bims-axbals 2025-01-26 papers

bims-axbals

Biomed News

on Axonal biology and ALS

Issue of 2025–01–26
29 papers selected by
TJ Krzystek, ALS Therapy Development Institute

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.
TDP-43 transports ferritin heavy chain mRNA to regulate oxidative stress in neuronal axons.
Altered cytoskeleton dynamics in patient-derived iPSC-based model of PCDH19 clustering epilepsy.
Somatic CAG repeat expansion in blood associates with biomarkers of neurodegeneration in Huntington's disease decades before clinical motor diagnosis.
Fis1 is required for the development of the dendritic mitochondrial network in pyramidal cortical neurons.
Derivation and Characterization of Isogenic OPA1 Mutant and Control Human Pluripotent Stem Cell Lines.
Deep learning analyses of splicing variants identify the link of PCP4 with amyotrophic lateral sclerosis.
ALS: A Silent Slayer of Motor Neurons. Traditional Chinese Herbal Medicine as an Effective Therapy.
The mitochondrial choline transporter, SLC25A48, regulates urine and blood choline levels in humans.
CRMP/UNC-33 maintains neuronal microtubule arrays by promoting individual microtubule rescue.
How close is autophagy-targeting therapy for Alzheimer's disease to clinical use? A summary of autophagy modulators in clinical studies.
The levels of the long non-coding RNA MALAT1 affect cell viability and modulate TDP-43 binding to mRNA in the nucleus.
Hypotonic Swelling Method for the Isolation of Pure Mitochondria From Primary Human Skeletal Myoblasts for Proteomic Studies.
Comparisons of neurodegenerative disease biomarkers across different biological fluids from patients with Huntington's disease.
Imeglimin, unlike metformin, does not perturb differentiation of human induced pluripotent stem cells towards pancreatic β-like cells and rather enhances gain in β cell identity gene sets.
Application of antisense oligonucleotide drugs in amyotrophic lateral sclerosis and Huntington's disease.
Rapid human oogonia-like cell specification via transcription factor-directed differentiation.
Mitochondria and its epigenetic dynamics: Insight into synaptic regulation and synaptopathies.
Mouse totipotent blastomere-like cells model embryogenesis from zygotic genome activation to post implantation.
Dysfunctional BCAA degradation triggers neuronal damage through disrupted AMPK-mitochondrial axis due to enhanced PP2Ac interaction.
Direct and Indirect Protein Interactions Link FUS Aggregation to Histone Post-Translational Modification Dysregulation and Growth Suppression in an ALS/FTD Yeast Model.
Multiple regulators constrain the abundance of C. elegans DLK-1 in ciliated sensory neurons.
Tofersen and other antisense oligonucleotides in ALS.
Advances in physiological and clinical relevance of hiPSC-derived brain models for precision medicine pipelines.
Synaptic protein expression in bipolar disorder patient-derived neurons implicates PSD-95 as a marker of lithium response.
Long somatic DNA-repeat expansion drives neurodegeneration in Huntington's disease.
The utilisation of biliary organoids for biomedical applications.
The Role of Autophagy in Copper-Induced Apoptosis and Developmental Neurotoxicity in SH-SY5Y Cells.
Transcriptomic and Functional Landscape of Adult Human Spinal Cord NSPCs Compared to iPSC-Derived Neural Progenitor Cells.

Sci Adv. 2025 Jan 24. 11(4): eadu5787

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST.

Felix Kraus, Yuchen He, Sharan Swarup, Katherine A Overmyer, Yizhi Jiang, Johann Brenner, Cristina Capitanio, Anna Bieber, Annie Jen, Nicole M Nightingale, Benton J Anderson, Chan Lee, Joao A Paulo, Ian R Smith, Jürgen M Plitzko, Steven P Gygi, Brenda A Schulman, Florian Wilfling, Joshua J Coon, J Wade Harper.

Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multiomic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lysophosphatidylcholine species and multilamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs.

DOI: https://doi.org/10.1126/sciadv.adu5787
Neurochem Int. 2025 Jan 17. pii: S0197-0186(25)00007-5. [Epub ahead of print] 105934

TDP-43 transports ferritin heavy chain mRNA to regulate oxidative stress in neuronal axons.

Jyunki Jinno, Rehab F Abdelhamid, Junko Morita, Ryoko Saga, Yusuke Yamasaki, Atsushi Kadowaki, Kotaro Ogawa, Yasuyoshi Kimura, Kensuke Ikenaka, Goichi Beck, Kousuke Baba, Yoshitaka Nagai, Emiko Kasahara, Atsuo Sekiyama, Tasuku Hirayama, Isao Hozumi, Tatsuya Hasegawa, Toshiyuki Araki, Hideki Mochizuki, Seiichi Nagano.

  Amyotrophic lateral sclerosis (ALS) is characterized by the mislocalization and abnormal deposition of TAR DNA-binding protein 43 (TDP-43). This protein plays important roles in RNA metabolism and transport in motor neurons and glial cells. In addition, abnormal iron accumulation and oxidative stress are observed in the brain and spinal cord of patients with ALS exhibiting TDP-43 pathology and in animal models of ALS. We have previously demonstrated that TDP-43 downregulation significantly affects the expression of ferritin heavy chain (Fth1) mRNA in the axonal regions of neurons. Nevertheless, the mechanisms by which TDP-43 contributes to oxidative stress and iron accumulation in the central nervous system remain elusive. In this study, we aimed to investigate whether Fth1 mRNA is a target transported to the axon by TDP-43 using biophysical and biochemical analyses. Our results revealed Fth1 mRNA as a target mRNA transported to axons by TDP-43. Moreover, we demonstrated that TDP-43 regulates iron homeostasis and oxidative stress in neurons via Fth1 mRNA transport to the axons, possibly followed by a local translation of the ferritin heavy chain in the axons. This study suggests that TDP-43 plays an important role in preventing iron-mediated oxidative stress in neurons, with its loss contributing to ALS pathogenesis.

Keywords:  Amyotrophic lateral sclerosis; Fenton reaction; TDP-43; ferritin heavy chain; reactive oxygen species

DOI:  https://doi.org/10.1016/j.neuint.2025.105934
Front Cell Dev Biol. 2024 ;12 1518533

Altered cytoskeleton dynamics in patient-derived iPSC-based model of PCDH19 clustering epilepsy.

Rossella Borghi, Stefania Petrini, Valentina Apollonio, Marina Trivisano, Nicola Specchio, Sandra Moreno, Enrico Bertini, Marco Tartaglia, Claudia Compagnucci.

  Protocadherin 19 (PCDH19) is an adhesion molecule involved in cell-cell interaction whose mutations cause a drug-resistant form of epilepsy, named PCDH19-Clustering Epilepsy (PCDH19-CE, MIM 300088). The mechanism by which altered PCDH19 function drive pathogenesis is not yet fully understood. Our previous work showed that PCDH19 dysfunction is associated with altered orientation of the mitotic spindle and accelerated neurogenesis, suggesting a contribution of altered cytoskeleton organization in PCDH19-CE pathogenesis in the control of cell division and differentiation. Here, we evaluate the consequences of altered PCDH19 function on microfilaments and microtubules organization, using a disease model obtained from patient-derived induced pluripotent stem cells. We show that iPSC-derived cortical neurons are characterized by altered cytoskeletal dynamics, suggesting that this protocadherin has a role in modulating stability of MFs and MTs. Consistently, the levels of acetylated-tubulin, which is related with stable MTs, are significantly increased in cortical neurons derived from the patient's iPSCs compared to control cells, supporting the idea that the altered dynamics of the MTs depends on their increased stability. Finally, performing live-imaging experiments using fluorescence recovery after photobleaching and by monitoring GFP-tagged end binding protein 3 (EB3) "comets," we observe an impairment of the plus-end polymerization speed in PCDH19-mutated cortical neurons, therefore confirming the impaired MT dynamics. In addition to altering the mitotic spindle formation, the present data unveil that PCDH19 dysfunction leads to altered cytoskeletal rearrangement, providing therapeutic targets and pharmacological options to treat this disorder.

Keywords:  IPSC-derived neurons; PCDH19; cytoskeletal dynamics; epilepsy; microfilaments; microtubules; neurodevelopment

DOI:  https://doi.org/10.3389/fcell.2024.1518533
Nat Med. 2025 Jan 17.

Somatic CAG repeat expansion in blood associates with biomarkers of neurodegeneration in Huntington's disease decades before clinical motor diagnosis.

Rachael I Scahill, Mena Farag, Michael J Murphy, Nicola Z Hobbs, Michela Leocadi, Christelle Langley, Harry Knights, Marc Ciosi, Kate Fayer, Mitsuko Nakajima, Olivia Thackeray, Johan Gobom, John Rönnholm, Sophia Weiner, Yara R Hassan, Nehaa K P Ponraj, Carlos Estevez-Fraga, Christopher S Parker, Ian B Malone, Harpreet Hyare, Jeffrey D Long, Amanda Heslegrave, Cristina Sampaio, Hui Zhang, Trevor W Robbins, Henrik Zetterberg, Edward J Wild, Geraint Rees, James B Rowe, Barbara J Sahakian, Darren G Monckton, Douglas R Langbehn, Sarah J Tabrizi.

Huntington's disease (HD) is an autosomal dominant neurodegenerative disease with the age at which characteristic symptoms manifest strongly influenced by inherited HTT CAG length. Somatic CAG expansion occurs throughout life and understanding the impact of somatic expansion on neurodegeneration is key to developing therapeutic targets. In 57 HD gene expanded (HDGE) individuals, ~23 years before their predicted clinical motor diagnosis, no significant decline in clinical, cognitive or neuropsychiatric function was observed over 4.5 years compared with 46 controls (false discovery rate (FDR) > 0.3). However, cerebrospinal fluid (CSF) markers showed very early signs of neurodegeneration in HDGE with elevated neurofilament light (NfL) protein, an indicator of neuroaxonal damage (FDR = 3.2 × 10-12), and reduced proenkephalin (PENK), a surrogate marker for the state of striatal medium spiny neurons (FDR = 2.6 × 10-3), accompanied by brain atrophy, predominantly in the caudate (FDR = 5.5 × 10-10) and putamen (FDR = 1.2 × 10-9). Longitudinal increase in somatic CAG repeat expansion ratio (SER) in blood was a significant predictor of subsequent caudate (FDR = 0.072) and putamen (FDR = 0.148) atrophy. Atypical loss of interruption HTT repeat structures, known to predict earlier age at clinical motor diagnosis, was associated with substantially faster caudate and putamen atrophy. We provide evidence in living humans that the influence of CAG length on HD neuropathology is mediated by somatic CAG repeat expansion. These critical mechanistic insights into the earliest neurodegenerative changes will inform the design of preventative clinical trials aimed at modulating somatic expansion. ClinicalTrials.gov registration: NCT06391619 .

DOI: https://doi.org/10.1038/s41591-024-03424-6
bioRxiv. 2025 Jan 07. pii: 2025.01.07.631801. [Epub ahead of print]

Fis1 is required for the development of the dendritic mitochondrial network in pyramidal cortical neurons.

Klaudia Strucinska, Parker Kneis, Travis Pennington, Katarzyna Cizio, Patrycja Szybowska, Abigail Morgan, Joshua Weertman, Tommy L Lewis.

Mitochondrial ATP production and calcium buffering are critical for metabolic regulation and neurotransmission making the formation and maintenance of the mitochondrial network a critical component of neuronal health. Cortical pyramidal neurons contain compartment-specific mitochondrial morphologies that result from distinct axonal and dendritic mitochondrial fission and fusion profiles. We previously showed that axonal mitochondria are maintained at a small size as a result of high axonal mitochondrial fission factor (Mff) activity. However, loss of Mff activity had little effect on cortical dendritic mitochondria, raising the question of how fission/fusion balance is controlled in the dendrites. Thus, we sought to investigate the role of another fission factor, fission 1 (Fis1), on mitochondrial morphology, dynamics and function in cortical neurons. We knocked down Fis1 in cortical neurons both in primary culture and in vivo , and unexpectedly found that Fis1 depletion decreased mitochondrial length in the dendrites, without affecting mitochondrial size in the axon. Further, loss of Fis1 activity resulted in both increased mitochondrial motility and dynamics in the dendrites. These results argue Fis1 exhibits dendrite selectivity and plays a more complex role in neuronal mitochondrial dynamics than previously reported. Functionally, Fis1 loss resulted in reduced mitochondrial membrane potential, increased sensitivity to complex III blockade, and decreased mitochondrial calcium uptake during neuronal activity. The altered mitochondrial network culminated in elevated resting calcium levels that increased dendritic branching but reduced spine density. We conclude that Fis1 regulates morphological and functional mitochondrial characteristics that influence dendritic tree arborization and connectivity.

DOI: https://doi.org/10.1101/2025.01.07.631801
Cells. 2025 Jan 17. pii: 137. [Epub ahead of print]14(2):

Derivation and Characterization of Isogenic OPA1 Mutant and Control Human Pluripotent Stem Cell Lines.

Katherine A Pohl, Xiangmei Zhang, Johnny Jeonghyun Ji, Linsey Stiles, Alfredo A Sadun, Xian-Jie Yang.

  Dominant optic atrophy (DOA) is the most commonly inherited optic neuropathy. The majority of DOA is caused by mutations in the OPA1 gene, which encodes a dynamin-related GTPase located to the mitochondrion. OPA1 has been shown to regulate mitochondrial dynamics and promote fusion. Within the mitochondrion, proteolytically processed OPA1 proteins form complexes to maintain membrane integrity and the respiratory chain complexity. Although OPA1 is broadly expressed, human OPA1 mutations predominantly affect retinal ganglion cells (RGCs) that are responsible for transmitting visual information from the retina to the brain. Due to the scarcity of human RGCs, DOA has not been studied in depth using the disease affected neurons. To enable studies of DOA using stem-cell-derived human RGCs, we performed CRISPR-Cas9 gene editing to generate OPA1 mutant pluripotent stem cell (PSC) lines with corresponding isogenic controls. CRISPR-Cas9 gene editing yielded both OPA1 homozygous and heterozygous mutant ESC lines from a parental control ESC line. In addition, CRISPR-mediated homology-directed repair (HDR) successfully corrected the OPA1 mutation in a DOA patient's iPSCs. In comparison to the isogenic controls, the heterozygous mutant PSCs expressed the same OPA1 protein isoforms but at reduced levels; whereas the homozygous mutant PSCs showed a loss of OPA1 protein and altered mitochondrial morphology. Furthermore, OPA1 mutant PSCs exhibited reduced rates of oxygen consumption and ATP production associated with mitochondria. These isogenic PSC lines will be valuable tools for establishing OPA1-DOA disease models in vitro and developing treatments for mitochondrial deficiency associated neurodegeneration.

Keywords:  CRISPR-Cas9 editing; OPA1 gene; dominant optic atrophy; isogenic human pluripotent stem cell lines; mitochondria

DOI:  https://doi.org/10.3390/cells14020137
Brain. 2025 Jan 24. pii: awaf025. [Epub ahead of print]

Deep learning analyses of splicing variants identify the link of PCP4 with amyotrophic lateral sclerosis.

Xuelin Tang, Yan Chen, Yongfei Ren, Wanli Yang, Wendi Yu, Yu Zhou, Jingyan Guo, Jiali Hu, Xi Chen, Yuqi Gu, Chuyi Wang, Yi Dong, Hong Yang, Christine Sato, Ji He, Dongsheng Fan, Linya You, Lorne Zinman, Ekaterina Rogaeva, Yelin Chen, Ming Zhang.

  Amyotrophic lateral sclerosis (ALS) is a severe motor neuron disease, with most sporadic cases lacking clear genetic causes. Abnormal pre-mRNA splicing is a fundamental mechanism in neurodegenerative diseases. For example, TAR DNA-binding protein 43 (TDP-43) loss-of-function (LOF) causes widespread RNA mis-splicing events in ALS. Additionally, splicing mutations are major contributors to neurological disorders. However, the role of intronic variants driving RNA mis-splicing in ALS remains poorly understood. To address this, we developed Spliformer to predict RNA splicing. Spliformer is a transformer-based deep learning model trained and tested on splicing events from the GENCODE database, as well as RNA-seq data from blood and central nervous system tissues. We benchmarked Spliformer against SpliceAI and Pangolin using testing datasets and paired whole-genome sequencing (WGS) with RNA-seq data. We further developed the Spliformer-motif model to identify splicing regulatory motifs. We analyzed Clinvar dataset to identify the link of splicing variants with disease pathogenicity. Additionally, we analyzed WGS data of ALS patients and controls to identify common intronic splicing variants linked to ALS risk or disease phenotypes. We also profiled rare intronic splicing variants in ALS patients to identify known or novel ALS-associated genes. Minigene assays were employed to validate candidate splicing variants. Finally, we measured spine density in neurons with a specific gene knockdown or those expressing a TDP-43 disease-causing mutant. Spliformer accurately predicts the possibilities of a nucleotide within a pre-mRNA sequence being a splice donor, acceptor, or neither. Spliformer outperformed SpliceAI and Pangolin in both speed and accuracy in tested splicing events and/or paired WGS/RNA-seq data. Spliformer-motif successfully identified canonical and novel splicing regulatory motifs. In Clinvar dataset, splicing variants are highly related to disease pathogenicity. Genome-wide analyses of common intronic splicing variants nominated one variant linked to ALS progression. Deep learning analyses of WGS data from 1,370 ALS patients revealed rare splicing variants in reported ALS genes (such as PTPRN2 and CFAP410, validated through minigene assays and RNA-seq), and TDP-43 LOF related RNA mis-splicing genes (such as PTPRD). Further genetic analysis and minigene assays nominated PCP4 and TMEM63A as ALS-associated genes. Functional assays demonstrated that PCP4 is critical for maintaining spine density and can rescue spine loss in neurons expressing a disease-causing TDP-43 mutant. In summary, we developed Spliformer and Spliformer-motif that accurately predict and interpret pre-mRNA splicing. Our findings highlight an intronic genetic mechanism driving RNA mis-splicing in ALS and nominate PCP4 as an ALS-associated gene.

Keywords:  RNA mis-splicing; amyotrophic lateral sclerosis; deep learning; genomics; multi-omics; splicing variants

DOI:  https://doi.org/10.1093/brain/awaf025
Curr Pharm Des. 2025 Jan 17.

ALS: A Silent Slayer of Motor Neurons. Traditional Chinese Herbal Medicine as an Effective Therapy.

Anjali Rai, Shivang Shukla, Ramesh Kumar Gupta, Anuradha Mishra.

  Amyotrophic Lateral Sclerosis (ALS), is a progressive neurodegenerative disease characterized by motor symptoms, and cognitive impairment. The complexity in treating ALS arises from genetic and environmental factors, contributing to the gradual decline of lower and upper motor neurons. The anticipated pharmaceutical market valuation for ALS is projected to reach $1,038.94 million by 2032. This projection underscores the escalating impact of ALS on global healthcare systems. ALS prevalence is expected to surge to 376,674 cases by 2040. In 2022, India ranked among the top 3 Asian-Pacific nations, while North America dominated the global ALS market. Ongoing investigations explore the potential of neuroprotective drugs like riluzole and edaravone in ALS treatment. Recently approved drugs, Relyvrio (sodium phenylbutyrate and taurursodiol) and Tofersen (Qalsody) have completed the trials, and others are currently undergoing extensive clinical trials. Continuous research and exploration of therapeutic avenues, including gene therapy and neuroprotective treatments, are imperative to address the challenges posed by ALS and other neurodegenerative diseases. Traditional Chinese Medicine (TCM) approaches and clinical trials are being explored for treating ALS symptoms, targeting neuroinflammation, oxidative damage, and muscle weakness, showcasing the potential benefits of integrating traditional and modern approaches in ALS management.

Keywords:  Amyotrophic lateral sclerosis; clinical trials; gene therapy; motor symptoms; traditional Chinese medicine.

DOI:  https://doi.org/10.2174/0113816128329141241205063352
Kidney Int. 2025 Feb;pii: S0085-2538(24)00811-1. [Epub ahead of print]107(2): 225-227

The mitochondrial choline transporter, SLC25A48, regulates urine and blood choline levels in humans.

Soumya Maity, Kumar Sharma.

Choline is an essential nutrient for the biosynthesis of phospholipids and neurotransmitters and controls several physiological functions in mammals. It is metabolized in the organelles within cells, including mitochondria. However, its subcellular distribution and mode of mitochondrial transport remain poorly understood. Patil et al. identified SLC25A48 as a mitochondrial choline transporter, and its loss-of-function mutations were associated with elevated urine and plasma choline levels in humans.

DOI: https://doi.org/10.1016/j.kint.2024.11.014
Curr Biol. 2025 Jan 11. pii: S0960-9822(24)01698-1. [Epub ahead of print]

CRMP/UNC-33 maintains neuronal microtubule arrays by promoting individual microtubule rescue.

Xing Liang, Regina Agulto, Kelsie Eichel, Caitlin Ann Taylor, Victor Alexander Paat, Huichao Deng, Kassandra Ori-McKenney, Kang Shen.

  Microtubules (MTs) are intrinsically dynamic polymers. In neurons, staggered individual microtubules form stable, polarized acentrosomal MT arrays spanning the axon and dendrite to support long-distance intracellular transport. How the stability and polarity of these arrays are maintained when individual MTs remain highly dynamic is still an open question. Here, we visualize MT arrays in vivo in C. elegans neurons with single MT resolution. We find that the CRMP family homolog UNC-33 is essential for the stability and polarity of MT arrays in neurites. In unc-33 mutants, MTs exhibit dramatically reduced rescue after catastrophe, develop gaps in coverage, and lose their polarity, leading to trafficking defects. UNC-33 is stably anchored on the cortical cytoskeleton and forms patch-like structures along the dendritic shaft. These discrete and stable UNC-33 patches concentrate free tubulins and correlate with MT rescue sites. In vitro, purified UNC-33 preferentially associates with MT tips and increases MT rescue frequency. Together, we propose that UNC-33 functions as a microtubule-associated protein (MAP) to promote individual MT rescue locally. Through this activity, UNC-33 prevents the loss of individual MTs, thereby maintaining the coverage and polarity of MT arrays throughout the lifetime of neurons.

Keywords:  CRMPs; UNC-33; microtubule dynamic instability; microtubule-associated proteins; neuronal microtubule; neuronal polarity

DOI:  https://doi.org/10.1016/j.cub.2024.12.030
Front Cell Dev Biol. 2024 ;12 1520949

How close is autophagy-targeting therapy for Alzheimer's disease to clinical use? A summary of autophagy modulators in clinical studies.

Sofia Miranda Fernandes, Johanna Mayer, Per Nilsson, Makoto Shimozawa.

  Alzheimer's disease (AD) is a neurodegenerative disorder clinically characterized by progressive decline of memory and cognitive functions, and it is the leading cause of dementia accounting for 60%-80% of dementia patients. A pathological hallmark of AD is the accumulation of aberrant protein/peptide aggregates such as extracellular amyloid plaques containing amyloid-beta peptides and intracellular neurofibrillary tangles composed of hyperphosphorylated tau. These aggregates result from the failure of the proteostasis network, which encompasses protein synthesis, folding, and degradation processes. Autophagy is an intracellular self-digesting system responsible for the degradation of protein aggregates and damaged organelles. Impaired autophagy is observed in most neurodegenerative disorders, indicating the link between autophagy dysfunction and these diseases. A massive accumulation of autophagic vacuoles in neurons in Alzheimer's brains evidences autophagy impairment in AD. Modulating autophagy has been proposed as a therapeutic strategy for AD because of its potential to clear aggregated proteins. However, autophagy modulation therapy for AD is not yet clinically available. This mini-review aims to summarize clinical studies testing potential autophagy modulators for AD and to evaluate their proximity to clinical use. We accessed clinicaltrials.gov provided by the United States National Institutes of Health to identify completed and ongoing clinical trials. Additionally, we discuss the limitations and challenges of these therapies.

Keywords:  Alzheimer’s disease; autophagy impairment; autophagy modulators; clinical studies; protein homeostasis

DOI:  https://doi.org/10.3389/fcell.2024.1520949
J Biol Chem. 2025 Jan 19. pii: S0021-9258(25)00054-7. [Epub ahead of print] 108207

The levels of the long non-coding RNA MALAT1 affect cell viability and modulate TDP-43 binding to mRNA in the nucleus.

Adarsh Balaji, Aileen C Button, Simone D Hall, Jonathan Zhu, Lauren Ellis, Ellen Lavorando, Ethan L Ashley, Raul Johnson, Einollah Sarikhani, Zeinab Jahed, Colleen A McHugh.

  TAR DNA-binding protein (TDP-43) and Metastasis Associated Lung Adenocarcinoma Transcript (MALAT1) RNA are both abundantly expressed in the human cell nucleus. Increased interaction of TDP-43 and MALAT1, as well as dysregulation of TDP-43 function, was previously identified in brain samples from patients with neurodegenerative disease compared to healthy brain tissues. We hypothesized that TDP-43 function may depend in part on MALAT1 expression levels. Here, we find that alterations in MALAT1 expression affect cell viability and can modulate TDP-43 binding to other mRNAs in HEK293 and SH-SH5Y human cell lines. Disruption of either MALAT1 or TDP-43 expression induces cell death, indicating that both macromolecules contribute positively to survival. Depletion of MALAT1 RNA results in increased binding of TDP-43 to other mRNA transcripts at the 3' UTR. Finally, we examined the contribution of MALAT1 expression to survival in a cell culture model of neurodegeneration using MPP+ treatment in SH-SY5Y cells. Depletion of MALAT1 RNA protects against toxicity in a cellular model of neurodegeneration and modulates TDP-43 binding to mRNA transcripts involved in apoptotic cell death. Taken together, we find that MALAT1 RNA and TDP-43 interactions can affect mRNA levels and cell viability. A tightly regulated network of non-coding RNA, messenger RNA, and protein interactions could provide a mechanism to maintain appropriate RNA expression levels and contribute to neuronal function.

Keywords:  Long non-coding RNA; MALAT1; RNA binding protein; RNA-protein interaction; TAR DNA-binding protein 43 (TDP-43) (TARDBP); gene expression; mRNA; mRNA stability; neurodegeneration

DOI:  https://doi.org/10.1016/j.jbc.2025.108207
J Cell Mol Med. 2025 Jan;29(2): e70370

Hypotonic Swelling Method for the Isolation of Pure Mitochondria From Primary Human Skeletal Myoblasts for Proteomic Studies.

Evrim Aksu-Menges, Eray Taha Kumtepe, Gurler Akpinar, Burcu Balci-Hayta.

  Mitochondria play a fundamental role in energy metabolism, particularly in high-energy-demand tissues such as skeletal muscle. Understanding the proteomic composition of mitochondria in these cells is crucial for elucidating the mechanisms underlying muscle physiology and pathology. However, effective isolation of mitochondria from primary human skeletal muscle cells has been challenging due to the complex cellular architecture and the propensity for contamination with other organelles. Here, we compared four different methods to isolate mitochondria from primary human skeletal myoblasts regarding total protein yield, mitochondrial enrichment capacity and purity of the isolated fraction. We presented a modified method that combines differential centrifugation with a hypotonic swelling step and a subsequent purification process to minimise cellular contamination. We validated our method by demonstrating its ability to obtain highly pure mitochondrial fractions, as confirmed by Western Blot with mitochondrial, cytosolic and nuclear markers. We demonstrated that proteomic analysis can be performed with isolated mitochondria. Our approach provides a valuable tool for investigating mitochondrial dynamics, biogenesis and function in the context of skeletal muscle biology in health and disease. This methodological advancement opens new avenues for mitochondrial research and its implications in myopathies, sarcopenia, cachexia and metabolic disorders.

Keywords:  differential centrifugation; hypotonic swelling method; mitochondria isolation; primary human skeletal myoblasts

DOI:  https://doi.org/10.1111/jcmm.70370
J Neurol. 2025 Jan 23. 272(2): 158

Comparisons of neurodegenerative disease biomarkers across different biological fluids from patients with Huntington's disease.

Alison R Bamford, Georgia M Parkin, Jody Corey-Bloom, Elizabeth A Thomas.

  Fluid biomarkers play important roles in many aspects of neurodegenerative diseases, such as Huntington's disease (HD). However, a main question relates to how well levels of biomarkers measured in CSF are correlated with those measured in peripheral fluids, such as blood or saliva. In this study, we quantified levels of four neurodegenerative disease-related proteins, neurofilament light (NfL), total tau (t-tau), glial fibrillary acidic protein (GFAP) and YKL-40 in matched CSF, plasma and saliva samples from Huntingtin (HTT) gene-positive individuals (n = 21) using electrochemiluminescence assays. In addition, salivary levels of NfL, t-tau, and GFAP were quantified from a larger cohort (n = 95). We found both positive and negative correlations in the levels of these biomarkers among different biofluids. Most notably, in contrast to the significant positive correlations observed between CSF and plasma levels for NfL and GFAP, we detected significant negative correlations between the CSF and saliva levels of NfL and GFAP. With regard to clinical measures, both plasma and CSF levels of NfL were significantly positively correlated with Total Motor Score and chorea, whereas saliva levels of NfL showed significant correlations in the opposite direction. Additional correlations between salivary biomarkers with clinical data, adjusting for age, sex and CAG repeat length, confirmed that salivary NfL was significantly negatively associated with chorea scores in manifest HD, but not premanifest (PM), individuals. In contrast, salivary t-tau was positively associated with measures of cognition in PM participants. These findings suggest that salivary levels of NfL and t-tau proteins may exemplify non-invasive biomarkers for disease symptoms at different stages of illness. Further, these findings highlight the notion that different forms of disease proteins exist in different biological fluids.

Keywords:  Biomarker; Neurodegeneration; Neurodegenerative; Neurofilament; Saliva; Tau

DOI:  https://doi.org/10.1007/s00415-024-12785-4
J Diabetes Investig. 2025 Jan 20.

Imeglimin, unlike metformin, does not perturb differentiation of human induced pluripotent stem cells towards pancreatic β-like cells and rather enhances gain in β cell identity gene sets.

Tasuku Imada, Shugo Sasaki, Hiroki Yamaguchi, Ayaka Ueda, Dan Kawamori, Naoto Katakami, Iichiro Shimomura.

   AIMS/INTRODUCTION: Metformin treatment for hyperglycemia in pregnancy (HIP) beneficially improves maternal glucose metabolism and reduces perinatal complications. However, metformin could impede pancreatic β cell development via impaired mitochondrial function. A new anti-diabetes drug imeglimin, developed based on metformin, improves mitochondrial function. Here we examine the effect of imeglimin on β cell differentiation using human induced pluripotent stem cell (iPSC)-derived pancreatic islet-like spheroid (SC-islet) models.
MATERIALS AND METHODS: Human iPSCs are differentiated into SC-islets by three-dimensional culture with and without imeglimin or metformin. Differentiation efficiencies of SC-islets were analyzed by flow cytometry, immunostaining, quantitative PCR, and insulin secretion assay. RNA sequencing and oxygen consumption rate were obtained for further characterization of SC-islets. SC-islets were cultured with proinflammatory cytokines, in part mimicking the uterus environment in HIP.
RESULTS: Metformin perturbed SC-islet differentiation while imeglimin did not alter it. Furthermore, imeglimin enhanced the gene expressions of β cell lineage markers. Maintenance of mitochondrial function and optimization of TGF-β and Wnt signaling were considered potential mechanisms for augmented β cell maturation by imeglimin. In the presence of proinflammatory cytokines, imeglimin ameliorated β cell differentiation impaired by cytokines and metformin.
CONCLUSIONS: Imeglimin does not perturb differentiation of SC-islet cells and rather enhances gain in β cell identity gene sets in contrast to metformin. This may lead to the improvement of in vitro β cell differentiation protocols.

Keywords:  Imeglimin; Metformin; β cell differentiation

DOI:  https://doi.org/10.1111/jdi.14410
Transl Neurodegener. 2025 Jan 21. 14(1): 4

Application of antisense oligonucleotide drugs in amyotrophic lateral sclerosis and Huntington's disease.

Kaili Ou, Qingqing Jia, Dandan Li, Shihua Li, Xiao-Jiang Li, Peng Yin.

  Amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD) are diverse in clinical presentation and are caused by complex and multiple factors, including genetic mutations and environmental factors. Numerous therapeutic approaches have been developed based on the genetic causes and potential mechanisms of ALS and HD. Currently, available treatments for various neurodegenerative diseases can alleviate symptoms but do not provide a definitive cure. Gene therapy, which aims to modify or express specific proteins for neuroprotection or correction, is considered a powerful tool in managing neurodegenerative conditions. To date, antisense oligonucleotide (ASO) drugs targeting the pathological genes associated with ALS and HD have shown promising results in numerous animal studies and several clinical trials. This review provides a comprehensive overview of the development, mechanisms of action, limitations, and clinical applications of ASO drugs in neurodegenerative diseases, with a specific focus on ALS and HD therapeutic strategies.

Keywords:  Amyotrophic lateral sclerosis; Antisense oligonucleotide; Clinical trial; Huntington’s disease

DOI:  https://doi.org/10.1186/s40035-025-00466-9
EMBO Rep. 2025 Jan 23.

Rapid human oogonia-like cell specification via transcription factor-directed differentiation.

Merrick Pierson Smela, Christian C Kramme, Patrick R J Fortuna, Bennett Wolf, Shrey Goel, Jessica Adams, Carl Ma, Sergiy Velychko, Ursula Widocki, Venkata Srikar Kavirayuni, Tianlai Chen, Sophia Vincoff, Edward Dong, Richie E Kohman, Mutsumi Kobayashi, Toshi Shioda, George M Church, Pranam Chatterjee.

  The generation of germline cells from human induced pluripotent stem cells (hiPSCs) represents a milestone toward in vitro gametogenesis. Methods to recapitulate germline development beyond primordial germ cells in vitro have relied on long-term cell culture, such as 3-dimensional organoid co-culture for ~four months. Using a pipeline with highly parallelized screening, this study identifies combinations of TFs that directly and rapidly convert hiPSCs to induced oogonia-like cells (iOLCs). We demonstrate that co-expression of five TFs - namely, ZNF281, LHX8, SOHLH1, ZGLP1, and ANHX, induces high efficiency DDX4-positive iOLCs in only four days in a feeder-free monolayer culture condition. We also show improved production of human primordial germ cell-like cells (hPGCLCs) from hiPSCs by expression of DLX5, HHEX, and FIGLA. We characterize these TF-based iOLCs and hPGCLCs via gene and protein expression analyses and demonstrate their similarity to in vivo and in vitro-derived oogonia and primordial germ cells. Together, these results identify new regulatory factors that enhance human germ cell specification in vitro, and further establish unique computational and experimental tools for human in vitro oogenesis research.

Keywords:  Differentiation; Induced Pluripotent Stem Cells; Oogonia; Primordial Germ Cells; Transcription Factors

DOI:  https://doi.org/10.1038/s44319-025-00371-2
Funct Integr Genomics. 2025 Jan 23. 25(1): 26

Mitochondria and its epigenetic dynamics: Insight into synaptic regulation and synaptopathies.

Shiwangi Gupta, Abhinoy Kishore, Vikas Rishi, Aanchal Aggarwal.

Mitochondria, the cellular powerhouses, are pivotal to neuronal function and health, particularly through their role in regulating synaptic structure and function. Spine reprogramming, which underlies synapse development, depends heavily on mitochondrial dynamics-such as biogenesis, fission, fusion, and mitophagy as well as functions including ATP production, calcium (Ca2+) regulation, and retrograde signaling. Mitochondria supply the energy necessary for assisting synapse development and plasticity, while also regulating intracellular Ca2+ homeostasis to prevent excitotoxicity and support synaptic neurotransmission. Additionally, the dynamic processes of mitochondria ensure mitochondrial quality and adaptability, which are essential for maintaining effective synaptic activity. Emerging evidence highlights the significant role of epigenetic modifications in regulating mitochondrial dynamics and function. Epigenetic changes influence gene expression, which in turn affects mitochondrial activity, ensuring coordinated responses necessary for synapse development. Furthermore, metabolic changes within mitochondria can impact the epigenetic machinery, thereby modulating gene expression patterns that support synaptic integrity. Altered epigenetic regulation affecting mitochondrial dynamics and functions is linked to several neurological disorders, including Amyotrophic Lateral Sclerosis, Huntington's, Alzheimer's, and Parkinson's diseases, emphasizing its crucial function. The review delves into the molecular machinery involved in mitochondrial dynamics, ATP and Ca2+ regulation, highlighting the role of key proteins that facilitate the processes. Additionally, it also shed light on the emerging epigenetic factors influencing these regulations. It provides a thorough summary on the current understanding of the role of mitochondria in synapse development and emphasizes the importance of both molecular and epigenetic mechanisms in maintaining synaptic integrity.

DOI: https://doi.org/10.1007/s10142-025-01530-3
Cell Stem Cell. 2025 Jan 10. pii: S1934-5909(24)00446-6. [Epub ahead of print]

Mouse totipotent blastomere-like cells model embryogenesis from zygotic genome activation to post implantation.

Bing Peng, Qingyi Wang, Feixiang Zhang, Hui Shen, Peng Du.

  Embryo development begins with zygotic genome activation (ZGA), eventually generating blastocysts for implantation. However, in vitro systems modeling the pre-implantation development are still absent and challenging. Here, we used mouse totipotent blastomere-like cells (TBLCs) to develop spontaneous differentiation and blastoid formation systems, respectively. We found Wnt signaling enabled the rapid expansion of TBLCs and the optimization of their culture medium. We successfully developed a TBLC-spontaneous differentiation system in which mouse TBLCs (mTBLCs) firstly converted into two types of ZGA-like cells (ZLCs) distinguished by Zscan4 expression. Surprisingly, Zscan4-, but not Zscan4+, ZLCs further passed through intermediate 4-cell and then 8-cell/morula stages to produce epiblast, primitive endoderm, and trophectoderm lineages. Significantly, single TBLCs underwent expansion, compaction, and polarization to efficiently generate blastocyst-like structures and even post-implantation egg-cylinder-like structures. Conclusively, we established TBLC-based differentiation and embryo-like structure formation systems to model early embryonic development, offering criteria for evaluating and understanding totipotency.

Keywords:  Wnt signaling; blastoid; preimplantation; splicing inhibition; spontaneous differentiation; totipotent; totipotent blastomere-like cell

DOI:  https://doi.org/10.1016/j.stem.2024.12.006
Commun Biol. 2025 Jan 21. 8(1): 105

Dysfunctional BCAA degradation triggers neuronal damage through disrupted AMPK-mitochondrial axis due to enhanced PP2Ac interaction.

Shih-Cheng Wu, Yan-Jhen Chen, Shih-Han Su, Pai-Hsiang Fang, Rei-Wen Liu, Hui-Ying Tsai, Yen-Jui Chang, Hsing-Han Li, Jian-Chiuan Li, Chun-Hong Chen.

Metabolic and neurological disorders commonly display dysfunctional branched-chain amino acid (BCAA) metabolism, though it is poorly understood how this leads to neurological damage. We investigated this by generating Drosophila mutants lacking BCAA-catabolic activity, resulting in elevated BCAA levels and neurological dysfunction, mimicking disease-relevant symptoms. Our findings reveal a reduction in neuronal AMP-activated protein kinase (AMPK) activity, which disrupts autophagy in mutant brain tissues, linking BCAA imbalance to brain dysfunction. Mechanistically, we show that excess BCAA-induced mitochondrial reactive oxygen species (ROS) triggered the binding of protein phosphatase 2 A catalytic subunit (PP2Ac) to AMPK, suppressing AMPK activity. This initiated a dysregulated feedback loop of AMPK-mitochondrial interactions, exacerbating mitochondrial dysfunction and oxidative neuronal damage. Our study identifies BCAA imbalance as a critical driver of neuronal damage through AMPK suppression and autophagy dysfunction, offering insights into metabolic-neuronal interactions in neurological diseases and potential therapeutic targets for BCAA-related neurological conditions.

DOI: https://doi.org/10.1038/s42003-025-07457-6
J Fungi (Basel). 2025 Jan 14. pii: 58. [Epub ahead of print]11(1):

Direct and Indirect Protein Interactions Link FUS Aggregation to Histone Post-Translational Modification Dysregulation and Growth Suppression in an ALS/FTD Yeast Model.

Seth A Bennett, Samantha N Cobos, Raven M A Fisher, Elizaveta Son, Rania Frederic, Rianna Segal, Huda Yousuf, Kaitlyn Chan, David K Dansu, Mariana P Torrente.

  Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are incurable neurodegenerative disorders sharing pathological and genetic features, including mutations in the FUS gene. FUS is an RNA-binding protein that mislocalizes to the cytoplasm and aggregates in ALS/FTD. In a yeast model, FUS proteinopathy is connected to changes in the epigenome, including reductions in the levels of H3S10ph, H3K14ac, and H3K56ac. Exploiting the same model, we reveal novel connections between FUS aggregation and epigenetic dysregulation. We show that the histone-modifying enzymes Ipl1 and Rtt109-responsible for installing H3S10ph and H3K56ac-are excluded from the nucleus in the context of FUS proteinopathy. Furthermore, we found that Ipl1 colocalizes with FUS, but does not bind it directly. We identified Nop1 and Rrp5, a histone methyltransferase and rRNA biogenesis protein, respectively, as FUS binding partners involved in the growth suppression phenotype connected to FUS proteinopathy. We propose that the nuclear exclusion of Ipl1 through indirect interaction with FUS drives the dysregulation of H3S10ph as well as H3K14ac via crosstalk. We found that the knockdown of Nop1 interferes with these processes. In a parallel mechanism, Rtt109 mislocalization results in reduced levels of H3K56ac. Our results highlight the contribution of epigenetic mechanisms to ALS/FTD and identify novel targets for possible therapeutic intervention.

Keywords:  FUS; Ipl1; Nop1; Rtt109; amyotrophic lateral sclerosis; epigenetics; frontotemporal dementia; histone post-translational modifications

DOI:  https://doi.org/10.3390/jof11010058
G3 (Bethesda). 2025 Jan 24. pii: jkaf004. [Epub ahead of print]

Multiple regulators constrain the abundance of C. elegans DLK-1 in ciliated sensory neurons.

Yue Sun, Junxiang Zhou, Arunima Debnath, Bokun Xie, Zhiping Wang, Yishi Jin.

  The conserved MAP3K DLKs are widely known for their functions in synapse formation, axonal regeneration and degeneration, and neuronal survival, notably under traumatic injury and chronic disease conditions. In contrast, their roles in other neuronal compartments are much less explored. Through an unbiased forward genetic screening in C. elegans for altered patterns of GFP-tagged DLK-1 expressed from the endogenous locus, we have recently uncovered a mechanism by which the abundance of DLK-1 is tightly regulated by intraflagellar transport in ciliated sensory neurons. Here, we report additional mutants identified from the genetic screen. Most mutants exhibit increased accumulation of GFP::DLK-1 in sensory endings, and the levels of misaccumulated GFP::DLK-1 are exacerbated by loss of function in cebp-1, the b-Zip transcription factor acting downstream of DLK-1. We identify several new mutations in genes encoding proteins functioning in intraflagellar transport and cilia assembly, in components of BBSome, MAPK-15 and DYF-5 kinases. We report a novel mutation in the chaperone HSP90 that causes misaccumulation of GFP::DLK-1 and up-regulation of CEBP-1 selectively in ciliated sensory neurons. We also find that the guanylate cyclase ODR-1 constrains GFP::DLK-1 abundance throughout cilia and dendrites of AWC neurons. Moreover, in odr-1 mutants, AWC cilia display distorted morphology, which is ameliorated by loss of function in dlk-1 or cebp-1. These data expand the landscape of DLK-1 signaling in ciliated sensory neurons and underscore a high degree of cell- and neurite- specific regulation.

Keywords:  BBSome; HSP-90; Intraflagellar transport; MAPK-15; ODR-1

DOI:  https://doi.org/10.1093/g3journal/jkaf004
Ther Adv Neurol Disord. 2025 ;18 17562864251313915

Tofersen and other antisense oligonucleotides in ALS.

Albert Ludolph, Maximilian Wiesenfarth.

  The advent of antisense oligonucleotide (ASO) therapies in neurodegenerative disorders is associated with enormous hope. Nusinersen treatment was a breakthrough intervention in the recessive disease spinal muscular atrophy, and superoxide dismutase 1 (SOD1) amyotrophic lateral sclerosis (ALS) seems to be the paradigm disease in dominant degenerative diseases. The results of treatment with the ASO tofersen in SOD1-ALS show that the drug has a convincing beneficial effect on ALS caused by SOD1 mutations, that preclinical studies in rodents predicted the therapeutic effect in the human disease, and that clinical efficacy is associated with a specific sequence of effects of the drug on mechanistic and degenerative biomarkers and, subsequently, functional outcomes such as weight stabilization and ALSFRS-R. Therefore, the enthusiasm seems to be justified; but this should be followed by an attempt to obtain further insights with the goal to improve this therapy. In particular, the following issues are only partially resolved: Which mechanisms are responsible for the clinical effect following the downregulation of SOD1 protein by ASOs? Is long-term downregulation of SOD1 function associated with side effects? Is there an autoimmune response caused by this and other ASO? Is prevention of SOD1-associated ALS possible?

Keywords:  amyotrophic lateral sclerosis; antisense oligonucleotides; superoxide dismutase; tofersen

DOI:  https://doi.org/10.1177/17562864251313915
Front Cell Neurosci. 2024 ;18 1478572

Advances in physiological and clinical relevance of hiPSC-derived brain models for precision medicine pipelines.

Negin Imani Farahani, Lisa Lin, Shama Nazir, Alireza Naderi, Leanne Rokos, Anthony Randal McIntosh, Lisa M Julian.

  Precision, or personalized, medicine aims to stratify patients based on variable pathogenic signatures to optimize the effectiveness of disease prevention and treatment. This approach is favorable in the context of brain disorders, which are often heterogeneous in their pathophysiological features, patterns of disease progression and treatment response, resulting in limited therapeutic standard-of-care. Here we highlight the transformative role that human induced pluripotent stem cell (hiPSC)-derived neural models are poised to play in advancing precision medicine for brain disorders, particularly emerging innovations that improve the relevance of hiPSC models to human physiology. hiPSCs derived from accessible patient somatic cells can produce various neural cell types and tissues; current efforts to increase the complexity of these models, incorporating region-specific neural tissues and non-neural cell types of the brain microenvironment, are providing increasingly relevant insights into human-specific neurobiology. Continued advances in tissue engineering combined with innovations in genomics, high-throughput screening and imaging strengthen the physiological relevance of hiPSC models and thus their ability to uncover disease mechanisms, therapeutic vulnerabilities, and tissue and fluid-based biomarkers that will have real impact on neurological disease treatment. True physiological understanding, however, necessitates integration of hiPSC-neural models with patient biophysical data, including quantitative neuroimaging representations. We discuss recent innovations in cellular neuroscience that can provide these direct connections through generative AI modeling. Our focus is to highlight the great potential of synergy between these emerging innovations to pave the way for personalized medicine becoming a viable option for patients suffering from neuropathologies, particularly rare epileptic and neurodegenerative disorders.

Keywords:  biomarkers; brain disorders; brain organoids; generative AI; hiPSCs; neurophysiology; precision medicine

DOI:  https://doi.org/10.3389/fncel.2024.1478572
Neuropharmacology. 2025 Jan 15. pii: S0028-3908(25)00019-X. [Epub ahead of print]268 110313

Synaptic protein expression in bipolar disorder patient-derived neurons implicates PSD-95 as a marker of lithium response.

Kayla E Rohr, Himanshu K Mishra, Johansen Amin, Timothy Nakhla, Michael J McCarthy.

  Bipolar disorder (BD) is a severe mental illness characterized by recurrent episodes of depression and mania. Lithium is the gold standard pharmacotherapy for BD, but outcomes are variable, and the relevant therapeutic mechanisms underlying successful treatment response remain uncertain. To identify synaptic markers of BD and lithium response, we measured the effects of lithium on induced pluripotent stem cell-derived neurons from BD patients and controls. We determined that baseline expression of synapsin I (SYN1) and PSD-95 is reduced in BD neurons compared to controls. In control neurons, lithium treatment had modest, transient effects increasing SYN1 and PSD-95 expression. In BD neurons, lithium increased SYN1 expression regardless of lithium response history. However, lithium only increased PSD-95 expression selectively in neurons from lithium-responders and not in neurons from lithium non-responders, leading to group differences in the colocalization of SYN1 and PSD-95. In conclusion, this preliminary work indicates synaptic protein markers are associated with BD pathology and correction of post-synaptic protein expression may be an important mechanism underlying lithium response.

Keywords:  Bipolar disorder; Lithium; Neuron; Stem cell; Synapse

DOI:  https://doi.org/10.1016/j.neuropharm.2025.110313
Cell. 2025 Jan 14. pii: S0092-8674(24)01379-5. [Epub ahead of print]

Long somatic DNA-repeat expansion drives neurodegeneration in Huntington's disease.

Robert E Handsaker, Seva Kashin, Nora M Reed, Steven Tan, Won-Seok Lee, Tara M McDonald, Kiely Morris, Nolan Kamitaki, Christopher D Mullally, Neda R Morakabati, Melissa Goldman, Gabriel Lind, Rhea Kohli, Elisabeth Lawton, Marina Hogan, Kiku Ichihara, Sabina Berretta, Steven A McCarroll.

  In Huntington's disease (HD), striatal projection neurons (SPNs) degenerate during midlife; the core biological question involves how the disease-causing DNA repeat (CAG)n in the huntingtin (HTT) gene leads to neurodegeneration after decades of biological latency. We developed a single-cell method for measuring this repeat's length alongside genome-wide RNA expression. We found that the HTT CAG repeat expands somatically from 40-45 to 100-500+ CAGs in SPNs. Somatic expansion from 40 to 150 CAGs had no apparent cell-autonomous effect, but SPNs with 150-500+ CAGs lost positive and then negative features of neuronal identity, de-repressed senescence/apoptosis genes, and were lost. Our results suggest that somatic repeat expansion beyond 150 CAGs causes SPNs to degenerate quickly and asynchronously. We conclude that in HD, at any one time, most neurons have an innocuous but unstable HTT gene and that HD pathogenesis is a DNA process for almost all of a neuron's life.

Keywords:  CAG; DNA repeats; Huntington’s disease; neurodegeneration; repeat instability; single-nucleus RNA-seq; somatic expansion; striatal projection neurons; triplet repeat disorders

DOI:  https://doi.org/10.1016/j.cell.2024.11.038
Front Bioeng Biotechnol. 2024 ;12 1501829

The utilisation of biliary organoids for biomedical applications.

Zhongwen Lei, Yijun Yang, Yang Xiang.

  Biliary duct injury, biliary atresia (BA), biliary tract tumors, primary sclerosing cholangitis (PSC), and other diseases are commonly encountered in clinical practice within the digestive system. To gain a better understanding of the pathogenesis and development of these diseases and explore more effective treatment methods, organoid technology has recently garnered significant attention. Organoids are three-dimensional structures derived from stem/progenitor cells that can faithfully mimic the intricate structure and physiological function of tissues or organs in vitro. They provide a valuable platform for studying the pathogenesis of biliary tract diseases and offer novel possibilities for repairing and regenerating biliary tract injuries. The main seed cells used to construct biliary tract organoids include primary human biliary tract epithelial cells as well as pluripotent stem cells. The construction of these organoids involves various techniques such as traditional embedding technology, rotary culture technology, hanging drop culture technology, along with emerging approaches like organ chip technology, three-dimensional (3D) printing technology, and four-dimensional (4D) printing technology. This article comprehensively reviews the construction methods of biliary tract organoids while discussing their applications in disease modeling research on disease mechanisms drug screening tissue/organ repair; it also highlights current challenges and suggests future research directions regarding biliary tract organoids which will serve as references for treating common refractory digestive system diseases in clinical practice.

Keywords:  drug screening; mechanisms of disease; organoids; regenerative medicine; tissue engineering

DOI:  https://doi.org/10.3389/fbioe.2024.1501829
Toxics. 2025 Jan 17. pii: 63. [Epub ahead of print]13(1):

The Role of Autophagy in Copper-Induced Apoptosis and Developmental Neurotoxicity in SH-SY5Y Cells.

Lu Lu, Ying Zhang, Wei Shi, Qian Zhou, Zhuoqi Lai, Yuepu Pu, Lihong Yin.

  Copper (Cu) is a global environmental pollutant that poses a serious threat to humans and ecosystems. Copper induces developmental neurotoxicity, but the underlying molecular mechanisms are unknown. Neurons are nonrenewable, and they are unable to mitigate the excessive accumulation of pathological proteins and organelles in cells, which can be ameliorated by autophagic degradation. In this study, we established an in vitro model of Cu2+-exposed (0, 15, 30, 60 and 120 μM) SH-SY5Y cells to explore the role of autophagy in copper-induced developmental neurotoxicity. The results showed that copper resulted in the reduction and shortening of neural synapses in differentiated cultured SH-SY5Y cells, a downregulated Wnt signaling pathway, and nuclear translocation of β-catenin. Exposure to Cu2+ increased autophagosome accumulation and autophagic flux blockage in terms of increased sequestosome 1 (p62/SQSTM1) and microtubule-associated protein 1 light chain 3B (LC3B) II/LC3BI expressions and inhibition of the phosphatidylinositol 3-kinase (PI3K)/Akt/mTOR pathway. Furthermore, copper induced apoptosis, characterized by increased expressions of Bcl2 X protein (Bax), caspase 3, and Poly (ADP-ribose) polymerase (PARP) and decreased expression of B-cell lymphoma 2 (Bcl2). Compared with the 120 μM Cu2+ exposure group alone, autophagy activator rapamycin pretreatment increased expression of Wnt and β-catenin nuclear translocation, decreased expression of LC3BII/LC3BI and p62, as well as upregulated expression of Bcl2 and downregulated expressions of caspase 3 and PARP. In contrast, after autophagy inhibitor chloroquine pretreatment, expressions of Wnt and β-catenin nuclear translocation were decreased, expression levels of LC3BII/LC3BI and p62 were upregulated, expression of Bcl2 was decreased, while expression levels of caspase 3, Bax, and PARP were increased. In conclusion, the study demonstrated that autophagosome accumulation and autophagic flux blockage were associated with copper-induced developmental neurotoxicity via the Wnt signaling pathway, which might deepen the understanding of the developmental neurotoxicity mechanism of environmental copper exposure.

Keywords:  Wnt signaling pathway; autophagy; copper; developmental neurotoxicity

DOI:  https://doi.org/10.3390/toxics13010063
Cells. 2025 Jan 07. pii: 64. [Epub ahead of print]14(2):

Transcriptomic and Functional Landscape of Adult Human Spinal Cord NSPCs Compared to iPSC-Derived Neural Progenitor Cells.

Sasi Kumar Jagadeesan, Ahmad Galuta, Ryan Vimukthi Sandarage, Eve Chung Tsai.

  The adult human spinal cord harbors diverse populations of neural stem/progenitor cells (NSPCs) essential for neuroregeneration and central nervous system repair. While induced pluripotent stem cell (iPSC)-derived NSPCs offer significant therapeutic potential, understanding their molecular and functional alignment with bona fide spinal cord NSPCs is crucial for developing autologous cell therapies that enhance spinal cord regeneration and minimize immune rejection. In this study, we present the first direct transcriptomic and functional comparison of syngeneic adult human NSPC populations, including bona fide spinal cord NSPCs and iPSC-derived NSPCs regionalized to the spinal cord (iPSC-SC) and forebrain (iPSC-Br). RNA sequencing analysis revealed distinct transcriptomic profiles and functional disparities among NSPC types. iPSC-Br NSPCs exhibited a close resemblance to bona fide spinal cord NSPCs, characterized by enriched expression of neurogenesis, axon guidance, synaptic signaling, and voltage-gated calcium channel activity pathways. Conversely, iPSC-SC NSPCs displayed significant heterogeneity, suboptimal regional specification, and elevated expression of neural crest and immune response-associated genes. Functional assays corroborated the transcriptomic findings, demonstrating superior neurogenic potential in iPSC-Br NSPCs. Additionally, we assessed donor-specific influences on NSPC behavior by analyzing gene expression and differentiation outcomes across syngeneic populations from multiple individuals. Donor-specific factors significantly modulated transcriptomic profiles, with notable variability in the alignment of iPSC-derived NSPCs to bona fide spinal cord NSPCs. Enrichment of pathways related to neurogenesis, axon guidance, and synaptic signaling varied across donors, highlighting the impact of genetic and epigenetic individuality on NSPC behavior.

Keywords:  cellular heterogeneity; differentiation potential; induced pluripotent stem cells; neural stem/progenitor cells; neurogenesis; patient-specific variability; proliferation dynamics; regenerative medicine; spinal cord injury; transcriptomics

DOI:  https://doi.org/10.3390/cells14020064