.
    Keywords:  Beta oscillations; cognition; functional inhibition; large-scale interactions; oscillatory bursts; top–down control
    DOI:  https://doi.org/10.1016/j.tics.2024.03.010
  83. Med. 2024 Apr 23. pii: S2666-6340(24)00132-6. [Epub ahead of print]
    Closed-loop automated drug infusion regulator: A clinically translatable, closed-loop drug delivery system for personalized drug dosing.
    Louis B DeRidder, Kyle A Hare, Aaron Lopes, Josh Jenkins, Nina Fitzgerald, Emmeline MacPherson, Niora Fabian, Josh Morimoto, Jacqueline N Chu, Ameya R Kirtane, Wiam Madani, Keiko Ishida, Johannes L P Kuosmanen, Naomi Zecharias, Christopher M Colangelo, Hen-Wei Huang, Makaya Chilekwa, Nikhil B Lal, Shriya S Srinivasan, Alison M Hayward, Brian M Wolpin, David Trumper, Troy Quast, Douglas A Rubinson, Robert Langer, Giovanni Traverso.
       BACKGROUND: Dosing of chemotherapies is often calculated according to the weight and/or height of the patient or equations derived from these, such as body surface area (BSA). Such calculations fail to capture intra- and interindividual pharmacokinetic variation, which can lead to order of magnitude variations in systemic chemotherapy levels and thus under- or overdosing of patients.
    METHODS: We designed and developed a closed-loop drug delivery system that can dynamically adjust its infusion rate to the patient to reach and maintain the drug's target concentration, regardless of a patient's pharmacokinetics (PK).
    FINDINGS: We demonstrate that closed-loop automated drug infusion regulator (CLAUDIA) can control the concentration of 5-fluorouracil (5-FU) in rabbits according to a range of concentration-time profiles (which could be useful in chronomodulated chemotherapy) and over a range of PK conditions that mimic the PK variability observed clinically. In one set of experiments, BSA-based dosing resulted in a concentration 7 times above the target range, while CLAUDIA keeps the concentration of 5-FU in or near the targeted range. Further, we demonstrate that CLAUDIA is cost effective compared to BSA-based dosing.
    CONCLUSIONS: We anticipate that CLAUDIA could be rapidly translated to the clinic to enable physicians to control the plasma concentration of chemotherapy in their patients.
    FUNDING: This work was supported by MIT's Karl van Tassel (1925) Career Development Professorship and Department of Mechanical Engineering and the Bridge Project, a partnership between the Koch Institute for Integrative Cancer Research at MIT and the Dana-Farber/Harvard Cancer Center.
    Keywords:  Foundational research; cancer; chemotherapy; closed-loop system; drug delivery; personalized dosing
    DOI:  https://doi.org/10.1016/j.medj.2024.03.020
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