bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2025–11–09
forty-five papers selected by
Fawaz Alzaïd, Sorbonne Université



  1. Cell. 2025 Nov 05. pii: S0092-8674(25)01178-X. [Epub ahead of print]
      Chromatin structure is a key determinant of gene expression in eukaryotes, but it has not been possible to define the structure of cis-regulatory elements at the scale of the proteins that bind them. Here, we generate multidimensional chromosome conformation capture (3C) maps at base-pair resolution using Micro Capture-C ultra (MCCu). This can resolve contacts between individual transcription factor motifs within cis-regulatory elements. Using degron systems, we show that removal of Mediator complex components alters fine-scale promoter structure and that nucleosome depletion plays a key role in transcription factor-driven enhancer-promoter contacts. We observe that chromatin is partitioned into nanoscale domains by nucleosome-depleted regions. This structural conformation is reproduced by chemically specific coarse-grained molecular dynamics simulations of the physicochemical properties of chromatin. Combining MCCu with molecular dynamics simulations and super-resolution microscopy allows us to propose a unified model in which the biophysical properties of chromatin orchestrate contacts between cis-regulatory elements.
    Keywords:  chromatin structure; chromosome conformation capture; cis-regulatory elements; enhancer-promoter interactions; gene regulation; mediator complex; molecular dynamics simulations; nuclear organization; transcription factors
    DOI:  https://doi.org/10.1016/j.cell.2025.10.013
  2. Nature. 2025 Nov 05.
      Microglia, the innate immune cells of the brain, play a defining role in the progression of Alzheimer's disease (AD)1. The microglial response to amyloid plaques in AD can range from neuroprotective to neurotoxic2. Here we show that the protective function of microglia is governed by the transcription factor PU.1, which becomes downregulated following microglial contact with plaques. Lowering PU.1 expression in microglia reduces the severity of amyloid disease pathology in mice and is linked to the expression of immunoregulatory lymphoid receptor proteins, particularly CD28, a surface receptor that is critical for T cell activation3,4. Microglia-specific deficiency in CD28, which is expressed by a small subset of plaque-associated PU.1low microglia, promotes a broad inflammatory microglial state that is associated with increased amyloid plaque load. Our findings indicate that PU.1low CD28-expressing microglia may operate as suppressive microglia that mitigate the progression of AD by reducing the severity of neuroinflammation. This role of CD28 and potentially other lymphoid co-stimulatory and co-inhibitory receptor proteins in governing microglial responses in AD points to possible immunotherapy approaches for treating the disease by promoting protective microglial functions.
    DOI:  https://doi.org/10.1038/s41586-025-09662-z
  3. Nat Commun. 2025 Nov 03. 16(1): 9484
      α/β-hydrolase domain-containing protein 11 (ABHD11) is a mitochondrial hydrolase that maintains the catalytic function of α-ketoglutarate dehydrogenase (α-KGDH), and its expression in CD4 + T-cells has been linked to remission status in rheumatoid arthritis (RA). However, the importance of ABHD11 in regulating T-cell metabolism and function is yet to be explored. Here, we show that pharmacological inhibition of ABHD11 dampens cytokine production by human and mouse T-cells. Mechanistically, the anti-inflammatory effects of ABHD11 inhibition are attributed to increased 24,25-epoxycholesterol (24,25-EC) biosynthesis and subsequent liver X receptor (LXR) activation, which arise from a compromised TCA cycle. The impaired cytokine profile established by ABHD11 inhibition is extended to two patient cohorts of autoimmunity. Importantly, using murine models of accelerated type 1 diabetes (T1D), we show that targeting ABHD11 suppresses cytokine production in antigen-specific T-cells and delays the onset of diabetes in vivo in female mice. Collectively, our work provides pre-clinical evidence that ABHD11 is an encouraging drug target in T-cell-mediated inflammation.
    DOI:  https://doi.org/10.1038/s41467-025-65417-4
  4. Mol Cell. 2025 Nov 06. pii: S1097-2765(25)00853-6. [Epub ahead of print]
      Cytosolic translation activity is fine-tuned by environmental conditions primarily through signaling pathways that target translation initiation factors. Although mitochondria possess their own translation machinery, they lack an autonomous signaling network analogous to their cytosolic counterpart for regulating translation activity. Consequently, our understanding of how mitochondrial translation activity is adjusted under different metabolic environments remains very limited. Here, we report a noncanonical mechanism for regulating mitochondrial translation activity via metabolism-dependent changes in the mitochondrial ribosome (mitoribosome) in S. cerevisiae. These changes arise from a metabolism-modulated mitoribosome assembly pathway that regulates the composition and conformation of the mitoribosome, thereby adjusting its translation activity to meet metabolic demands. Moreover, the translation activity of the mitoribosome feeds back to regulate the biogenesis of nuclear-encoded mitochondrial proteins, influencing mitochondrial functions and aging. Such a ribosomal remodeling-based "gear-switching" mechanism represents an orthogonal mode of translation regulation, compensating for the absence of a translation-modulating signaling network within mitochondria.
    Keywords:  aging; metabolism; mitochondria; mitoribosome; translation activity
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.012
  5. Nature. 2025 Nov 03.
      Somatically acquired mutations in the E1 ubiquitin-activating enzyme UBA1 within hematopoietic stem and progenitor cells (HSPCs) were recently identified as the cause of the adult-onset autoinflammatory syndrome VEXAS (vacuoles, E1 enzyme, X linked, autoinflammatory, somatic)1. UBA1 mutations in VEXAS lead to clonal expansion within the HSPC and myeloid, but not lymphoid, compartments. Despite its severity and prevalence, the mechanisms whereby UBA1 mutations cause multiorgan autoinflammation and hematologic disease are unknown. Here, we employ somatic gene editing approaches to model VEXAS-associated UBA1 mutations in primary macrophages and HSPCs. Uba1-mutant macrophages exposed to inflammatory stimuli underwent aberrant apoptotic and necroptotic cell death mediated by Caspase-8 and RIPK3-MLKL, respectively. Accordingly, in mice challenged with TNF or LPS, the UBA1 inhibitor TAK-243 exacerbated inflammation in a RIPK3-Caspase-8-dependent manner. In contrast, Uba1 mutation in HSPCs induced an unfolded protein response and myeloid bias independently of RIPK3-Caspase-8. Mechanistically, aberrant cell death of Uba1-mutant macrophages coincided with a kinetic defect in Lys63/Met1 (i.e., linear) polyubiquitylation of inflammatory signaling complexes. Collectively, our results link VEXAS pathogenesis with that of rarer monogenic autoinflammatory syndromes; highlight specific ubiquitin-associated defects stemming from an apical mutation in the ubiquitylation cascade; and support therapeutic targeting of the inflammatory cell death axis in VEXAS.
    DOI:  https://doi.org/10.1038/s41586-025-09815-0
  6. Nature. 2025 Nov 03.
      
    Keywords:  Alzheimer's disease; Medical research; Neuroscience; Public health
    DOI:  https://doi.org/10.1038/d41586-025-03596-2
  7. Nat Commun. 2025 Nov 03. 16(1): 9688
      Satellite DNA comprises ~11% of the mouse genome and is primarily located in centromeres and pericentromeres. We present comprehensive genomic and epigenomic maps of these regions utilizing Hifiasm assemblies, CUT&RUN-seq, DNA methylation analysis, and RNA-seq alongside recent mouse telomere-to-telomere assembly drafts. We show that 120-mer Minor satellites (MiSats) occupy core centromeres, while MiSat length variants localize at centromere-pericentric junctions. Pericentromeres contain mostly homogeneous Major satellites (MaSats), with divergent MaSats concentrated near pericentric non-satellite repeat islands and pericentric-chromosomal junctions. Most centromeres contain higher-order repeats (HORs), with shorter HORs more common. Centromeres are hypomethylated compared to pericentromeres, and transcripts are detected from a small subset of satellites with lower DNA methylation. CENP-A is highly enriched at 120-mer MiSats but reduced at MiSat length variants. Homogeneous MaSats are enriched with H3K9me3, whereas divergent MaSats are associated with H3K9me3 and H3K27me3. Finally, the density and type of satellite sequence motifs correlate with chromatin signatures.
    DOI:  https://doi.org/10.1038/s41467-025-64689-0
  8. Nat Commun. 2025 Nov 03. 16(1): 9674
      Human inflammatory response reflects adaptive alteration of immune-cell regulatory elements during human evolution. Yet the impact of the deeper evolutionary history of these elements, within primate genomes reshaped by transposon expansions, remains unclear. Tracing sequence changes in human immune-cell enhancers back to macaque and analysing proinflammatory transcription factor binding, we show that primate-specific endogenous retroviruses and Alu transposons introduced functional NF-κB and IRF1 motifs, contributing most to the great-ape-specific pool. After the human-macaque split, these motifs tend to evolve toward higher predicted binding affinity. In modern humans, positive selection favoured alleles, often Alu-derived, that increase enhancer affinity for NF-κB, and Alu-containing enhancers are enriched in signatures of adaptation. Highly mutable, Alus disproportionately contribute to the pool of adaptive alleles, including at enhancers linked to inflammatory diseases. We propose that primate-specific transposons facilitated the evolution of inflammatory responses in great apes, with Alus shaping adaptive potential in modern humans.
    DOI:  https://doi.org/10.1038/s41467-025-64690-7
  9. Nat Commun. 2025 Nov 06. 16(1): 9750
      Our understanding of how the body communicates with the brain to coordinate their functions is remarkably limited. At the blood-brain barrier (BBB), brain endothelial cells (BECs) are ideally positioned to mediate signaling between blood and brain parenchyma via direct communication with astrocyte perivascular processes (endfeet). We develop a method to define the mouse in vivo astrocyte endfoot proteome, which in combination with BEC-specific RNA-seq, reveal BEC to astrocyte endfoot ligand-receptor pairs that are modulated when mice are exposed to a peripheral inflammatory insult with lipopolysaccharide. We show that over 80% of these mouse BEC-endfoot ligand-receptor pairs are also found in the human BBB, with a subset of them differentially expressed in human multiple sclerosis or Alzheimer's disease compared to healthy individuals. Our findings reveal dynamic BEC-endfoot communication pathways that are relevant to human physiology and provide methodology and datasets for the translational study of BEC-astrocyte crosstalk in health and disease.
    DOI:  https://doi.org/10.1038/s41467-025-65487-4
  10. Cell Metab. 2025 Nov 04. pii: S1550-4131(25)00436-X. [Epub ahead of print]37(11): 2099-2101
      Emerging evidence challenges the view of obesity as a uniform metabolic risk. Spotlighting the recent Nature Medicine study by Chami et al.,1 this piece discusses how "uncoupling" adiposity from its cardiometabolic consequences reveals biologically distinct subtypes of obesity. Integrating imaging and multi-omics offers a promising path toward personalized obesity management and deeper mechanistic insight.
    DOI:  https://doi.org/10.1016/j.cmet.2025.10.002
  11. Sci Immunol. 2025 Nov 07. 10(113): eaed4910
      An MS twin study links ileal Lachnospiraceae to spontaneous CNS autoimmunity in mice receiving a human microbiome transplant.
    DOI:  https://doi.org/10.1126/sciimmunol.aed4910
  12. Nature. 2025 Nov 05.
      
    Keywords:  Authorship; Institutions; Research management
    DOI:  https://doi.org/10.1038/d41586-025-03617-0
  13. Science. 2025 Nov 06. 390(6773): 570-571
      A protein complex promotes the expansion of lipid droplets during the formation of mature adipocytes.
    DOI:  https://doi.org/10.1126/science.aec4109
  14. Sci Immunol. 2025 Nov 07. 10(113): eaed4909
      Repeated dengue infections elicit broadly neutralizing antibodies that are protective against severe disease.
    DOI:  https://doi.org/10.1126/sciimmunol.aed4909
  15. J Clin Invest. 2025 Nov 03. pii: e190635. [Epub ahead of print]135(21):
      Both adipocytes and hepatocytes have the capacity to store fat, but the factor(s) that determine fat distribution between these cell types remain unknown. In mice fed a high-fat diet, fat initially accumulates predominantly in adipocytes, while hepatic fat accumulation mainly emerges after the onset of epididymal adipocyte death that results in elevated free fatty acids to promote lipid accumulation in hepatocytes. However, it remains unclear whether other signals after adipocyte death are required to direct and/or promote hepatocytes to store fat and subsequently trigger metabolic dysfunction-associated steatotic liver disease (MASLD, formerly known as nonalcoholic fatty liver disease). Using genetically modified mouse models combined with bulk and single-cell RNA-Seq analysis, we demonstrated that visceral adipocyte death induced an accumulation of S100A8+ macrophages in the liver, which was partially induced by fatty acids and apoptotic adipocyte-derived extracellular vesicles. Macrophage-specific deletion of the S100a8 gene reduced hepatic fat accumulation and MASLD severity in mice. Mechanistically, S100A8+ macrophages suppressed cellular communication network factor 3 (CCN3), a negative regulator of CD36, thereby enhancing CD36 expression in hepatocytes. In conclusion, adipocyte death promotes hepatic infiltration of S100A8+ macrophages, which drive hepatocyte lipid storage and subsequently promote MASLD progression through CD36 upregulation, partially mediated by CCN3 suppression.
    Keywords:  Adipose tissue; Gastroenterology; Hepatology; Macrophages
    DOI:  https://doi.org/10.1172/JCI190635
  16. Nat Genet. 2025 Nov 03.
      The vast majority of recurrent somatic mutations arising in tumors affect protein-coding genes in the nuclear genome. Here, through population-scale analysis of 14,106 whole tumor genomes, we report the discovery of highly recurrent mutations affecting both the small (12S, MT-RNR1) and large (16S, MT-RNR2) mitochondrial RNA subunits of the mitochondrial ribosome encoded within mitochondrial DNA (mtDNA). Compared to non-hotspot positions, mitochondrial rRNA hotspots preferentially affected positions under purifying selection in the germline and demonstrated structural clustering within the mitoribosome at mRNA and tRNA interacting positions. Using precision mtDNA base editing, we engineered models of an exemplar MT-RNR1 hotspot mutation, m.1227G>A. Multimodal profiling revealed a heteroplasmy-dependent decrease in mitochondrial function and loss of respiratory chain subunits from a heteroplasmic dosage of ~10%. Mutation of conserved positions in ribosomal RNA that disrupt mitochondrial translation therefore represent a class of functionally dominant, pathogenic mtDNA mutations that are under positive selection in cancer genomes.
    DOI:  https://doi.org/10.1038/s41588-025-02374-0
  17. Nat Metab. 2025 Nov 04.
      Neurodegenerative disorders alter mitochondrial functions, including the production of reactive oxygen species (ROS). Mitochondrial complex III (CIII) generates ROS implicated in redox signalling, but its triggers, temporal dynamics, targets and disease relevance are not clear. Here, using site-selective suppressors and genetic manipulations together with live mitochondrial ROS imaging and multiomic profiling, we show that CIII is a dominant source of ROS production in astrocytes exposed to neuropathology-related stimuli. Astrocytic CIII ROS production is dependent on nuclear factor-κB and the mitochondrial sodium-calcium exchanger (NCLX) and causes oxidation of select cysteines within immune- and metabolism-associated proteins linked to neurological disease. CIII ROS amplify metabolomic and pathology-associated transcriptional changes in astrocytes, with STAT3 activity as a major mediator, and facilitate neuronal toxicity. Therapeutic suppression of CIII ROS in mice decreases dementia-linked tauopathy and neuroimmune cascades and extends lifespan. Our findings establish CIII ROS as an important immunometabolic signal transducer and tractable therapeutic target in neurodegenerative disease.
    DOI:  https://doi.org/10.1038/s42255-025-01390-y
  18. Nat Commun. 2025 Nov 04. 16(1): 9402
      Multimorbidity is projected to continue increasing in England and many other countries. Here, we use a validated microsimulation model to quantify the potential impact of improving exposure levels of eight risk factors on the burden of major illness among adults aged 30+ in England between 2023-2043. We find that the biggest contributors to incident major illness are body mass index, smoking, systolic blood pressure, and physical inactivity. Theoretical minimum risk exposure levels of all risk factors could reduce 2043 major illness prevalence by 2 percentage points (95% uncertainty intervals: 1.3, 2.7) compared to the continuing trends (base-case) scenario; under a 10% improvement in all risk factors, we project a 0.3 percentage points (0.2, 0.4) reduction in major illness. The impact on health inequalities is mixed. Our findings show that large improvements in risk factors are unlikely to substantially reduce the major illness burden by 2043 due to population ageing.
    DOI:  https://doi.org/10.1038/s41467-025-64820-1
  19. Immunity. 2025 Oct 31. pii: S1074-7613(25)00465-0. [Epub ahead of print]
      Expression of the IgE BCR is associated with increased B cell apoptosis, yet in persistent allergy, sustained production of IgE antibodies in the absence of allergen exposure suggests the existence of long-lived IgE plasma cells (PCs). Here we studied the development and localization of IgE PCs in mouse models of allergy. After immunization, IgE PCs underwent maturation in spleen and lymph nodes, acquiring a stable MHCIIloCD93+CD98hiBCRlo phenotype. Mature IgE PCs had a distinct transcriptional profile adapted to high protein synthesis, glycosylation, and survival and resisted BCR-crosslinking-induced apoptosis. Immunization induced a burst of short-lived IgE PC formation, followed by a reduced differentiation rate over time, compared with IgG1 PCs. Timestamping of PCs revealed long-lived IgE PCs that localize to the spleen, in addition to the bone marrow (BM). Thus, immune challenge can generate both short-lived and long-lived IgE PCs, with long-lived IgE PCs in spleen and BM contributing to allergy persistence.
    Keywords:  IgE plasma cells; allergy persistence; long-lived plasma cells; spleen niche; timestamping
    DOI:  https://doi.org/10.1016/j.immuni.2025.10.011
  20. Nature. 2025 Nov 05.
      Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes1. Although these methods are conceptually similar, by analysing association studies of 209 quantitative traits in the UK Biobank2-4, we show that they systematically prioritize different genes. This raises the question of how genes should ideally be prioritized. We propose two prioritization criteria: (1) trait importance - how much a gene quantitatively affects a trait; and (2) trait specificity - the importance of a gene for the trait under study relative to its importance across all traits. We find that GWAS prioritize genes near trait-specific variants, whereas burden tests prioritize trait-specific genes. Because non-coding variants can be context specific, GWAS can prioritize highly pleiotropic genes, whereas burden tests generally cannot. Both study designs are also affected by distinct trait-irrelevant factors, complicating their interpretation. Our results illustrate that burden tests and GWAS reveal different aspects of trait biology and suggest ways to improve their interpretation and usage.
    DOI:  https://doi.org/10.1038/s41586-025-09703-7
  21. Elife. 2025 Nov 03. pii: RP89596. [Epub ahead of print]12
      In pancreatic islet β cells, molecular motors use cytoskeletal polymers microtubules as tracks for intracellular transport of insulin secretory granules. The β-cell microtubule network has a complex architecture and is nondirectional, which provides insulin granules at the cell periphery for rapid secretion response, yet to avoid oversecretion and subsequent hypoglycemia. We have previously characterized a peripheral sub-membrane microtubule array, which is critical for the withdrawal of excessive insulin granules from the secretion sites. Microtubules in β cells originate at the Golgi in the cell interior, and how the peripheral array is formed remains unknown. Here, we demonstrate that kinesin KIF5B, a motor protein with the capacity to transport microtubules as cargos, is needed to align sub-membrane microtubules in clonal mouse β cells MIN6 and β cells within intact mouse islets. Real-time imaging and photokinetics approaches indicate that KIF5B actively slides existing microtubules to the β-cell periphery. Moreover, like many physiological β-cell features, microtubule sliding is facilitated by a high glucose stimulus. These new data, together with our previous report that high glucose destabilizes the sub-membrane microtubule array to allow for robust secretion, indicate that MT sliding is another integral part of glucose-triggered microtubule remodeling, likely replacing destabilized peripheral microtubules to prevent their loss over time and β-cell malfunction.
    Keywords:  cell biology; developmental biology; insulin secretion; kinesin; microtubule; mouse; trafficking; β cell
    DOI:  https://doi.org/10.7554/eLife.89596
  22. Cell Metab. 2025 Nov 04. pii: S1550-4131(25)00438-3. [Epub ahead of print]37(11): 2097-2098
      Mechanisms that preserve glucose homeostasis are highly conserved across species, with the brain playing a central role in regulating these counterregulatory responses. However, the exact neural circuits underlying this regulation remain poorly understood. The previewed papers illuminate how the ventromedial hypothalamus orchestrates glycemic responses through brain-liver communication during periods of increased glucose demand.
    DOI:  https://doi.org/10.1016/j.cmet.2025.10.004
  23. Nat Commun. 2025 Nov 03. 16(1): 9667
      Reduced nicotinamide adenine dinucleotide phosphate (NADPH) metabolism is independently regulated in different compartments in endothelial cells (EC). The metabolic profile and functional impact of NADPH during EC senescence remain largely unknown. Using a genetically encoded fluorescent indicator, we find that cytosolic, but not mitochondrial, NADPH level increases during EC senescence. Upregulation of glucose-6-phosphate dehydrogenase (G6PD) further elevates cytosolic NADPH level during EC senescence. Suppression of G6PD S-nitrosylation at C385 potentiates G6PD activity. G6PD overexpression alleviates, while its knockdown aggravates, vascular aging. NADPH is indispensable for G6PD to protect against vascular aging through increasing reduced glutathione and inhibiting HDAC3 activity. Among 1419 FDA-approved drugs, folic acid, catalyzed by methylenetetrahydrofolate dehydrogenase to generate NADPH, effectively alleviates vascular aging in angiotensin II-infused mice and naturally aged mice. The connection between NADPH metabolism and EC senescence provides a unique angle for understanding vascular aging and an efficient target for therapy.
    DOI:  https://doi.org/10.1038/s41467-025-64652-z
  24. Commun Biol. 2025 Nov 05. 8(1): 1528
      Spatial transcriptomics has enabled the study of mRNA distributions within cells, a key aspect of cellular function. However, there is a dearth of tools that can identify and interpret functionally relevant spatial patterns of subcellular transcript distribution. To address this, we present CellSP, a computational framework for identifying, visualizing, and characterizing consistent subcellular spatial patterns of mRNA. CellSP introduces the concept of "gene-cell modules", which are gene sets with coordinated subcellular transcript distributions in many cells. It provides intuitive visualizations of the captured patterns and offers functional insights into each discovered module. We demonstrate that CellSP reliably identifies functionally significant modules across diverse tissues and technologies. We use the tool to discover subcellular spatial phenomena related to myelination, axonogenesis, and synapse formation in the mouse brain. We find immune response-related modules that change between kidney cancer and healthy samples, and myelination-related modules specific to mouse models of Alzheimer's Disease.
    DOI:  https://doi.org/10.1038/s42003-025-08891-2
  25. Sci Transl Med. 2025 Nov 05. 17(823): eadu6015
      Extrafollicular age-associated B cells (ABCs) excessively expand and produce autoantibodies in systemic lupus erythematosus (SLE), and the regulatory mechanism remains elusive. We found that the m6A demethylase fat mass and obesity-associated protein (FTO) was highly expressed in ABCs from patients with SLE, which was positively associated with renal immune damage. FTO overexpression in murine and human B cells facilitated ABC expansion and exacerbated SLE in lupus-prone mice, whereas FTO ablation ameliorated ABC-driven autoimmunity. FTO expression was up-regulated upon activation of the toll-like receptor 7-myeloid differentiation primary response protein 88 (TLR7-MyD88) signaling pathway. FTO, in turn, promoted TLR7-driven ABC differentiation by targeting ATPase H+ transporting V1 subunit G1 (ATP6V1G1), a subunit of the vacuolar H+-ATPase (V-ATPase), in an m6A-dependent manner. Mechanistically, FTO deficiency impaired lysosomal autophagy by reducing ATP6V1G1-mediated V-ATPase activity. The accumulation of damaged mitochondria led to mitochondrial dysfunction in human and murine B cells, characterized by reduced oxidative phosphorylation and elevated reactive oxygen species. This dysfunction limited cell proliferation and blocked ABC differentiation by dampening cellular responsiveness to interleukin-12. Thus, TLR7-FTO-ATP6V1G1 signaling metabolically shapes extrafollicular ABCs in SLE, providing a potential therapeutic target.
    DOI:  https://doi.org/10.1126/scitranslmed.adu6015
  26. Nature. 2025 Nov;647(8088): 213-227
      The ability to spatially map multiple layers of omics information across developmental timepoints enables exploration of the mechanisms driving brain development1, differentiation, arealization and disease-related alterations. Here we used spatial tri-omic sequencing, including spatial ATAC-RNA-protein sequencing and spatial CUT&Tag-RNA-protein sequencing, alongside multiplexed immunofluorescence imaging (co-detection by indexinng (CODEX)) to map dynamic spatial remodelling during brain development and neuroinflammation. We generated a spatiotemporal tri-omic atlas of the mouse brain from postnatal day 0 (P0) to P21 and compared corresponding regions with the human developing brain. In the cortex, we identified temporal persistence and spatial spreading of chromatin accessibility for a subset of layer-defining transcription factors. In the corpus callosum, we observed dynamic chromatin priming of myelin genes across subregions and identified a role for layer-specific projection neurons in coordinating axonogenesis and myelination. In a lysolecithin neuroinflammation mouse model, we detected molecular programs shared with developmental processes. Microglia exhibited both conserved and distinct programs for inflammation and resolution, with transient activation observed not only at the lesion core but also at distal locations. Overall, this study reveals common and differential mechanisms underlying brain development and neuroinflammation, providing a rich resource for investigating brain development, function and disease.
    DOI:  https://doi.org/10.1038/s41586-025-09663-y
  27. Geroscience. 2025 Nov 04.
      Non-lethal exposure to mitochondrial stress has been shown to have beneficial effects due to activation of signaling pathways, including the mitochondrial unfolded protein response (UPRmt). Activation of UPRmt restores the function of the mitochondria and improves general health and longevity in multiple model systems, termed mitohormesis. In C. elegans, mitohormesis can be accomplished by electron transport chain inhibition, a decline in mitochondrial translation, decreased mitochondrial import, and numerous other methods that activate UPRmt. However, not all methods that activate UPRmt promote longevity. These and other studies have started to question whether UPRmt is directly correlated with longevity. Here, we attempt to address this controversy by unraveling the complex molecular regulation of longevity of the nematode under different mitochondrial stressors that induce mitochondrial stress by performing RNA sequencing to profile transcriptome changes. Using this comprehensive and unbiased approach, we aim to determine whether specific transcriptomic changes can reveal a correlation between UPRmt and longevity. Altogether, this study will provide mechanistic insights on mitohormesis and how it correlates with the lifespan of C. elegans.
    Keywords:  Aging; Caenorhabditis elegans; Mitohormesis; UPRmt
    DOI:  https://doi.org/10.1007/s11357-025-01912-2
  28. Nature. 2025 Nov 06.
      The nuclear export of messenger RNA (mRNA) is an important step in eukaryotic gene expression1. Despite recent molecular insights into how newly transcribed mRNAs are packaged into ribonucleoprotein complexes (mRNPs)2,3, the subsequent events that govern mRNA export are poorly understood. Here, we uncover the molecular basis underlying key events of human mRNA export, including the remodeling of mRNP-bound transcription-export complexes (TREX), the formation of export-competent mRNPs, the docking of mRNPs at the nuclear pore complex (NPC), and the release of mRNPs at the NPC to initiate their export. Our biochemical and structural data show that the ATPase DDX39/UAP56 acts as a central molecular switch that directs nucleoplasmic mRNPs from TREX to NPC-anchored TREX-2 complexes through its ATP-gated mRNA-binding cycle. Collectively, these findings establish a mechanistic framework for a general and evolutionarily conserved mRNA export pathway.
    DOI:  https://doi.org/10.1038/s41586-025-09832-z